Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients.

Background: Metagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale. Methods: From January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections. Results: Combined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280). Conclusions: Our findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.

Combination of metagenomic next-generation sequencing and conventional tests unraveled pathogen profiles in infected patients undergoing allogeneic hematopoietic stem cell transplantation in Jilin Province of China.

Background: Infection is the main cause of death for patients after allogeneic hematopoietic stem cell transplantation (HSCT). However, pathogen profiles still have not been reported in detail due to their heterogeneity caused by geographic region. Objective: To evaluate the performance of metagenomic next-generation sequencing (mNGS) and summarize regional pathogen profiles of infected patients after HSCT. Methods: From February 2021 to August 2022, 64 patients, admitted to the Department of Hematology of The First Hospital of Jilin University for HSCT and diagnosed as suspected infections, were retrospectively enrolled. Results: A total of 38 patients were diagnosed as having infections, including bloodstream (n =17), pulmonary (n =16), central nervous system (CNS) (n =4), and chest (n =1) infections. Human betaherpesvirus 5 (CMV) was the most common pathogen in both bloodstream (n =10) and pulmonary (n =8) infections, while CNS (n =2) and chest (n =1) infections were mainly caused by Human gammaherpesvirus 4 (EBV). For bloodstream infection, Mycobacterium tuberculosis complex (n =3), Staphylococcus epidermidis (n =1), and Candida tropicalis (n =1) were also diagnosed as causative pathogens. Furthermore, mNGS combined with conventional tests can identify more causative pathogens with high sensitivity of 82.9% (95% CI 70.4-95.3%), and the total coincidence rate can reach up to 76.7% (95% CI 64.1-89.4%). Conclusions: Our findings emphasized the importance of mNGS in diagnosing, managing, and ruling out infections, and an era of more rapid, independent, and impartial diagnosis of infections after HSCT can be expected.

Randomized controlled trial on the effects of mindfulness-based respiratory decompression therapy in claustrophobic patients undergoing MRI inspection.

Background: Claustrophobia is a psychological disease. It is estimated to occur in 2.1-14.3% of all magnetic resonance imaging (MRI) examinations. Mindfulness decompression is an effective means to treat and reduce fear and anxiety. There is a rare report on the application of mindfulness-based stress reduction therapy in the magnetic resonance examinations of patients with claustrophobia to date. Purpose: The purpose of this study is to explore the intervention effect of mindfulness respiratory decompression therapy on the MRI inspection of patients with claustrophobia. Methods: A total of 86 patients with claustrophobia requiring MRI in our hospital from January 2018 to December 2020 were divided into two groups. The control group was given routine psychological nursing, and the observation group was given a mindfulness breathing technique on the basis of the control group. Before and after the intervention, we compared the intervention effect, satisfaction with nurses' psychological intervention technique, severe autonomic nervous symptoms during the examination, self-rating anxiety scale (SAS) scores, and profile of mood states revised (POMS-R) scores. Results: The total effective rate of intervention in the observation group was 90.90%, which was significantly higher (χ2 = 6.857, p = 0.00004) than that in the control group (26.19%). Severe autonomic nervous symptoms in the observation group were significantly lower than those in the control group (p < 0.05). After the intervention, SAS scores and POMS-R scores in the observation group decreased with statistical significance (p < 0.05). Conclusion: Mindfulness respiratory decompression therapy can effectively help claustrophobic patients complete an MRI examination, which may be worthy of wide promotion and application in the clinic.

Effect of visceral fat area on the accuracy of preoperative CT-N staging of colorectal cancer.

OBJECTIVE: To investigate the effect of visceral fat area (VFA) on the accuracy of preoperative CT-N staging of colorectal cancer. METHODS: We retrospectively reviewed the clinical and imaging data of 385 CRC patients who underwent surgical resection for colorectal cancer between January 2018 and July 2021. Preoperative CT-N staging and imaging features were determined independently by two radiologists. Using postoperative pathology as the gold standard, patients were divided into accurately and incorrectly staged groups, and clinical and imaging characteristics were compared between the two groups. VFA and subcutaneous fat area (SFA) at the L3 vertebral level, sex, age, BMI, tumor location, size, and tumor circumference ratio (TCR) were included. Logistic regression analysis was used to evaluate the independent factors influencing the accuracy of preoperative N staging of colorectal cancer. RESULTS: Of the 385 patients enrolled, 259 (67.27%) were in the preoperative N-stage accurate staging group, and 126 (32.73%) were in the incorrectly staged group. Univariate analysis showed that there were significant differences in BMI, tumor location, VFA, SFA, size and TCR between the two groups (P<0.05). Logistic regression analysis showed that VFA (95% CI: 1.277, 3.813; P=0.005) and TCR (95% CI: 1.649, 17.545; P=0.005) were independent factors affecting the accuracy of N staging. The optimal cutoff points for VFA and TCR in predicting incorrect staging were 110 cm2 and 0.675, respectively. CONCLUSIONS: Colorectal cancer patients with lower VFA and higher TCR and preoperative CT-N staging had an increased risk for diagnostic errors.

Dexlansoprazole prevents pulmonary artery hypertension by inhibiting pulmonary artery smooth muscle cell to fibroblast transition.

OBJECTIVES: To validate that dexlansoprazole, an anti-acid drug, can prevent pulmonary artery hypertension (PAH) in preclinical animal models and find the possible mechanism of action of dexlansoprazole for this new indication. METHODS: The efficacy of dexlansoprazole to attenuate PAH in vivo was evaluated in PAH animal models. Plasma guanosine 3', 5'-cyclic phosphate (cGMP) in PAH rats was measured by enzyme linked immunosorbent assay (ELISA). To investigate the anti-PAH effect of dexlansoprazole in vitro, proliferation and migration assays of primary cultured pulmonary artery smooth muscle cells (PASMCs) were performed. Furthermore, dexlansoprazole's function on fibroblast transition of vascular smooth muscle cells (VSMC) was explored by single cell ribonucleic acid (RNA) sequencing and RNAscope. RESULTS: Dexlansoprazole could attenuate the pathologic process in monocrotaline (MCT)-, hypoxia-induced PAH rats and SU5416/hypoxia (SuHy)-induced PAH mice. The intervention with dexlansoprazole significantly inhibited elevated right ventricular systolic pressure (RVSP), right ventricular hypertrophy, and pulmonary vascular wall thickness. Furthermore, plasma cGMP in MCT-induced PAH rats was restored after receiving dexlansoprazole. In vitro, dexlansoprazole could inhibit PASMCs' proliferation and migration stimulated by platelet derived growth factor-BB (PDGF-BB). Moreover, dexlansoprazole significantly ameliorated pulmonary vascular remodeling by inhibiting VSMC phenotypic transition to fibroblast-like cells in a VSMC-specific multispectral lineage-tracing mouse. CONCLUSIONS: Dexlansoprazole can prevent PAH through promoting cGMP generation and inhibiting pulmonary vascular remodeling through restraining PASMCs' proliferation, migration, and phenotypic transition to fibroblast-like cells. Consequently, PAH might be a new indication for dexlansoprazole.

Rational Nanomedicine Design Enhances Clinically Physical Treatment-Inspired or Combined Immunotherapy.

Independent of tumor type and non-invasive or minimally-invasive feature, current physical treatments including ultrasound therapy, microwave ablation (MWA), and radiofrequency ablation (RFA) are widely used as the local treatment methods in clinics for directly killing tumors and activating systematic immune responses. However, the activated immune responses are inadequate and incompetent for tumor recession, and the incomplete thermal ablation even aggravates the immunosuppressive tumor microenvironment (ITM), resulting in the intractable tumor recurrence and metastasis. Intriguingly, nanomedicine provides a powerful platform as they can elevate energy utilization efficiency and augment oncolytic effects for mitigating ITM and potentiating the systematic immune responses. Especially after combining with clinical immunotherapy, the anti-tumor killing effect by activating or enhancing the human anti-tumor immune system is reached, enabling the effective prevention against tumor recurrence and metastasis. This review systematically introduces the cutting-edge progress and direction of nanobiotechnologies and their corresponding nanomaterials. Moreover, the enhanced physical treatment efficiency against tumor progression, relapse, and metastasis via activating or potentiating the autologous immunity or combining with exogenous immunotherapeutic agents is exemplified, and their rationales are analyzed. This review offers general guidance or directions to enhance clinical physical treatment from the perspectives of immunity activation or magnification.

An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome.

BACKGROUND: Ubiquitination is essential for many cellular processes in eukaryotes, including 26S proteasome-dependent protein degradation, cell cycle progression, transcriptional regulation, and signal transduction. Although numerous ubiquitinated proteins have been empirically identified, their cognate ubiquitin E3 ligases remain largely unknown. RESULTS: Here, we generate a complete ubiquitin E3 ligase-encoding open reading frames (UbE3-ORFeome) library containing 98.94% of the 1515 E3 ligase genes in the rice (Oryza sativa L.) genome. In the test screens with four known ubiquitinated proteins, we identify both known and new E3s. The interaction and degradation between several E3s and their substrates are confirmed in vitro and in vivo. In addition, we identify the F-box E3 ligase OsFBK16 as a hub-interacting protein of the phenylalanine ammonia lyase family OsPAL1-OsPAL7. We demonstrate that OsFBK16 promotes the degradation of OsPAL1, OsPAL5, and OsPAL6. Remarkably, we find that overexpression of OsPAL1 or OsPAL6 as well as loss-of-function of OsFBK16 in rice displayed enhanced blast resistance, indicating that OsFBK16 degrades OsPALs to negatively regulate rice immunity. CONCLUSIONS: The rice UbE3-ORFeome is the first complete E3 ligase library in plants and represents a powerful proteomic resource for rapid identification of the cognate E3 ligases of ubiquitinated proteins and establishment of functional E3-substrate interactome in plants.

Application of Contrast-Enhanced 3-Dimensional T2-Weighted Volume Isotropic Turbo Spin Echo Acquisition Sequence in the Diagnosis of Prolactin-Secreting Pituitary Microadenomas.

OBJECTIVE: This study aimed to investigate the value of contrast-enhanced 3-dimensional (3D) T2-weighted (T2W) Volume Isotropic Turbo Spin Echo Acquisition (VISTA) sequence in prolactin-secreting pituitary adenoma diagnosis. METHODS: We enrolled 158 patients with hyperprolactinemia. Coronal dynamic contrast-enhanced (DCE) T1 spin echo and T2W VISTA sequences were performed. The detection of pituitary microadenomas in 3 imaging groups (DCE magnetic resonance imaging [MRI], VISTA, and DCE MRI + VISTA) were compared using McNemar test and χ2 test. RESULTS: The DCE MRI + VISTA group detected 28 more pituitary microlesions than DCE MRI alone. Among these, 20 lesions were clearly observed on VISTA images but were negative on DCE MRI. The combined sequences showed higher sensitivity (85.3%) and diagnostic accuracy (89.2%) for adenoma detection than any of the sequences alone (P < 0.01). We noted that in 65.7% of the patients with adenoma (46 of 70), a "hypointense rim" was present around the lesion on the VISTA images. Of them, 11 patients underwent surgery. Histopathology confirmed that the "hypointense rim" was a pseudocapsular structure at the edge of the adenoma. CONCLUSIONS: For patients with hyperprolactinemia, the 3D T2W VISTA sequence is an important supplement to DCE MRI, because it could improve the detection rate of pituitary microadenomas.

A phosphate starvation response-centered network regulates mycorrhizal symbiosis.

To secure phosphorus (P) from soil, most land plants use a direct phosphate uptake pathway via root hairs and epidermis and an indirect phosphate uptake pathway via mycorrhizal symbiosis. The interaction between these two pathways is unclear. Here, we mapped a network between transcription factors and mycorrhizal symbiosis-related genes using Y1H. Intriguingly, this gene regulatory network is governed by the conserved P-sensing pathway, centered on phosphate starvation response (PHR) transcription factors. PHRs are required for mycorrhizal symbiosis and regulate symbiosis-related genes via the P1BS motif. SPX-domain proteins suppress OsPHR2-mediated induction of symbiosis-related genes and inhibit mycorrhizal infection. In contrast, plants overexpressing OsPHR2 show improved mycorrhizal infection and are partially resistant to P-mediated inhibition of symbiosis. Functional analyses of network nodes revealed co-regulation of hormonal signaling and mycorrhizal symbiosis. This network deciphers extensive regulation of mycorrhizal symbiosis by endogenous and exogenous signals and highlights co-option of the P-sensing pathway for mycorrhizal symbiosis.

Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development.

Seed development is an important process of reproductive development and consists of embryo and endosperm development; both comprise several key processes. To determine and investigate the functions of the dynamic DNA methylome during seed development, we profiled the DNA methylation genome wide in a series of developmental stages of rice (Oryza sativa) embryo and endosperm by methylcytosine immunoprecipitation followed by Illumina sequencing. The results showed that embryo is hypermethylated predominantly around non-transposable element (TE) genes, short DNA-TEs, and short interspersed TEs compared with endosperm, and non-TE genes have the most diverse methylation status across seed development. In addition, lowly expressed genes are significantly enriched in hypermethylated genes, but not vice versa, confirming the crucial role of DNA methylation in suppressing gene transcription. Further analysis revealed the significantly decreased methylation at early developing stages (from 2 to 3 d after pollination), indicating a predominant role of demethylation during early endosperm development and that genes with a consistent negative correlation between DNA methylation change and expression change may be potentially directly regulated by DNA methylation. Interestingly, comparative analysis of the DNA methylation profiles revealed that both rice indica and japonica subspecies showed robust fluctuant profiles of DNA methylation levels in embryo and endosperm across seed development, with the highest methylation level at 6 d after pollination (2 d after pollination of endosperm in japonica as well), indicating that a complex and finely controlled methylation pattern is closely associated with seed development regulation. The systemic characterization of the dynamic DNA methylome in developing rice seeds will help us understand the effects and mechanism of epigenetic regulation in seed development.

[Comparison between pathological findings and MR diffusion-weighted imaging in primary hepatocellular carcinoma after transcatheter arterial chemoembolization].

OBJECTIVE: To explore the pathological basis of diffusion-weighted imaging (DWI) findings in hepatocellular carcinoma (HCC) after transcatheter arterial chemoembolization (TACE). METHODS: DWI was performed in 15 patients with HCC treated by TACE within 24 - 48 hours before II-phase operation. The DWI findings of the liver lesions were analyzed and correlated with pathological findings including macroscopic observation, HE staining and immunohistochemical staining for bFGF. RESULTS: (1) The viable tumor area showed mostly hypersignal intensity (12/15), whereas coagulative necrotic lesions showed hyposignal (8/15) or isosignal intensity (6/15). The ADC values of zones of viable tumor and necrosis in tumor were (1.42 +/- 0.16) x 10(-3) mm(2)/s and (1.58 +/- 0.18) x 10(-3) mm(2)/s, respectively. There was a significant difference of ADC values between the two zones (t = 2.618, P < 0.05). (2) There was a significant difference in ADC values of viable tumor between well and poorly differentiated tumors (t = -2.646, P < 0.05). The distinction of ADC values of the whole tumor was significant among tumors with different degree of necrosis (chi(2) = 7.236, P < 0.05). (3) A negative correlation was observed between bFGF protein expression index and ADC values of viable parts of the tumors in the study group (r = -0.552, P = 0.033). CONCLUSION: DWI shows certain characteristic features of the HCC after TACE, and can be used to distinguish viable and necrotic tumor tissues in HCC after TACE.