Hypoxia-induced ALKBH5 aggravates synovial aggression and inflammation in rheumatoid arthritis by regulating the m6A modification of CH25H

Previous studies have shown that epigenetic factors are involved in the occurrence and development of rheumatoid arthritis (RA). However, the role of N6-methyladenosine (m6A) methylation in RA has not been determined. The aim of this study was to investigate the role and regulatory mechanisms of hypoxia-induced expression of the m6A demethylase alkB homolog 5 (ALKBH5) in RA fibroblast-like synoviocytes (FLSs). Synovial tissues were collected from RA and osteoarthritis (OA) patients, and RA FLSs were obtained. ALKBH5 expression in RA FLSs and collagen-induced arthritis (CIA) model rats was determined using quantitative reverse transcription-PCR (qRT-PCR), western blotting and immunohistochemistry (IHC). Using ALKBH5 overexpression and knockdown, we determined the role of ALKBH5 in RA FLS aggression and inflammation. The role of ALKBH5 in RA FLS regulation was explored using m6A-methylated RNA sequencing and methylated RNA immunoprecipitation coupled with quantitative real-time PCR. The expression of ALKBH5 was increased in RA synovial tissues, CIA model rats and RA FLSs, and a hypoxic environment increased the expression of ALKBH5 in FLSs. Increased expression of ALKBH5 promoted the proliferation and migration of RA-FLSs and inflammation. Conversely, decreased ALKBH5 expression inhibited the migration of RA-FLSs and inflammation. Mechanistically, hypoxia-induced ALKBH5 expression promoted FLS aggression and inflammation by regulating CH25H mRNA stability. Our study elucidated the functional roles of ALKBH5 and mRNA m6A methylation in RA and revealed that the HIF1α/2α-ALKBH5-CH25H pathway may be key for FLS aggression and inflammation. This study provides a novel approach for the treatment of RA by targeting the HIF1α/2α-ALKBH5-CH25H pathway.

[Epidemiological and clinical features of newly reported advanced schistosomiasis cases in Sichuan Province from 2011 to 2022]

OBJECTIVE

To analyze the epidemiological characteristics of newly reported advanced schistosomiasis cases in Sichuan Province, so as to provide the evidence for analyzing the causes and formulating targeted control measures of newly reported advanced schistosomiasis cases.

METHODS

Individual case investigation forms for advanced schistosomiasis cases were collected from the Sichuan Provincial Epidemic Annual Report System from 2011 to 2022, and patients' demographics, previous medical history and liver parenchymal grading were retrieved. All advanced schistosomiasis cases' medical records were reviewed, and the subtypes of schistosomiasis-endemic villages where the cases' household registration were, floating population, survival and death and time of death were collected.

RESULTS

A total of 321 newly reported advanced schistosomiasis cases were found in Sichuan Province from 2011 to 2022, with a male to female ratio of 0.99 to 1. There were 274 cases at ages of over 50 years (85.4%), with the highest proportion seen at ages of 60 to 69 years (87 cases, 27.1%), and splenomegaly was the most common type (180 cases, 56.1%), with no dwarfism type detected. The highest number of cases was reported in 2011 (78 cases), followed by in 2022 (74 cases), and the highest number of cases were reported in Meishan City (199 cases, 62.0%), Dongpo District (131 cases, 40.8%), and hilly subtype areas (136 cases, 42.4%). As of the end of 2022, there were 111 deaths due to advanced schistosomiasis, with the highest number of deaths seen in 2018 (25 deaths), and the highest mortality was seen among patients with the ascites type (41.2%). There were 47 (37.3%), 40 (59.5%) and 4 (23.5%) cases with grade III liver parenchyma among patients with splenomegaly, ascites, and colonic proliferation types, respectively, and there was a significant difference in the grading of III liver parenchyma among three types of patients (H = 12.092, P < 0.05), with more severe liver parenchyma injuries seen among patients with the ascites type than among those with splenomegaly and colonic proliferation type (Z = 24.262 and 44.738, both Padjusted values < 0.05).

CONCLUSIONS

There have been newly reported advanced schistosomiasis cases in Sichuan Province during recent years, and patients with the ascites type should be given a high priority among advanced schistosomiasis cases in Sichuan Province. Intensified clue surveys are needed for early identification and treatment of advanced schistosomiasis cases, so as to increase the survival rate and improve the quality of life.

R-loops act as regulatory switches modulating transcription of COLD-responsive genes in rice

COLD is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in crops. R-loops function in various cellular processes, including development and stress responses, in plants. However, how R-loops function in COLD responses is largely unknown in COLD susceptible crops like rice (Oryza sativa L.). We conducted DRIP-Seq along with other omics data (RNA-Seq, DNase-Seq and ChIP-Seq) in rice with or without COLD treatment. COLD treatment caused R-loop reprogramming across the genome. COLD-biased R-loops had higher GC content and novel motifs for the binding of distinct transcription factors (TFs). Moreover, R-loops can directly/indirectly modulate the transcription of a subset of COLD-responsive genes, which can be mediated by R-loop overlapping TF-centered or cis-regulatory element-related regulatory networks and lncRNAs, accounting for c. 60% of COLD-induced expression of differential genes in rice, which is different from the findings in Arabidopsis. We validated two R-loop loci with contrasting (negative/positive) roles in the regulation of two individual COLD-responsive gene expression, as potential targets for enhanced COLD resistance. Our study provides detailed evidence showing functions of R-loop reprogramming during COLD responses and provides some potential R-loop loci for genetic and epigenetic manipulation toward breeding of rice varieties with enhanced COLD tolerance.

Prevalence and influencing factors of depressive and anxiety symptoms among hospital-based healthcare workers during the surge period of the COVID-19 pandemic in the Chinese mainland: a multicenter cross-sectional study

BACKGROUND

From November 2022 to February 2023, the Chinese mainland experienced a surge in COVID-19 infection and hospitalization, and the hospital-based healthcare workers (HCWs) might suffer serious psychological crisis during this period. This study aims to assess the depressive and anxiety symptoms among HCWs during the surge of COVID-19 pandemic and to provide possible reference on protecting mental health of HCWs in future infectious disease outbreaks.

METHODS

A multicenter cross-sectional study was carried out among hospital-based HCWs in the Chinese mainland from 5 January to 9 February 2023. The PHQ-9 (nine-item Patient Health Questionnaire) and GAD-7 (seven-item Generalized Anxiety Disorder Questionnaire) were used to measure depressive and anxiety symptoms. Ordinal logistic regression analysis was performed to identify influencing factors.

RESULTS

A total of 6522 hospital-based HCWs in the Chinse mainland were included in this survey. The prevalence of depressive symptoms among the HCWs was 70.75%, and anxiety symptoms was 47.87%. The HCWs who perceived higher risk of COVID-19 infection and those who had higher work intensity were more likely to experience depressive and anxiety symptoms. Additionally, higher levels of mindfulness, resilience and perceived social support were negatively associated with depressive and anxiety symptoms.

CONCLUSION

This study revealed that a high proportion of HCWs in the Chinese mainland suffered from mental health disturbances during the surge of the COVID-19 pandemic. Resilience, mindfulness and perceived social support are important protective factors of HCWs' mental health. Tailored interventions, such as mindfulness practice, should be implemented to alleviate psychological symptoms of HCWs during the COVID-19 pandemic or other similar events in the future.

Microglia and complement mediate early corticostriatal synapse loss and cognitive dysfunction in Huntington's disease

Huntington's disease (HD) is a devastating monogenic neurodegenerative disease characterized by early, selective pathology in the basal ganglia despite the ubiquitous expression of mutant huntingtin. The molecular mechanisms underlying this region-specific neuronal degeneration and how these relate to the development of early cognitive phenotypes are poorly understood. Here we show that there is selective loss of synaptic connections between the cortex and striatum in postmortem tissue from patients with HD that is associated with the increased activation and localization of complement proteins, innate immune molecules, to these synaptic elements. We also found that levels of these secreted innate immune molecules are elevated in the cerebrospinal fluid of premanifest HD patients and correlate with established measures of disease burden.In preclinical genetic models of HD, we show that complement proteins mediate the selective elimination of corticostriatal synapses at an early stage in disease pathogenesis, marking them for removal by microglia, the brain's resident macrophage population. This process requires mutant huntingtin to be expressed in both cortical and striatal neurons. Inhibition of this complement-dependent elimination mechanism through administration of a therapeutically relevant C1q function-blocking antibody or genetic ablation of a complement receptor on microglia prevented synapse loss, increased excitatory input to the striatum and rescued the early development of visual discrimination learning and cognitive flexibility deficits in these models. Together, our findings implicate microglia and the complement cascade in the selective, early degeneration of corticostriatal synapses and the development of cognitive deficits in presymptomatic HD; they also provide new preclinical data to support complement as a therapeutic target for early intervention.

Stimulator of interferon genes (STING): Key therapeutic targets in ischemia/reperfusion injury

The Stimulator of Interferon Genes (STING) is predominantly expressed in immune cells, including macrophages, natural killer cells, dendritic cells, and T cells, functioning as a pattern recognition receptor. STING activation upon detecting cytosolic DNA released from damaged cells initiates downstream pathways, leading to the production of inflammatory cytokines such as IFNs, IL-6, and TNF-α. Dysregulated STING activation has been implicated in inflammatory and metabolic diseases. Ischemia/reperfusion injury (I/RI) is common in stroke, acute myocardial infarction, organ transplantation, and surgeries for certain end-stage diseases. Recent studies suggest that STING could be a novel therapeutic target for I/RI treatment. In this review, we provide a concise overview of the cGAS-STING signaling pathway's general functions and summarize STING's role in I/RI across various organs, including the heart, liver, kidney, and lung. Moreover, we explore potential therapeutic approaches for I/RI by targeting STING.

Multivariable model of postoperative delirium in cardiac surgery patients: proteomic and demographic contributions

Background

Delirium following cardiac surgery is common, morbid, and costly, but may be prevented with risk stratification and targeted intervention. Preoperative protein signatures may identify patients at increased risk for worse postoperative outcomes, including delirium. In this study, we aimed to identify plasma protein biomarkers and develop a predictive model for postoperative delirium in older patients undergoing cardiac surgery, while also uncovering possible pathophysiological mechanisms.

Methods

SOMAscan analysis of 1,305 proteins in the plasma from 57 older adults undergoing cardiac surgery requiring cardiopulmonary bypass was conducted to define delirium-specific protein signatures at baseline (PREOP) and postoperative day 2 (POD2). Selected proteins were validated in 115 patients using the ELLA multiplex immunoassay platform. Proteins were combined with clinical and demographic variables to build multivariable models that estimate the risk of postoperative delirium and bring light to the underlying pathophysiology.

Results

A total of 115 and 85 proteins from SOMAscan analyses were found altered in delirious patients at PREOP and POD2, respectively (p<0.05). Using four criteria including associations with surgery, delirium, and biological plausibility, 12 biomarker candidates (Tukey's fold change (|tFC|)>1.4, Benjamini-Hochberg (BH)-p<0.01) were selected for ELLA multiplex validation. Eight proteins were significantly altered at PREOP, and seven proteins at POD2 (p<0.05), in patients who developed postoperative delirium compared to non-delirious patients. Statistical analyses of model fit resulted in the selection of a combination of age, sex, and three proteins (angiopoietin-2 (ANGPT2); C-C motif chemokine 5 (CCL5); and metalloproteinase inhibitor 1 (TIMP1); AUC=0.829) as the best performing predictive model for delirium at PREOP. The delirium-associated proteins identified as biomarker candidates are involved with inflammation, glial dysfunction, vascularization, and hemostasis, highlighting the multifactorial pathophysiology of delirium.

Conclusion

Our study proposes a model of postoperative delirium that includes a combination of older age, female sex, and altered levels of three proteins. Our results support the identification of patients at higher risk of developing postoperative delirium after cardiac surgery and provide insights on the underlying pathophysiology. ClinicalTrials.gov ( NCT02546765 ).

High-performance multilayer WSe2/SnS2p-n heterojunction photodetectors by two step confined space chemical vapor deposition

Two-dimensional (2D) p-n heterojunctions have attracted great attention due to their outstanding properties in electronic and optoelectronic devices, especially in photodetectors. Various types of heterojunctions have been constituted by mechanical exfoliation and stacking. However, achieving controlled growth of heterojunction structures remains a tremendous challenge. Here, we employed a two-step KI-assisted confined-space chemical vapor deposition method to prepare multilayer WSe2/SnS2p-n heterojunctions. Optical characterization results revealed that the prepared WSe2/SnS2vertical heterostructures have clear interfaces as well as vertical heterostructures. The electrical and optoelectronic properties were investigated by constructing the corresponding heterojunction devices, which exhibited good rectification characteristics and obtained a high detectivity of 7.85 × 1012Jones and a photoresponse of 227.3 A W-1under visible light irradiation, as well as a fast rise/fall time of 166/440μs. These remarkable performances are likely attributed to the ultra-low dark current generated in the depletion region at the junction and the high direct tunneling current during illumination. This work demonstrates the value of multilayer WSe2/SnS2heterojunctions for applications in high-performance photodetectors.

High-Responsivity and Broadband MoS2 Photodetector Using Interfacial Engineering

Combining MoS2 with mature silicon technology is an effective method for preparing high-performance photodetectors. However, the previously studied MoS2/silicon-based heterojunction photodetectors cannot simultaneously demonstrate high responsivity, a fast response time, and broad spectral detection. We constructed a broad spectral n-type MoS2/p-type silicon-based heterojunction photodetector. The SiO2 dielectric layer on the silicon substrate was pretreated with soft plasma to change its thickness and surface state. The pretreated SiO2 dielectric layer and the silicon substrate constitute a multilayer heterostructure with a high carrier concentration and responsiveness. Taking silicon-based and n-type MoS2 heterojunction photodetectors as examples, its responsivity can reach 4.05 × 104 A W1- at 637 nm wavelength with a power density of 2 μW mm-2, and the detectable spectral range is measured from 447 to 1600 nm. This pretreated substrate was proven applicable to other n-type TMDCs, such as MoTe2, ReS2, etc., with certain versatility.

Overall Survival Prediction in Stereotactic Radiosurgery Patients with Glioblastoma Via a Deep-Learning Approach

PURPOSE/OBJECTIVE(S)

Accurate and automated early survival prediction is critical for glioblastoma (GBM) patients as their poor prognosis requires timely treatment decision-making. We have developed a deep learning (DL)-based GBM overall survival (OS) prediction model based on a multi-institutional public dataset using only pre-operative basic structural multi-parametric magnetic resonance images (MRIs). The purpose of this study is to evaluate this DL-based OS prediction model with an institutional stereotactic radiosurgery (SRS) clinical trial dataset.

MATERIALS/METHODS

The task of this study is to classify GBM patients into 3 OS classes: long-survivors (>15 months), mid-survivors (between 10 and 15 months) and short-survivors (< 10 months). The proposed OS prediction model is an ensemble of a ResNet-based classifier and a K-NN classifier. The ResNet-based classifier is trained in a Siamese fashion to explore inter-class differences. During testing, training sample features are implemented with a K-NN classifier to ensemble with the ResNet-based classifier. A public dataset from Medical Image Computing and Computer Assisted Intervention (MICCAI) Brain Tumor Segmentation (BraTS) challenge 2020 (235 patients) were used for model establishing and initial validation. Then the validated model was evaluated on 19 GBM patients from an institutional SRS clinical trial. Each data entry consists of pre-operative basic structural multi-parametric MRIs and survival days, as well as patient ages for BraTS data and basic clinical characteristics for institutional data. GBM sub-regions, including contrast-enhancing tumor, peri-tumoral edema, and necrotic/non-enhancing tumor core, were segmented in the multi-parametric MRIs by an in-house DL model for both datasets. The OS prediction model was trained on 90% of the segmented BraTS data and validated on the rest 10%, then further evaluated on the institutional data. The model performance was assessed by prediction accuracy (ACC) and the area under the curve (AUC).

RESULTS

For this 3-class OS classification task, our DL-based prediction model achieved an ACC of 65.22% and an AUC of 0.81 on the BraTS dataset compared with the top-ranked result from the BraTS challenge 2020 (Rank 1st: ACC 61.7%), and an ACC of 52.63% and an AUC of 0.69 on the institutional dataset. Further analysis of the institutional dataset found that the predicted OS class had a statistically significant correlation with treatment volume (p = 0.012) and age (p = 0.006), which matches the analysis that the patients' ground truth OS class is statistical significantly correlated with treatment volume (p = 0.045).

CONCLUSION

Our DL-based OS prediction model for GBM using basic structural multi-parametric pre-operative MRIs has demonstrated promising performance in both public and institutional dataset with minimal manual processing requirements. This OS prediction model can be potentially applied to assist timely clinical decision-making.

Cardiac Sparing with Volumetric Modulated Arc Therapy Enabled Total Body Irradiation (CS VMAT-TBI)

PURPOSE/OBJECTIVE(S)

Volumetric modulated arc therapy (VMAT) enabled total body irradiation (TBI) has replaced conventional TBI in our institution given the improved treatment accuracy, patient comfort, and dose modulation ability. The risk of cardiovascular disease is several folds higher among transplant patients who receive TBI, likely related to dose to the heart. We hypothesize that a cardiac-sparing (CS) VMAT-TBI technique is feasible and can meaningfully reduce dose to the heart while still adequately covering nearby lymphatic tissue.

MATERIALS/METHODS

VMAT-TBI is delivered via multi-isocentric external beams in a frame-based setup. Heart is contoured as per published guidelines. A lymph node contour, which includes tonsils, neck nodal stations, mediastinal, abdominal, retroperitoneal, and pelvic nodes is created. Coverage of the lymph node contour is prioritized over organ-sparing during inverse optimization; with a goal of V90% greater than 99.5% and mean dose less than 800 cGy for the lymph nodes and heart, respectively. An IRB-approved retrospective review was performed with mean heart dose collected for all patients treated with CS VMAT-TBI and compared to a representative cohort of five patients treated with VMAT-TBI without cardiac sparing.

RESULTS

Thirty-one patients were treated with CS VMAT-TBI between 2020-2022 with a median follow up time of 11.5 months. Mean heart dose was 796 ± 71 cGy in the CS VMAT-TBI compared to 1247 ± 29 cGy in the VMAT-TBI group without cardiac sparing (p < 0.001). Of those treated with CS VMAT-TBI, three patients relapsed; one relapse occurred in bone marrow only, one relapse occurred in bone marrow and cervical, thoracic, and intra-abdominal lymphoid tissues, and one patient was simulated but never received induction therapy due to overt progression. 100-day relapse-free survival and overall survival were 82.5% and 86.2%, respectively. Median survival time has not been met.

CONCLUSION

Cardiac sparing is feasible in VMAT-TBI and is associated with significant decrease in mean heart dose of ∼450 cGy. This is estimated to confer a 33.3% decreased absolute risk for lifetime major coronary events compared to patients treated with VMAT-TBI without cardiac sparing. Although limited by short follow-up time, there does not appear to be a significant risk for early relapse despite de-escalating cardiac tissue, likely due to prioritizing coverage of lymph nodes. Prospective clinical studies are needed to further validate cardiac and other organ at risk sparing VMAT-TBI techniques.

ZmBELL10 interacts with other ZmBELLs and recognizes specific motifs for transcriptional activation to modulate internode patterning in maize

Plant height is an important agronomic trait that affects crop yield. Elucidating the molecular mechanism underlying plant height regulation is also an important question in developmental biology. Here, we report that a BELL transcription factor, ZmBELL10, positively regulates plant height in maize (Zea mays). Loss of ZmBELL10 function resulted in shorter internodes, fewer nodes, and smaller kernels, while ZmBELL10 overexpression increased plant height and hundred-kernel weight. Transcriptome analysis and chromatin immunoprecipitation followed by sequencing showed that ZmBELL10 recognizes specific sequences in the promoter of its target genes and activates cell division- and cell elongation-related gene expression, thereby influencing node number and internode length in maize. ZmBELL10 interacted with several other ZmBELL proteins via a spatial structure in its POX domain to form protein complexes involving ZmBELL10. All interacting proteins recognized the same DNA sequences, and their interaction with ZmBELL10 increased target gene expression. We identified the key residues in the POX domain of ZmBELL10 responsible for its protein-protein interactions, but these residues did not affect its transactivation activity. Collectively, our findings shed light on the functions of ZmBELL10 protein complexes and provide potential targets for improving plant architecture and yield in maize.

An Online AI-Powered Interactive Histological Image Annotation Platform for Analyzing Intestinal Regenerating Crypts in Post-Irradiated Mice

PURPOSE/OBJECTIVE(S)

The goal of this project is to build an online AI-powered interactive annotation platform to accurately and efficiently annotate intestinal regenerating crypts in histological images of mice after abdominal irradiation.

MATERIALS/METHODS

The proposed platform is developed by the seamless integration of a front-end web client and a back-end server. Such client/server design allows the users to access the platform without software installation on local computers. Our front-end client is developed with SvelteJS + WebGL technology stack, allowing access from any common web browsers and enabling user interaction, such as image importing/visualization, interactive crypt annotating, and annotation saving/deleting. The back-end server is responsible for executing the tasks requested from the web client, for instance, image pre-processing, AI-based crypts automatic identification, and database management. The image preprocessing is designed to extract a single cross section image using morphological operations because multiple hematoxylin and eosin (H&E) stained jejunum cross sections from post-irradiated mice are scanned within one slide. The auto-crypt identification is powered by a trained and validated AI engine U-Net, classifying image grid tiles into two groups with and without regenerating crypts. The database is implemented with the self-contained SQLite to support recording and indexing the annotated grid tiles with regenerating crypts. The workflow for crypt analysis on this interactive platform has 5 steps: 1) manually import a whole H&E slide image; 2) auto-preprocess the slide by extracting single cross-section images; 3) auto-identify regenerating crypts with an AI engine; 4) interactively annotate (add, delete, modify) auto-identified crypt markers; 5) save and/or output the annotation to the database or the local drive.

RESULTS

The performance of the developed interactive crypt analysis platform was evaluated in aspects of accuracy and efficiency. The AI-powered crypt auto-identification accuracy was assessed by computing the mean absolute error (MAE) on crypt number per cross section between manual and auto annotation using a testing dataset containing 80 cross sections. It achieved an MAE of 3.5±4.8 crypts per cross section, and 81.25% of the cross sections have no more than 5 crypts difference. The efficiency was assessed under two conditions with the server on the cloud and a local computer. It took about 2-3 minutes to finish the entire workflow on the cloud, while 1-2 minutes on the local by saving ∼1 minute on image uploading.

CONCLUSION

The developed web client/server platform enables online automatic identification and interactive annotation of mice crypts in minutes. It is a convenient tool that allows accurate and efficient crypt analysis and can be extended for other histologic image analyses.

Green Tea Derivative (-)-Epigallocatechin-3-Gallate (EGCG) for Prevention of Acute Radiation-Induced Intestinal Injury: A Prospective Phase II Clinical Study in Pelvic Cancer Patients

PURPOSE/OBJECTIVE(S)

Radiation-induced intestinal injury (RIII) remains the most common dose-limiting toxicity following radiotherapy (RT) for pelvic malignancies. However, few efficient and safe methods for the prevention of RIII are available in the clinical practice. Our previous study proved that the green tea polyphenol (-)-epigallocatechin-3-gallate (EGCG) efficiently attenuates radiation-induced intestinal injury (RIII) in animal level. Therefore, this prospective phase II clinical study (ChiCTR2100053703) evaluated the efficacy of EGCG in the prevention of RIII.

MATERIALS/METHODS

Cervical or endometrial cancer patients who received adjuvant or radical RT in our department were enrolled, 400mg EGCG was taken daily, and RIII was evaluated weekly according to the RTOG criteria.

RESULTS

Between February 2022 to January 2023, 37 patients were enrolled (30 were cervical cancer and the other 7 were endometrial cancer), and were followed-up regularly. Among them, the majority patients (75.7%, 28 patients) developed grade 0 or 1 RIII, for which no medical intervention was required. Meanwhile, the occurrence of grade 2 RIII was 24.3% (9 patients), which was significantly lower than that in the historical controls (usually 60% to 80%). Besides that, no patients developed grade 3 or worse RIII.

CONCLUSION

In this phase II clinical trial, compared to historical controls, the prophylactic use of EGCG significantly reduced the incidence and severity of RIII in patients receiving pelvic RT. Therefore, EGCG has the potential to become a novel medical countermeasure for the prevention of RIII for pelvic cancer patients.

Multi-Institutional Phase II Trial Using Dose Escalated Five Fraction Stereotactic Partial Breast Irradiation (S-PBI) with GammaPodTM for Early-Stage Breast Cancer

PURPOSE/OBJECTIVE(S)

We report on our early experience of a multi-institutional phase II study of dose escalated five fraction stereotactic partial breast irradiation (S-PBI) for early-stage breast cancer after partial mastectomy using the GammaPodTM stereotactic radiation system.

MATERIALS/METHODS

Patient eligibility included DCIS or invasive epithelial histologies, AJCC clinical stage 0, I, or II with tumor size < 3 cm, and negative margins. Prior safety of Phase I dose escalation has been reported. Dose was 40 Gy delivered in 5 fractions to the CTV, and minimum dose 30 Gy in 5 fractions to the PTV. CTV margin was 1 cm and PTV margin 3 mm. For PTV cavities larger than 100cc, dose was reduced to 35Gy in 5 fractions to the CTV and 30 Gy in 5 fractions to the PTV. Primary endpoint of the study is to determine the 3-year patient global cosmesis score (4-point scale excellent, good, fair, or poor) and adverse cosmesis using a dose escalated approach with smaller PTV margins than conventional methods. Both patients and physicians completed baseline and subsequent cosmesis outcome questionnaires. Treatment related toxicity was graded using the NCI version 4.0 and RTOG/EORTC late radiation scale.

RESULTS

From 3/2019-10/2021, 74 patients were treated respectively. Of these, 38 were treated to 40Gy and 36 were treated to 35 Gy. Median follow up (f/u) was 24 months (mo), range (r) 3-39mo. Median age was 63 years (r 43-77). Histology included 28 DCIS, and 46 invasive carcinomas. 45/46 invasive tumors were ER+. 60/74 (81%) patients received endocrine therapy, and 7/74 patient received chemotherapy. There were 221 acute grade 1 toxicities, and 28 Grade 2 toxicities. No grade 3 or higher acute toxicities were reported (< 90 days). The most common Grade 2 toxicities were radiation dermatitis (10), breast pain (8), blister (4), skin infection (2), nipple discharge (2), and fatigue (2). In the late period, there were 54 Grade 1 late toxicities, 4 Grade 2 late toxicities, and no Grade 3 or higher late toxicities. Grade 2 toxicities included fibrosis (2), and pain (2). Two patients developed grade 1 asymptomatic nonpalpable fat necrosis both diagnosed at 12 months after radiation treatments. The most common grade 1 late toxicities were breast pain (14), hyperpigmentation (8), fibrosis (10), and fatigue (5). Physicians scored cosmesis excellent or good 70/73 (95.8%), 58/60 (96.7%), 36/36 (100%),17/17(100%) respectively at baseline, 12 months, 24 months, and 36months post SBRT, while patients scored the same periods 62/71 (83.7%), 53/59 (89.8%), 33/36 (91.6%), 17/18 (94.4%). There have been no reports of disease recurrences.

CONCLUSION

Results at 24-month median follow-up, of our dose escalated stereotactic partial breast 5 fraction regimen, has low acute and late toxicity, while maintaining high proportion of excellent/good cosmetic outcomes. Continued analysis of all cohorts is in progress.

CLINICAL TRIALS

gov identifier is NCT03581136.

Deep Learning-Based Pipeline for Automatic Identification of Intestinal Regenerating Crypts in Mouse Histological Images

PURPOSE/OBJECTIVE(S)

A classical approach for evaluating normal tissue radiation response is to count the number of intestinal regenerating crypts in mouse histological images acquired after abdominal radiation. However, manual counting is time-consuming and subject to inter-observer variations. The goal of this study is to build a deep learning-based pipeline for automatically identifying intestinal regenerating crypts to facilitate high-throughput studies.

MATERIALS/METHODS

Sixty-six healthy C57BL/6 female mice underwent 16 MeV whole abdominal electron irradiation. The small bowel was collected from each mouse 4 days post-irradiation, and 9 jejunal cross-sections from each were processed together in a single slide. The slides were stained with hematoxylin and eosin (H&E) and subsequently scanned (x20), providing one electronic histological image per mouse. Regenerating crypts, consisting of more than 10 basophilic crypt epithelial cells, were manually identified using point annotations in histological images. The pipeline was built to take the input of the image containing 9 cross sections and automatically identify the regenerating crypts on each cross section. It mainly consists of two components, cross section segmentation using intensity thresholding and morphological operations and crypt identification using a UNet. The dataset was randomly split into 46, 10, and 10 slide images for UNet training, validation, and testing. Each slide image was split into grid tiles with a voxel size of 200 × 200, and 40 × 40 square masks were placed with centers at manual point annotations on tiles with regenerating crypts. 5203/5198 tiles (w/wo crypt mask) were extracted to train UNet by minimizing dice loss. The mask probability map generated by the UNet was post-processed to identify the crypt position. Postprocessing hyperparameters were tuned using the validation dataset. The model accuracy was evaluated using the testing dataset by computing the mean absolute error (MAE) of the crypt number averaged across all cross sections.

RESULTS

The number of regenerating crypts on testing cross sections ranges from 1 to 63. The testing cross-section-wise MAE achieved by the platform is 3.5±4.8 crypts. 81.25% of testing cross sections have absolute number differences less than or equal to 5 crypts.

CONCLUSION

Our established deep learning-based pipeline can accurately count the number of regenerating crypts in mouse intestinal histological images. We have integrated it into an online platform that enables automatic crypt identification and allows users to interactively modify auto-identified crypt annotations. The acquired annotations from the platform will be used to finetune the deep learning model to achieve better identification performance.

Equivalent Dose Estimation in FLASH Irradiation with a Deep Learning Approach

PURPOSE/OBJECTIVE(S)

Ultra-high dose rate (FLASH) irradiation has been reported to provide decreased normal tissue toxicity without compromising tumor control compared with conventional (CONV) irradiation. However, a comprehensive understanding of the FLASH biological effect requires precise quantification of radiobiology. The study is to explore whether deep learning (DL) can tackle the task. As a proof of concept, we investigate a DL model for estimating FLASH dose to its equivalent CONV dose.

MATERIALS/METHODS

Healthy C57Bl/6 female mice underwent FLASH (200Gy/s; n = 43) or CONV (0.12Gy/s; n = 41) whole abdominal irradiation using ∼16 MeV electron beams with a dose escalation scheme of 5 groups (n = 8 or 9) at 1Gy increments: 12-16Gy FLASH, 11-15Gy CONV. 4 days post-irradiation, 9 jejunum cross-sections per mouse were H&E stained for histological analysis. Each cross-section image was processed to remove lumen background and oversampled into multiple large-scale and small-scale patches along jejunal circumference. In CONV dataset, we randomly selected the data of 32 mice (80%) for model training and the rest (20%) for model validation. A ResNet101-based DL model, pre-trained with an unsupervised contrastive learning scheme, was retrained with only CONV training set to estimate corresponding CONV dose. For comparison, a crypt counting (CC) approach was implemented by manually counting the number of regenerating crypts on each cross-section image. An exponential function of dose vs crypt number was fitted with the CONV training set and used for dose estimation on the testing set. Mean squared error (MSE) was used to assess the accuracy of DL and CC approaches in estimating dose levels in CONV irradiation. The validated DL model was applied to the FLASH set to project FLASH dose into corresponding CONV dose that results in equivalent biological response.

RESULTS

The CONV dose estimated by DL and CC approaches and DL-estimated FLASH equivalent dose were summarized in Table 1. The DL model achieved an MSE of 0.21 Gy2 on CONV testing set compared with 0.32 Gy2 of the CC approach. FLASH equivalent dose estimated by DL model for 12, 13, 14, 15 and 16Gy were 12.16±0.40, 12.53±0.32, 12.72±0.24, 12.85±0.20 and 13.04±0.27 Sv, respectively.

CONCLUSION

Our proposed DL model can accurately estimate the CONV dose based on histological images. The DL predictions of FLASH dataset demonstrate that FLASH may reduce normal tissue toxicity with a lower equivalent dose, especially at high irradiated dose levels. Our study indicates that deep learning can be potentially used to assess the equivalent dose of FLASH irradiation to normal tissue.

Assessment of Cardiac Radiation Dose in the Co-60 Prone Based Stereotactic Partial Breast Irradiation (CP-sPBI) Using the Distance from the Heart to the Planning Treatment Volume as a Surrogate Marker

PURPOSE/OBJECTIVE(S)

Irradiation of the breast has shown to provide sharp dose gradients using Co-60 prone based stereotactic partial breast irradiation (CP-sPBI), a contemporary device for stereotactic radiotherapy for breast cancer (BC) for accelerated partial breast irradiation (APBI). In addition, the precise setup of CP-sPBI permits a small planning treatment volume (PTV) margin of 3 mm creating a greater distance from PTV to organs at risk. However, to date the factors that influence dose gradients and subsequent cardiac doses of ionizing radiation using CP-sPBI have not been well-studied. Here we evaluate distance of the heart to the lumpectomy PTV cavity and how this effects cardiac dose.

MATERIALS/METHODS

A retrospective database of 113 consecutive patients treated by CP-sPBI for APBI from March 2019 to February 2023 who were treated with 30 Gy in 5 fractions were queried for analysis. The minimum distance from the heart to the PTV (hP) was measured in either the axial or sagittal view. A group of 28 patient cases were randomly selected to achieve an even distribution of 28 cases with hP < 2.75 cm and hP ≥ 2.75 cm to compare cardiac toxicities based on hP. Descriptive analyses were performed to evaluate various cardiac dosimetric parameters based on laterality of BC and hP, using the student's t test.

RESULTS

The mean (range) hP was 4.58 cm (0.80-12.23) for all cases. The subgroup analyses of 28 patient cases with cardiac parameters showed the heart mean (range) dose of 1.20 Gy (0.01-2.11). The mean and max heart dose to the left-sided BC were similar to those to the right-sided BC (mean dose: 1.20 vs. 1.19 Gy; P = 0.97 and max dose: 10.47 vs. 5.66 Gy; P = 0.06). An inverse correlation between hP and mean heart dose was shown with the correlation coefficient of -0.81. Using a cutoff of 2.75 cm hP, the differences between hP < 2.75 and hP ≥ 2.75 cm for all cardiac dosimetric evaluations were all statistically significant, including mean (1.67 vs. 0.79 Gy; p<0.01) and maximal heart dose (14.48 vs. 4.11 Gy; p<0.01) CONCLUSION: CP-sPBI treatment delivery system was able to achieve acceptable clinically relevant heart dosimetric parameters when delivering 5 fraction APBI with a mean heart dose of 1.20 Gy for all locations of PTV cavity volume in the breast. Due to CP-sPBIs excellent dose fall-off characteristics, APBI using CP-SPBI showed clinically acceptable cardiac dosimetric parameters, particularly for PTVs located > 2.75 cm from the heart.

Financial Toxicity and Patient Experience Outcomes on a Multi-Institutional Phase I Single Fraction Stereotactic Partial Breast Irradiation Protocol for Early-Stage Breast Cancer

PURPOSE/OBJECTIVE(S)

Given the demonstrated financial toxicity (FT) of radiation treatment on breast cancer patients shown in both conventional and our recent 5 fraction stereotactic APBI (S-PBI) study, we assessed the FT, as well as patient-reported utility, quality-of-life and patient experience measures, on patients treated in our phase I single fraction S-PBI trial.

MATERIALS/METHODS

A phase I single fraction dose escalation trial of S-PBI for early-stage breast cancer was conducted. Women with in-situ or stage I-II (AJCC 6) invasive breast cancer following breast conserving surgery were treated with S-PBI in 1 fraction to a total dose of 22.5, 26.5 or 30 Gy (Clinical trials.gov ID NCT02685332). At one month follow-up, patients were asked to complete our novel "Patient Perspective Cost and Convenience of Care Questionnaire". Patients also completed the EQ-5D-5L, including the visual analogue scale of overall health (VAS), at enrollment, 6, 12-, 24-, 36-, and 48-month follow-up.

RESULTS

Of 29 patients enrolled and treated, questionnaire data was available for all patients. Our trial encompassed a wide range of annual household incomes, education, and employment status. Overall, 44.8% (n = 13/29) of patients reported that radiation treatment presented a financial burden. Interestingly, no demographic information, such as patient race, marital status, education, household income, or employment during treatment predicted perceived FT. Patients reporting FT trended towards younger age (median 64 vs 70.5) and having a cancer related co-pay similar to our 5 fraction S-PBI FT trial; however, due to the small size of this study, this did not reach significance (p = 0.24 and 0.10, respectively). VAS and utility scores were calculated per the EQ-5D-5L and remained unchanged from baseline through 4-year follow-up. Likewise, there was no difference in the utility or VAS between patients who reported FT and those who did not. Interestingly, while patient reported cosmesis was similar for all patients at enrollment, patients who reported FT noted significantly worse cosmesis scores (fair/poor vs good/excellent) at 6 month and 2-year follow-ups (p = 0.01 and 0.04, respectively). Finally, patients were surveyed on treatment related disruption to their daily activities and enjoyment of life. The median values were 0 (scale 0-10, with 0 being no disruption) regardless of perceived FT. Patients were also uniformly satisfied with treatment time with a median score of 10 (scale 0-10, 10 being most satisfied).

CONCLUSION

Here, we show that despite using SPBI in a single fraction, nearly half of the patients treated still reported FT of treatment. Importantly, single fraction S-PBI has no negative impact on patient VAS or utility scores, and all patients were uniformly satisfied with treatment time without significant disruption to their life.

Predicting Neurocognitive Decline in Multiple Brain Metastases Patients Undergoing Distributed Stereotactic Radiosurgery

PURPOSE/OBJECTIVE(S)

Stereotactic radiosurgery (SRS) is the standard of care for treating a limited number (<3) of brain metastasis (BMs), which offers reduced neurotoxicity compared to whole brain radiotherapy (WBRT). Contemporary advancements in SRS made it possible to also commonly treat multiple (>4) BMs (mBMs). Emphasizing the value of preserving quality of life (QoL) after SRS, there is an urgent need for a systematic study of potential neurocognitive decline in patients receiving SRS treatment for mBMs. The purpose of this study is to use routine MRIs to predict neurocognitive decline for patients treated with distributed SRS, allowing for timely and effective treatment strategy design.

MATERIALS/METHODS

This study uses data from an institutional phase I/II clinical trial to determine the neurocognitive decline in patients with (>6) mBMs treated with distributed SRS. In the first 12 months post-SRS, participants are followed and evaluated with routine MRIs and the Hopkins Verbal Learning Test-Revised (HVLT-R) at 2 to 3-month intervals. Changes in HVLT-Delayed Recall scores between two visits are used to define neurocognitive decline. For each visit, an in-house deep learning model segments 66 cortical and 55 subcortical brain regions of interest (ROIs) from the T1 structural MRI and extracts 253 ROI features, including the surface area and thickness of cortical ROIs, and the volume of all ROIS. The difference in ROI features between two visits, together with other clinical factors (e.g., prescription, number of BMs, etc.), is considered as one sample. The study included 22 subjects with 91 visits, resulting in 171 samples with neurocognitive decline labels. The entire sample set is split into 10 folds on patient level for cross validation. In each fold, feature engineering is conducted to remove redundancy and to select the most-important features. The top 20% most frequently selected features are applied with Support Vector Machine to predict the neurocognitive decline label of each sample.

RESULTS

As a preliminary result, the proposed method achieves an accuracy of 76%, with an area under the curve (AUC) of 0.75, sensitivity of 0.65 and specificity of 0.83 for predicting neurocognitive decline in mBMs SRS patients using only routine T1 MRIs. The volume of lateral occipital complex, the thickness of inferior parietal lobe and postcentral gyrus, and the surface area of lateral orbitofrontal cortex and pars triangularis are identified as the 5 most important features for this task.

CONCLUSION

Our method shows promising findings for post-SRS neurocognitive decline prediction solely based on routine baseline and follow-up MRIs. In addition, it can identify critical brain ROIs associated with the post-SRS cognitive function. This method has the potential to assist treatment planning strategy to help preserve patients' QoL.

A Comprehensive Deep Learning Framework for Automatic Target Volumes Segmentation in Post-Operative Stereotactic Partial Breast Irradiation (S-PBI)

PURPOSE/OBJECTIVE(S)

In S-PBI, accurate delineation of post-surgical tumor bed volume (TBV) and clinical target volume (CTV) are crucial tasks to achieve effective radiotherapy outcomes. However, manual contouring is labor intensive, time consuming, and largely relies on the experience of clinicians. We aimed to propose a deep learning (DL) approach which mimics physicians' contouring practice to accurately segment target volumes in post-operative breast CT images.

MATERIALS/METHODS

Our approach incorporated domain knowledge into a 3D U-Net based DL model for breast target volumes (TBV and CTV) delineation. Our TBV segmentation approach was inspired by the marker-guidance procedure in manual delineation, where the visual clues provided by the markers assist physicians in defining TBV. For this purpose, a distance-transformation coupled with a Gaussian filter was adopted to convert markers' locations on the CT images to saliency maps. Subsequently, the CT images and the corresponding saliency maps formed a two-channel input for the segmentation model. For CTV segmentation, TBV was incorporated as an input in addition to the CT images, guiding the model to encode the location-related image features. The architecture allowed the network to emulate the oncologist's manual delineation where CTV is derived from TBV via a margin expansion, followed by correcting the extensions for anatomical barriers of tumor invasion (e.g., skin, chest wall). We retrospectively collected 175 prone CT images from 35 post-operative breast cancer patients who received 5-fraction partial breast irradiation (PBI) regimen on a Co-60 prone based S-PBI unit. The 35 patients were randomly split into 25, 5, and 5 for model training, validation, and testing respectively.

RESULTS

We evaluated the performance of the developed DL model on the testing dataset by comparing the predicted volumes with the manually delineated contours (ground truth) using Dice similarity coefficient (DSC), 95th percentile Hausdorff distance (HD95), and average symmetric surface distance (ASD). For TBV segmentation, our model achieved mean (standard deviation) of 0.76 (±2.7), 6.76 (±1.83) mm, and 1.9 (±0.66) mm for DSC, HD95, and ASD respectively. For CTV segmentation, our model achieved 0.94 (±0.02), 2.46 (±0.5) mm, and 0.53 (±0.14) mm for DSC, HD95, and ASD respectively. The proposed auto-segmentation approach generated TBV and CTV masks in ∼11 seconds per CT volume, implying significantly improved efficiency compared to manual contouring.

CONCLUSION

We developed a comprehensive DL framework mimicking clinical contouring practice for auto-segmentation of target volumes in S-PBI. The results demonstrated high levels of agreement between the predicted contours and physicians' manual contours. The approach is promising for improving the efficiency and accuracy of the on-line treatment planning workflow, such as adaptive based S-PBI.

Prospective Clinical Adoption of Artificial Intelligence for Organ Contouring in Head and Neck Radiation Treatment Planning

PURPOSE/OBJECTIVE(S)

Patients that undergo head and neck (H&N) radiation therapy (RT) require laborious delineation of organs-at-risk (OARs) on computed tomography (CT) scans in a treatment planning system (TPS) to minimize radiation to normal tissue. This task can be completed rapidly and accurately with recently developed artificial intelligence-based semantic segmentation models. The current study aims to deploy and evaluate a strategy for improving clinical practice with this technology.

MATERIALS/METHODS

Deep learning models were trained and tested with CT scans and OAR contours from previous H&N RT cases at our clinic. Two medical physicists vetted the models and selected a 2.5D U-Net for further implementation. The model was embedded in a dedicated server at the hospital, programmed to read H&N CT scans staged for import into the TPS, generate auto-contours, and write them into a TPS-compatible format made available alongside the scan. In the pilot implementation, the auto-contouring service was utilized for more than 60 cases, prospectively. The auto-contours were quantitatively evaluated against the treatment-approved contours to determine how much modification was performed by the clinical team.

RESULTS

The 2.5D U-Net selected for clinical integration segments 21 OARs in less than 3 minutes per scan. Across all the prospective cases, the mean Dice score and mean 95th percentile Hausdorff distance (mm) between the auto-contour and treatment-approved contour for each of the 21 OARs were as follows, respectively: brainstem (0.93, 1.94), optic chiasm (0.70, 2.96), left cochlea (0.69, 2.37), right cochlea (0.68, 2.44), esophagus (0.88, 2.46), left globe (0.93, 1.50), right globe (0.93, 1.63), glottis (0.91, 2.13), larynx (0.93, 2.76), mandible (0.90, 4.86), left optic nerve (0.78, 1.64), right optic nerve (0.82, 1.65), oral cavity (0.86, 8.46), left parotid gland (0.91, 2.78), right parotid gland (0.91, 2.39), pharynx (0.85, 2.39), spinal cord (0.87, 2.27), left submandibular gland (0.85, 3.46), right submandibular gland (0.83, 3.69), left temporal lobe (0.94, 2.20), and right temporal lobe (0.95, 2.09). The auto-contours for the optic chiasm, optic nerves, cochleas, and submandibular glands differed substantially from the final contours, a finding corroborated by the clinical team; the rest were clinically acceptable with minor or no edits necessary.

CONCLUSION

The proposed strategy provides a sophisticated starting point for treatment planning that has garnered overall favorable feedback from the participating radiation oncologists and dosimetrists. Consequently, the technique is being extended to other treatment sites.

Effects of biochar and vermicompost on growth and economic benefits of continuous cropping pepper at karst yellow soil region in Southwest China

Recently, biochar (B) and vermicompost (V) have been widely used as amendments to improve crop productivity and soil quality. However, the ameliorative effects of biochar and vermicompost on the continuous cropping of pepper under open-air conditions, particularly in the karst areas of southwestern China, remain unclear. A field experiment was conducted to study the effects of biochar and vermicompost application, alone or in combination, on the yield, quality, nutrient accumulation, fertilizer utilization, and economic benefits of continuous pepper cropping from 2021 to 2022. The experiment included six treatments: CK (no fertilizer), TF (traditional fertilization of local farmers), TFB (TF combined with biochar of 3000 kg·ha-1), TFV (TF combined with vermicompost of 3000 kg·ha-1), TFBV1 (TF combined with biochar of 1500 kg·ha-1 and vermicompost of 1500 kg·ha-1), and TFBV2 (TF combined with biochar of 3000 kg·ha-1 and vermicompost of 3000 kg·ha-1). Compared with the TF treatment, biochar and vermicompost application alone or in combination increased the yield of fresh pod pepper by 24.38-50.03% and 31.61-88.92% in 2021 and 2022, respectively, whereas the yield of dry pod pepper increased by 14.69-40.63% and 21.44-73.29% in 2021 and 2022, respectively. The application of biochar and vermicompost reduced the nitrate content and increased the vitamin C (VC) and soluble sugar content of the fruits, which is beneficial for improving their quality. Biochar and vermicompost application alone or in combination not only increased nutrient uptake but also significantly improved agronomic efficiency (AE) and recovery efficiency (RE). In addition, although the application of biochar or vermicompost increased production costs, the increase in yield improved net income (ranging from 0.77 to 22.34% in 2021 and 8.82 to 59.96% in 2022), particularly in the TFBV2 treatment. In conclusion, the use of biochar and vermicompost amendments had a positive effect on the productivity and economic benefits of continuous pepper cropping, and the co-application of biochar and vermicompost could be an effective nutrient management strategy for the continuous cropping of pepper in the karst mountain areas of southwest China.

[Efficacy of non-surgical comprehensive treatment for locally advanced hypopharyngeal carcinoma with cervical esophagus invasion]

Objective: To analyze the treatment effects and side effects of non-surgical comprehensive treatment for locally advanced hypopharyngeal carcinoma invading cervical esophagus. Methods: A retrospective analysis was performed on sixty-six patients with locally advanced hypopharyngeal carcinoma invade the esophagus. These patients were treated in the Department of Otolaryngology, Head and Neck Surgery of Chinese People's Liberation Army General Hospital between January 2011 and May 2022, including sixty-five males and one female, aged 43-71 years. Treatment regimen consisted of induction chemotherapy and concurrent chemoradiothrapy and epidermal growth factor receptor (EGFR)-targeted therapy, three of these cases were treated with programmed cell death 1 (PD-1) immunotherapy. The Kaplan-Meier method was used for survival analysis. Side effects were evaluated with the established CTCAE (Common Terminology Criteria for Adverse Events) 5.0 criteria. The factors affecting prognosis were analyzed by Cox multivariate regression analysis. Results: Sixty-four (97.0%, 64/66) patients completed the radiotherapy and chemotherapy plan. The most common grade three side effects were radioactive oropharyngeal mucositis (89.1%, 57/64) and leukopenia (23.4%, 15/64). Five (7.8%, 5/64) patients showed grade three hoarseness; two patients (3.1%, 2/64) suffered from grade three swallowing dysfunction and required feeding tube and intravenous nutrition; the remaining patients(89.1%) retained good vocal and swallowing functions. The overall survival (OS) of all patients was 81.5% after one year, 54.0% after three years, and 39.9% after five years; the progression-free survival (PFS) was 78.3% after one year, 54.9% after three years, and 42.6% after five years; local control rate (LCR) was 80.9% after one year, 62.5% after three years, and 52.0% after five years. T4a patients showed better OS, PFS and LCR than T4b patients, with statistically significant differences (χ2=8.10, 8.27, and 6.64, respectively, all P<0.05). Cox multivariate regression analysis showed that lymph node metastasis was an independent factor affecting prognosis (χ2=10.21, P<0.05). Conclusion: Non-surgical comprehensive treatment can provide with another option of radical treatment for locally advanced hypopharyngeal carcinoma with cervical esophagus invasion, offering the patients higher rate of larynx and esophageal preservation with tolerable side effects.

BAC Transgenic Expression of Human TREM2-R47H Remodels Amyloid Plaques but Unable to Reprogram Plaque-associated Microglial Reactivity in 5xFAD Mice

Background

Genetic study of late-onset Alzheimer's disease (AD) reveals that a rare Arginine-to-Histamine mutation at amino acid residue 47 (R47H) in Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) results in increased disease risk. TREM2 plays critical roles in regulating microglial response to amyloid plaques in AD, leading to their clustering and activation surrounding the plaques. We previously showed that increasing human TREM2 gene dosage exerts neuroprotective effects against AD-related deficits in amyloid depositing mouse models of AD. However, the in vivo effects of the R47H mutation on human TREM2-mediated microglial reprogramming and neuroprotection remains poorly understood.

Method

Here we created a BAC transgenic mouse model expressing human TREM2 with the R47H mutation in its cognate genomic context (BAC-TREM2-R47H). Importantly, the BAC used in this study was engineered to delete critical exons of other TREM-like genes on the BAC to prevent confounding effects of overexpressing multiple TREM-like genes. We crossed BAC-TREM2- R47H mice with 5xFAD [1], an amyloid depositing mouse model of AD, to evaluate amyloid pathologies and microglial phenotypes, transcriptomics and in situ expression of key TREM2 -dosage dependent genes. We also compared the key findings in 5xFAD/BAC-TREM2-R47H to those observed in 5xFAD/BAC-TREM2 mice.

Result

Both BAC-TREM2 and BAC-TREM2-R47H showed proper expression of three splicing isoforms of TREM2 that are normally found in human. In 5xFAD background, elevated TREM2-R47H gene dosages significantly reduced the plaque burden, especially the filamentous type. The results were consistent with enhanced phagocytosis and altered NLRP3 inflammasome activation in BAC- TREM2-R47H microglia in vitro. However, unlike TREM2 overexpression, elevated TREM2- R47H in 5xFAD failed to ameliorate cognitive and transcriptomic deficits. In situ analysis of key TREM2 -dosage dependent genes and microglial morphology uncovered that TREM2-R47H showed a loss-of-function phenotype in reprogramming of plaque-associated microglial reactivity and gene expression in 5xFAD.

Conclusion

Our study demonstrated that the AD-risk variant has a previously unknown, mixture of partial and full loss of TREM2 functions in modulating microglial response in AD mouse brains. Together, our new BAC-TREM2-R47H model and prior BAC-TREM2 mice are invaluable resource to facilitate the therapeutic discovery that target human TREM2 and its R47H variant to ameliorate AD and other neurodegenerative disorders.

Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice

Heterosis has been widely used in multiple crops. However, the molecular mechanism and prediction of heterosis remains elusive. We generated five F1 hybrids [four showing better-parent heterosis (BPH) and one showing mid-parent heterosis], and performed the transcriptomic and methylomic analyses to identify the candidate genes for BPH and explore the molecular mechanism of heterosis and the potential predictors for heterosis. Transcriptomic results showed that most of the differentially expressed genes shared in the four better-parent hybrids were significantly enriched into the terms of molecular function, and the additive and dominant effects played crucial roles for BPH. DNA methylation level, especially in CG context, significantly and positively correlated with grain yield per plant. The ratios of differentially methylated regions in CG context in exons to transcription start sites between the parents exhibited significantly negative correlation with the heterosis levels of their hybrids, as was further confirmed in 24 pairwise comparisons of other rice lines, implying that this ratio could be a feasible predictor for heterosis level, and this ratio of less than 5 between parents in early growth stages might be a critical index for judging that their F1 hybrids would show BPH. Additionally, we identified some important genes showing differential expression and methylation, such as OsDCL2, Pi5, DTH2, DTH8, Hd1 and GLW7 in the four better-parent hybrids as the candidate genes for BPH. Our findings helped shed more light on the molecular mechanism and heterosis prediction.

Evidence for Band Renormalizations in Strong-Coupling Superconducting Alkali-Fulleride Films

There has been a long-standing debate about the mechanism of the unusual superconductivity in alkali-intercalated fullerides. In this Letter, using high-resolution angle-resolved photoemission spectroscopy, we systematically investigate the electronic structures of superconducting K_{3}C_{60} thin films. We observe a dispersive energy band crossing the Fermi level with the occupied bandwidth of about 130 meV. The measured band structure shows prominent quasiparticle kinks and a replica band involving the Jahn-Teller active phonon modes, which reflects strong electron-phonon coupling in the system. The electron-phonon coupling constant is estimated to be about 1.2, which dominates the quasiparticle mass renormalization. Moreover, we observe an isotropic nodeless superconducting gap beyond the mean-field estimation (2Δ/k_{B}T_{c}≈5). Both the large electron-phonon coupling constant and large reduced superconducting gap suggest a strong-coupling superconductivity in K_{3}C_{60}, while the electronic correlation effect is suggested by the observation of a waterfall-like band dispersion and the small bandwidth compared with the effective Coulomb interaction. Our results not only directly visualize the crucial band structure but also provide important insights into the mechanism of the unusual superconductivity of fulleride compounds.

6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication

N6-methyladenine (6mA) DNA methylation has emerged as an important epigenetic modification in eukaryotes. Nevertheless, the evolution of the 6mA methylation of homologous genes after species and after gene duplications remains unclear in plants. To understand the evolution of 6mA methylation, we detected the genome-wide 6mA methylation patterns of four lotus plants (Nelumbo nucifera) from different geographic origins by nanopore sequencing and compared them to patterns in Arabidopsis and rice. Within lotus, the genomic distributions of 6mA sites are different from the widely studied 5mC methylation sites. Consistently, in lotus, Arabidopsis and rice, 6mA sites are enriched around transcriptional start sites, positively correlated with gene expression levels, and preferentially retained in highly and broadly expressed orthologs with longer gene lengths and more exons. Among different duplicate genes, 6mA methylation is significantly more enriched and conserved in whole-genome duplicates than in local duplicates. Overall, our study reveals the convergent patterns of 6mA methylation evolution based on both lineage and duplicate gene divergence, which underpin their potential role in gene regulatory evolution in plants.

Single-cell RNA-seq of Lotus japonicus provide insights into identification and function of root cell types of legume

The roots of legume plant play a crucial role in nitrogen fixation. However, the transcriptomes of different cell types of legume root and their functions remain largely unknown. Here, we performed single-cell RNA sequencing and profiled more than 22,000 single cells from root tips of Lotus japonicus, a model species of legume. We identified seven clusters corresponding to seven major cell types, which were validated by in situ hybridization. Further analysis revealed regulatory programs including phytohormone and nodulation associated with specific cell types, and revealed conserved and diverged features for the cell types. Our results represent the first single-cell resolution transcriptome for legume root tips and a valuable resource for studying the developmental and physiological functions of various cell types in legumes.

Imaging diagnosis of intravenous leiomyomatosis: an institutional experience

AIM

To review and summarise the clinical and imaging characteristics of intravenous leiomyomatosis (IVL), a rare smooth muscle tumour originating from the uterus.

MATERIALS AND METHODS

Twenty-seven patients with a histopathological diagnosis of IVL who underwent surgery were reviewed retrospectively. All patients underwent pelvic ultrasonography, inferior vena cava (IVC) ultrasonography, and echocardiography before surgery. Computed tomography (CT) with contrast enhancement was performed in patients with extrapelvic IVL. Some patients underwent pelvic magnetic resonance imaging (MRI).

RESULTS

Mean age was 44.81 years. Clinical symptoms were non-specific. IVL was intrapelvic in seven patients and extrapelvic in 20. Preoperative pelvic ultrasonography missed the diagnosis in 85.7% of patients with intrapelvic IVL. Pelvic MRI was useful to evaluate the parauterine vessels. Incidence of cardiac involvement was 59.26%. Echocardiography showed a highly mobile sessile mass in the right atrium with moderate-to-low echogenicity that originates from the IVC. Ninety per cent of extrapelvic lesions showed unilateral growth. The most common growth pattern was via the right uterine vein-internal iliac vein-IVC pathway.

CONCLUSION

The clinical symptoms of IVL are non-specific. For patients with intrapelvic IVL, early diagnosis is difficult. Pelvic ultrasound should focus on the parauterine vessels, the iliac and ovarian veins should be explored carefully. MRI has obvious advantages in evaluating parauterine vessel involvement, which is helpful for early diagnosis. For patients with extrapelvic IVL, CT should be performed before surgery as part of a comprehensive evaluation. IVC ultrasonography and echocardiography are recommended when IVL is highly suspected.

Folate shapes plant root architecture by affecting auxin distribution

Folate (vitamin B9) is important for plant root development, but the mechanism is largely unknown. Here we characterized a root defective mutant, folb2, in Arabidopsis, which has severe developmental defects in the primary root. The root apical meristem of the folb2 mutant is impaired, and adventitious roots are frequently found at the root-hypocotyl junction. Positional cloning revealed that a 61-bp deletion is present in the predicted junction region of the promoter and the 5' untranslated region of AtFolB2, a gene encoding a dihydroneopterin aldolase that functions in folate biosynthesis. This mutation leads to a significant reduction in the transcript level of AtFolB2. Liquid chromatography-mass spectrometry analysis showed that the contents of the selected folate compounds were decreased in folb2. Arabidopsis AtFolB2 knockdown lines phenocopy the folb2 mutant. On the other hand, the application of exogenous 5-formyltetrahydrofolic acid could rescue the root phenotype of folb2, indicating that the root phenotype is indeed related to the folate level. Further analysis revealed that folate could promote rootward auxin transport through auxin transporters and that folate may affect particular auxin/indole-3-acetic acid proteins and auxin response factors. Our findings provide new insights into the important role of folic acid in shaping root structure.

[Efficacy and safety of various doses of hybutimibe monotherapy or in combination with atorvastatin for primary hypercholesterolemia: a multicenter, randomized, double-blind, double-dummy, parallel-controlled phase Ⅲ clinical trial]

Objective: To evaluate the efficacy and safety of hybutimibe monotherapy or in combination with atorvastatin in the treatment of primary hypercholesterolemia. Methods: This was a multicenter, randomized, double-blind, double-dummy, parallel-controlled phase Ⅲ clinical trial of patients with untreated primary hypercholesterolemia from 41 centers in China between August 2015 and April 2019. Patients were randomly assigned, at a ratio of 1∶1∶1∶1∶1∶1, to the atorvastatin 10 mg group (group A), hybutimibe 20 mg group (group B), hybutimibe 20 mg plus atorvastatin 10 mg group (group C), hybutimibe 10 mg group (group D), hybutimibe 10 mg plus atorvastatin 10 mg group (group E), and placebo group (group F). After a dietary run-in period for at least 4 weeks, all patients were administered orally once a day according to their groups. The treatment period was 12 weeks after the first dose of the study drug, and efficacy and safety were evaluated at weeks 2, 4, 8, and 12. After the treatment period, patients voluntarily entered the long-term safety evaluation period and continued the assigned treatment (those in group F were randomly assigned to group B or D), with 40 weeks' observation. The primary endpoint was the percent change in low density lipoprotein cholesterol (LDL-C) from baseline at week 12. Secondary endpoints included the percent changes in high density lipoprotein cholesterol (HDL-C), triglyceride (TG), apolipoprotein B (Apo B) at week 12 and changes of the four above-mentioned lipid indicators at weeks 18, 24, 38, and 52. Safety was evaluated during the whole treatment period. Results: Totally, 727 patients were included in the treatment period with a mean age of (55.0±9.3) years old, including 253 males. No statistical differences were observed among the groups in demographics, comorbidities, and baseline blood lipid levels. At week 12, the percent changes in LDL-C were significantly different among groups A to F (all P<0.01). Compared to atorvastatin alone, hybutimibe combined with atorvastatin could further improve LDL-C, TG, and Apo B (all P<0.05). Furthermore, there was no significant difference in percent changes in LDL-C at week 12 between group C and group E (P=0.991 7). During the long-term evaluation period, there were intergroup statistical differences in changes of LDL-C, TG and Apo B at 18, 24, 38, and 52 weeks from baseline among the statins group (group A), hybutimibe group (groups B, D, and F), and combination group (groups C and E) (all P<0.01), with the best effect observed in the combination group. The incidence of adverse events was 64.2% in the statins group, 61.7% in the hybutimibe group, and 71.0% in the combination group during the long-term evaluation period. No treatment-related serious adverse events or adverse events leading to death occurred during the 52-week study period. Conclusions: Hybutimibe combined with atorvastatin showed confirmatory efficacy in patients with untreated primary hypercholesterolemia, which could further enhance the efficacy on the basis of atorvastatin monotherapy, with a good overall safety profile.

Integration of high-throughput phenotyping, GWAS, and predictive models reveals the genetic architecture of plant height in maize

Plant height (PH) is an essential trait in maize (Zea mays) that is tightly associated with planting density, biomass, lodging resistance, and grain yield in the field. Dissecting the dynamics of maize plant architecture will be beneficial for ideotype-based maize breeding and prediction, as the genetic basis controlling PH in maize remains largely unknown. In this study, we developed an automated high-throughput phenotyping platform (HTP) to systematically and noninvasively quantify 77 image-based traits (i-traits) and 20 field traits (f-traits) for 228 maize inbred lines across all developmental stages. Time-resolved i-traits with novel digital phenotypes and complex correlations with agronomic traits were characterized to reveal the dynamics of maize growth. An i-trait-based genome-wide association study identified 4945 trait-associated SNPs, 2603 genetic loci, and 1974 corresponding candidate genes. We found that rapid growth of maize plants occurs mainly at two developmental stages, stage 2 (S2) to S3 and S5 to S6, accounting for the final PH indicators. By integrating the PH-association network with the transcriptome profiles of specific internodes, we revealed 13 hub genes that may play vital roles during rapid growth. The candidate genes and novel i-traits identified at multiple growth stages may be used as potential indicators for final PH in maize. One candidate gene, ZmVATE, was functionally validated and shown to regulate PH-related traits in maize using genetic mutation. Furthermore, machine learning was used to build predictive models for final PH based on i-traits, and their performance was assessed across developmental stages. Moderate, strong, and very strong correlations between predictions and experimental datasets were achieved from the early S4 (tenth-leaf) stage. Colletively, our study provides a valuable tool for dissecting the spatiotemporal formation of specific internodes and the genetic architecture of PH, as well as resources and predictive models that are useful for molecular design breeding and predicting maize varieties with ideal plant architectures.

Development of a laser-based angle-resolved-photoemission spectrometer with sub-micrometer spatial resolution and high-efficiency spin detection

Angle-resolved photoemission spectroscopy with sub-micrometer spatial resolution (μ-ARPES), has become a powerful tool for studying quantum materials. To achieve sub-micrometer or even nanometer-scale spatial resolution, it is important to focus the incident light beam (usually from synchrotron radiation) using x-ray optics, such as the zone plate or ellipsoidal capillary mirrors. Recently, we developed a laser-based μ-ARPES with spin-resolution (LMS-ARPES). The 177 nm laser beam is achieved by frequency-doubling a 355 nm beam using a KBBF crystal and subsequently focused using an optical lens with a focal length of about 16 mm. By characterizing the focused spot size using different methods and performing spatial-scanning photoemission measurement, we confirm the sub-micron spatial resolution of the system. Compared with the μ-ARPES facilities based on the synchrotron radiation, our LMS-ARPES system is not only more economical and convenient, but also with higher photon flux (>5 × 10¹³ photons/s), thus enabling the high-resolution and high-statistics measurements. Moreover, the system is equipped with a two-dimensional spin detector based on exchange scattering at a surface-passivated iron film grown on a W(100) substrate. We investigate the spin structure of the prototype topological insulator Bi₂Se₃ and reveal a high spin-polarization rate, confirming its spin-momentum locking property. This lab-based LMS-ARPES will be a powerful research tool for studying the local fine electronic structures of different condensed matter systems, including topological quantum materials, mesoscopic materials and structures, and phase-separated materials.

Association of non-alcoholic fatty liver disease with total testosterone in non-overweight/obese men with type 2 diabetes mellitus

PURPOSE

Non-alcoholic fatty liver disease (NAFLD) is considered as both a vital risk factor and a consequence of type 2 diabetes mellitus (T2DM). Low total testosterone (TT) is common in men with T2DM, contributing to increased risks of metabolic diseases. This study aimed to investigate the association between TT levels and the prevalence of NAFLD in men with T2DM.

METHODS

In this cross-sectional study, 1005 men with T2DM were enrolled in National Metabolic Management Center (MMC) of First Affiliated Hospital of Wenzhou Medical University between January 2017 and August 2021. NAFLD was diagnosed using ultrasound as described by the Chinese Liver Disease Association. Overweight/obesity was defined as body mass index (BMI) ≥ 25 kg/m² according to WHO BMI classifications.

RESULTS

Individuals without NAFLD had higher serum TT levels than those with NAFLD. After adjustments for potential confounding factors, the top tertile was significantly associated with lower prevalence of NAFLD compared with the bottom tertile of TT level [odds ratio (OR) 0.303, 95% confidence interval (CI) 0.281-0.713; P < 0.001]. The association between TT with NAFLD in individuals with normal weight (OR 0.175, 95% CI 0.098-0.315; P < 0.001) was stronger than in individuals with overweight/obesity (OR 0.509, 95% CI 0.267-0.971; P = 0.040). There was a significant interaction of TT with overweight/obesity (P for interaction = 0.018 for NAFLD).

CONCLUSION

Higher serum TT was significantly associated with a lower prevalence of NAFLD in men with T2DM. We found that the relationship of TT and NAFLD was stronger in individuals with non-overweight/obesity.

Novelties in Microthyriaceae (Microthyriales): Two New Asexual Genera with Three New Species from Freshwater Habitats in Guizhou Province, China

Microthyriaceae is typified by the sexual genus Microthyrium, with eight asexual genera. Three interesting isolates were collected during our investigation of freshwater fungi from the wetlands in Guizhou Province, southwest China. Three new asexual morphs are identified. Phylogenetic analyses using ITS and LSU gene regions revealed the placement of these isolates in Microthyriaceae (Microthyriales, Dothideomycetes). Based on the morphology and phylogenetic evidence, two new asexual genera, Paramirandina and Pseudocorniculariella, and three new species, Pa. aquatica, Pa. cymbiformis, and Ps. guizhouensis, are introduced. Descriptions and illustrations of the new taxa are provided, with a phylogenetic tree of Microthyriales and related taxa.

Silver-Ion-Passivated Black Phosphorus Photodetector to Improve Response Time

We present a remarkable improvement in the photoresponse time of few-layer black phosphorus (BP) following treatment with silver nitrate solution, with the rise time being reduced from 1.71 s to...

Association between Iodized Salt Intake and Cognitive Function in Older Adults in China

OBJECTIVES

To investigate the association between iodized salt intake and cognitive function in older adults.

DESIGN

A cross-sectional study.

SETTINGS

Individuals from the Zhejiang Major Public Health Surveillance Program (ZPHS).

PARTICIPANTS

Data of 10,217 participants (including 4,680 coastal residents and 5,537 inland residents) aged ≥ 60 years were analyzed.

MEASUREMENTS

Salt intake was evaluated using a questionnaire, and participants were stratified into the following three groups: iodized salt, non-iodized salt, and mixed salt. Cognitive function was assessed through the Mini-Mental State Examination and defined using education-specific cut-off points. Logistic regression models controlling for an extensive range of potential confounders were generated to examine the association between salt intake and cognitive function among all participants.

RESULTS

Data from 10,217 participants with a 16.1% prevalence of cognitive impairment were analyzed. Compared with non-iodized salt intake, consumption of iodized salt was inversely associated with cognitive impairment (odds ratio [OR], 0.410; 95% confidence interval [CI], 0.351-0.480; P < 0.001) in all participants after multivariable adjustment. An association between iodized salt intake and cognitive impairment was observed in coastal (OR, 0.441; 95% CI, 0.340-0.572; P < 0.001) and inland residents (OR, 0.569; 95% CI, 0.439-0.738; P < 0.001). Despite the insufficient sample size, the results for individuals consuming mixed salt suggested an inverse association between mixed salt intake and cognitive impairment among coastal residents (OR, 0.598; 95% CI, 0.405-0.885; P = 0.010) after multivariable adjustment.

CONCLUSION

Our results indicate that iodized salt intake may reduce the risk of cognitive impairment in older adults living in coastal or inland areas, and the protective effect of iodized salt intake is greater in coastal areas than in inland areas.

Silencing PARP-1 binding protein Inhibits Cell Migration and Invasion via Suppressing UBE2C in Nasopharyngeal Cancer Cells

BACKGROUND

Nasopharyngeal carcinoma (NPC) is a malignancy with a 2 per 100 000 incidence rate in the world. Overall survival (OS) of patients in stage I-II disease is around 80%, whereas OS of patients in stage III-IVB disease drops to 60%, implying the importance of diagnosis to reduce NPC mortality. However, more than 70% patients of NPC were diagnosed at advanced stages (stage III and IV) in clinics, and it definitely contributes to little substantial improvement in the 5-year survival rates although NPC is sensitive to radio-and chemotherapy. Hence, development of novel biomarkers and targetable genes in NPC is eagerly awaited.

METHODS

We had analyzed the dataset GSE12452 and found hundreds of genes trans-activated in NPC. Among them, this study focused on PARP-1 binding protein (PARPBP) whose overexpression was also validated in GSE13597 and GSE53819 datasets.

RESULTS

Knockdown of PARPBP significantly reduced cell viability in NPC and also identified hundreds of differentially expressed genes including 377 downregulated and 518 upregulated genes in HONE-1 cells with stably knockdown PARPBP. Furthermore, PARPBP might promote cell migration and invasion in NPC through positive regulation of ubiquitin-conjugating enzyme 2C (UBE2C).

CONCLUSION

The results demonstrate the aberrant expression of PARPBP in NPC, and imply its importance in nasopharyngeal carcinogenesis which further opens up the possibility of PARPBP as a novel diagnostic biomarker for NPC therapy.

Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes

BACKGROUND

The Lycophyta species are the extant taxa most similar to early vascular plants that were once abundant on Earth. However, their distribution has greatly diminished. So far, the absence of chromosome-level assembled lycophyte genomes has hindered our understanding of evolution and environmental adaption of lycophytes.

FINDINGS

We present the reference genome of the tetraploid aquatic quillwort, Isoetes sinensis, a lycophyte. This genome represents the first chromosome-level assembled genome of a tetraploid seed-free plant. Comparison of genomes between I. sinensis and Isoetestaiwanensis revealed conserved and different genomic features between diploid and polyploid lycophytes. Comparison of the I. sinensis genome with those of other species representing the evolutionary lineages of green plants revealed the inherited genetic tools for transcriptional regulation and most phytohormones in I. sinensis. The presence and absence of key genes related to development and stress responses provide insights into environmental adaption of lycophytes.

CONCLUSIONS

The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic and environmental studies of not only I. sinensis but also other lycophytes.

Diagnostic gene signatures and aberrant pathway activation based on m6A methylation regulators in rheumatoid arthritis

Purpose

Rheumatoid arthritis (RA) is a chronic autoimmune disease (AD) characterized by persistent synovial inflammation, bone erosion and progressive joint destruction. This research aimed to elucidate the potential roles and molecular mechanisms of N6-methyladenosine (m6A) methylation regulators in RA.

Methods

An array of tissues from 233 RA and 126 control samples was profiled and integrated for mRNA expression analysis. Following quality control and normalization, the cohort was split into training and validation sets. Five distinct machine learning feature selection methods were applied to the training set and validated in validation sets.

Results

Among the six models, the LASSO_λ-1se model not only performed better in the validation sets but also exhibited more stringent performance. Two m6A methylation regulators were identified as significant biomarkers by consensus feature selection from all four methods. IGF2BP3 and YTHDC2, which are differentially expressed in patients with RA and controls, were used to predict RA diagnosis with high accuracy. In addition, IGF2BP3 showed higher importance, which can regulate the G2/M transition to promote RA-FLS proliferation and affect M1 macrophage polarization.

Conclusion

This consensus of multiple machine learning approaches identified two m6A methylation regulators that could distinguish patients with RA from controls. These m6A methylation regulators and their target genes may provide insight into RA pathogenesis and reveal novel disease regulators and putative drug targets.

Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips

BACKGROUND

Root development and function have central roles in plant adaptation to the environment. The modification of root traits has additionally been a major driver of crop performance since the green revolution; however, the molecular underpinnings and the regulatory programmes defining root development and response to environmental stress remain largely unknown. Single-cell reconstruction of gene regulatory programmes provides an important tool to understand the cellular phenotypic variation in complex tissues and their response to endogenous and environmental stimuli. While single-cell transcriptomes of several plant organs have been elucidated, the underlying chromatin landscapes associated with cell type-specific gene expression remain largely unexplored.

RESULTS

To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-seq (scATAC-seq) to 46,758 cells from rice root tips under normal and heat stress conditions. Our data revealed cell type-specific accessibility variance across most of the major cell types and allowed us to identify sets of transcription factors which associate with accessible chromatin regions (ACRs). Using root hair differentiation as a model, we demonstrate that chromatin and gene expression dynamics during cell type differentiation correlate in pseudotime analyses. In addition to developmental trajectories, we describe chromatin responses to heat and identify cell type-specific accessibility changes to this key environmental stimulus.

CONCLUSIONS

We report chromatin landscapes during rice root development at single-cell resolution. Our work provides a framework for the integrative analysis of regulatory dynamics in this important crop organ at single-cell resolution.

Plant synthetic epigenomic engineering for crop improvement

Efforts have been directed to redesign crops with increased yield, stress adaptability, and nutritional value through synthetic biology-the application of engineering principles to biology. A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops, thus heralding the promise of "synthetic epigenetics." In this review, we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques, epigenetic editing, and deep learning-driven predictive tools can rapidly extend these insights. We also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.