RNAcontacts: A Pipeline for Predicting Contacts from RNA Proximity Ligation Assays

High-throughput RNA proximity ligation assays are molecular methods that are used to simultaneously analyze the spatial proximity of many RNAs in living cells. Their principle is based on cross-linking, fragmentation, and subsequent religation of RNAs, followed by high-throughput sequencing. The generated fragments have two different types of splits, one resulting from pre-mRNA splicing and the other formed by the ligation of spatially close RNA strands. Here, we present RNAcontacts, a universal pipeline for detecting RNA-RNA contacts in high-throughput RNA proximity ligation assays. RNAcontacts circumvents the inherent problem of mapping sequences with two distinct types of splits using a two-pass alignment, in which splice junctions are inferred from a control RNA-seq experiment on the first pass and then provided to the aligner as bona fide introns on the second pass. Compared to previously developed methods, our approach allows for a more sensitive detection of RNA contacts and has a higher specificity with respect to splice junctions that are present in the biological sample. RNAcontacts automatically extracts contacts, clusters their ligation points, computes the read support, and generates tracks for visualizing through the UCSC Genome Browser. The pipeline is implemented in Snakemake, a reproducible and scalable workflow management system for rapid and uniform processing of multiple datasets. RNAcontacts is a generic pipeline for the detection of RNA contacts that can be used with any proximity ligation method as long as one of the interacting partners is RNA. RNAcontacts is available via the GitHub repository https://github.com/smargasyuk/ RNAcontacts/.

UCHL1 Impairs Periodontal Ligament Stem Cell Osteogenesis in Periodontitis

Periodontitis comprises a series of inflammatory responses resulting in alveolar bone loss. The suppression of osteogenesis of periodontal ligament stem cells (PDLSCs) by inflammation is responsible for impaired alveolar bone regeneration, which remains an ongoing challenge for periodontitis therapy. Ubiquitin C-terminal hydrolase L1 (UCHL1) belongs to the family of deubiquitinating enzymes, which was found to play roles in inflammation previously. In this study, the upregulation of UCHL1 was identified in inflamed PDLSCs isolated from periodontitis patients and in healthy PDLSCs treated with tumor necrosis factor-α or interleukin-1β, and the higher expression level of UCHL1 was accompanied with the impaired osteogenesis of PDLSCs. Then UCHL1 was inhibited in PDLSCs using the lentivirus or inhibitor, and the osteogenesis of PDLSCs suppressed by inflammation was rescued by UCHL1 inhibition. Mechanistically, the negative effect of UCHL1 on the osteogenesis of PDLSCs was attributable to its negative regulation of mitophagy-dependent bone morphogenetic protein 2/Smad signaling pathway in periodontitis-associated inflammation. Furthermore, a ligature-induced murine periodontitis model was established, and the specific inhibitor of UCHL1 was administrated to periodontitis mice. The histological results showed increased active osteoblasts on alveolar bone surface and enhanced alveolar bone regeneration when UCHL1 was inhibited in periodontitis mice. Besides, the therapeutic effects of UCHL1 inhibition on ameliorating periodontitis were verified, as indicated by less bone loss and reduced inflammation. Altogether, our study proved UCHL1 to be a key negative regulator of the osteogenesis of PDLSCs in periodontitis and suggested that UCHL1 inhibition holds promise for alveolar bone regeneration in periodontitis treatment.

Prognostic value of plasma circulating tumor DNA fraction across four common cancer types: a real-world outcomes study

BACKGROUND

Genomic analysis of circulating tumor DNA (ctDNA) is increasingly incorporated into the clinical management of patients with advanced cancer. Beyond tumor profiling, ctDNA analysis also can enable calculation of circulating tumor fraction (TF), which has previously been found to be prognostic. While most prognostic models in metastatic cancer are tumor type specific and require significant patient-level data, quantification of TF in ctDNA has the potential to serve as a pragmatic, tumor-agnostic prognostic tool.

PATIENTS AND METHODS

This study utilized a cohort of patients in a nationwide de-identified clinico-genomic database with metastatic castration-resistant prostate cancer (mCRPC), metastatic breast cancer (mBC), advanced non-small-cell lung cancer (aNSCLC), or metastatic colorectal cancer (mCRC) undergoing liquid biopsy testing as part of routine care. TF was calculated based on single-nucleotide polymorphism aneuploidy across the genome. Clinical, disease, laboratory, and treatment data were captured from the electronic health record. Overall survival (OS) was evaluated by TF level while controlling for relevant covariables.

RESULTS

A total of 1725 patients were included: 198 mCRPC, 402 mBC, 902 aNSCLC, and 223 mCRC. TF ≥10% was highly correlated with OS in univariable analyses for all cancer types: mCRPC [hazard ratio (HR) 3.3, 95% confidence interval (CI) 2.04-5.34, P < 0.001], mBC (HR 2.4, 95% CI 1.71-3.37, P < 0.001), aNSCLC (HR 1.68, 95% CI 1.34-2.1, P < 0.001), and mCRC (HR 2.11, 95% CI 1.39-3.2, P < 0.001). Multivariable assessments of TF had similar point estimates and CIs, suggesting a consistent and independent association with survival. Exploratory analysis showed that TF remained consistently prognostic across a wide range of cutpoints.

CONCLUSIONS

Plasma ctDNA TF is a pragmatic, independent prognostic biomarker across four advanced cancers with potential to guide clinical conversations around expected treatment outcomes. With further prospective validation, ctDNA TF could be incorporated into care paradigms to enable precision escalation and de-escalation of cancer therapy based on patient-level tumor biology.

Relationship between Social Support, Sarcopenia, and Cognitive Impairment in Chinese Community-Dwelling Older Adults

BACKGROUND

Cognitive impairment and sarcopenia have become important challenges for the growing aging population. Social support has been shown to protect against cognitive impairment, but its impact on sarcopenia remains unknown. The purpose of this study was to explore the correlation between social support, sarcopenia, and cognitive impairment in Chinese older adults.

METHOD

A multi-stage whole group sampling method was used to conduct a cross-sectional survey of 720 community-dwelling older people in Shanghai. The definition of sarcopenia was in accordance with the criteria of the Asian Working Group for Sarcopenia (AWGS) 2019. Cognitive impairment was evaluated using a computerized neuropsychological assessment device that had been previously validated. Social support was assessed using the Social Support Rate Scale. Logistic regression analyses were conducted to explore the relationship between social support cognitive impairment and sarcopenia, fully adjusting for all potential confounding factors.

RESULTS

Our study found that 230 (31.94%) of the participants had cognitive impairment and 97 (13.47%) of the participants had sarcopenia. The mean social support score was 35.10 ± 7.54. Besides, the results showed that cognitive impairment was associated with sarcopenia (OR:1.650, 95% CI: 1.048, 2.596, P=0.030) after adjusting for confounding factors. Older adults with high level social support had the lowest risk of cognitive impairment (OR: 0.297, 95% CI: 0.115, 0.680, P=0.021) and sarcopenia (OR: 0.113, 95% CI: 0.031, 0.407, P=0.001), respectively.

CONCLUSION

Our analysis revealed that high level social support was negatively associated with sarcopenia and cognitive impairment. These findings provide strong support for the health promotion effect of social networks against sarcopenia and cognitive impairment in Chinese community-dwelling older adults, with important implications for healthcare policy makers.

Genetic polymorphisms in MIR1208 and MIR5708 are associated with susceptibility to COPD in the Chinese population

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by limited airflow and is influenced by genetic and environmental factors. The purpose of this study was to investigate the effects of gene polymorphisms in MIR5708 and MIR1208 on COPD risk.

METHODS

Four single nucleotide polymorphisms (SNPs) in MIR5708 (rs6473227 and rs16907751) and MIR1208 (rs2608029 and rs13280095) were selected and genotyped among 315 COPD patients and 314 healthy controls using the Agena MassARRAY platform. SPSS 18.0 was used for statistical analysis and data processing. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the association between genetic variants of MIR1208 and MIR5708 and COPD risk.

RESULTS

The results suggested that rs16907751 variants in MIR5708 contributed to an increased susceptibility to COPD in the allelic (P = 0.001), co-dominant (homozygous) (P = 0.001), dominant (P = 0.017), recessive (P = 0.002), and additive (P = 0.002) models. The effects of MIR5708 and MIR1208 gene polymorphisms on the risk of COPD were age-, sex-, smoking status-, and BMI-related. Furthermore, the C-A and G-A haplotypes of rs2608029 and rs13280095 in MIR1208 were identified as risk factors for COPD in the population over 70 years (P = 0.029) and in women (P = 0.049), respectively. Finally, significant associations between rs16907751genotypes with pulse rate and forced expiratory volume in 1 s were found among COPD patients.

CONCLUSION

Genetic polymorphisms in MIR5708 and MIR1208 are associated with increased risk of COPD in China.

Study of the Semileptonic Decay Λ_{c}^{+}→Λe^{+}ν_{e}

The study of the Cabibbo-favored semileptonic decay Λ_{c}^{+}→Λe^{+}ν_{e} is reported using a 4.5  fb^{-1} data sample of e^{+}e^{-} annihilations collected at center-of-mass energies ranging from 4.600 GeV to 4.699 GeV with the BESIII detector at the BEPCII collider. The branching fraction of the decay is measured to be B(Λ_{c}^{+}→Λe^{+}ν_{e})=(3.56±0.11_{stat}±0.07_{syst})%, which is the most precise measurement to date. Furthermore, we perform an investigation of the internal dynamics in Λ_{c}^{+}→Λe^{+}ν_{e}. We provide the first direct comparisons of the differential decay rate and form factors with those predicted from lattice quantum chromodynamics (LQCD) calculations. Combining the measured branching fraction with a q^{2}-integrated rate predicted by LQCD, we determine |V_{cs}|=0.936±0.017_{B}±0.024_{LQCD}±0.007_{τ_{Λ_{c}}}.

Gap-Free Nuclear and Mitochondrial Genomes of Ustilaginoidea virens JS60-2, a Fungal Pathogen Causing Rice False Smut

Rice false smut (RFS), caused by Ustilaginoidea virens, has become a major disease in recent years, and mycotoxins produced by U. virens often threaten food safety. To study fungal pathogenesis and identify potential targets for developing new fungicides, gap-free nuclear and complete mitochondrial genomes of U. virens JS60-2 were sequenced and assembled. Using the second and third generation sequencing data, we assembled a 38.02-Mb genome that consists of seven contigs with the contig N₅₀ being 6.32-Mb. In total, 8,486 protein-coding genes were annotated in the genome, including 21 secondary metabolism gene clusters. We also assembled the complete mitochondrial genome, which is 102,498 bp, with 28% GC content. The JS60-2 genomes assembled in this study will facilitate research on U. virens and contribute to RFS control. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Measurement of the Absolute Branching Fraction and Decay Asymmetry of Λ→nγ

The radiative hyperon decay Λ→nγ is studied using (10087±44)×10^{6}  J/ψ events collected with the BESIII detector operating at BEPCII. The absolute branching fraction of the decay Λ→nγ is determined to be (0.832±0.038_{stat}±0.054_{syst})×10^{-3}, which is a factor of 2.1 lower and 5.6 standard deviations different than the previous measurement. By analyzing the joint angular distribution of the decay products, the first determination of the decay asymmetry α_{γ} is reported with a value of -0.16±0.10_{stat}±0.05_{syst}.

Observation of an Isoscalar Resonance with Exotic J^{PC}=1^{-+} Quantum Numbers in J/ψ→γηη^{'}

Using a sample of (10.09±0.04)×10^{9}  J/ψ events collected with the BESIII detector operating at the BEPCII storage ring, a partial wave analysis of the decay J/ψ→γηη^{'} is performed. The first observation of an isoscalar state with exotic quantum numbers J^{PC}=1^{-+}, denoted as η_{1}(1855), is reported in the process J/ψ→γη_{1}(1855) with η_{1}(1855)→ηη^{'}. Its mass and width are measured to be (1855±9_{-1}^{+6})  MeV/c^{2} and (188±18_{-8}^{+3})  MeV, respectively, where the first uncertainties are statistical and the second are systematic, and its statistical significance is estimated to be larger than 19σ.

Prevalence of USP and hlyA Genes and Association with Drug Resistance in Uropathogenic Escherichia coli Isolated from Patients in a Tertiary Hospital from Southeast China

E. coli was cultured from the urine of patients from the tertiary hospital located in Southeast China from 2017 to 2019. The species were identified, drug sensitivity test was performed, and the presence of the virulence genes USP and hlyA was determined. A total of 483 strains of E. coli were isolated, including 132 from patients with urinary tract infection (UTI). The resistance to ciprofloxacin was more common in non-UTI patients, while resistance to gentamycin was significantly higher in the UTI group. In the UTI group, the proportions of isolated bacteria with the virulence USP (40.15%) and hlyA (8.33%) genes were significantly higher than in the non-UTI group (19.60 and 2.56%, respectively). The rate of resistance of E. coli toward levofloxacin in the USP⁺ group was significantly (p<0.05) higher than in the USP- group. Thus, we revealed the differences in the rate of drug resistance and prevalence of USP and hlyA between the UTI and non-UTI groups. Furthermore, the presence of the USP gene was found to be associated with greater resistance to levofloxacin.

Observation of an a_{0}-like State with Mass of 1.817 GeV in the Study of D_{s}^{+}→K_{S}^{0}K^{+}π^{0} Decays

Using e^{+}e^{-} annihilation data corresponding to an integrated luminosity of 6.32  fb^{-1} collected at center-of-mass energies between 4.178 and 4.226 GeV with the BESIII detector, we perform the first amplitude analysis of the decay D_{s}^{+}→K_{S}^{0}K^{+}π^{0} and determine the relative branching fractions and phases for intermediate processes. We observe an a_{0}-like state with mass of 1.817 GeV in its decay to K_{S}^{0}K^{+} for the first time. In addition, we measure the ratio {B[D_{s}^{+}→K[over ¯]^{*}(892)^{0}K^{+}]/B[D_{s}^{+}→K[over ¯]^{0}K^{*}(892)^{+}]} to be 2.35_{-0.23stat}^{+0.42}±0.10_{syst}. Finally, we provide a precision measurement of the absolute branching fraction B(D_{s}^{+}→K_{S}^{0}K^{+}π^{0})=(1.46±0.06_{stat}±0.05_{syst})%.

Circadian nuclear receptor Rev-erbalpha is expressed by platelets and potentiates platelet activation and thrombus formation

Background

Adverse cardiovascular events have day/night patterns with peaks in the morning, potentially related to endogenous circadian clock control of platelet activation. Circadian nuclear receptor Rev-erbα is an essential and negative component of the circadian clock.

Purpose

We aim to investigate the expression profile and biological function of Rev-erbα in platelets.

Methods and results

Here we report the presence and functions of circadian nuclear receptor Rev-erbα in human and mouse platelets. Both human and mouse platelet Rev-erbα showed a circadian rhythm that positively correlated with platelet aggregation. Global Rev-erbα knockout and platelet-specific Rev-erbα knockout mice exhibited defective in hemostasis as assessed by prolonged tail-bleeding times. Rev-erbα deletion also reduced ferric chloride-induced carotid arterial occlusive thrombosis, prevented collagen/epinephrine-induced pulmonary thromboembolism, and protected against microvascular microthrombi obstruction and infarct expansion in an acute myocardial infarction model. In vitro thrombus formation assessed by CD41-labeled platelet fluorescence intensity was significantly reduced in Rev-erbα knockout mouse blood. Platelets from Rev-erbα knockout mice exhibited impaired agonist-induced aggregation responses, integrin αIIbβ3 activation and α-granule release. Consistently, pharmacological inhibition of Rev-erbα by specific antagonists decreased platelet activation markers in both mouse and human platelets. Mechanistically, mass spectrometry and co-immunoprecipitation analyses revealed that Rev-erbα potentiated platelet activation via oligophrenin-1-mediated RhoA/ERM (ezrin/radixin/moesin) pathway.

Conclusion

We provide the first evidence that circadian protein Rev-erbα is functionally expressed in platelets and potentiates platelet activation and thrombus formation. Rev-erbα may serve as a novel therapeutic target for managing thrombosis-based cardiovascular disease.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): This work was supported by grants from the National Science Fund for Distinguished Young Scholars (81625002), the National Natural Science Foundation of China (81930007).

Diagnostic performance of on-site computation of quantitative flow ratio by a coronary computed tomography angiography based algorithm: comparison of distal and lesion-specific measurements

Introduction

Guidelines recommend secondary ischemia assessment following a coronary computed tomography angiography (CTA) with suspected obstructive coronary artery disease (CAD). Coronary CTA-derived quantitative flow ratio (CT-QFR) is an on-site technique performed on acquired CTA images that estimates the functional severity of a coronary stenosis. However, CT-QFR measurements are available throughout the coronary vessel with no clear recommendations as to which specific values should be used for identifying obstructive CAD, e.g. most distal or lesion-specific values.

Purpose

First, to investigate the feasibility of CT-QFR and the correlation and agreement with invasive fractional flow reserve (FFR). Secondly, to compare the diagnostic performance of distal versus lesion-specific CT-QFR for identifying obstructive CAD defined by invasive coronary angiography (ICA) with FFR.

Methods

A total of 1732 prospectively included patients with symptoms suggestive of CAD referred for CTA were included. All patients with ≥50% diameter stenosis (DS) on CTA were subsequently referred for ICA with conditional FFR in lesions with 30–89%DS. Obstructive CAD was defined by ICA as FFR ≤0.80 or high-grade stenosis by visual assessment (≥90%DS). A blinded analysis of CT-QFR was performed in patients referred to ICA with measurements at the distal end of a vessel (distal CT-QFR) and 1 cm distal to stenotic lesions on CTA (lesion-specific). CT-QFR ≤0.80 was defined as abnormal. For correlation analyses to invasive FFR, CT-QFR was assessed corresponding to the position of the invasive pressure sensor.

Results

In total, 445/1732 (25%) patients had suspected obstructive CAD at CTA and underwent subsequent ICA. CT-QFR analysis was feasible in 423/445 (95%) patients. CT-QFR correlated (Pearson's rho 0.54, p&lt;0.001) and agreed (mean difference –0.02±0.09) to FFR with CT-QFR overestimating FFR (Fig. 1). Obstructive CAD was identified in 190/423 (44%) patients by ICA. Distal and lesion-specific CT-QFR classified 196 (46%) and 171 (40%) patients as abnormal, respectively. Areas under the receiver-operating characteristic curves for distal versus lesion-specific CT-QFR were similar (0.86 (95% CI: 0.82–0.89) vs. 0.86 (0.82–0.90), p=0.80). Sensitivities for distal and lesion-specific CT-QFR were 78% (95% CI: 71–84) vs. 74% (67–80), p=0.01, respectively, and specificities 79% (95% CI: 74–84) vs. 87% (82–91), p&lt;0.01, respectively. Distal and lesion-specific CT-QFR had similar diagnostic accuracy (79 (95% CI: 75–83), vs. 81 (77–85), p=0.07) (Fig. 2).

Conclusion

In patients with suspected obstructive CAD on CTA, non-invasive estimation of FFR using CT-QFR is feasible with moderate correlation and good agreement with invasive FFR. Overall diagnostic performance of distal and lesion-specific values for discriminating obstructive CAD by invasive FFR are similar. The use of CT-QFR could therefore potentially reduce the need for referral to invasive angiography after CTA.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): Aarhus UniversityRegion Mid Jutland

The gene LpBCP increased NaHCO3 resistance by enhancing lignin or ROS scavenging in the Nicotiana benthamiana

Lilium pumilum is an excellent wildflower germplasm resource with high resistance to salinity stress. The gene LpBCP plays an important role in salinity tolerance of L. pumilum. Studying the molecular mechanism of salinity resistance in L. pumilum will provide insights into multiple aspects, including breeding better varieties, environmental protection, improving soil conditions, etc. Conventional methods were used to determine different physiological indicators of Nicotiana benthamiana after NaHCO₃ treatment, i.e. chlorophyll content, soluble phenol content and lignin content. RT-qPCR was carried out to find expression of LpBCP in different organs and under abiotic stresses. DAB was used to detect H₂ O₂ in leaves in situ. A yeast two-hybrid system was used to screen for LpBCP interacting proteins. LpBCP was cloned from bulbs of L. pumilum. The highest expression of LpBCP was in roots and bulbs of transgenic plants. LpBCP-overexpressed plants showed less wilting, compared to WT plants. LpBCP transgenic plants have higher chlorophyll, soluble phenol and lignin content, and lower relative conductivity under 500 mM NaHCO₃ stress. In addition, H₂ O₂ scavenging in transgenic plants was much improved, indicating increased resistance to NaHCO₃ stress. Thirteen LpBCP-interacting proteins were screened using the yeast two-hybrid method and five were associated with salt stress. Based on our findings, LPBCP could be a key gene that can be used to improve L. pumilum salt tolerance.

A secreted fungal subtilase interferes with rice immunity via degradation of SUPPRESSOR OF G2 ALLELE OF skp1

Serine protease subtilase, found widely in both eukaryotes and prokaryotes, participates in various biological processes. However, how fungal subtilase regulates plant immunity is a major concern. Here, we identified a secreted fungal subtilase, UvPr1a, from the rice false smut (RFS) fungus Ustilaginoidea virens. We characterized UvPr1a as a virulence effector localized to the plant cytoplasm that inhibits plant cell death induced by Bax. Heterologous expression of UvPr1a in rice (Oryza sativa) enhanced plant susceptibility to rice pathogens. UvPr1a interacted with the important rice protein SUPPRESSOR OF G2 ALLELE OF skp1 (OsSGT1), a positive regulator of innate immunity against multiple rice pathogens, degrading OsSGT1 in a protease activity-dependent manner. Furthermore, host-induced gene silencing of UvPr1a compromised disease resistance of rice plants. Our work reveals a previously uncharacterized fungal virulence strategy in which a fungal pathogen secretes a subtilase to interfere with rice immunity through degradation of OsSGT1, thereby promoting infection. These genetic resources provide tools for introducing RFS resistance and further our understanding of plant-pathogen interactions.

Precise Measurements of Decay Parameters and CP Asymmetry with Entangled Λ-Λ[over ¯] Pairs

Based on 10 billion J/ψ events collected at the BESIII experiment, a search for CP violation in Λ decay is performed in the difference between CP-odd decay parameters α_{-} for Λ→pπ^{-} and α_{+} for Λ[over ¯]→p[over ¯]π^{+} by using the process e^{+}e^{-}→J/ψ→ΛΛ[over ¯]. With a five-dimensional fit to the full angular distributions of the daughter baryon, the most precise values for the decay parameters are determined to be α_{-}=0.7519±0.0036±0.0024 and α_{+}=-0.7559±0.0036±0.0030, respectively. The Λ and Λ[over ¯] averaged value of the decay parameter is extracted to be α_{avg}=0.7542±0.0010±0.0024 with unprecedented accuracy. The CP asymmetry A_{CP}=(α_{-}+α_{+})/(α_{-}-α_{+}) is determined to be -0.0025±0.0046±0.0012, which is one of the most precise measurements in the baryon sector. The reported results for the decay parameter will play an important role in the studies of the polarizations and CP violations for the strange, charmed and beauty baryons.

First Observation of the Direct Production of the χ_{c1} in e^{+}e^{-} Annihilation

We study the direct production of the J^{PC}=1^{++} charmonium state χ_{c1}(1P) in electron-positron annihilation by carrying out an energy scan around the mass of the χ_{c1}(1P). The data were collected with the BESIII detector at the BEPCII collider. An interference pattern between the signal process e^{+}e^{-}→χ_{c1}(1P)→γJ/ψ→γμ^{+}μ^{-} and the background processes e^{+}e^{-}→γ_{ISR}J/ψ→γ_{ISR}μ^{+}μ^{-} and e^{+}e^{-}→γ_{ISR}μ^{+}μ^{-} is observed by combining all the data samples. The χ_{c1}(1P) signal is observed with a significance of 5.1σ. This is the first observation of a C-even state directly produced in e^{+}e^{-} annihilation. The electronic width of the χ_{c1}(1P) resonance is determined to be Γ_{ee}=(0.12_{-0.08}^{+0.13})  eV, which is of the same order of magnitude as theoretical calculations.

[Epidemiological characteristics of notifiable infectious diseases in Beijing, 2021]

Objective: To understand the epidemiological characteristics of notifiable infectious diseases reported in Beijing in 2021 under the influence of the novel coronavirus pneumonia epidemic prevention and control policy, and provide reference evidence for the prevention and control of notifiable infectious diseases. Methods: Descriptive epidemiological methods were used to analyze the morbidity of notifiable infectious diseases reported in Beijing in 2021, with software R 4.1.2 for data process and ArcGIS 10.8 for visualization. Results: The morbidity of notifiable infectious diseases in Beijing in 2021 was 290.51/100 000, a decrease of 43.29% compared with 2020 and a decrease of 71.45% compared with the average during 2017-2019. The top 5 reported diseases with high morbidity were other infectious diarrhea, influenza, hand foot and mouth disease, pulmonary tuberculosis and syphilis. From the perspective of transmission route, intestinal infectious diseases were the main diseases, accounting for 50.15% (31 898/63 601) of the total cases. From the perspective of pathogens, viral infectious diseases were the main diseases, accounting for 59.63% (25 259/42 356) of the total cases. The laboratory diagnosis rate of notifiable infectious diseases reported in Beijing increased from the average of 16.47% (36 289/220 371) during 2017-2019 to 35.36% (22 490/63 601) in 2021. The laboratory diagnosis rate of parasitic infectious diseases was 83.33%. The districts with high incidence of intestinal infectious diseases were Pinggu, Miyun and Fengtai; Natural foci and insect borne infectious diseases were mainly reported in Yanqing, Mentougou, Fangshan and Daxing. Conclusion: The morbidity of notifiable infectious diseases in Beijing in 2021 showed a decrease trend. The laboratory confirmation rate of reported notifiable infectious disease cases increased, and there were great differences in the laboratory confirmation rate among different diseases. It is very necessary to improve the laboratory confirmation rate of the cases. The diseases with different transmission routes showed different geographical distributions. It is necessary to conduct the targeted prevention and control of infectious diseases in different areas.