AVCAPIR: A Novel Procalcific PIWI-Interacting RNA in Calcific Aortic Valve Disease

BACKGROUND

Calcification of the aortic valve leads to increased leaflet stiffness and consequently results in the development of calcific aortic valve disease (CAVD). However, the underlying molecular and cellular mechanisms of calcification remain unclear. Here, we identified a novel aortic valve calcification-associated PIWI-interacting RNA (piRNA; AVCAPIR) that increases valvular calcification and promotes CAVD progression.

METHODS

Using piRNA sequencing, we identified piRNAs contributing to the pathogenesis of CAVD that we termed AVCAPIRs. High-cholesterol diet-fed ApoE-/- mice with AVCAPIR knockout were used to examine the role of AVCAPIR in aortic valve calcification (AVC). Gain- and loss-of-function assays were conducted to determine the role of AVCAPIR in the induced osteogenic differentiation of human valvular interstitial cells. To dissect the mechanisms underlying AVCAPIR-elicited procalcific effects, we performed various analyses, including an RNA pulldown assay followed by liquid chromatography-tandem mass spectrometry, methylated RNA immunoprecipitation sequencing, and RNA sequencing. RNA pulldown and RNA immunoprecipitation assays were used to study piRNA interactions with proteins.

RESULTS

We found that AVCAPIR was significantly upregulated during AVC and exhibited potential diagnostic value for CAVD. AVCAPIR deletion markedly ameliorated AVC in high-cholesterol diet-fed ApoE-/- mice, as shown by reduced thickness and calcium deposition in the aortic valve leaflets, improved echocardiographic parameters (decreased peak transvalvular jet velocity and mean transvalvular pressure gradient, as well as increased aortic valve area), and diminished levels of osteogenic markers (Runx2 and Osterix) in aortic valves. These results were confirmed in osteogenic medium-induced human valvular interstitial cells. Using unbiased protein-RNA screening and molecular validation, we found that AVCAPIR directly interacts with FTO (fat mass and obesity-associated protein), subsequently blocking its N6-methyladenosine demethylase activity. Further transcriptomic and N6-methyladenosine modification epitranscriptomic screening followed by molecular validation confirmed that AVCAPIR hindered FTO-mediated demethylation of CD36 mRNA transcripts, thus enhancing CD36 mRNA stability through the N6-methyladenosine reader IGF2BP1 (insulin-like growth factor 2 mRNA binding protein 1). In turn, the AVCAPIR-dependent increase in CD36 stabilizes its binding partner PCSK9 (proprotein convertase subtilisin/kexin type 9), a procalcific gene, at the protein level, which accelerates the progression of AVC.

CONCLUSIONS

We identified a novel piRNA that induced AVC through an RNA epigenetic mechanism and provide novel insights into piRNA-directed theranostics in CAVD.

Prophylactic Supplementation with Lactobacillus Reuteri or Its Metabolite GABA Protects Against Acute Ischemic Cardiac Injury

The gut microbiome has emerged as a potential target for the treatment of cardiovascular disease. Ischemia/reperfusion (I/R) after myocardial infarction is a serious complication and whether certain gut bacteria can serve as a treatment option remains unclear. Lactobacillus reuteri (L. reuteri) is a well-studied probiotic that can colonize mammals including humans with known cholesterol-lowering properties and anti-inflammatory effects. Here, the prophylactic cardioprotective effects of L. reuteri or its metabolite γ-aminobutyric acid (GABA) against acute ischemic cardiac injury caused by I/R surgery are demonstrated. The prophylactic gavage of L. reuteri or GABA confers cardioprotection mainly by suppressing cardiac inflammation upon I/R. Mechanistically, GABA gavage results in a decreased number of proinflammatory macrophages in I/R hearts and GABA gavage no longer confers any cardioprotection in I/R hearts upon the clearance of macrophages. In vitro studies with LPS-stimulated bone marrow-derived macrophages (BMDM) further reveal that GABA inhibits the polarization of macrophages toward the proinflammatory M1 phenotype by inhibiting lysosomal leakage and NLRP3 inflammasome activation. Together, this study demonstrates that the prophylactic oral administration of L. reuteri or its metabolite GABA attenuates macrophage-mediated cardiac inflammation and therefore alleviates cardiac dysfunction after I/R, thus providing a new prophylactic strategy to mitigate acute ischemic cardiac injury.

[Prediction of pathological remission of head and neck squamous cell carcinoma patients after neoadjuvant immunochemotherapy and construction of clinical model based on clinical features and inflammatory markers]

Objective: To analyze the potential clinical biological factors influencing the major pathological response (MPR) to neoadjuvant immunochemotherapy in patients with resectable head and neck squamous cell carcinoma (HNSCC). Methods: This retrospective study enrolled patients with resectable HNSCC who underwent neoadjuvant immunochemotherapy at Sun Yat-sen University Cancer Center from June 1, 2019 to December 31, 2021. Binary logistic regression was used to analyze the correlation between clinical characteristics, inflammatory markers and MPR, and a nomogram model was constructed. The calibration curve and decision curve analysis were used to verify the predictive ability and accuracy of the nomogram model. Results: A total of 173 patients were included in the study, with 141 males and 32 females, aged from 22 to 83 years. After pathological assessment, the patients were divided into two groups: MPR group (108 cases) and non MPR group (65 cases). Logistics regression analysis indicated that the patients with HPV+oropharyngeal cancer, partial response or complete response by imaging assessment, low pre-treatment platelet/lymphocyte ratio, low pre-treatment C reactive protein/albumin ratio and lower pre-and post-treatment C reactive protein/albumin ratio difference were more likely to have MPR (all P<0.05). Nomogram model was constructed based on the above factors, with a C-index of 0.826 (95%CI: 0.760-0.892), and the calibration curve and decision curve analysis confirmed the prediction accuracy of the model. Conclusion: This study shows that many factors are related to MPR of patients with resectable HNSCC receiving neoadjuvant immunochemotherapy and the constructed nomogram model helps to develop personalized treatment strategies for the patients.

Genome-wide association studies and Mendelian randomization analyses provide insights into the causes of early-onset colorectal cancer

BACKGROUND

The incidence of early-onset colorectal cancer (EOCRC; diagnosed <50 years of age) is rising globally; however, the causes underlying this trend are largely unknown. CRC has strong genetic and environmental determinants, yet common genetic variants and causal modifiable risk factors underlying EOCRC are unknown. We conducted the first EOCRC-specific genome-wide association study (GWAS) and Mendelian randomization (MR) analyses to explore germline genetic and causal modifiable risk factors associated with EOCRC.

PATIENTS AND METHODS

We conducted a GWAS meta-analysis of 6176 EOCRC cases and 65 829 controls from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), the Colorectal Transdisciplinary Study (CORECT), the Colon Cancer Family Registry (CCFR), and the UK Biobank. We then used the EOCRC GWAS to investigate 28 modifiable risk factors using two-sample MR.

RESULTS

We found two novel risk loci for EOCRC at 1p34.1 and 4p15.33, which were not previously associated with CRC risk. We identified a deleterious coding variant (rs36053993, G396D) at polyposis-associated DNA repair gene MUTYH (odds ratio 1.80, 95% confidence interval 1.47-2.22) but show that most of the common genetic susceptibility was from noncoding signals enriched in epigenetic markers present in gastrointestinal tract cells. We identified new EOCRC-susceptibility genes, and in addition to pathways such as transforming growth factor (TGF) β, suppressor of Mothers Against Decapentaplegic (SMAD), bone morphogenetic protein (BMP) and phosphatidylinositol kinase (PI3K) signaling, our study highlights a role for insulin signaling and immune/infection-related pathways in EOCRC. In our MR analyses, we found novel evidence of probable causal associations for higher levels of body size and metabolic factors-such as body fat percentage, waist circumference, waist-to-hip ratio, basal metabolic rate, and fasting insulin-higher alcohol drinking, and lower education attainment with increased EOCRC risk.

CONCLUSIONS

Our novel findings indicate inherited susceptibility to EOCRC and suggest modifiable lifestyle and metabolic targets that could also be used to risk-stratify individuals for personalized screening strategies or other interventions.

Scanning near-field optical microscopy measurements and simulations of regularly arranged silver nanoparticles

Silver nanoparticles on a glass substrate are experimentally investigated by aperture scanning near-field optical microscopy (a-SNOM). To understand the experimental results, finite-element-method simulations are performed building a theoretical model of the a-SNOM geometry. We systematically vary parameters like aperture size, aluminum-coating thickness, tip cone angle, and tip-surface distance and discuss their influence on the near-field enhancement. All these investigations are performed comparatively for constant-height and constant-gap scanning modes. In the end, we establish a reliable and stable optical model for simulating a-SNOM measurements, which is capable of reproducing trends observed in experimental data.

A human mitofusin 2 mutation can cause mitophagic cardiomyopathy

Cardiac muscle has the highest mitochondrial density of any human tissue, but mitochondrial dysfunction is not a recognized cause of isolated cardiomyopathy. Here, we determined that the rare mitofusin (MFN) 2 R400Q mutation is 15-20× over-represented in clinical cardiomyopathy, whereas this specific mutation is not reported as a cause of MFN2 mutant-induced peripheral neuropathy, Charcot-Marie-Tooth disease type 2A (CMT2A). Accordingly, we interrogated the enzymatic, biophysical, and functional characteristics of MFN2 Q400 versus wild-type and CMT2A-causing MFN2 mutants. All MFN2 mutants had impaired mitochondrial fusion, the canonical MFN2 function. Compared to MFN2 T105M that lacked catalytic GTPase activity and exhibited normal activation-induced changes in conformation, MFN2 R400Q and M376A had normal GTPase activity with impaired conformational shifting. MFN2 R400Q did not suppress mitochondrial motility, provoke mitochondrial depolarization, or dominantly suppress mitochondrial respiration like MFN2 T105M. By contrast to MFN2 T105M and M376A, MFN2 R400Q was uniquely defective in recruiting Parkin to mitochondria. CRISPR editing of the R400Q mutation into the mouse Mfn2 gene induced perinatal cardiomyopathy with no other organ involvement; knock-in of Mfn2 T105M or M376V did not affect the heart. RNA sequencing and metabolomics of cardiomyopathic Mfn2 Q/Q400 hearts revealed signature abnormalities recapitulating experimental mitophagic cardiomyopathy. Indeed, cultured cardiomyoblasts and in vivo cardiomyocytes expressing MFN2 Q400 had mitophagy defects with increased sensitivity to doxorubicin. MFN2 R400Q is the first known natural mitophagy-defective MFN2 mutant. Its unique profile of dysfunction evokes mitophagic cardiomyopathy, suggesting a mechanism for enrichment in clinical cardiomyopathy.

Outcomes and Failure Patterns after Chemoradiotherapy for Locally Advanced Rectal Cancer with Positive Lateral Pelvic Lymph Nodes: A Propensity Score-Matched Analysis

PURPOSE/OBJECTIVE(S)

Locally advanced rectal cancer (LARC) combined with positive lateral pelvic lymph nodes (LPLN) tends to present worse prognosis. However, for those patients it remains unclear whether other combination high-risk factors affect the prognosis. This study aimed to use propensity score matching (PSM) to examine long-term outcomes and failure patterns in patients with positive vs. negative LPLN.

MATERIALS/METHODS

Patients with LARC were retrospectively divided into LPLN-positive and LPLN-negative groups. LPLN-positivity was defined as lymph node short diameter greater than or equal to 7 mm with specific morphological features. Clinical characteristics were compared between the groups using the chi-square test. PSM was applied to balance these differences. Progression-free survival (PFS) and overall survival (OS), and local-regional recurrence (LRR) and distant metastasis (DM) rates were compared between the groups using the Kaplan-Meier method and log-rank tests.

RESULTS

Prior to PSM, a total of 651 LARC patients were included. The LPLN-positive group had higher rates of lower location (53.1% vs. 43.0%, P = 0.025), mesorectal fascia (MRF)-positive (53.9% vs. 35.4%, P<0.001) and extramural venous invasion (EMVI)-positive (51.2% vs. 27.2%, P<0.001) disease than the LPLN-negative group. After PSM, there were 114 patients for each group along with the balanced clinical factors, and both groups had comparable surgery, pathologic complete response (pCR), and ypN stage rates. The median follow-up time was 45.9 months, 3-year OS (88.3% vs. 92.1%, P = 0.276) and LRR (5.7% vs. 2.8%, P = 0.172) rates were comparable between LPLN-positive and LPLN-negative groups. Meanwhile, despite no statistical difference, 3-year PFS (78.8% vs. 85.9%, P = 0.065) and DM (20.4% vs. 13.3%, P = 0.061) rates slightly differed between the groups. Among 10 patients with LRR, seven (70.0%) had lateral pelvic recurrence, among them, five patients were LPLN-positive, and four (80.0%) of these patients did not receive simultaneous integrated boost intensity-modulated radiotherapy (SIB- IMRT).45 patients were diagnosed with DM, 11 (40.7%) LPLN-positive and 3 (17.6%) LPLN-negative patients were diagnosed with oligometastases (P = 0.109).

CONCLUSION

Our study shows there is a tendency of worse PFS and DM in LPLN-positive than LPLN-negative patients, for LPLN-positive patients, oligometastases account for a large proportion of all distant metastases.

4D-MRI Guided Stereotactic Body Radiation Therapy for Unresectable Colorectal Liver Metastases

PURPOSE/OBJECTIVE(S)

This study evaluated the feasibilities and outcomes following four-dimensional magnetic resonance imaging (4D-MRI) guided stereotactic body radiation therapy (SBRT) for unresectable colorectal liver metastases (CRLM).

MATERIALS/METHODS

From March 2018 to January 2022, we identified 76 unresectable CRLM patients with 123 lesions who received 4D-MRI guided SBRT in our institution. 4D-MRI simulation with or without abdominal compression was conducted for all patients. The prescription dose was 50-65 Gy in 5-12 fractions. The image quality of computed tomography (CT) and MRI were compared using the Clarity Score. Clinical outcomes and toxicity profiles were evaluated.

RESULTS

The 4D-MRI significantly improved the image quality compared with CT images (mean Clarity Score: 1.67 vs 2.88, P < 0.001). The abdominal compression significantly reduced motions in cranial-caudal direction (P = 0.03) with 2 phase T2 weighted images assessing tumor motion. The median follow-up time was 12.5 months. For 98 lesions assessed for best response, the complete response, partial response and stable disease rate were 57.1 %, 30.6 % and 12.2 %, respectively. The local control (LC) rate at 2 year was 97.3%. 46.1% of patients experienced grade 1-2 toxicities and only 2.6% patients experienced grade 3 hematologic toxicities.

CONCLUSION

The 4D-MRI technique allowed precise target delineation and motion tracking in unresectable CRLM patients. High LC rate and mild toxicities were achieved. This study provided evidence for using 4D-MRI guided SBRT as an alternative treatment in unresectable CRLM.

SIRT2 counteracts primate cardiac aging via deacetylation of STAT3 that silences CDKN2B

Aging is a major risk factor contributing to pathophysiological changes in the heart, yet its intrinsic mechanisms have been largely unexplored in primates. In this study, we investigated the hypertrophic and senescence phenotypes in the hearts of aged cynomolgus monkeys as well as the transcriptomic and proteomic landscapes of young and aged primate hearts. SIRT2 was identified as a key protein decreased in aged monkey hearts, and engineered SIRT2 deficiency in human pluripotent stem cell-derived cardiomyocytes recapitulated key senescence features of primate heart aging. Further investigations revealed that loss of SIRT2 in human cardiomyocytes led to the hyperacetylation of STAT3, which transcriptionally activated CDKN2B and, in turn, triggered cardiomyocyte degeneration. Intra-myocardial injection of lentiviruses expressing SIRT2 ameliorated age-related cardiac dysfunction in mice. Taken together, our study provides valuable resources for decoding primate cardiac aging and identifies the SIRT2-STAT3-CDKN2B regulatory axis as a potential therapeutic target against human cardiac aging and aging-related cardiovascular diseases.

[The mediating role of resilience between social capital at work and anxiety of medical staff]

Objective: To explore the influence of social capital at work on anxiety of medical staff, and the mediating role of resilience. Methods: From March to May 2022, a total of 201 medical staff in the Affiliated Hospital of Jining Medical University were investigated with the General Information Questionnaire, Workplace Social Capital Scale, Connor-Davidson Resilience Scale (CD-RISC-10) and Generalized Anxiety Disorder-7 (GAD-7) . K-S method was used for normdity test of econometic voriobles, and normal distribution data were represented by Mean±SD, Pearson correlation analysis and linear regression analysis were used to test correlation between variables and mediating effect, and Bootstrap method was carried out by SPSS macro program PROCESS v3.5 to verify the mediating effect. Results: The detection rate of anxiety was 59.20% (119/201) in medical staff. The scores of social capital at work (28.90±5.83) and resilience (31.55±4.98) were negatively correlated with the score of anxiety (7.20±2.06) (r=-0.338, -0.510, P<0.001) , while the score of social capital at work was positively correlated with resilience (r=0.392, P<0.001) . Workplace social capital positively predicted resilience (β=0.392, P<0.001) , and both workplace social capital (β=-0.222, P=0.001) and resilience at work (β=-0.423, P<0.001) negatively predicted anxiety score. The direct effect of social capital in the workplace of medical staff on anxiety was -0.222 (95%CI: -0.349~-0.095, P=0.001) , and the indirect effect of resilience on anxiety was -0.166 (95%CI: -0.265~-0.080) . The resilience of medical staff had a partial mediating effect between workplace social capital and anxiety, which accounted for 42.78% of the total effect. Conclusion: The resilience of medical staff has a partial mediating effect between workplace social capital and anxiety. Workplace social capital can not only directly affect the anxiety of medical staff, but also indirectly affect it through resilience.

Efficient Mining of Anticancer Peptides from Gut Metagenome

The gut microbiome plays a crucial role in modulating host health and disease. It serves as a vast reservoir of functional molecules that hold great potential for clinical applications. One specific area of interest is identifying anticancer peptides (ACPs) for innovative cancer therapies. However, ACPs discovery is hindered by a heavy reliance on experimental methodologies. To overcome this limitation, we here employed a novel approach by leveraging the overlap between ACPs and antimicrobial peptides (AMPs). By combining well-established AMP prediction methods with mining techniques in metagenomic cohorts, a total of 40 potential ACPs is identified. Out of the identified ACPs, 39 demonstrated inhibitory effects against at least one cancer cell line, exhibiting significant differences from known ACPs. Moreover, the therapeutic potential of the two most promising peptides in a mouse xenograft cancer model is evaluated. Encouragingly, the peptides exhibit effective tumor inhibition without any detectable toxic effects. Interestingly, both peptides display uncommon secondary structures, highlighting its distinctive characteristics. This findings highlight the efficacy of the multi-center mining approach, which effectively uncovers novel ACPs from the gut microbiome. This approach has significant implications for expanding treatment options not only for CRC, but also for other cancer types.

MAVS Antagonizes Human Stem Cell Senescence as a Mitochondrial Stabilizer

Mitochondrial dysfunction is a hallmark feature of cellular senescence and organ aging. Here, we asked whether the mitochondrial antiviral signaling protein (MAVS), which is essential for driving antiviral response, also regulates human stem cell senescence. To answer this question, we used CRISPR/Cas9-mediated gene editing and directed differentiation techniques to generate various MAVS-knockout human stem cell models. We found that human mesenchymal stem cells (hMSCs) were sensitive to MAVS deficiency, as manifested by accelerated senescence phenotypes. We uncovered that the role of MAVS in maintaining mitochondrial structural integrity and functional homeostasis depends on its interaction with the guanosine triphosphatase optic atrophy type 1 (OPA1). Depletion of MAVS or OPA1 led to the dysfunction of mitochondria and cellular senescence, whereas replenishment of MAVS or OPA1 in MAVS-knockout hMSCs alleviated mitochondrial defects and premature senescence phenotypes. Taken together, our data underscore an uncanonical role of MAVS in safeguarding mitochondrial homeostasis and antagonizing human stem cell senescence.

Breast cancer diagnosis and prognosis using a high b-value non-Gaussian continuous-time random-walk model

AIM

To compare the diagnostic performance of mono-exponential model-derived apparent diffusion coefficient (ADC), continuous-time random-walk (CTRW) model-derived D_m, α, β and their combinations in discriminating malignancy of breast lesions, and investigate the association between model-derived parameters and prognosis-related immunohistochemical indices.

MATERIALS AND METHODS

A total of 85 patients with breast lesions (51 malignant, 34 benign) were analysed in this retrospective study. Clinical characteristics include oestrogen receptor (ER), progesterone receptor (PR), human epidermal receptor 2 (HER2), and Ki-67. The ADC was fitted using a mono-exponential model (b-values = 0, 800 s/mm²), while D_m, α, and β were fitted using a CTRW model. Independent Student's t-test and the Mann-Whitney U-test were used for the comparison of parameters. Discrimination performance was accomplished by receiver operating characteristic (ROC) analysis, and Spearman's correlation analysis was used to explore the association between immunohistochemical indices and diffusion parameters, the statistical significance level was p<0.05.

RESULTS

D_m and ADC demonstrated similar performance in differentiating malignant and benign lesions (AUC = 0.928 versus 0.930), while the combination of D_m, α, and β could improve the AUC to 0.969. The combined parameter generated by ADC, D_m, α, and β was effective in identifying the ER+/ER- and PR+/PR- patients. Temporal heterogeneity parameter α correlated significantly with the expression of PR.

CONCLUSION

Diffusion parameters derived from the CTRW model could effectively discriminate the malignancy of breast lesions. Meanwhile, the hormone receptor expression could be distinguished by combined diffusion parameters, and have the potential to reflect the prognosis.

Biomarkers of aging

Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant.

Acting on ethics and governance of aging research

Rapid advances in aging research and clinical translation come with numerous ethical and societal issues that the current regulatory framework may not be sufficient to address. To fill this gap, we propose a responsible and comprehensive governance framework to cope with these issues while maximizing the benefits of aging research.

Resurrection of endogenous retroviruses during aging reinforces senescence

Whether and how certain transposable elements with viral origins, such as endogenous retroviruses (ERVs) dormant in our genomes, can become awakened and contribute to the aging process is largely unknown. In human senescent cells, we found that HERVK (HML-2), the most recently integrated human ERVs, are unlocked to transcribe viral genes and produce retrovirus-like particles (RVLPs). These HERVK RVLPs constitute a transmissible message to elicit senescence phenotypes in young cells, which can be blocked by neutralizing antibodies. The activation of ERVs was also observed in organs of aged primates and mice as well as in human tissues and serum from the elderly. Their repression alleviates cellular senescence and tissue degeneration and, to some extent, organismal aging. These findings indicate that the resurrection of ERVs is a hallmark and driving force of cellular senescence and tissue aging.

[Predictive value of SYNTAX-Ⅱ score on prognosis of patients with chronic total occlusion undergoing percutaneous coronary intervention]

Objective: To investigate the predictive value of SYNTAX-Ⅱ score on long term prognosis of patients diagnosed with chronic total occlusion (CTO) and received percutaneous coronary intervention (PCI). Methods: Patients undergoing CTO-PCI in Fuwai hospital from January 2010 to December 2013 were enrolled in this retrospective analysis. The SYNTAX-Ⅱ score of the patients was calculated. According to SYNTAX-Ⅱ score tertiles, patients were stratified as follows: SYNTAX-Ⅱ≤20, 20<SYNTAX-Ⅱ≤27, SYNTAX-Ⅱ>27. Primary endpoint was major adverse cardiac events (MACCE), including all-cause death, myocardial infarction, stroke and any revascularization. Secondary endpoints included stent thrombosis, heart failure and target lesion failure (TLF). Patients were followed up by outpatient visit or telephone call at 1 month, 6 months and 1 year after PCI, and annually up to 5 years. Multivariate Cox regression model was used to analyze the independent risk factors of all-cause death in patients undergoing CTO-PCI. The predictive value of SYNTAX score with SYNTAX-Ⅱ score for all-cause death was evaluated by the receiver operating characteristic (ROC) curve and the area under the curve (AUC). Results: A total of 2 391 patients with CTO and received PCI were enrolled in this study. The mean age was (57.0±10.5) years, 1 994 (83.40%) patients were male. There were 802 patients in lower tertile group (SYNTAX-Ⅱ≤20), 798 patients in intermediate group (20<SYNTAX-Ⅱ≤27) and 791 patients in upper tertile group (SYNTAX-Ⅱ>27). At the end of 5-year follow-up, the loss to follow-up rate of the three groups was 9.10%(73/802), 10.78%(86/798)and 8.85%(70/791), respectively. The rate of all-cause mortality (1.78% (13/729) vs. 3.65% (26/712) vs. 9.02% (65/721), P<0.001), cardiac death (1.37% (10/729) vs. 2.11% (15/712) vs. 4.85% (35/721), P<0.001), target vessel myocardial infarctions (4.25% (31/729) vs. 4.49% (32/712) vs. 7.07% (51/721), P=0.03), probable stent thrombosis (1.51% (11/729) vs. 2.81% (20/712) vs. 3.61% (26/721), P=0.04) and heart failure (1.78% (13/729) vs. 1.97% (14/712) vs. 5.41% (39/721), P<0.001) increased in proportion to increasing SYNTAX-Ⅱ score (all P<0.05). Multivariable Cox regression analysis indicated that female (HR=2.05, 95%CI 1.12-3.73, P=0.01), left ventricular ejection fraction (HR=0.97, 95%CI 0.95-1.00, P=0.05) and SYNTAX-Ⅱ score (HR=1.07, 95%CI 1.02-1.11,P=0.01) were independent predictors for all-cause mortality in patients undergoing CTO-PCI. The predicted value of the SYNTAX-Ⅱ score for all-cause death was significantly higher than the SYNTAX score (AUC 0.71 vs. 0.60, P=0.003). Conclusion: For CTO patients who underwent percutaneous coronary intervention, SYNTAX-Ⅱ score is an independent predictor for 5-year all-cause death, and SYNTAX-Ⅱ serves as an important predictor for all-cause death in these patients.

National audit of non-melanoma skin cancer excisions performed by plastic surgery in the UK

A national, multi-centre audit of non-melanoma skin cancer excisions by plastic surgery.

Single-nucleus transcriptomics reveals a gatekeeper role for FOXP1 in primate cardiac aging

Aging poses a major risk factor for cardiovascular diseases, the leading cause of death in the aged population. However, the cell type-specific changes underlying cardiac aging are far from being clear. Here, we performed single-nucleus RNA-sequencing analysis of left ventricles from young and aged cynomolgus monkeys to define cell composition changes and transcriptomic alterations across different cell types associated with age. We found that aged cardiomyocytes underwent a dramatic loss in cell numbers and profound fluctuations in transcriptional profiles. Via transcription regulatory network analysis, we identified FOXP1, a core transcription factor in organ development, as a key downregulated factor in aged cardiomyocytes, concomitant with the dysregulation of FOXP1 target genes associated with heart function and cardiac diseases. Consistently, the deficiency of FOXP1 led to hypertrophic and senescent phenotypes in human embryonic stem cell-derived cardiomyocytes. Altogether, our findings depict the cellular and molecular landscape of ventricular aging at the single-cell resolution, and identify drivers for primate cardiac aging and potential targets for intervention against cardiac aging and associated diseases.

4E-BP1 counteracts human mesenchymal stem cell senescence via maintaining mitochondrial homeostasis

Although the mTOR-4E-BP1 signaling pathway is implicated in aging and aging-related disorders, the role of 4E-BP1 in regulating human stem cell homeostasis remains largely unknown. Here, we report that the expression of 4E-BP1 decreases along with the senescence of human mesenchymal stem cells (hMSCs). Genetic inactivation of 4E-BP1 in hMSCs compromises mitochondrial respiration, increases mitochondrial reactive oxygen species (ROS) production, and accelerates cellular senescence. Mechanistically, the absence of 4E-BP1 destabilizes proteins in mitochondrial respiration complexes, especially several key subunits of complex III including UQCRC2. Ectopic expression of 4E-BP1 attenuates mitochondrial abnormalities and alleviates cellular senescence in 4E-BP1-deficient hMSCs as well as in physiologically aged hMSCs. These f indings together demonstrate that 4E-BP1 functions as a geroprotector to mitigate human stem cell senescence and maintain mitochondrial homeostasis, particularly for the mitochondrial respiration complex III, thus providing a new potential target to counteract human stem cell senescence.

[Association of glutamate receptor metabotropic 5 polymorphisms with schizophrenia susceptibility in a Chinese Han population]

Objectives: To investigate the association of single nucleotide polymorphisms (SNP) of glutamate receptor metabotropic 5 (GRM5) gene with schizophrenia susceptibility(SZ) in a Chinese Han population. Methods: Twenty-two SNPs located in GRM5 gene in 528 paranoid SZ patients and 528 control subjects recruited from northern Henanwere analyzed. The clinical features of 267 first-episode SZ patients were assessed with the Positive and Negative Syndrome Scale (PANSS). Results: The SZ group included 264 males and 264 females, aged (27±8) years; the healthy control group had 264 males and 264 females, aged (28±8) years.The differences in the genotypic and allelic frequencies of two SNPs (rs567990 and rs12421343) were statistically significant between the SZ patients and control groups (all P<0.05). The allele frequency of rs504183 was also statistically different between the two groups (P=0.030). When the subjects were stratified by sex, the genotypic and allelic frequencies of rs12421343 in female subjects were statistically different between the SZ patients and control groups. The allele frequencies of SNPs (rs12422021, rs567990, and rs7101540) were also statisticallydifferent between the two groups (all P<0.05). Meanwhile, rs567990 AG+GG carriers had a higher risk for SZ than AA carriers in female subjects(OR=1.946, 95%CI: 1.264-2.995). In addition, the patients with different genotypes (GG, AA+AG) of rs12422021 showed statistically significant differences in PANSS total score(84.8±24.4 vs 75.3±18.6), positive (16.2±4.3 vs 14.4±4.2), excitement (12.4±5.1 vs 10.2±4.1) and cognitive impairment factor scores (15.2±6.8 vs 13.3±3.9) (all P<0.05). The patients with AC and the other two genotypes (AA and CC) of rs504183 showed statistically significant differences in PANSS negative factor score(27.4±9.9 vs 24.7±8.4 and 23.4±8.1, both P<0.05). Conclusion: The current study provides further evidence that GRM5 is associated with SZ, and suggests a putative sex difference.

[The clinical value of oral robotic surgery in the treatment of oropharyngeal squamous cell carcinoma]

Objective: To explore the therapeutic effects of transoral robotic surgery (TORS) and traditional surgical modes in oropharyngeal squamous cell carcinoma (OPSCC). Methods: The clinicopathological data of patients with oropharyngeal squamous cell carcinoma treated at Sun Yat-sen University Cancer Center from 2010 to 2018 were retrospectively analyzed. 135 cases were treated with traditional surgery (non-TORS group), while 52 cases were treated with TORS (TORS group). The prognosis of the two groups of patients were analyzed by Kaplan-Meier method and Log rank test, the influencing factors were analyzed by Cox regression model. Results: The 2-year overall survival (OS, 94.2%) and 2-year progression-free survival (PFS, 93.8%) of patients in the TORS group were better than those in the non-TORS group (71.4% and 71.4%, respectively, P<0.05). The 2-year OS (93.3%) and 2-year PFS (92.8%) of TORS group patients in T1-2 stage were better than those of non-TORS group (73.1% and 72.8%, respectively, P<0.05). The 2-year OS (95.8%) and 2-year PFS (95.2%) of patients with stage Ⅰ to Ⅱ in the TORS group were not significantly different from those in the non-TORS group (84.1% and 83.9%, respectively, P>0.05). The 2-year OS (92.9%) and 2-year PFS rate (92.7%) of patients with stage Ⅲ to Ⅳ in the TORS group were better than those in the non-TORS group (64.7% and 63.9%, respectively, P<0.05). The 2-year OS (94.4%) of HPV-positive patients in the TORS group was not significantly different from that in the non-TORS group (83.3%, P=0.222). The 2-year OS of HPV-negative patients in the TORS group (94.1%) was significantly different from that in the non-TORS group (43.7%, P<0.001). HPV status was an independent prognostic factor (P=0.008). Conclusions: TORS has a better prognosis in the treatment of oropharyngeal squamous cell carcinoma compared with the traditional treatment methods. The patients with T1-T2 can achieve better survival benefits after TORS treatment. The HPV-positive OPSCC patients has a better prognosis than that of HPV-negative OPSCC patients, and regardless of HPV status, OPSCC patients in the TORS group could obtain a better survival prognosis.

Vitronectin-Derived Peptide Promotes Reparative Dentin Formation

Exposed dental pulp can maintain its vitality through a pulp-capping procedure with biocompatible materials, followed by reparative dentin formation. Our previous study demonstrated that a vitronectin-derived peptide (VnP-16) promotes osteoblast differentiation and concomitantly restrains osteoclast differentiation and resorptive function. In this study, we aimed to demonstrate that VnP-16 promotes odontoblast differentiation, mineralization, and reparative dentin formation in a pulp exposure model using a rat tooth. VnP-16 showed no cytotoxicity and promoted cellular behavior in human dental pulp cells, enhancing their differentiation into odontoblast-like cells and mineralization, effects that are comparable to those obtained with vitronectin. In a rat pulp exposure model, VnP-16 showed mild inflammatory responses at 2 and 4 wk or none. Mineral trioxide aggregate (MTA) demonstrated a tendency of early formation of reparative dentin at 2 wk when compared with recombinant human bone morphogenetic protein 2 (rhBMP-2) and VnP-16. However, VnP-16 induced reparative dentin formation similar to MTA and rhBMP-2 without inflammation at 4 wk. In addition, VnP-16 showed a thicker and homogeneous reparative dentin formation versus MTA and rhBMP-2. Collectively, these results suggest that VnP-16 can be a useful, direct pulp-capping agent for highly qualified reparative dentin formation by promoting cell behavior and odontoblastic differentiation of human dental pulp cells.

Numerical Optimization of a Nanophotonic Cavity by Machine Learning for Near-Unity Photon Indistinguishability at Room Temperature

Room-temperature (RT), on-chip deterministic generation of indistinguishable photons coupled to photonic integrated circuits is key for quantum photonic applications. Nevertheless, high indistinguishability (I) at RT is difficult to obtain due to the intrinsic dephasing of most deterministic single-photon sources (SPS). Here, we present a numerical demonstration of the design and optimization of a hybrid slot-Bragg nanophotonic cavity that achieves a theoretical near-unity I and a high coupling efficiency (β) at RT for a variety of single-photon emitters. Our numerical simulations predict modal volumes in the order of 10^-3(λ/2n)³, allowing for strong coupling of quantum photonic emitters that can be heterogeneously integrated. We show that high I and β should be possible by fine-tuning the quality factor (Q) depending on the intrinsic properties of the single-photon emitter. Furthermore, we perform a machine learning optimization based on the combination of a deep neural network and a genetic algorithm (GA) to further decrease the modal volume by almost 3 times while relaxing the tight dimensions of the slot width required for strong coupling. The optimized device has a slot width of 20 nm. The design requires fabrication resolution in the limit of the current state-of-the-art technology. Also, the condition for high I and β requires a positioning accuracy of the quantum emitter at the nanometer level. Although the proposal is not a scalable technology, it can be suitable for experimental demonstration of single-photon operation.

[Retropharyngeal lymph node dissection in head and neck cancers treated with transoral robotic surgery]

Objective: To evaluate the indications, safety, feasibility, and surgical technique for patients with head and neck cancers undergoing transoral robotic retropharyngeal lymph node (RPLN) dissection. Methods: The current study enrolled 12 consecutive head and neck cancer patients (seven males and four females) who underwent transoral robotic RPLN dissection with the da Vinci surgical robotic system at the Sun Yat-sen University Cancer Center from May 2019 to July 2020. Seven patients were diagnosed as nasopharyngeal carcinoma with RPLN metastasis after initial treatments, 4 patients were diagnosed as thyroid carcinoma with RPLN metastasis after initial treatments, and one patient was diagnosed as oropharyngeal carcinoma with RPLN metastasis before initial treatments. The operation procedure and duration time, intraoperative blood loss volume and complications, nasogastric feeding tube dependence, tracheostomy dependence, postoperative complications, and hospitalization time were recorded and analyzed. Results: All patients were successfully treated by transoral robotic dissection of the metastatic RPLNs, none of which was converted to open surgery. RPLNs were completely resected in 10 patients, and partly resected in 2 patients (both were nasopharyngeal carcinoma patients). The mean number of RPLN dissected was 1.7. The operation duration time and intraoperative blood loss volume were (191.3±101.1) min and (150.0±86.6) ml, respectively. There was no severe intraoperative complication such as massive haemorrhage or adjacent organ injury during surgery. Nasogastric tube use was required in all patients with (17.1±10.6) days of dependence, while tracheotomy was performed in 8 patients with (11.6±10.7) days of dependence. The postoperative hospitalization stay was (8.5±5.7) days. Postoperative complications occurred in 4 patients, including 2 of retropharyngeal incision and 2 of dysphagia. During a follow-up of (6.5±5.1) months, disease-free progression was observed in all patients, 10 patients were disease-free survival and other 2 patients were survival with tumor burden. Conclusions: The transoral robotic RPLN dissection is safety and feasible. Compared with the traditional open surgical approach, it is less traumatic and safer, has fewer complications and good clinical application potentiality. The indications for transoral robotic RPLN dissection include thyroid carcinoma, oropharyngeal carcinoma, and some selected nasopharyngeal carcinoma and other head and neck cancers. Metastatic RPLNs from some nasopharyngeal carcinoma with incomplete capsule, unclear border and adhesion to the surrounding vessels are not suitable for transoral robotic RPLN dissection.

Heterochronic parabiosis induces stem cell revitalization and systemic rejuvenation across aged tissues

The young circulatory milieu capable of delaying aging in individual tissues is of interest as rejuvenation strategies, but how it achieves cellular- and systemic-level effects has remained unclear. Here, we constructed a single-cell transcriptomic atlas across aged tissues/organs and their rejuvenation in heterochronic parabiosis (HP), a classical model to study systemic aging. In general, HP rejuvenated adult stem cells and their niches across tissues. In particular, we identified hematopoietic stem and progenitor cells (HSPCs) as one of the most responsive cell types to young blood exposure, from which a continuum of cell state changes across the hematopoietic and immune system emanated, through the restoration of a youthful transcriptional regulatory program and cytokine-mediated cell-cell communications in HSPCs. Moreover, the reintroduction of the identified rejuvenating factors alleviated age-associated lymphopoiesis decline. Overall, we provide comprehensive frameworks to explore aging and rejuvenating trajectories at single-cell resolution and revealed cellular and molecular programs that instruct systemic revitalization by blood-borne factors.

Single-Cell Analysis Reveals Transcriptomic Reprogramming in Aging Cardiovascular Endothelial Cells

The senescence of cardiovascular endothelial cells (ECs) is a major risk factor in the development of aging-related cardiovascular diseases. However, the molecular dynamics in cardiovascular EC aging are poorly understood. Here, we characterized the transcriptomic landscape of cardiovascular ECs during aging and observed that ribosome biogenesis, inflammation, apoptosis and angiogenesis-related genes and pathways changed with age. We also highlighted the importance of collagen genes in the crosstalk between ECs and other cell types in cardiovascular aging. Moreover, transcriptional regulatory network analysis revealed Jun as a candidate transcription factor involved in murine cardiovascular senescence and we validated the upregulation of Jun in aged cardiovascular ECs both in vitro and in vivo. Altogether, our study reveals the transcriptomic reprogramming in the aging murine cardiovascular ECs, which deepens the understanding of the molecular mechanisms of cardiovascular aging and provides new insights into potential therapeutic targets against age-related cardiovascular diseases.

[Application of transoral robotic surgery in treatment of oropharyngeal squamous cell carcinoma]

Objective: To evaluate the therapeutic and prognostic outcomes of transoral robotic surgery (TORS) for oropharyngeal squamous cell carcinoma (OSCC). Methods: A retrospective study of 99 OSCC patients treated with TORS in Department of Head and Neck Surgery, Sun Yat-sen University Cancer Center between April 2017 and May 2021 was conducted. There were 84 males and 15 females, with an age range of 35-85 years. Patients' clinical characteristics, including clinical staging, HPV infection status, perioperative management and postoperative adjuvant treatment, were recorded. The overall survival (OS) and progression-free survival (PFS) were analyzed. The survival outcomes were analyzed with Kaplan-Meier method and Log-rank test. Results: The hospital stay of OSCC patients with TORS was (5.3±2.9) days and the average time of postoperative nasal feeding tube indwelling was (15.2±10.8) days. Among the 99 patients, 21 (21.2%) received tracheotomy and the average time of tracheotomy tube indwelling was (11.9±11.4) days. The two-year OS and PFS in patients with follow-up over two years were 94.0% and 87.7%, respectively and the three-year OS and PFS of patients with follow-up over three years were 94.0% and 78.9%, respectively. The two-year OS and PFS were respectively 97.4% and 88.9%, for patients with stages I-II and 86.8% and 88.9% for patients with stages III-IV. HPV-negative and HPV-positive patients had respectively two-year OS (100.0% vs. 91.5%) and PFS (88.9% vs. 87.2%). There was no significantly statistical difference in survival between patients with and without adjuvant radiotherapy after TORS (82.6% vs. 90.5%, HR=0.52, 95%CI: 0.12-2.23, P=0.400). Conclusions: TORS is more suitable for the treatment of patients with early (Ⅰ-Ⅱ) or HPV-positive oropharyngeal squamous cell carcinoma, and the recovery after TORS treatment is good.

[Clinical and molecular pathological features of bronchopulmonary large cell neuroendocrine carcinoma]

Objective: To investigate the clinical manifestations, imaging, pathological and molecular features of bronchopulmonary large-cell neuroendocrine carcinoma (LCNEC). Methods: The clinical data of 216 LCNEC patients in the First Affiliated Hospital of Zhengzhou University from 2011 to 2021 were analyzed retrospectively. The clinical manifestations, tumor location and size, characteristics of CT images, immunohistochemical and molecular pathological features were analyzed and compared with 115 cases of mixed small cell carcinoma (M-SCLC) diagnosed in the same period. Results: Among the 216 LCNEC patients, there were 190 males and 26 females, with a median age of 65 years. The first symptoms of the patients were mainly cough (106 cases, 49.1%) and bloody sputum (48 cases, 22.2%). The median tumor length were 4.7cm, including 55 cases of nodular type (25.5%) and 161 cases of mass-forming type (74.5%). CT imaging results showed that LCNEC lesions had soft tissue density, and the proportion of slight enhancement lesions was significantly lower than that in M-SCLC group (52.3% vs 74.8%, P<0.001). In contrast, the proportion of necrosis (87.0% vs 58.3%, P<0.001) and calcification (26.9% vs 2.6%, P<0.001) in LCNEC patients was significantly higher than that in M-SCLC group. Immunohistochemical results showed that the positive rate of CK in LCNEC was significantly higher than that in M-SCLC (99.0 % vs 90.5%, P<0.05), while the positive rate of TTF-1 was significantly lower than that in M-SCLC (51.6% vs 67.0%, P<0.05). In LCNEC group, the proportion of patients with Ki-67 positive index between 50% and 80% was significantly higher than that of M-SCLC (41.2% vs 25.2%), while the proportion between 80% and 100% was lower than that of M-SCLC (51.9% vs 72.2%). There was no significant difference in the positive rates of CD56 (91.7% vs 94.6%, P=0.336), Syn (83.8% vs 84.7%, P=0.838) and CgA (54.8% vs 50.0%, P=0.632) in both tumor types. Molecular pathology results showed that frequent mutatios were TP53 (54.5%), RB1 (36.4%), KEAP1 (18.2%), MYC(18.2%), and PTEN (14.3%), and the rate of tumor mutation burden which is more than 25 mutation/Mb was 27.3%. Conclusions: LCNEC lacks specific clinical manifestations. CT imaging is powerful in distinguishing LCNEC from M-SCLC. LCNEC contains a specific mutation spectrum. Pathology combined with immunohistochemical staining is still the gold standard for LCNEC diagnosis, and the differentiation from M-SCLC mainly depends on cell size and nuclear chromatin pattern with light microscopy.

Gut microbiota production of trimethyl-5-aminovaleric acid reduces fatty acid oxidation and accelerates cardiac hypertrophy

Numerous studies found intestinal microbiota alterations which are thought to affect the development of various diseases through the production of gut-derived metabolites. However, the specific metabolites and their pathophysiological contribution to cardiac hypertrophy or heart failure progression still remain unclear. N,N,N-trimethyl-5-aminovaleric acid (TMAVA), derived from trimethyllysine through the gut microbiota, was elevated with gradually increased risk of cardiac mortality and transplantation in a prospective heart failure cohort (n = 1647). TMAVA treatment aggravated cardiac hypertrophy and dysfunction in high-fat diet-fed mice. Decreased fatty acid oxidation (FAO) is a hallmark of metabolic reprogramming in the diseased heart and contributes to impaired myocardial energetics and contractile dysfunction. Proteomics uncovered that TMAVA disturbed cardiac energy metabolism, leading to inhibition of FAO and myocardial lipid accumulation. TMAVA treatment altered mitochondrial ultrastructure, respiration and FAO and inhibited carnitine metabolism. Mice with γ-butyrobetaine hydroxylase (BBOX) deficiency displayed a similar cardiac hypertrophy phenotype, indicating that TMAVA functions through BBOX. Finally, exogenous carnitine supplementation reversed TMAVA induced cardiac hypertrophy. These data suggest that the gut microbiota-derived TMAVA is a key determinant for the development of cardiac hypertrophy through inhibition of carnitine synthesis and subsequent FAO.

Intestinal microbiota alterations may affect heart function through the production of gut-derived metabolites. Here the authors found that gut microbiota-derived TMAVA is a key determinant for the development of cardiac hypertrophy through inhibition of carnitine synthesis and subsequent fatty acid oxidation.

Destabilizing heterochromatin by APOE mediates senescence

Apolipoprotein E (APOE) is a component of lipoprotein particles that function in the homeostasis of cholesterol and other lipids. Although APOE is genetically associated with human longevity and Alzheimer's disease, its mechanistic role in aging is largely unknown. Here, we used human genetic, stress-induced and physiological cellular aging models to explore APOE-driven processes in stem cell homeostasis and aging. We report that in aged human mesenchymal progenitor cells (MPCs), APOE accumulation is a driver for cellular senescence. By contrast, CRISPR-Cas9-mediated deletion of APOE endows human MPCs with resistance to cellular senescence. Mechanistically, we discovered that APOE functions as a destabilizer for heterochromatin. Specifically, increased APOE leads to the degradation of nuclear lamina proteins and a heterochromatin-associated protein KRAB-associated protein 1 via the autophagy-lysosomal pathway, thereby disrupting heterochromatin and causing senescence. Altogether, our findings uncover a role of APOE as an epigenetic mediator of senescence and provide potential targets to ameliorate aging-related diseases.

Kansl1 haploinsufficiency impairs autophagosome-lysosome fusion and links autophagic dysfunction with Koolen-de Vries syndrome in mice

Koolen-de Vries syndrome (KdVS) is a rare disorder caused by haploinsufficiency of KAT8 regulatory NSL complex subunit 1 (KANSL1), which is characterized by intellectual disability, heart failure, hypotonia, and congenital malformations. To date, no effective treatment has been found for KdVS, largely due to its unknown pathogenesis. Using siRNA screening, we identified KANSL1 as an essential gene for autophagy. Mechanistic study shows that KANSL1 modulates autophagosome-lysosome fusion for cargo degradation via transcriptional regulation of autophagosomal gene, STX17. Kansl1^+/− mice exhibit impairment in the autophagic clearance of damaged mitochondria and accumulation of reactive oxygen species, thereby resulting in defective neuronal and cardiac functions. Moreover, we discovered that the FDA-approved drug 13-cis retinoic acid can reverse these mitophagic defects and neurobehavioral abnormalities in Kansl1^+/− mice by promoting autophagosome-lysosome fusion. Hence, these findings demonstrate a critical role for KANSL1 in autophagy and indicate a potentially viable therapeutic strategy for KdVS.

Here the authors show that the Koolen-de Vries syndrome associated gene KANSL1 modulates autophagosome-lysosome fusion via transcriptional regulation of autophagosomal gene Syntaxin17, and that 13-cis retinoic acid can reverses mitophagic defects and neurobehavioural abnormalities of mice lacking Kansl1.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.

A single-cell transcriptomic landscape of the lungs of patients with COVID-19

The lung is the primary organ targeted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), making respiratory failure a leading coronavirus disease 2019 (COVID-19)-related mortality. However, our cellular and molecular understanding of how SARS-CoV-2 infection drives lung pathology is limited. Here we constructed multi-omics and single-nucleus transcriptomic atlases of the lungs of patients with COVID-19, which integrate histological, transcriptomic and proteomic analyses. Our work reveals the molecular basis of pathological hallmarks associated with SARS-CoV-2 infection in different lung and infiltrating immune cell populations. We report molecular fingerprints of hyperinflammation, alveolar epithelial cell exhaustion, vascular changes and fibrosis, and identify parenchymal lung senescence as a molecular state of COVID-19 pathology. Moreover, our data suggest that FOXO3A suppression is a potential mechanism underlying the fibroblast-to-myofibroblast transition associated with COVID-19 pulmonary fibrosis. Our work depicts a comprehensive cellular and molecular atlas of the lungs of patients with COVID-19 and provides insights into SARS-CoV-2-related pulmonary injury, facilitating the identification of biomarkers and development of symptomatic treatments.

Regeneration Roadmap: database resources for regenerative biology

Regeneration plays an instrumental role in biological development and damage repair by constructing and replacing cells, tissues, and organs. Since regenerative capacity declines with age, promoting regeneration is heralded as a potential strategy for delaying aging. On this premise, mechanisms that regulate regeneration have been extensively studied across species and in different tissues. However, an open and comprehensive database collecting and standardizing the abundant data generated in regeneration research, such as high-throughput sequencing data, remains to be developed. In this work, we constructed Regeneration Roadmap to systematically and comprehensively collect such information over 2.38 million data entries across 11 species and 36 tissues, including regeneration-related genes, bulk and single-cell transcriptomics, epigenomics, and pharmacogenomics data. In this database, users can explore regulatory and expression changes of regeneration-associated genes in different species and tissues. Regeneration Roadmap provides the research community with a long-awaited and valuable data resource featuring convenient computing and visualizing tools, which is publicly available at https://ngdc.cncb.ac.cn/regeneration/index.