T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese.

Since its initial release in 2001, the human reference genome has undergone continuous improvement in quality, and the recently released telomere-to-telomere (T2T) version - T2T-CHM13 - reaches its highest level of continuity and accuracy after 20 years of effort by working on a simplified, nearly homozygous genome of a hydatidiform mole cell line. Here, to provide an authentic complete diploid human genome reference for the Han Chinese, the largest population in the world, we assembled the genome of a male Han Chinese individual, T2T-YAO, which includes T2T assemblies of all the 22 + X + M and 22 + Y chromosomes in both haploid. The quality of T2T-YAO is much better than all currently available diploid assemblies, and its haploid version, T2T-YAO-hp, generated by selecting the better assembly for each autosome, reaches the top quality of fewer than one error per 29.5 Mb, even higher than that of T2T-CHM13. Derived from an individual living in the aboriginal region of the Han population, T2T-YAO shows clear ancestry and potential genetic continuity from the ancient ancestors. Each haplotype of T2T-YAO possesses ∼ 330-Mb exclusive sequences, ∼ 3100 unique genes, and tens of thousands of nucleotide and structural variations as compared with CHM13, highlighting the necessity of a population-stratified reference genome. The construction of T2T-YAO, a truly accurate and authentic representative of the Chinese population, would enable precise delineation of genomic variations and advance our understandings in the hereditability of diseases and phenotypes, especially within the context of the unique variations of the Chinese population.

Prognosis Prediction of Lung Adenocarcinoma Patients Based on Molecular Subgroups of DNA Methylation.

Lung adenocarcinoma (LUAD) is a malignant tumor with high mortality. At present, the clinicopathologic feature is the main breakthrough to assess the prognosis of LUAD patients. However, in most cases, the results are less than satisfactory. Cox regression analysis was conducted in this study to obtain methylation sites with significant prognostic relevance based on mRNA expression, DNA methylation data, and clinical data of LUAD from The Cancer Genome Atlas Program database. LUAD patients were grouped into 4 subtypes according to different methylation levels using K-means consensus cluster analysis. By survival analysis, patients were grouped into high-methylation and low-methylation groups. Later, 895 differentially expressed genes (DEGs) were obtained. Eight optimal methylation signature genes associated with prognosis were screened by Cox regression analysis, and a risk assessment model was constructed based on these genes. Samples were then classified into high-risk and low-risk groups depending on the risk assessment model, and prognostic, predictive ability was assessed using survival and receiver operating characteristic (ROC) curves. The results showed that this risk model had a great efficacy in predicting the prognosis of patients, and it was, therefore, able to be an independent prognostic factor. At last, the enrichment analysis demonstrated that the signaling pathways, including cell cycle, homologous recombination, P53 signaling pathway, DNA replication, pentose phosphate pathway, and glycolysis gluconeogenesis were remarkably activated in the high-risk group. In general, we construct an 8-gene model based on DNA methylation molecular subtypes by a series of bioinformatics methods, which can provide new insights for predicting the prognosis of patients with LUAD.

Metabolic landscape dysregulation in bronchoalveolar lavage fluid of checkpoint inhibitor pneumonitis.

BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is a potentially fatal adverse event resulting from immunotherapy in patients with malignant tumors. However, the pathogenesis of CIP remains poorly understood. METHODS: We collected bronchoalveolar lavage fluid (BALF) from cohorts of patients with CIP, new-onset lung cancer (LC), and idiopathic pulmonary fibrosis (IPF). Non-targeted metabolomics analysis was conducted to analyze metabolic signatures. Flow cytometry was used to evaluate immune cell subsets. RESULTS: Lymphocytes were predominant in the BALF of patients with CIP. A total of 903 metabolites were identified, among which lipid compounds were the most abundant. In a comparison between patients with CIP and LC, enrichment analysis of the altered metabolites showed suppressed amino sugar metabolism, and spermidine and spermine biosynthesis in the CIP group. Metabolism of alpha linolenic acid, linoleic acid, and their fatty acid derivatives was enriched in the CIP group relative to the IPF group. The twelve metabolites found to be enriched in the CIP group were positively correlated with the proportion of CD8+ T cells. One cluster of BALF metabolites, 57.14% of which were lipid molecules, was inversely correlated with the proportion of natural killer cells. CONCLUSIONS: In this study, the metabolomic landscape of BALF in patients with CIP was determined. We elucidated suppressed tumor metabolic signatures, enhanced pulmonary inflammatory signaling, and the characteristics of responsible immune cells, which helps to understand the pathogenesis of CIP.

Clinical Characteristics and Treatment of Adult Idiopathic Carpal Tunnel Syndrome Accompanied with Trigger Digit.

Purpose: To investigate the clinical characteristics and treatment of adult idiopathic carpal tunnel syndrome (CTS) accompanied with trigger digit. Materials and Methods: A retrospective analysis was performed on a total of 74 patients with adult idiopathic CTS accompanied with trigger digit admitted to and treated at the Hand Surgery Department of Ningbo No. 6 Hospital from January 1, 2017 to December 31, 2019. Data on patients' gender, age, occupation, course of the disease, menstruation, surgeries, examination-related information, complications, treatment methods, and prognoses during follow-up were recorded and subsequently used to analyze the pathogeneses, clinical characteristics, and treatment. Results: A total of 74 patients (72 females and 2 males) were included. Among female patients, 51 were postmenopausal and 18 were non-postmenopausal. There were 101 fingers with trigger digit, including 14 patients with trigger digit in both hands, and 115 wrists affected by the CTS. The average course of CTS was 34.5 ± 49.3 months, and that of trigger digit was 10.5 ± 22.4 months. Seventy had both trigger digit and CTS in one hand, while among patients with both hands involved, only 4 had trigger digit or CTS in one hand. Eighty-nine fingers underwent A1 pulley release, and 104 hands underwent carpal tunnel surgery, with steroids being injected under the adventitia of the median nerve during the surgery. All patients who underwent surgeries had I/A-healed incisions, and 14 of them had obvious synovial hyperplasia observed in the carpal tunnel and flexor tendon sheath during surgeries. Follow-up visits, which lasted 3 to 35 months, had an average duration of 1.34 years and included 72 patients. In 63 patients (63/72), the syndrome of tenosynovitis and numbness disappeared and normal hand functions were restored; in 6 patients, the numbness in hands greatly improved and normal hand functions were almost completely restored, while no improvement in numbness of hands and limited hand functions were still observed in 3 patients. Conclusion: CTS accompanied with trigger digit was more common in postmenopausal females, and the course of CTS was longer than that of trigger digit. CTS and trigger digit were more likely to simultaneously occur in the same hand, while some patients might not have obvious synovial hyperplasia in the carpal tunnel. Surgeries were effective in severe cases.

MicroRNA-9-5p Facilitates Lung Adenocarcinoma Cell Malignant Progression via Targeting STARD13.

We aimed to elucidate binding of microRNA-9-5p and STARD13 in lung adenocarcinoma (LUAD) cells and discuss their impact on malignant progression of LUAD, so as to provide evidence for identifying new therapeutic targets for LUAD. Bioinformatics analysis was introduced for analysis of differentially expressed miRNAs in LUAD tissue, and potential downstream target gene was predicted with TargetScan and other databases. MicroRNA-9-5p and STARD13 mRNA levels at cellular level was analyzed with qRT-PCR assay. Lipofectamine 2000 was applied for cell transfection. Proliferation, migration and invasion of LUAD cells were assayed with CCK-8, wound healing and Transwell assays, respectively. Protein expression of STARD13 was assessed with western blot. Binding of microRNA-9-5p and STARD13 was identified with dual-luciferase assay. Compared with normal human bronchial cells, microRNA-9-5p level in LUAD cells was noticeably increased, and STARD13 level was noticeably decreased. MicroRNA-9-5p could significantly promote malignant progression of LUAD cells, while forced STARD13 level markedly repress malignant progression of LUAD cells. Dual-luciferase gene assay showed that microRNA-9-5p had a direct targeting relationship with STARD13, and it was also found that microRNA-9-5p enhanced malignant behaviors of LUAD cells through modulating STARD13. STARD13 was a target of microRNA-9-5p in LUAD. MicroRNA-9-5p fostered malignant behaviors of LUAD cells by targeting STARD13. Therefore, microRNA-9-5p may become a new target for LUAD, and microRNA-9-5p inhibition may be a new treatment method.

Free thoracodorsal artery polyfoliate perforator flaps for repairing multiple soft tissue defects in the hand.

BACKGROUND: Hand injury is commonly associated with multiple soft tissue defects. Polyfoliate flaps grafting is the optimal approach for multiple wounds.The feasibility of clinical using of free thoracodorsal artery polyfoliate perforator flaps for repairing multiple soft tissue defects in the hand needs to be confirmed in clinical practice. METHODS: Fifteen patients with hand soft tissue defects that were repaired using free thoracodorsal artery polyfoliate perforator flaps from January 2015 to February 2018 was retrospectively analysed. The survival rate, the operative time, the appearance and sensory recovery of the flaps, and hand function were evaluated. RESULTS: The flaps of all 15 patients survived. Vascular crisis occurred in one patient, and the flap was saved after exploratory operation. The 15 patients were followed up for 12-26 months. Sensation in the flaps was partially recovered in all 15 patients. The wound in the donor area was closed directly with sutures. Mean score of scars at the donor site were assessed using the modified Vancouver scar scale (VSS) was 2.7. A puffed appearance in the recipient area was noted in four patients. To obtain a more satisfactory appearance, revision of the flap was performed once in these four patients. The Total Active Movement (TAM) evaluation system was used to assess the results, which were considered excellent in seven patients, good in six patients, fair in two patients, and poor in none of the patients. Ten of the 15 patients returned to their primary jobs. CONCLUSION: Free thoracodorsal artery polyfoliate perforator flaps are appropriate for repairing multiple soft tissue defects in the hand, offer a satisfactory appearance, require a short operative time, and have little impact on the function and aesthetics of the donor site.

Screening for obstructive sleep apnea using a contact-free system compared with polysomnography.

STUDY OBJECTIVES: To evaluate the utility of a contact-free device in screening for obstructive sleep apnea. METHODS: Three hundred fifty-nine participants (mean age 46 ± 13 years, body mass index 26.1 ± 4.2 kg/m², 67.7% male) underwent overnight monitoring using a contact-free device, the OrbSense, and polysomnography (PSG) in the sleep laboratory simultaneously. The OrbSense recordings were analyzed automatically, and PSG was scored based on recommended guidelines. RESULTS: The respiratory event index from the OrbSense was lower than the apnea-hypopnea index (AHI) from PSG (25.5 ± 20.7 vs 27.0 ± 25.2 events/h; P = .007) and was significantly correlated with AHI (Pearson coefficient, 0.92; P < .0001). Bland-Altman analysis showed a mean difference of 1.5 events/h, and the limit of agreement was -18.6 to 21.5 events/h. Use of the OrbSense resulted in larger underestimates of AHI and lower negative predictive values at higher AHI values (especially when AHI ≥ 30 events/h). When we used a PSG diagnostic criterion of AHI > 5 events/h, the optimal diagnostic cutoff value from the OrbSense was 8 events/h, with a sensitivity of 90.4%, a specificity of 77.6%, a 94.6% positive predictive value, and a 65% negative predictive value. For patients with moderate to severe obstructive sleep apnea whose AHI was > 15 events/h, the OrbSense cutoff was 16.6 events/h, with a sensitivity of 87.1% and a specificity of 89.7%. Among the 359 participants, 250 patients (69.6%) had the same obstructive sleep apnea severity division classified by both PSG and the OrbSense. CONCLUSIONS: The contact-free device OrbSense can detect respiratory events during sleep and has close agreement with in-laboratory PSG in screening for obstructive sleep apnea. Further studies are warranted to test its utility in community-based settings and at home.

Myricitrin regulates proliferation, apoptosis and inflammation of chondrocytes treated with IL-1ß.

Osteoarthritis (OA) is a clinical disease which seriously affects the quality of life of sufferers. Although the pathogenesis of OA has not been fully unraveled, it is may be due to increased levels of pro-inflammatory cytokines, activation of inflammation-related signaling pathways, and degradation of extracellular matrix. Osteoarthritis is characterized by chronic joint pain, swelling, stiffness, limited movement or joint deformity, all of which seriously affect the quality of life and health of the affected individuals. Myroside (Myr) is a polyphenolic hydroxyflavone glycoside extracted from the fruits, bark and leaves of myroside and other natural plants. It has many pharmacological properties, especially anti-inflammatory effects. In the present study, primary chondrocytes of IL-1ß rats were used to simulate pathological environment of chondrocytes in OA, and to explore the effect of Myr on chondrocytes. It was found that Myr improved the viability and proliferation of chondrocytes, and also inhibited apoptosis in these cells. Moreover, Myr reduced the expressions of inflammatory factors, and inhibited inflammatory reactions in chondrocytes. These findings provide good experimental basis for the clinical application of Myr in the prevention and treatment of progressive degeneration of cartilage in OA.

[Anatomy of the free descending genicular artery perforator flap and its clinical application for soft-tissue defects at extremities].

OBJECTIVE: To investigate the feasibility of free descending genicular artery perforator flaps in the soft tissue defects at extremities. METHODS: Ten fresh cadavers were injected with lead oxide-gelatin mixture for three-dimensional visualization reconstruction using a 16-slice spiral computed tomography scanner and specialized volume-rendering software ( Materiaise's interactive medical image control system, MIMICS). The origin, course and distribution of the perforators in the thigh and leg region were observed. 11 patients with skin defects at the distal part of extremities were treated. The flap size ranged from 5 cm x 8 cm to 6 cm x 15 cm. Six flaps were pedicled with the descending genicular artery and the others were pedicled with the perforator of the descending genicular artery. All flaps were transferred by end to end anastomosis. RESULTS The follow-up period ranged from 6 to 18 months. All the flaps survived. The appearance and texture of the flaps were good with sensory recovery of S3. CONCLUSIONS: Free descending genicular artery perforator flap has a reliable blood supply and suitable thickness for the treatment of soft tissue defects at extremities. The technique is easily performed with reliable results.