Histone modifications of circulating nucleosomes are associated with changes in cell-free DNA fragmentation patterns.

The analysis of tissues of origin of cell-free DNA (cfDNA) is of research and diagnostic interest. Many studies focused on bisulfite treatment or immunoprecipitation protocols to assess the tissues of origin of cfDNA. DNA loss often occurs during such processes. Fragmentomics of cfDNA molecules has uncovered a wealth of information related to tissues of origin of cfDNA. There is still much room for the development of tools for assessing contributions from various tissues into plasma using fragmentomic features. Hence, we developed an approach to analyze the relative contributions of DNA from different tissues into plasma, by identifying characteristic fragmentation patterns associated with selected histone modifications. We named this technique as FRAGmentomics-based Histone modification Analysis (FRAGHA). Deduced placenta-specific histone H3 lysine 27 acetylation (H3K27ac)-associated signal correlated well with the fetal DNA fraction in maternal plasma (Pearson's r = 0.96). The deduced liver-specific H3K27ac-associated signal correlated with the donor-derived DNA fraction in liver transplantation recipients (Pearson's r = 0.92) and was significantly increased in patients with hepatocellular carcinoma (HCC) (P < 0.01, Wilcoxon rank-sum test). Significant elevations of erythroblasts-specific and colon-specific H3K27ac-associated signals were observed in patients with ß-thalassemia major and colorectal cancer, respectively. Furthermore, using the fragmentation patterns from tissue-specific H3K27ac regions, a machine learning algorithm was developed to enhance HCC detection, with an area under the curve (AUC) of up to 0.97. Finally, genomic regions with H3K27ac or histone H3 lysine 4 trimethylation (H3K4me3) were found to exhibit different fragmentomic patterns of cfDNA. This study has shed light on the relationship between cfDNA fragmentomics and histone modifications, thus expanding the armamentarium of liquid biopsy.

Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs.

Cell-free DNA (cfDNA) fragmentation is nonrandom, at least partially mediated by various DNA nucleases, forming characteristic cfDNA end motifs. However, there is a paucity of tools for deciphering the relative contributions of cfDNA cleavage patterns related to underlying fragmentation factors. In this study, through non-negative matrix factorization algorithm, we used 256 5' 4-mer end motifs to identify distinct types of cfDNA cleavage patterns, referred to as "founder" end-motif profiles (F-profiles). F-profiles were associated with different DNA nucleases based on whether such patterns were disrupted in nuclease-knockout mouse models. Contributions of individual F-profiles in a cfDNA sample could be determined by deconvolutional analysis. We analyzed 93 murine cfDNA samples of different nuclease-deficient mice and identified six types of F-profiles. F-profiles I, II, and III were linked to deoxyribonuclease 1 like 3 (DNASE1L3), deoxyribonuclease 1 (DNASE1), and DNA fragmentation factor subunit beta (DFFB), respectively. We revealed that 42.9% of plasma cfDNA molecules were attributed to DNASE1L3-mediated fragmentation, whereas 43.4% of urinary cfDNA molecules involved DNASE1-mediated fragmentation. We further demonstrated that the relative contributions of F-profiles were useful to inform pathological states, such as autoimmune disorders and cancer. Among the six F-profiles, the use of F-profile I could inform the human patients with systemic lupus erythematosus. F-profile VI could be used to detect individuals with hepatocellular carcinoma, with an area under the receiver operating characteristic curve of 0.97. F-profile VI was more prominent in patients with nasopharyngeal carcinoma undergoing chemoradiotherapy. We proposed that this profile might be related to oxidative stress.

Epigenetic analysis of cell-free DNA by fragmentomic profiling.

Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation patterns to predict cytosine-phosphate-guanine (CpG) methylation of cfDNA, obviating the use of bisulfite treatment and associated risks of DNA degradation. This study investigated the cfDNA cleavage profile surrounding a CpG (i.e., within an 11-nucleotide [nt] window) to analyze cfDNA methylation. The cfDNA cleavage proportion across positions within the window appeared nonrandom and exhibited correlation with methylation status. The mean cleavage proportion was ∼twofold higher at the cytosine of methylated CpGs than unmethylated ones in healthy controls. In contrast, the mean cleavage proportion rapidly decreased at the 1-nt position immediately preceding methylated CpGs. Such differential cleavages resulted in a characteristic change in relative presentations of CGN and NCG motifs at 5' ends, where N represented any nucleotide. CGN/NCG motif ratios were correlated with methylation levels at tissue-specific methylated CpGs (e.g., placenta or liver) (Pearson's absolute r > 0.86). cfDNA cleavage profiles were thus informative for cfDNA methylation and tissue-of-origin analyses. Using CG-containing end motifs, we achieved an area under a receiver operating characteristic curve (AUC) of 0.98 in differentiating patients with and without hepatocellular carcinoma and enhanced the positive predictive value of nasopharyngeal carcinoma screening (from 19.6 to 26.8%). Furthermore, we elucidated the feasibility of using cfDNA cleavage patterns to deduce CpG methylation at single CpG resolution using a deep learning algorithm and achieved an AUC of 0.93. FRAGmentomics-based Methylation Analysis (FRAGMA) presents many possibilities for noninvasive prenatal, cancer, and organ transplantation assessment.

Nomogram based on clinical characteristics and ultrasound indicators for predicting severe postpartum hemorrhage in patients with anterior placenta previa combined with previous cesarean section: a retrospective case-control study.

BACKGROUND: Placental accreta spectrum disorders (PAS) are a high-risk group for severe postpartum hemorrhage (SPPH), with the incidence of PAS increasing annually. Given that cesarean section and anterior placenta previa are the primary risk factors for PAS, therefore, our study aims to investigate the predictive value of clinical characteristics and ultrasound indicators for SPPH in patients with anterior placenta previa combined with previous cesarean section, providing a theoretical basis for early prediction of SPPH. METHODS: A total of 450 patients with anterior placenta previa combined with previous cesarean section were retrospectively analyzed at Shengjing Hospital affiliated with China Medical University between January 2018 and March 2022. Clinical data and ultrasound indicators were collected. Patients were categorized into SPPH (blood loss >2000mL, 182 cases) and non-SPPH (blood loss ≤ 2000mL, 268 cases) groups based on the blood loss within 24 h postpartum. The population was randomly divided into training and validation cohorts at a 7:3 ratio. LASSO and multifactorial logistic regression analyses were utilized to identify independent risk factors for SPPH. Accordingly, a nomogram prediction model was constructed, the predictive performance was assessed using receiver operating characteristic (ROC) curves, calibration curves and decision curve analysis (DCA). RESULTS: Among the 450 patients, 182 experienced SPPH (incidence rate, 40.44%). Preoperative systemic immune-inflammatory index, preoperative D-dimer level, preoperative placenta accreta spectrum ultrasound scoring system (PASUSS) score, and one-step-conservative surgery were identified as independent risk factors for SPPH in patients with anterior placenta previa combined with previous cesarean section. A nomogram was constructed based on these factors. The areas under the ROC curves for the training and validation cohorts were 0.844 (95%CI: 0.801-0.888) and 0.863 (95%CI: 0.803-0.923), respectively. Calibration curves and DCA indicated that this nomogram demonstrated good predictive accuracy. CONCLUSIONS: This nomogram presents an effective and convenient prediction model for identifying SPPH in patients with anterior placenta previa combined with previous cesarean section. It can guide surgical planning and improve prognosis.

Uptake of COVID-19 and influenza vaccines in relation to preexisting chronic conditions in the European countries.

BACKGROUND: The suboptimal uptake of COVID-19 and influenza vaccines among those with non-communicable chronic diseases is a public health concern, because it poses a higher risk of severe illness for individuals with underlying health conditions, emphasizing the need to address barriers to vaccination and ensure adequate protection for this vulnerable population. In the present study, we aimed to identify whether people with chronic illnesses are more likely to get vaccinated against COVID-19 and influenza in the European Union. METHODS: Cross-sectional data on 49,253 men (n = 20,569) and women (n = 28,684) were obtained from the ninth round of the Survey of Health, Ageing and Retirement in Europe (June - August, 2021). The outcome variables were self-reported COVID-19 and influenza vaccine uptake status. The association between the uptake of the vaccines and six preexisting conditions including high blood pressure, high blood cholesterol, chronic lung disease, diabetes, chronic bronchitis, and asthma was estimated using binary logistic regression methods. RESULTS: The vaccination coverage for COVID-19 ranged from close to 100% in Denmark (98.2%) and Malta (98.2%) to less than 50% in Bulgaria (19.1%) and Romania (32.7%). The countries with the highest percentage of participants with the influenza vaccine included Malta (66.7%), Spain (63.7%) and the Netherlands (62.5%), and those with the lowest percentage included Bulgaria (3.7%), Slovakia (5.8%) and Poland (9.2%). Participants with high blood pressure were 3% less likely [Risk difference (RD) = -0.03, 95% CI = -0.04, -0.03] to report taking COVID-19 and influenza [RD = -0.03, 95% CI= -0.04, -0.01] vaccine. Those with chronic lung disease were 4% less likely [RD = -0.04, 95% CI= -0.06, -0.03] to report taking COVID-19 and 2% less likely [RD= -0.02, 95% CI = -0.04, -0.01] to report taking influenza vaccine. Men and women with high blood pressure were 3% less likely to have reported taking both of the vaccines. CONCLUSIONS: Current findings indicate a suboptimal uptake of COVID-19 and influenza vaccines among adult men and women in the EU countries. Those with preexisting conditions, including high blood pressure and chronic lung disease are less likely to take the vaccines.

[Peripheral blood lymphocyte subsets are associated with the prognosis of prostate cancer].

OBJECTIVE: To explore the relationship between peripheral lymphocyte subsets and the survival of PCa patients. METHODS: Using the Kaplan-Meier curve and log-rank test, we compared the overall survival (OS) and progression-free survival (PFS) of 100 PCa patients with different levels of lymphocytes. Meanwhile, we investigated the prognostic factors by univariate and multivariate Cox regression analyses, and counted the peripheral lymphocyte subsets by flow cytometry. RESULTS: Both OS and PFS were significantly prolonged in the PCa patients with high levels of lymphocytes (≥747/µl), CD3+T cells (≥528/µl), CD4+T cells (≥315/µl), CD8+T cells (≥226/µl), B cells (≥105/µl) and NK cells (≥168/µl)(P < 0.001). Univariate and multivariate Cox regression analyses indicated that CD4+T cells ≤ 315/µl was an independent factor for the poor prognosis of PCa (HR=12.58, 95% CI: 3.00－52.73). CONCLUSION: Decreased absolute count of peripheral lymphocyte subsets is associated with the poor prognosis of PCa.

[Causes of missed diagnosis of clinically significant prostate cancer by targeted biopsy].

OBJECTIVE: To retrospectively analyze the causes of missed diagnosis of clinically significant PCa (csPCa) by targeted biopsy (TB). METHODS: This retrospective study included 652 males aged (71.32 ± 16.53) years with elevated PSA and abnormal MRI signals detected in our hospital from June 2018 to December 2020. We further examined the patients by transperineal prostatic TB and systematic biopsy (SB), analyzed the detection rates of PCa and csPCa by TB and SB, and investigated the causes of missed diagnosis of csPCa in TB using the fishbone diagram. RESULTS: The total detection rate of PCa and csPCa by TB combined with SB was 45.7% (298/652), and that of csPCa was 37.4% (244/652), with 38 cases of csPCa missed in TB, including 23 cases of negative TB and 15 cases of low ISUP grade. The causes of missed diagnosis of csPCa by TB included low MRI image quality, PSA density ≤0.15 ng/ml/cm3, target area <10 mm, and PI-RADS 2 score ≤3. The detection rate of csPCa by TB alone was 31.6%, which was increased by 5.8% (P = 0.027) when TB combined with SB. CONCLUSION: TB combined with SB yields a higher detection rate of csPCa than either used alone. Missed diagnosis of csPCa by TB is closely related to the characteristics of tumor and MR image of the target area.

Cervical cancer screening aided by artificial intelligence, China.

Objective: To implement and evaluate a large-scale online cervical cancer screening programme in Hubei Province, China, supported by artificial intelligence and delivered by trained health workers. Methods: The screening programme, which started in 2017, used four types of health worker: sampling health workers, slide preparation technicians, diagnostic health workers and cytopathologists. Sampling health workers took samples from the women on site; slide preparation technicians prepared slides for liquid-based cytology; diagnostic health workers identified negative samples and classified positive samples based on the Bethesda System after cytological assessment using online artificial intelligence; and cytopathologists reviewed positive samples and signed reports of the results online. The programme used fully automated scanners, online artificial intelligence, an online screening management platform, and mobile telephone devices to provide screening services. We evaluated the sustainability, performance and cost of the programme. Results: From 2017 to 2021, 1 518 972 women in 16 cities in Hubei Province participated in the programme, of whom 1 474 788 (97.09%) had valid samples for the screening. Of the 86 648 women whose samples were positive, 30 486 required a biopsy but only 19 495 had one. The biopsy showed that 2785 women had precancerous lesions and 191 had invasive cancers. The cost of screening was 6.31 United States dollars (US$) per woman for the public payer: US$ 1.03 administrative costs and US$ 5.28 online screening costs. Conclusion: Cervical cancer screening using artificial intelligence in Hubei Province provided a low-cost, accessible and effective service, which will contribute to achieving universal cervical cancer screening coverage in China.

Opening KATP channels induces inflammatory tolerance and prevents chronic pain.

Current treatments for chronic pain are unsatisfactory, therefore, new therapeutics are urgently needed. Our previous study indicated that KATP channel openers have analgesic effects, but the underlying mechanism has not been elucidated. We speculated that KATP channel openers might increase suppressor of cytokine signaling (SOCS)-3 expression to induce inflammatory tolerance and attenuate chronic pain. Postoperative pain was induced by plantar incision to establish a chronic pain model. Growth arrest-specific 6 (Gas6)-/- and Axl-/- mice were used for signaling studies. The microglia cell line BV-2 was cultured for the in vitro experiments. The KATP channel opener significantly attenuated incision-induced mechanical allodynia in mice associated with the upregulated expression of SOCS3. Opening KATP channels induced the expression of SOCS3 in the Gas6/Axl signaling pathway in microglia, inhibited incision-induced mechanical allodynia by activating the Gas6/Axl-SOCS3 signaling pathway, and induced inflammatory tolerance to relieve neuroinflammation and postoperative pain. We demonstrated that opening of the KATP channel opening activated Gas6/Axl/SOCS3 signaling to induce inflammatory tolerance and relieve chronic pain. We explored a new target for anti-inflammatory and analgesic effects by regulating the innate immune system and provided a theoretical basis for clinical preemptive analgesia.

Platelet-rich Plasma Improves Radiotherapy-induced Emotional Disorder and Cognitive Dysfunction, Neuroinflammation in Aged Rats by Inhibiting the Activation of NLRP3 Inflammasomes.

Although radiotherapy (RT) is the preferred treatment for elderly patients with brain tumors, certain negative effects can't be ignored. Fortunately, platelet-rich plasma (PRP) presents with a promising potential for the treatment of neurological diseases. Therefore, this study aimed to explore the effect of PRP on neuroinflammation, emotional disorder and cognitive dysfunction induced by RT in aged rats. Firstly, whole brain RT (WBRT) model was established by whole brain irradiation with 10 Gy of 6-MeV electron beam in rats. Next, twenty 20-month-old female SD rats were divided into four groups (sham group, PRP group, WBRT group, and WBRT + PRP group) according different treatments. After that, the cognitive dysfunction and depression-like behavior of rats were examined by novel object recognition test (NORT), Morris water maze test (MWM), open field test (OFT) and elevated plus maze test (EPM). Besides, immunohistochemistry was used to detect the expression of microglial marker protein Iba-1 in rat hippocampus; enzyme linked immunosorbent assay (ELISA) to examine the levels of pro-inflammatory cytokines tumor necrosis factor-alpha (TNF-α), interleukin (IL)-1 beta (IL-1ß), IL-18, and monocyte chemoattractant protein 1 (MCP-1) in rat hippocampus; real-time quantitative reverse transcription PCR (qRT-PCR) and western blot to measure the levels of neurotrophic factors brain-derived neurotrophic factor (BDNF), tropomyosin-related kinase B receptor (TrkB), and nerve growth factor (NGF) in rat hippocampus; and western blot also to observe the protein expression levels of NOD-like receptor protein 3 (NLRP3), caspase-1, apoptosis-associated speck-like protein containing a CARD (ASC), and IL-1ß in rat hippocampus. After experiments, some results obtained were shown as follows. PRP could significantly improve learning and memory ability and depression-like behavior, increase the level of neurotrophic factors, inhibit the activation of microglia and decrease the level of pro-inflammatory factors in WBRT rats. In addition, PRP significantly inhibited the activation of NLRP3 inflammasomes. To sum up, PRP can ameliorate neuroinflammation, emotional disorder and cognitive dysfunction induced by RT in aged rats, and the mechanism may be related to its inhibitory effect on NLRP3 inflammasome activation.

Identification and characterization of extrachromosomal circular DNA in maternal plasma.

We explored the presence of extrachromosomal circular DNA (eccDNA) in the plasma of pregnant women. Through sequencing following either restriction enzyme or Tn5 transposase treatment, we identified eccDNA molecules in the plasma of pregnant women. These eccDNA molecules showed bimodal size distributions peaking at ∼202 and ∼338 bp with distinct 10-bp periodicity observed throughout the size ranges within both peaks, suggestive of their nucleosomal origin. Also, the predominance of the 338-bp peak of eccDNA indicated that eccDNA had a larger size distribution than linear DNA in human plasma. Moreover, eccDNA of fetal origin were shorter than the maternal eccDNA. Genomic annotation of the overall population of eccDNA molecules revealed a preference of these molecules to be generated from 5'-untranslated regions (5'-UTRs), exonic regions, and CpG island regions. Two sets of trinucleotide repeat motifs flanking the junctional sites of eccDNA supported multiple possible models for eccDNA generation. This work highlights the topologic analysis of plasma DNA, which is an emerging direction for circulating nucleic acid research and applications.

Pachymic acid ameliorates bleomycin-induced pulmonary fibrosis through inhibiting endoplasmic reticulum stress in rats.

The effect of pachymic acid (PA) on pulmonary fibrosis in rats was expected to be investigated in this study. Firstly, bleomycin (BLM) was used to establish pulmonary fibrosis rat model, then PA (10, 20, or 40 mg/kg) was intragastrically administered to the rats for 14 days. Subsequently, a variety of tests was performed to observe changes in sample tissues after different treatments. Briefly, the degree of pulmonary edema in rats was assessed through dry/wet weight ratio. Hematoxylin and eosin (H&E) staining and Masson's trichrome staining were used to observe the pathological injury and fibrosis of lung tissue. Biochemical kits were applied to measure the levels of hydroxyproline (Hyp), transforming growth factor beta-1 (TGFß-1), malondialdehyde (MDA), reactive oxygen species (ROS), and adenosine triphosphate (ATP) and the activities of superoxide dismutase (SOD) and catalase (CAT) in rat lung tissues of each group. The mitochondrial DNA (mtDNA) copy number in rat lung tissue was tested using qRT-PCR. Additionally, the western blot was employed to detect the expression levels of pulmonary fibrosis-related proteins and endoplasmic reticulum (ER) stress-related proteins in each group of rat lung tissue. By virtue of experimental verification above, PA was discovered to alleviate BLM-induced pulmonary edema, pulmonary fibrosis and histopathological damage. On the one hand, PA treatment decreased Hyp and TGF-ß1 levels and down-regulated pulmonary fibrosis-related protein expression [collagen I, α-smooth muscle actin (α-SMA), and fibronectin] in the lung tissue of BLM rats. On the other hand, it significantly increased the levels of SOD, CAT and ATP while decreased the activities of MDA and ROS in BLM rat lung tissues. In addition, the expression levels of ER stress-related proteins [glucose-regulated protein 78 (GRP78), C/EBP homologous protein (CHOP), Caspase 9, and activating transcription factor 4 (ATF4)] were significantly down-regulated in the lung tissue of BLM rats after PA treatment. Collectively, PA may ameliorate BLM-induced pulmonary fibrosis and histopathological damage in rats through inhibiting ER stress and improving mitochondrial function.

AMPK-autophagy-mediated inhibition of microRNA-30a-5p alleviates morphine tolerance via SOCS3-dependent neuroinflammation suppression.

BACKGROUND: The development of morphine tolerance is a clinical challenge for managing severe pain. Studies have shown that neuroinflammation is a critical aspect for the development of analgesic tolerance. We found that AMPK-autophagy activation could suppress neuroinflammation and improve morphine tolerance via the upregulation of suppressor of cytokine signaling 3 (SOCS3) by inhibiting the processing and maturation of microRNA-30a-5p. METHODS: CD-1 mice were utilized for the tail-flick test to evaluate morphine tolerance. The microglial cell line BV-2 was utilized to investigate the mechanism of AMPK-autophagy-mediated posttranscriptional regulation of SOCS3. Proinflammatory cytokines were measured by western blotting and real-time PCR. The levels of SOCS3 and miRNA-processing enzymes were evaluated by western blotting, real-time PCR and immunofluorescence staining. RESULTS: Based on experimental verification, miRNA-30a-5p could negatively regulate SOCS3. The AMPK activators AICAR, resveratrol and metformin downregulated miRNA-30a-5p. We found that AMPK activators specifically inhibited the processing and maturation of miRNA-30a-5p in microglia by degrading DICER and AGO2 via autophagy. Furthermore, a miRNA-30a-5p inhibitor significantly improved morphine tolerance via upregulation of SCOS3 in mice. It markedly increased the level of SOCS3 in the spinal cord of mice and subsequently inhibited morphine-induced phosphorylation of NF-κB p65. In addition, a miRNA-30a-5p inhibitor decreased the levels of IL-1ß and TNF-α caused by morphine in microglia. CONCLUSION: AMPK-autophagy activation suppresses neuroinflammation and improves morphine tolerance via the upregulation of SOCS3 by inhibiting miRNA-30a-5p.

The occurrence of COVID-19 is associated with air quality and relative humidity.

The association between meteorological factors and COVID-19 is important for the prevention and control of COVID-19. However, similar studies are relatively rare in China. This study aims to investigate the association between COVID-19 and meteorological factors, such as average temperature, relative humidity, and air quality index (AQI), and average wind speed. We collected the daily confirmed cases of COVID-19 and meteorological factors in Shanghai China from January 10, 2020 to March 31, 2020. A generalized additive model was fitted to quantify the associations between meteorological factors and COVID-19 during the study period. A negative association between average temperature and daily confirmed cases of COVID-19 was found on lag 13 days. In addition, we observed a significant positive correlation between meteorological factors (AQI, relative humidity) and daily confirmed cases of COVID-19. A 10 increase in AQI (lag1/7/8/9/10 days) was correlated with a 4.2%-9.0% increase in the daily confirmed cases of COVID-19. A 1% increase in relative humidity (lag1/4/7/8/9/10 days) was correlated with 1.7%-3.7% increase in the daily confirmed cases of COVID-19. However, the associations between average wind speed and the daily confirmed cases of COVID-19 is complex in different lag days. In summary, meteorological factors could affect the occurrence of COVID-19. Reducing the effects of meteorological factors on COVID-19 may be an important public health action for the prevention and control of COVID-19.

Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers.

Hippo-YAP signaling pathway functions in early lineage differentiation of pluripotent stem cells, but the detailed mechanisms remain elusive. We found that knockout (KO) of Mst1 and Mst2, two key components of the Hippo signaling in mouse embryonic stem cells (ESCs), resulted in a disruption of differentiation into mesendoderm lineage. To further uncover the underlying regulatory mechanisms, we performed a series of ChIP-seq experiments with antibodies against YAP, ESC master transcription factors and some characterized histone modification markers as well as RNA-seq assays using wild type and Mst KO samples at ES and day 4 embryoid body stage respectively. We demonstrate that YAP is preferentially co-localized with super-enhancer (SE) markers such as Nanog, Sox2, Oct4 and H3K27ac in ESCs. The hyper-activation of nuclear YAP in Mst KO ESCs facilitates the binding of Nanog, Sox2 and Oct4 as well as H3K27ac modification at the loci where YAP binds. Moreover, Mst depletion results in novel SE formation and enhanced liquid-liquid phase-separated Med1 condensates on lineage associated genes, leading to the upregulation of these genes and the distortion of ESC differentiation. Our study reveals a novel mechanism on how Hippo-YAP signaling pathway dictates ESC lineage differentiation.

Capturing the interactome of newly transcribed RNA.

We combine the labeling of newly transcribed RNAs with 5-ethynyluridine with the characterization of bound proteins. This approach, named capture of the newly transcribed RNA interactome using click chemistry (RICK), systematically captures proteins bound to a wide range of RNAs, including nascent RNAs and traditionally neglected nonpolyadenylated RNAs. RICK has identified mitotic regulators amongst other novel RNA-binding proteins with preferential affinity for nonpolyadenylated RNAs, revealed a link between metabolic enzymes/factors and nascent RNAs, and expanded the known RNA-bound proteome of mouse embryonic stem cells. RICK will facilitate an in-depth interrogation of the total RNA-bound proteome in different cells and systems.

Characteristics of Fetal Extrachromosomal Circular DNA in Maternal Plasma: Methylation Status and Clearance.

BACKGROUND: Although the characterization of cell-free extrachromosomal circular DNA (eccDNA) has gained much research interest, the methylation status of these molecules is yet to be elucidated. We set out to compare the methylation densities of plasma eccDNA of maternal and fetal origins, and between small and large molecules. The clearance of fetal eccDNA from maternal circulation was also investigated. METHODS: We developed a sequencing protocol for eccDNA methylation analysis using tagmentation and enzymatic conversion approaches. A restriction enzyme-based approach was applied to verify the tagmentation results. The efficiency of cell-free fetal eccDNA clearance was investigated by fetal eccDNA fraction evaluations at various postpartum time points. RESULTS: The methylation densities of fetal eccDNA (median: 56.3%; range: 40.5-67.6%) were lower than the maternal eccDNA (median: 66.7%; range: 56.5-75.7%) (P = 0.02, paired t-test). In addition, eccDNA molecules from the smaller peak cluster (180-230 bp) were of lower methylation levels than those from the larger peak cluster (300-450 bp). Both of these findings were confirmed using the restriction enzyme approach. We also observed comparable methylation densities between linear and eccDNA of both maternal and fetal origins. The average half-lives of fetal linear and eccDNA in the maternal blood were 30.2 and 29.7 min, respectively. CONCLUSIONS: We found that fetal eccDNA in plasma was relatively hypomethylated compared to the maternal eccDNA. The methylation densities of eccDNA were positively correlated with their sizes. In addition, fetal eccDNA was found to be rapidly cleared from the maternal blood after delivery, similar to fetal linear DNA.

Single Cell and Plasma RNA Sequencing for RNA Liquid Biopsy for Hepatocellular Carcinoma.

BACKGROUND: Human plasma contains RNA transcripts released by multiple cell types within the body. Single-cell transcriptomic analysis allows the cellular origin of circulating RNA molecules to be elucidated at high resolution and has been successfully utilized in the pregnancy context. We explored the application of a similar approach to develop plasma RNA markers for cancer detection. METHODS: Single-cell RNA sequencing was performed to decipher transcriptomic profiles of single cells from hepatocellular carcinoma (HCC) samples. Cell-type-specific transcripts were identified and used for deducing the cell-type-specific gene signature (CELSIG) scores of plasma RNA from patients with and without HCC. RESULTS: Six major cell clusters were identified, including hepatocyte-like, cholangiocyte-like, myofibroblast, endothelial, lymphoid, and myeloid cell clusters based on 4 HCC tumor tissues as well as their paired adjacent nontumoral tissues. The CELSIG score of hepatocyte-like cells was significantly increased in preoperative plasma RNA samples of patients with HCC (n = 14) compared with non-HCC participants (n = 49). The CELSIG score of hepatocyte-like cells declined in plasma RNA samples of patients with HCC within 3 days after tumor resection. Compared with the discriminating power between patients with and without HCC using the abundance of ALB transcript in plasma [area under curve (AUC) 0.72)], an improved performance (AUC: 0.84) was observed using the CELSIG score. The hepatocyte-specific transcript markers in plasma RNA were further validated by ddPCR assays. The CELSIG scores of hepatocyte-like cell and cholangiocyte trended with patients' survival. CONCLUSIONS: The combination of single-cell transcriptomic analysis and plasma RNA sequencing represents an approach for the development of new noninvasive cancer markers.

Targeted Delivery of CXCL9 and OX40L by Mesenchymal Stem Cells Elicits Potent Antitumor Immunity.

Major obstacles in immunotherapies include toxicities associated with systemic administration of therapeutic agents, as well as low tumor lymphocyte infiltration that hampers the efficacies. In this study, we report a mesenchymal stem cell (MSC)-based immunotherapeutic strategy in which MSCs specifically deliver T/natural killer (NK) cell-targeting chemokine CXCL9 and immunostimulatory factor OX40 ligand (OX40L)/tumor necrosis factor superfamily member 4 (TNFSF4) to tumor sites in syngeneic subcutaneous and azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced spontaneous colon cancer mouse models. This approach generated potent local antitumor immunity by increasing the ratios of tumor-infiltrating CD8+ T and NK cells and production of antitumor cytokines and cytolytic proteins in the tumor microenvironment. Moreover, it improved the efficacy of programmed death-1 (PD-1) blockade in a syngeneic mouse model and significantly suppressed the growth of major histocompatibility complex class I (MHC class I)-deficient tumors. Our MSC-based immunotherapeutic strategy simultaneously recruits and activates immune effector cells at the tumor site, thus overcoming the problems with toxicities of systemic therapeutic agents and low lymphocyte infiltration of solid tumors.

Sequencing Analysis of Plasma Epstein-Barr Virus DNA Reveals Nasopharyngeal Carcinoma-Associated Single Nucleotide Variant Profiles.

BACKGROUND: Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. Plasma EBV DNA is a validated screening tool for NPC. In screening, there are some individuals who do not have NPC but carry EBV DNA in plasma. Currently it is not known from screening if there may be any genotypic differences in EBV isolates from NPC and non-NPC subjects. Also, low concentrations of EBV DNA in plasma could pose challenge to such EBV genotypic analysis through plasma DNA sequencing. METHODS: In a training dataset comprised of plasma DNA sequencing data of NPC and non-NPC subjects, we studied the difference in the EBV single nucleotide variant (SNV) profiles between the two groups. The most differentiating SNVs across the EBV genome were identified. We proposed an NPC risk score to be derived from the genotypic patterns over these SNV sites. We subsequently analyzed the NPC risk scores in a testing set. RESULTS: A total of 661 significant SNVs across the EBV genome were identified from the training set. In the testing set, NPC plasma samples were shown to have high NPC risk scores, which suggested the presence of NPC-associated EBV SNV profiles. Among the non-NPC samples, there was a wide range of NPC risk scores. These results support the presence of diverse SNV profiles of EBV isolates from non-NPC subjects. CONCLUSION: EBV genotypic analysis is feasible through plasma DNA sequencing. The NPC risk score may be used to inform the cancer risk based on the EBV genome-wide SNV profile.