CT-Based Radiomics Models for Differentiation of Benign and Malignant Thyroid Nodules: A Multicenter Development-and-Validation.

Background: CT is increasingly detecting thyroid nodules. Prior studies indicated a potential role of CT-based radiomics models in characterizing thyroid nodules, although lacked external validation. Objectives: To develop and validate a CT-based radiomics model for the differentiation of benign and malignant thyroid nodules. Methods: This retrospective study included 378 patients (mean age, 46.3±13.9 years; 86 men, 292 women) with 408 resected thyroid nodules (145 benign, 263 malignant) from two centers (center 1: 293 nodules, January 2018-December 2022; center 2: 115 nodules, January 2020-December 2022), who underwent preoperative multiphase neck CT (noncontrast, arterial, and venous phases). Nodules from center 1 were divided into training (n=206) and internal validation (n=87) sets; all nodules from center 2 formed an external validation set. Radiologists assessed nodules for morphologic CT features. Nodules were manually segmented on all phases, and radiomic features were extracted. Conventional (clinical and morphologic CT), noncontrast radiomics, arterial-phase radiomics, venous-phase radiomics, multiphase radiomics, and combined (clinical, morphologic, and multiphase radiomics) models were established using feature selection methods and evaluated by ROC curve analysis, calibration curves, and decision-curve analysis. Results: The combined model included patient age, three morphologic features (cystic change, edge interruption sign, abnormal cervical lymph nodes), and 28 radiomic features (from all three phases). In the external validation set, the combined model had AUC of 0.923 and, at an optimal threshold derived in the training set, sensitivity of 84.0%, specificity of 94.1%, and accuracy of 87.0%. In the external validation set, AUC was significantly higher for the combined model than for the conventional model (0.827), noncontrast radiomics model (0.847), arterial-phase radimoics model (0.826), venous-phase radiomics model (0.773), and multiphase radiomics model (0.824) (all p<.05). In the external validation set, the calibration curves indicated lowest (i.e., best) Brier score for the combined model; in decision-curve analysis, the combined model had the highest net benefit for most of the range of threshold probabilities. Conclusion: A combined model incorporating clinical, morphologic CT, and multiphasic radiomics CT features, exhibited robust performing in differentiating benign and malignant thyroid nodules. Clinical Impact: The combined radiomics model may help guide further management for thyroid nodules detected on CT.

Perturb-tracing enables high-content screening of multiscale 3D genome regulators.

Three-dimensional (3D) genome organization becomes altered during development, aging, and disease1-23, but the factors regulating chromatin topology are incompletely understood and currently no technology can efficiently screen for new regulators of multiscale chromatin organization. Here, we developed an image-based high-content screening platform (Perturb-tracing) that combines pooled CRISPR screen, a new cellular barcode readout method (BARC-FISH), and chromatin tracing. We performed a loss-of-function screen in human cells, and visualized alterations to their genome organization from 13,000 imaging target-perturbation combinations, alongside perturbation-paired barcode readout in the same single cells. Using 1.4 million 3D positions along chromosome traces, we discovered tens of new regulators of chromatin folding at different length scales, ranging from chromatin domains and compartments to chromosome territory. A subset of the regulators exhibited 3D genome effects associated with loop-extrusion and A-B compartmentalization mechanisms, while others were largely unrelated to these known 3D genome mechanisms. We found that the ATP-dependent helicase CHD7, the loss of which causes the congenital neural crest syndrome CHARGE24 and a chromatin remodeler previously shown to promote local chromatin openness25-27, counter-intuitively compacts chromatin over long range in different genomic contexts and cell backgrounds including neural crest cells, and globally represses gene expression. The DNA compaction effect of CHD7 is independent of its chromatin remodeling activity and does not require other protein partners. Finally, we identified new regulators of nuclear architectures and found a functional link between chromatin compaction and nuclear shape. Altogether, our method enables scalable, high-content identification of chromatin and nuclear topology regulators that will stimulate new insights into the 3D genome functions, such as global gene and nuclear regulation, in health and disease.

H2S protects from oxidative stress-driven ACE2 expression and cardiac aging.

Cystathionine gamma-lyase (CSE)-derived hydrogen sulfide (H2S) plays an essential role in preserving cardiac functions. Angiotensin-converting enzyme 2 (ACE2) acts as the negative regulator of the renin-angiotensin system, exerting anti-oxidative stress and anti-inflammatory properties within the body. The interplays of CSE/H2S signaling and ACE2 in cardiac aging are unclear. In this study, the regulatory roles of H2S on ACE2 expression in mouse heart tissue and rat cardiomyocytes under different stress conditions were investigated. It was found that ACE2 protein level was lower in heart tissues from old mice (56-week-old) than young mice (8-week-old), and the knockout of CSE (CSE KO) induced moderate oxidative stress and further inhibited ACE2 protein level in mouse hearts at both young and old age. Incubation of rat cardiac cells (H9C2) with a low dose of H2O2 (50 µM) suppressed ACE2 protein level and induced cellular senescence, which was completely reversed by co-incubation with 30 µM NaHS (a H2S donor). Prolonged nutrient excess is an increased risk of heart disorders by causing metabolic dysfunction and cardiac remodeling. We further found high-fat diet feeding stimulated ACE2 expression and induced severe oxidative stress in CSE KO heart in comparison with wild-type heart. Lipid overload in H9C2 cells to mimic a status of nutrient excess also enhanced the expression of ACE2 protein and induced severe oxidative stress and cell senescence, which were significantly attenuated by the supplementation of exogenous H2S. Furthermore, the manipulation of ACE2 expression partially abolished the protective role of H2S against cellular senescence. These results demonstrate the dynamic roles of H2S in the maintenance of ACE2 levels under different levels of oxidative stress, pointing to the potential implications in targeting the CSE/H2S system for the interruption of aging and diabetes-related heart disorders.

H2S-mediated blockage of protein acetylation and oxidative stress attenuates lipid overload-induced cardiac senescence.

Hydrogen sulphide (H2S), a newly identified gasotransmitter, can be endogenously produced by cystathionine gamma-lyase (CSE) in the cardiovascular system. This study investigated the role of the CSE/H2S system on lipid overload-induced lipotoxicity and cardiac senescence. Lipid overload in rat cardiomyocyte cells (H9C2) promoted intracellular accumulation of lipid, oxidative stress, mitochondrial dysfunctions, lipid peroxidation and inhibited cell viability, all of which could be reversed by exogenously applied H2S. Further data revealed that H2S protected H9C2 cells from lipid overload-induced senescence by altering the expressions of lipid metabolism-related genes and inhibiting cellular acetyl-CoA and global protein acetylation. Enhancement of protein acetylation abolished the protective role of H2S on cardiac senescence. In vivo, knockout of the CSE gene strengthened cardiac lipid accumulation, protein acetylation, and cellular ageing in high fat diet-fed mice. Taken together, the CSE/H2S system is capable of maintaining lipid homeostasis and cellular senescence in heart cells under lipid overload.

Hydrogen sulfide guards myoblasts from ferroptosis by inhibiting ALOX12 acetylation.

Recognized as a novel and important gasotransmitter, hydrogen sulfide (H2S) is widely present in various tissues and organs. Cystathionine gamma-lyase (CSE)-derived H2S has been shown to regulate oxidative stress and lipid metabolism. The aim of the present study is to examine the role of H2S in ferroptosis and lipid peroxidation in mouse myoblasts and skeletal muscles. Ferroptosis agonist RSL3 inhibited the expressions of Gpx4 and reduced CSE/H2S signaling, which lead to increased oxidative stress, lipid peroxidation, and ferroptotic cell death. In addition, ferroptosis antagonist ferrostatin-1 (Fer-1) up-regulated the expression of CSE, scavenged the generation of reactive oxygen species (ROS) and lipid peroxidation, and improved cell viability. Exogenously applied NaHS was also able to block RSL3-induced ferroptotic cell death. Neither RSL3 nor H2S affected cell apoptosis. Furthermore, H2S reversed RSL3-induced Drp1 expression and mitochondrial damage, which lead to abnormal lipid metabolism as evidenced by altered expressions of ACSL4, FAS, ACC and CPT1 as well as higher acetyl-CoA contents in both cytoplasm and mitochondria. RSL3 promoted the protein expression and acetylation of ALOX12, a key protein in initiating membrane phospholipid oxidation, while the addition of NaHS attenuated ALOX12 acetylation and protected from membrane lipid peroxidation. Moreover, we observed that CSE deficiency alters the expressions of ferroptosis and lipid peroxidation-related proteins and enhances global protein acetylation in mouse skeletal muscles under aging or injury conditions. These results indicate that downregulation of CSE/H2S signaling would contribute to mitochondrial damage, abnormal lipid metabolism, membrane lipid peroxidation, and ferroptotic cell death. CSE/H2S system can be a target for preventing ferroptosis in skeletal muscle.

Hydrogen sulfide signaling in regulation of cell behaviors.

Recent advances in the biomedical importance of H2S have help us understand various cellular functions and pathophysiological processes from a new aspect. Specially, H2S has been demonstrated to play multiple roles in regulating cell behaviors, including cell survival, cell differentiation, cell senescence, cell hypertrophy, cell atrophy, cell metaplasia, and cell death, etc. H2S contributes to cell behavior changes via various mechanisms, such as histone modification, DNA methylation, non-coding RNA changes, DNA damage repair, transcription factor activity, and post-translational modification of proteins by S-sulfhydration, etc. In this review, we summarized the recent research progress on H2S signaling in control of cell behaviors and discussed the ways of H2S regulation of gene expressions. Given the key roles of H2S in both health and diseases, a better understanding of the regulation of H2S on cell behavior change and the underlying molecular mechanisms will help us to develop novel and more effective strategies for clinical therapy.