Sirtuin 6 ameliorates bleomycin-induced pulmonary fibrosis via activation of lipid catabolism.

Pulmonary fibrosis is a chronic and serious interstitial lung disease with little effective therapies currently. Our incomplete understanding of its pathogenesis remains obstacles in therapeutic developments. Sirtuin 6 (SIRT6) has been shown to mitigate multiple organic fibrosis. However, the involvement of SIRT6-mediated metabolic regulation in pulmonary fibrosis remains unclear. Here, we demonstrated that SIRT6 was predominantly expressed in alveolar epithelial cells in human lung tissues by using a single-cell sequencing database. We showed that SIRT6 protected against bleomycin-induced injury of alveolar epithelial cells in vitro and pulmonary fibrosis of mice in vivo. High-throughput sequencing revealed enriched lipid catabolism in Sirt6 overexpressed lung tissues. Mechanismly, SIRT6 ameliorates bleomycin-induced ectopic lipotoxicity by enhancing lipid degradation, thereby increasing the energy supply and reducing the levels of lipid peroxides. Furthermore, we found that peroxisome proliferator-activated receptor α (PPARα) was essential for SIRT6-mediated lipid catabolism, anti-inflammatory responses, and antifibrotic signaling. Our data suggest that targeting SIRT6-PPARα-mediated lipid catabolism could be a potential therapeutic strategy for diseases complicated with pulmonary fibrosis.

Single-cell landscape of peripheral immune response in patients with anti-melanoma differentiation-associated gene 5 dermatomyositis.

OBJECTIVE: Anti-melanoma differentiation-associated gene 5 (MDA5)-positive dermatomyositis (DM) is a rare but life-threatening autoimmune disorder with a high risk to develop rapidly progressive interstitial lung disease. Current empirical therapies have limited improvement on patients' survival, as little is known about the aetiology of MDA5 DM. To best understand its immune landscape, we applied single-cell RNA sequencing (scRNA-seq) to peripheral blood samples from DM patients and healthy controls. METHODS: Peripheral blood mononuclear cells (PBMCs) from eight DM patients, comprising three distinct subtypes, as well as two healthy donors, were sequenced by 10X Genomics platform. Additional scRNA-seq data of four healthy donors were incorporated for further bioinformatic analysis. RESULTS: Aberrant increased proportions of CD14+ monocyte and plasma cells were observed in MDA5 DM samples. Moreover, we found overactivated type I interferon response and antiviral immunity in both innate and adaptive immune cells derived from MDA5 DM patients, which was positively correlated with disease severity. Importantly, a unique subset of CD14+ monocyte that highly expressed interferon alpha-inducible protein 27 (IFI27, a biomarker for viral infection) and interferon induced with helicase C domain 1 (IFIH1, encodes MDA5) was specifically identified in MDA5 DM samples for the first time. CONCLUSION: Our study demonstrates the peripheral immune cell atlas of different DM subtypes, provides compelling evidence for viral infection-derived origin of MDA5 DM, and offers potential targets for innovative therapeutic interventions.

Exploring the correlation between genetic transcription and multi-temporal developmental autism spectrum disorder using resting-state functional magnetic resonance imaging.

Introduction: The present investigation aimed to explore the neurodevelopmental trajectory of autism spectrum disorder (ASD) by identifying the changes in brain function and gene expression associated with the disorder. Previous studies have indicated that ASD is a highly inherited neurodevelopmental disorder of the brain that displays symptom heterogeneity across different developmental periods. However, the transcriptomic changes underlying these developmental differences remain largely unknown. Methods: To address this gap in knowledge, our study employed resting-state functional magnetic resonance imaging (rs-fMRI) data from a large sample of male participants across four representative age groups to stratify the abnormal changes in brain function associated with ASD. Partial least square regression (PLSr) was utilized to identify unique changes in gene expression in brain regions characterized by aberrant functioning in ASD. Results: Our results revealed that ASD exhibits distinctive developmental trajectories in crucial brain regions such as the default mode network (DMN), temporal lobe, and prefrontal lobes during critical periods of neurodevelopment when compared to the control group. These changes were also associated with genes primarily located in synaptic tissues. Discussion: The findings of this study suggest that the neurobiology of ASD is uniquely heterogeneous across different ages and may be accompanied by distinct molecular mechanisms related to gene expression.

Protocol for siRNA-mediated TET1 knockdown during differentiation of human embryonic stem cells into definitive endoderm cells.

TET1-mediated active DNA demethylation is required for endogenous retrovirus (ERV) enhancer activation during human ES differentiation into definitive endoderm (DE) cells. Here we present a protocol for siRNA-mediated TET1 knockdown during this process to decipher TET1's role in ERV activation and DE differentiation. We describe steps for inducing ES into DE cells. We then detail steps for knocking down TET1 during differentiation and for examining the effects of TET1 knockdown on LTR6B methylation, cell morphology, and gene expression. For complete details on the use and execution of this protocol, please refer to Wu et al. (2022).1.

Loss of PHF8 induces a viral mimicry response by activating endogenous retrotransposons.

Immunotherapy has become established as major treatment modality for multiple types of solid tumors, including colorectal cancer. Identifying novel immunotherapeutic targets to enhance anti-tumor immunity and sensitize current immune checkpoint blockade (ICB) in colorectal cancer is needed. Here we report the histone demethylase PHD finger protein 8 (PHF8, KDM7B), a Jumonji C domain-containing protein that erases repressive histone methyl marks, as an essential mediator of immune escape. Ablation the function of PHF8 abrogates tumor growth, activates anti-tumor immune memory, and augments sensitivity to ICB therapy in mouse models of colorectal cancer. Strikingly, tumor PHF8 deletion stimulates a viral mimicry response in colorectal cancer cells, where the depletion of key components of endogenous nucleic acid sensing diminishes PHF8 loss-meditated antiviral immune responses and anti-tumor effects in vivo. Mechanistically, PHF8 inhibition elicits H3K9me3-dependent retrotransposon activation by promoting proteasomal degradation of the H3K9 methyltransferase SETDB1 in a demethylase-independent manner. Moreover, PHF8 expression is anti-correlated with canonical immune signatures and antiviral immune responses in human colorectal adenocarcinoma. Overall, our study establishes PHF8 as an epigenetic checkpoint, and targeting PHF8 is a promising viral mimicry-inducing approach to enhance intrinsic anti-tumor immunity or to conquer immune resistance.

Whole-body tumor segmentation from PET/CT images using a two-stage cascaded neural network with camouflaged object detection mechanisms.

BACKGROUND: Whole-body Metabolic Tumor Volume (MTVwb) is an independent prognostic factor for overall survival in lung cancer patients. Automatic segmentation methods have been proposed for MTV calculation. Nevertheless, most of existing methods for patients with lung cancer only segment tumors in the thoracic region. PURPOSE: In this paper, we present a Two-Stage cascaded neural network integrated with Camouflaged Object Detection mEchanisms (TS-Code-Net) for automatic segmenting tumors from whole-body PET/CT images. METHODS: Firstly, tumors are detected from the Maximum Intensity Projection (MIP) images of PET/CT scans, and tumors' approximate localizations along z-axis are identified. Secondly, the segmentations are performed on PET/CT slices that contain tumors identified by the first step. Camouflaged object detection mechanisms are utilized to distinguish the tumors from their surrounding regions that have similar Standard Uptake Values (SUV) and texture appearance. Finally, the TS-Code-Net is trained by minimizing the total loss that incorporates the segmentation accuracy loss and the class imbalance loss. RESULTS: The performance of the TS-Code-Net is tested on a whole-body PET/CT image data-set including 480 Non-Small Cell Lung Cancer (NSCLC) patients with five-fold cross-validation using image segmentation metrics. Our method achieves 0.70, 0.76, and 0.70, for Dice, Sensitivity and Precision, respectively, which demonstrates the superiority of the TS-Code-Net over several existing methods related to metastatic lung cancer segmentation from whole-body PET/CT images. CONCLUSIONS: The proposed TS-Code-Net is effective for whole-body tumor segmentation of PET/CT images. Codes for TS-Code-Net are available at: https://github.com/zyj19/TS-Code-Net.

Transposable elements activation triggers necroptosis in mouse embryonic stem cells.

Deficiency of the histone H3K9 methyltransferase SETDB1 induces RIPK3-dependent necroptosis in mouse embryonic stem cells (mESCs). However, how necroptosis pathway is activated in this process remains elusive. Here we report that the reactivation of transposable elements (TEs) upon SETDB1 knockout is responsible for the RIPK3 regulation through both cis and trans mechanisms. IAPLTR2_Mm and MMERVK10c-int, both of which are suppressed by SETDB1-dependent H3K9me3, act as enhancer-like cis-regulatory elements and their RIPK3 nearby members enhance RIPK3 expression when SETDB1 is knockout. Moreover, reactivated endogenous retroviruses generate excessive viral mimicry, which promotes necroptosis mainly through Z-DNA-binding protein 1 (ZBP1). These results indicate TEs play an important role in regulating necroptosis.

Lifelong deformities in an adult caused by vitamin D­dependent rickets type 1A: A case report.

Vitamin D-dependent rickets (VDDR) type 1A is a rare autosomal recessive disorder caused by cytochrome P450 family 27 subfamily B member 1 (CYP27B1) mutations and can lead to deficiencies in 1α-hydroxylase activity. The present study describes the case of a 39-year-old male patient who presented with rickets and deformities of limbs. Blood biochemical analysis revealed hypocalcemia and high serum parathyroid hormone (PTH) levels. Whole-exome Sanger sequencing using peripheral venous blood of this patient and his parents revealed exon1 c.182T>C, a novel mutation. Through physical examination, laboratory tests, imaging including lower limbs and lumbar spine X-ray and pelvis CT scan, and genetic testing, the patient was diagnosed with VDDR-1A. Following 1 month of treatment with 0.5 µg 1,25-dihydroxy-vitamin D3 twice daily and 0.6 g calcium carbonate once daily, follow-up examinations revealed that the patient's PTH and serum calcium levels had returned to normal. As the patient was diagnosed in his adulthood and missed the optimal treatment period, he developed irreversible deformities. If VDDR-1A can be diagnosed during infancy and childhood, skeletal deformities may be prevented. Therefore, the present report supports the proposal of early genetic sequencing in children with calcium deficiencies for the early diagnosis of rare diseases such as VDDR-1A, -1B and -2A and hereditary hypophosphatemic rickets. Since VDDR-1A diagnosed in adults is rare, the present case may provide clinicians with further insights into the characteristics of this rare disease.

Species-specific rewiring of definitive endoderm developmental gene activation via endogenous retroviruses through TET1-mediated demethylation.

Transposable elements (TEs) are the major sources of lineage-specific genomic innovation and comprise nearly half of the human genome, but most of their functions remain unclear. Here, we identify that a series of endogenous retroviruses (ERVs), a TE subclass, regulate the transcriptome at the definitive endoderm stage with in vitro differentiation model from human embryonic stem cell. Notably, these ERVs perform as enhancers containing binding sites for critical transcription factors for endoderm lineage specification. Genome-wide methylation analysis shows most of these ERVs are derepressed by TET1-mediated DNA demethylation. LTR6B, a representative definitive endoderm activating ERV, contains binding sites for FOXA2 and GATA4 and governs the primate-specific expression of its neighboring developmental genes such as ERBB4 in definitive endoderm. Together, our study proposes evidence that recently evolved ERVs represent potent de novo developmental regulatory elements, which, in turn, fine-tune species-specific transcriptomes during endoderm and embryonic development.

Regeneration of the human segmentation clock in somitoids in vitro.

Each vertebrate species appears to have a unique timing mechanism for forming somites along the vertebral column, and the process in human remains poorly understood at the molecular level due to technical and ethical limitations. Here, we report the reconstitution of human segmentation clock by direct reprogramming. We first reprogrammed human urine epithelial cells to a presomitic mesoderm (PSM) state capable of long-term self-renewal and formation of somitoids with an anterior-to-posterior axis. By inserting the RNA reporter Pepper into HES7 and MESP2 loci of these iPSM cells, we show that both transcripts oscillate in the resulting somitoids at ~5 h/cycle. GFP-tagged endogenous HES7 protein moves along the anterior-to-posterior axis during somitoid formation. The geo-sequencing analysis further confirmed anterior-to-posterior polarity and revealed the localized expression of WNT, BMP, FGF, and RA signaling molecules and HOXA-D family members. Our study demonstrates the direct reconstitution of human segmentation clock from somatic cells, which may allow future dissection of the mechanism and components of such a clock and aid regenerative medicine.

High Electromagnetic Shielding Effect of Carbon Nanotubes/Waterborne Polyurethane Composites Prepared by "Break-Adsorption" Method.

In recent years, conductive polymer composites have been widely studied for their electrical conductivity and electromagnetic shielding effects due to their advantages of light weight, simple preparation methods, and structural design versatility. In this study, oxidized multi-walled carbon nanotubes/waterborne polyurethane composites (OCNT/WPU) were prepared by grafting oxidized carbon nanotubes onto polyurethane molecular chains through in situ polymerization, using environmentally friendly waterborne polyurethane as the polymer matrix. Then, the OCNT/WPU structure was broken by high shear force, and the loading of CNTs was increased by adsorption, and a new composite structure was designed (denoted by OCWPU). The structure and morphology of OCNT/WPU and OCWPU were characterized by FT-IR and SEM. The structure and morphology of OCWPU with different multi-walled carbon nanotube loadings (CNTs/OCWPU) were characterized by SEM, Raman. Finally, the electrical conductivity and the electromagnetic shielding properties of the composites were investigated. It was found that after application of high shear force, the structure of OCWPU was disrupted and the surface activity of the material increased. With the increase in CNTs content, CNTs formed a rosette structure in the polyurethane matrix and covered the surface, and its electromagnetic shielding effect in X-bond (8.2-12.4 Ghz) would be able to reach 23 dB at 5% CNTs/OCWPU and 66.5 dB at 50% CNTs/OCWPU to meet the commercial needs. With 50% CNTs/OCWPU, an electrical conductivity of 5.1 S/cm could be achieved. This work provides a novel idea for the structural design of conductive polymer composites, which can achieve greater performance with the same carbon nanotube content.

Long-term Remission of Acute Intermittent Porphyria Treated with Gonadotropin-Releasing Hormone Analogues and Estrogen: a Case Report.

BACKGROUND: Acute intermittent porphyria (AIP) is an autosomal dominant hepatic porphyria characterized by a partial deficiency of hydroxymethylbilane synthase involved in heme biosynthesis. It is difficult for all patients to achieve complete control of AIP episodes. METHOD: We report on a 20-year-old female woman who suffered from recurrent abdominal pain and was diagnosed as "acute intermittent porphyria". She failed to respond to conventional symptomatic treatment and subsequently was treated with gonadotropin-releasing hormone analogues (GnRH) combined with estrogen for one year. RESULT: The case did not experience acute attacks and obtained long-term clinical remission to date. CONCLUSIONS: GnRH combined with estrogen, one of the treatment options for menstrual-associated AIP, might induce long-term remission.

Extensive Aortic Thromboembolism in a Patient With Erdheim-Chester Disease: A Case Report.

Background: Erdheim-Chester disease (ECD) is a rare disease that affects multiple systems and is characterized by non-Langerhans cell histiocytosis. Classic clinical signs include long bone infiltration, central nervous system involvement, diabetes insipidus, and sheathing of the entire aorta. However, thrombosis is not recognized as a typical cardiac manifestation of ECD. Here, we report the case of an ECD patient with extensive arterial thrombus formation and embolism in several sections of the aorta. Case: A 36-year-old woman was admitted due to recurrent fever and left finger cyanosis for 20 days. Laboratory tests revealed that her C-reactive protein and interleukin-6 levels were significantly elevated. Thoracic computed tomographic angiography (CTA) revealed thrombosis from the aortic arch to the left subclavian artery accompanied by severe stenosis of the left subclavian artery. Abdominal CTA revealed splenic infarction due to splenic artery embolism and thrombus formation in multiple abdominal arteries. She underwent emergent arterial thrombectomy. During hospitalization, she complained of polyuria. The desmopressin test and pituitary magnetic resonance imaging findings suggested diabetes insipidus. Furthermore, positron emission tomography-computed tomography and bone emission computed tomography showed long bone impairment, and pathological examination of the bone samples confirmed ECD. Steroids and tocilizumab were selected as the initial therapies; however, thrombosis continued to develop. After replacement of tocilizumab with interferon-α, her condition became stable. Conclusion: Although extremely rare, fatal thrombosis may be a significant cardiovascular manifestation of ECD.

H3K27ac mediated SS18/BAFs relocation regulates JUN induced pluripotent-somatic transition.

BACKGROUND: The exit from pluripotency or pluripotent-somatic transition (PST) landmarks an event of early mammalian embryonic development, representing a model for cell fate transition. RESULTS: In this study, using a robust JUN-induced PST within 8 h as a model, we investigate the chromatin accessibility dynamics (CAD) as well as the behaviors of corresponding chromatin remodeling complex SS18/BAFs, to probe the key events at the early stage of PST. Here, we report that, JUN triggers the open of 34661 chromatin sites within 4 h, accomplished with the activation of somatic genes, such as Anxa1, Fosl1. ChIP-seq data reveal a rapid relocation of SS18/BAFs from pluripotent loci to AP-1 associated ones. Consistently, the knockdown of Brg1, core component of BAF complexes, leads to failure in chromatin opening but not closing, resulting in delay for JUN induced PST. Notably, the direct interaction between SS18/BAFs and JUN-centric protein complexes is undetectable by IP-MS. Instead, we show that H3K27ac deposited by cJUN dependent process regulates SS18/BAFs complex to AP1-containing loci and facilitate chromatin opening and gene activation. CONCLUSIONS: These results reveal a rapid transfer of chromatin remodeling complexes BAF from pluripotent to somatic loci during PST, revealing a simple mechanistic aspect of cell fate control.

BMP4 drives primed to naïve transition through PGC-like state.

Multiple pluripotent states have been described in mouse and human stem cells. Here, we apply single-cell RNA-seq to a newly established BMP4 induced mouse primed to naïve transition (BiPNT) system and show that the reset is not a direct reversal of cell fate but goes through a primordial germ cell-like cells (PGCLCs) state. We first show that epiblast stem cells bifurcate into c-Kit+ naïve and c-Kit- trophoblast-like cells, among which, the naïve branch undergoes further transition through a PGCLCs intermediate capable of spermatogenesis in vivo. Mechanistically, we show that DOT1L inhibition permits the transition from primed pluripotency to PGCLCs in part by facilitating the loss of H3K79me2 from Gata3/6. In addition, Prdm1/Blimp1 is required for PGCLCs and naïve cells, while Gata2 inhibits PGC-like state by promoting trophoblast-like fate. Our work not only reveals an alternative route for primed to naïve transition, but also gains insight into germ cell development.

Diagnostic Potential of Plasma Extracellular Vesicle miR-483-3p and Let-7d-3p for Sepsis.

Background: microRNAs (miRNAs) from circulating extracellular vesicles (EVs) have been reported as disease biomarkers. This study aimed to identify the diagnostic value of plasma EV-miRNAs in sepsis. Methods: EVs were separated from the plasma of sepsis patients at admission and healthy controls. The expression of EV-miRNAs was evaluated by microarray and qRT-PCR. Results: A preliminary miRNA microarray of plasma EVs from a discovery cohort of 3 sepsis patients at admission and three healthy controls identified 11 miRNAs with over 2-fold upregulation in sepsis group. Based on this finding, EV samples from a validation cohort of 37 sepsis patients at admission and 25 healthy controls were evaluated for the expression of the 6 miRNAs relating injury and inflammation via qRT-PCR. Elevated expression of miR-483-3p and let-7d-3p was validated in sepsis patients and corroborated in a mouse model of sepsis. miR-483-3p and let-7d-3p levels positively correlated with the disease severity. Additionally, a combination of miR-483-3p and let-7d-3p had diagnostic value for sepsis. Furthermore, bioinformatic analysis and experimental validation showed that miR-483-3p and let-7d-3p target pathways regulating immune response and endothelial function. Conclusion: The present study reveals the potential role of plasma EV-miRNAs in the pathogenesis of sepsis and the utility of combining miR-483-3p and let-7d-3p as biomarkers for early sepsis diagnosis.

Lung adenocarcinoma: development of nomograms based on PET/CT images for prediction of epidermal growth factor receptor mutation status and subtypes.

OBJECTIVE: To develop nomograms that combine clinical characteristics, computed tomographic (CT) features and 18F-fluorodeoxyglucose PET (18F-FDG PET) metabolic parameters for individual prediction of epidermal growth factor receptor (EGFR) mutation status and exon 19 deletion mutation and exon 21 point mutation (21 L858R) subtypes in lung adenocarcinoma. METHODS: In total 124 lung adenocarcinoma patients who underwent EGFR mutation testing and whole-body 18F-FDG PET/CT were enrolled. Each patient's clinical characteristics (age, sex, smoking history, etc.), CT features (size, location, margins, etc.) and four metabolic parameters (SUVmax, SUVmean, MTV and TLG) were recorded and analyzed. Logistic regression analyses were performed to screen for significant predictors of EGFR mutation status and subtypes, and these predictors were presented as easy-to-use nomograms. RESULTS: According to the results of multiple regression analysis, three nomograms for individualized prediction of EGFR mutation status and subtypes were constructed. The area under curve values of three nomograms were 0.852 (95% CI, 0.783-0.920), 0.857 (95% CI, 0.778-0.937) and 0.893 (95% CI, 0.819-0.968) of EGFR mutation vs. wild-type, 19 deletion mutation vs. wild-type and 21 L858R vs. wild-type, respectively. Only calcification showed significant differences between the EGFR 19 deletion and 21 L858R mutations. CONCLUSION: EGFR 21 L858R mutation was more likely to be nonsolid texture with air bronchograms and pleural retraction on CT images. And they were more likely to be associated with lower FDG metabolic activity compared with those wild-types. The sex difference was mainly caused by the 19 deletion mutation, and calcification was more frequent in them.

Practical bioinformatics pipelines for single-cell RNA-seq data analysis.

Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool to explore cells. With an increasing number of scRNA-seq data analysis tools that have been developed, it is challenging for users to choose and compare their performance. Here, we present an overview of the workflow for computational analysis of scRNA-seq data. We detail the steps of a typical scRNA-seq analysis, including experimental design, pre-processing and quality control, feature selection, dimensionality reduction, cell clustering and annotation, and downstream analysis including batch correction, trajectory inference and cell-cell communication. We provide guidelines according to our best practice. This review will be helpful for the experimentalists interested in analyzing their data, and will aid the users seeking to update their analysis pipelines.

Epigenetic control of transposable elements and cell fate decision.

Transposable elements (TEs) are the most prevalent elements in mammalian genomes. Although potential risks for genome stability, they are a pool of potential regulatory sequences, chromatin control elements, protein-coding genes, and substrates for evolutionary processes. Consequently, a delicate balance is maintained between the potential benefits and deleterious aspects of TEs, and this balance is mediated by the epigenetic regulatory system. In this review, we introduce the role of heterochromatin associated epigentic modifications such as histone 3 lysine 9 trimethylation (H3K9me3) and DNA methylation in the silencing of TEs as well as epigenetic modifications such as histone 3 lysine 4 monomethylation (H3K4me1) and histone 3 lysine 27 acetylation (H3K27ac) in activation of TEs. Further, we elaborate the functions of TEs as binding sites of transcription factors and as anchors of chromosomal conformation in regulation of gene expression. We introduce the impact of TEs on the process of cell fate determination including natural embryonic development in vivo and artificial cell fate transition in vitro. We discuss the main challenges associated with computational TEs analysis and TEs functions exploration, as well as the different experimental and computational strategies in studying these processes. In all, this article provides a comprehensive review of the research advances and existing problems in study of transposable elements in epigenetic regulatory mechanisms, gene transcriptional regulation, and cell fate determination, thereby providing some references for researchers in the fields.