Most emerging viruses are spilled over from mammals. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of newly emerging viruses. This study systematically investigated the host proteins associated with the cross-species transmission of mammalian viruses based on 1,271 pairs of virus-mammal interactions including 382 viruses from 33 viral families and 73 mammal species from 11 orders. Numerous host proteins were found to contribute to the cross-species transmission of mammalian viruses. Host proteins potentially contributing to virus cross-species transmission are specific to viral families, and few overlaps of such host proteins are observed in different viral families. Based on these host proteins, the random-forest (RF) models were built to predict the cross-species transmission potential of mammalian viruses. Moderate performance was obtained when using all viruses together. However, when modeling by viral family, the performance of the RF models varied much among viral families. In 13 viral families such as Flaviviridae, Retroviridae, and Poxviridae, the AUC of the RF model was greater than 0.8. Finally, the contribution of virus receptors to cross-species transmission was evaluated, and the virus receptor was found to have a minor effect in predicting the cross-species transmission of mammalian viruses. The study deepens our understanding of the mechanism of virus cross-species transmission and provides a framework for predicting the cross-species transmission of mammalian viruses. IMPORTANCE Emerging viruses pose serious threats to humans. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of emerging viruses. This study systematically identified host factors associated with cross-species transmission of mammalian viruses and further built machine-learning models for predicting cross-species transmission of the viruses based on host factors including virus receptors. The study not only deepens our understanding of the mechanism of virus cross-species transmission but also provides a framework for predicting the cross-species transmission of mammalian viruses based on host factors.

Parkinson's disease (PD) is a kind of neurodegenerative disease that causes a huge burden to society. Previous studies have suggested the association between PD and multiple viruses. However, there is still a lack of a virome study about PD. This study systematically identified viruses from the public RNA‐sequencing data of more than 700 samples from both PD patients and the control group (most were healthy people). Only nine viruses such as human betaherpesvirus 5 and Merkel cell polyomavirus have been detected in several human brain tissues of the central nervous system, the appendix, and blood of PD patients, and all of these viruses were also detected in the control group. Most viruses were observed to have low abundance in no more than three tissues. No statistically significant differences were observed between the virus abundance in the PD patients and the control group for all viruses. The positive rates of most viruses in PD patients were higher or similar to that in the control group, although those were less than 5% for most viruses. Overall, this is the first study to systematically investigate the virome in PD patients, and provides new insights into the association between viruses and PD.

Virus-encoded small RNAs (vsRNAs) have been reported to play an important role in viral infections. Unfortunately, there is still a lack of a systematic characterization and resource of vsRNAs. Herein, we identified a total of 19 734 high-confidence vsRNAs including 2746 microRNAs (miRNAs) in 64 viral species from more than 800 samples of public small RNA-Seq data. The number of vsRNAs identified in viruses varied from 1 to 2489 with a median of 170. The length distribution of vsRNAs peaked at 21 and 22 nt. Plant viruses were found to express larger number and higher levels of vsRNAs than those of animal viruses. Besides, the number of vsRNAs identified increased as the viral infection persisted. Interestingly, the vsRNA showed strong expression specificity as little overlap was observed among vsRNAs identified in different strains of a virus, or in different hosts, cells, or tissues infected by the same virus. Little conservation was observed among vsRNAs of different viruses. The viral miRNAs were found to interact with host genes involved in multiple biological processes related to organization, development, action potential, polarity establishment, methylation, immune response, gene regulation, localization, and so on. To facilitate the usage of vsRNAs, a database named vsRNAdb was built for organizing and storing vsRNAs which is available at . Overall, the study deepens our understanding about the diversity and complexity of vsRNAs and provides a rich resource for further studies of vsRNAs.

Growing evidences have suggested the association between coronavirus infection and neurodegenerative diseases. However, the molecular mechanism behind the association is complex and remains to be clarified. This study integrated human genes involved in infections of three coronaviruses including SARS-CoV-2, SARS-CoV and MERS-CoV from multi-omics data, and investigated the shared genes and molecular functions between coronavirus infection and two neurodegenerative diseases, namely Alzheimer's Disease (AD) and Parkinson's Disease (PD). Seven genes including HSP90AA1, ALDH2, CAV1, COMT, MTOR, IGF2R and HSPA1A, and several inflammation and stress response-related molecular functions such as MAPK signaling pathway, NF-kappa B signaling pathway, responses to oxidative or chemical stress were common to both coronavirus infection and neurodegenerative diseases. These genes were further found to interact with more than 20 other viruses. Finally, drugs targeting these genes were identified. The study would not only help clarify the molecular mechanism behind the association between coronavirus infection and neurodegenerative diseases, but also provide novel targets for the development of broad-spectrum drugs against both coronaviruses and neurodegenerative diseases.

ABSTRACTCarcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) regulates collagen-mediated platelet activation through its cytoplasmic immunoreceptor tyrosine-based inhibition motifs (ITIMs). However, the function of CEACAM1’s extracellular cleavage fragments is currently unknown. In the present study, we used mass spectrometry (MS) to identify 9 cleavage fragments shed by matrix metallopeptidase 12 (MMP-12), and then we synthesized peptides with sequences corresponding to the fragments. QLSNGNRTLT (QLSN), a peptide from the A1-domain of CEACAM1, significantly attenuated collagen-induced platelet aggregation. QLSN also attenuated platelet static adhesion to collagen. Additionally, QLSN reduced human platelet secretion and integrin αIIbβ3 activation in response to glycoprotein VI (GPVI)–selective agonist, convulxin. Correspondingly, QLSN treatment significantly decreased convulxin-mediated phosphorylation of Src, protein kinase B (Akt), spleen tyrosine kinase (Syk) and phospholipase Cγ2 (PLCγ2) in human platelets. These data indicate that the CEACAM1-derived peptide QLSN inhibits GPVI-mediated human platelet activation. QLSN could potentially be developed as a novel antiplatelet agent.

Background: Acute coronary syndrome (ACS) occurs approximately every 40 seconds, and was an underlying cause of death in 1 out of every 7 deaths. More accurate indicators are needed to distinguish patients with ACS from patients manifesting negative changes in electrocardiogram (ECG) and myocardial enzymes. This study aimed to investigate whether the expression of platelet carcinoembryonic antigen cell adhesion molecule-5 (CEACAM5/CEA/CD66e) could help predict ACS. Material/Methods: We enrolled 82 participants (mean age 60 years, 33 females and 49 males). The expression of CEA on washed human platelets was assessed using two-color flow cytometry. The CEA levels on platelets and in serum of these 82 consecutive patients were detected using two-color whole-blood flow cytometry analysis and a custom-made Luminex multiplex assay, respectively. Results: CEA was expressed on the surface of human platelets. The expression of platelet CEA (P<0.01), but not serum CEA (P=0.30), was significantly higher in patients with ACS compared to patients with normal coronary artery. Increased platelet CEA levels could serve as a new independent indicator for ACS (P=0.0003). Platelet CEA testing (P=0.000002), as well as cardiac troponin I (cTnI) (P=0.0005), can diagnose ACS with high sensitivity and specificity, and, combined with cTnI (P<0.0001), can improve the diagnostic value. Conclusions: Platelet CEA expression was higher in individuals presenting with ACS. Hence, platelet CEA might be a novel and reliable biomarker for ACS. Large-scale studies are needed to confirm this hypothesis.

BackgroundSturge-Weber syndrome (SWS) is a rare and sporadic congenital neurocutaneous disorder, that is characterized by facial venous capillary malformation (port-wine birthmark), leptomeningeal venous malformation (angiomatosis), glaucoma, and neurologic problems. SWS can comorbid with other disorders in some patients, however, muscular abnormalities have still not been reported in patients with SWS.Case presentationA forty-one-year-old Chinese female who had left side port-wine stain, ipsilateral glaucoma, and hypothyroidism was included in the present study. The neurocutaneous and endocrine symptoms were consistent with the SWS diagnostic criteria. Meanwhile, the patient had progressive weakness on her both arms and legs, dramatically elevated creatine kinase (CK) and myoglobin levels, and elevated antinuclear and anti-Ro52 antibodies. Intravenous methylprednisolone (MP) (80mg/d), methotrexate, and intravenous cyclophosphamide were administrated and the weakness of the patient was gradually relieved with normal serum CK level.ConclusionsWe reported the first case of SWS comorbid with inflammatory myopathy. The underlying mechanism for SWS and idiopathic inflammatory myopathy is still not clear, and further researches need to be conducted to deeply explore the mentioned mechanism.