Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids.

BACKGROUND: Fragmentomics, the investigation of fragmentation patterns of cell-free DNA (cfDNA), has emerged as a promising strategy for the early detection of multiple cancers in the field of liquid biopsy. However, the clinical application of this approach has been hindered by a limited understanding of cfDNA biology. Furthermore, the prevalence of hematopoietic cell-derived cfDNA in plasma complicates the in vivo investigation of tissue-specific cfDNA other than that of hematopoietic origin. While conventional two-dimensional cell lines have contributed to research on cfDNA biology, their limited representation of in vivo tissue contexts underscores the need for more robust models. In this study, we propose three-dimensional organoids as a novel in vitro model for studying cfDNA biology, focusing on multifaceted fragmentomic analyses. RESULTS: We established nine patient-derived organoid lines from normal lung airway, normal gastric, and gastric cancer tissues. We then extracted cfDNA from the culture medium of these organoids in both proliferative and apoptotic states. Using whole-genome sequencing data from cfDNA, we analyzed various fragmentomic features, including fragment size, footprints, end motifs, and repeat types at the end. The distribution of cfDNA fragment sizes in organoids, especially in apoptosis samples, was similar to that found in plasma, implying occupancy by mononucleosomes. The footprints determined by sequencing depth exhibited distinct patterns depending on fragment sizes, reflecting occupancy by a variety of DNA-binding proteins. Notably, we discovered that short fragments (< 118 bp) were exclusively enriched in the proliferative state and exhibited distinct fragmentomic profiles, characterized by 3 bp palindromic end motifs and specific repeats. CONCLUSIONS: In conclusion, our results highlight the utility of in vitro organoid models as a valuable tool for studying cfDNA biology and its associated fragmentation patterns. This, in turn, will pave the way for further enhancements in noninvasive cancer detection methodologies based on fragmentomics.

A single-cell atlas of in vitro multiculture systems uncovers the in vivo lineage trajectory and cell state in the human lung.

We present an in-depth single-cell atlas of in vitro multiculture systems on human primary airway epithelium derived from normal and diseased lungs of 27 individual donors. Our large-scale single-cell profiling identified new cell states and differentiation trajectories of rare airway epithelial cell types in human distal lungs. By integrating single-cell datasets of human lung tissues, we discovered immune-primed subsets enriched in lungs and organoids derived from patients with chronic respiratory disease. To demonstrate the full potential of our platform, we further illustrate transcriptomic responses to various respiratory virus infections in vitro airway models. Our work constitutes a single-cell roadmap for the cellular and molecular characteristics of human primary lung cells in vitro and their relevance to human tissues in vivo.

Clinical Outcomes in Dogs Undergoing Cholecystectomy via a Transverse Incision: A Meta-Analysis of 121 Animals Treated between 2011 and 2021.

Although many studies have been conducted on the use of median and transverse incisions in various surgeries in the field of human medicine, related studies in veterinary medicine are lacking. This study aimed to present treatment options for dogs requiring cholecystectomy by reporting the pros and cons of 121 cholecystectomies performed via transverse incision at our hospital over 10 years. In most included cases, nonelective cholecystectomy was performed in an unstable emergency situation. The perioperative mortality rate was 23.14%, which was not significantly different from that of cholecystectomy performed via the conventional midline approach. However, the overall operation time (46.24 ± 6.13 min; range 35-65 min) was shortened by securing an adequate surgical field of view. The transverse incision approach facilitates fast and accurate surgery without increasing the fatality rate in small-breed dogs, in whom securing an adequate surgical field of view is difficult. Thus, transverse incision should be actively considered in dogs undergoing cholecystectomy due to emergency conditions, such as bile leakage or biliary tract obstruction, since prolonged anesthesia can be burdensome. This study may improve cholecystectomy outcomes in small-breed dogs with difficult-to-secure surgical fields.

Continuous electrolytic decarbonation and recovery of a carbonate salt solution from a metal-contaminated carbonate solution.

This work studied the characteristic changes of a continuous electrolytic decarbonation and recovery of a carbonate salt solution from a metal-contaminated carbonate solution with changes of operational variables in an electrolytic system which consisted of a cell-stacked electrolyzer equipped with a cation exchange membrane and a gas absorber. The system could completely recover the carbonate salt solution from a uranyl carbonato complex solution in a continuous operation. The cathodic feed rate could control the carbonate concentration of the recovered solution and it affected the most transient pH drop phenomenon of a well type within the gas absorber before a steady state was reached, which caused the possibility of a CO(2) gas slip from the gas absorber. The pH drop problem could be overcome by temporarily increasing the OH(-) concentration of the cathodic solution flowing down within the gas absorber only during the time required for a steady state to be obtained in the case without the addition of outside NaOH. An overshooting peak of the carbonate concentration in the recovered solution before a steady state was observed, which was ascribed to the decarbonation of the initial solution filled within the stacked cells by a redundant current leftover from the complete decarbonation of the feeding carbonate solution.

Precipitation characteristics of uranyl ions at different pHs depending on the presence of carbonate ions and hydrogen peroxide.

This work studied the dissolution of uranium dioxide and precipitation characteristics of uranyl ions in alkaline and acidic solutions depending on the presence of carbonate ions and H2O2 in the solutions at different pHs controlled by adding HNO3 or NaOH in the solution. The chemical structures of the precipitates generated in different conditions were evaluated and compared by using XRD, SEM, TG-DT, and IR analyses together. The sizes and forms of the precipitates in the solutions were evaluated, as well. The uranyl ions were precipitated in the various forms, depending on the solution pH and the presences of hydrogen peroxide and carbonate ions in the solution. In a 0.5 M Na2CO3 solution with H2O2, where the uranyl ions formed mixed uranyl peroxy-carbonato complexes, the uranyl ions were precipitated as a uranium peroxide of UO4(H20)4 at pH 3-4, and precipitated as a clarkeite of Na2U2Ox(OH)y(H2O)z above pH 13. In the same carbonate solution without H2O2, where the uranyl ions formed uranyl tris-carbonato complex, the uranyl ions were observed to be precipitated as a different form of clarkeite above pH 13. The precipitate of uranyl ions in a nitrate solution without carbonate ions and H2O2 at a high pH were studied together to compare the precipitate forms in the carbonate solutions.