Biology subjects

Song, T.

Publications and source records attributed to Song, T..

61 records · Page 4Linked to original sources

bioRxiv2019

Different subtypes of influenza A viruses target different human proteins and pathways leading to different pathogenic phenotypes

Different subtypes of Influenza A viruses cause different pathogenic phenotypes after infecting human bodies. Direct binary interactions between viral proteins and human proteins provide an important background for influenza viruses to cause complex pathologies of hosts. Here, we demonstrated the different impacts on the TNF--induced NF-{kappa}B activation of H1N1 and H5N1 virus proteins. By further examining the virus-host protein-protein interactions (PPI), we found that the same segment protein of the H1N1 and H5N1 viruses target on different host proteins. We then performed a yeast two-hybrid analysis of a highly pathogenic avian H5N1 influenza virus and human proteins. Influenza-host protein-protein interaction networks of three strains of influenza A viruses (including two other reported influenza-host PPI networks) were systematically compared and mapped on the network level and the pathway level. The results show subtype-specific characters of the influenza-host protein interactome, which may response for the specific pathogenic mechanisms of different subtypes of influenza viruses. ImportanceInfluenza A virus (IAV) can cause contagious respiratory illness, namely influenza (flu). The symptoms of infections from different subtypes of IAVs vary from mild to severe illness. The mechanism of these different pathogenic phenotypes remains poorly understood. Our results show that the same NA and NP segments from H1N1 and H5N1 virus cause different impacts on the TNF--induced NF-{kappa}B pathway. Furthermore, we generated a yeast two-hybrid protein-protein interaction (PPI) network between H5N1 and human proteins. By systematically comparing the influenza-host PPI networks of three strains of IAVs, we show that different subtypes of IAVs target different human proteins and pathways, which may have led to different pathogenic phenotypes.

microbiology↗

bioRxiv2019

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

The glucocorticoid receptor (GR) binds to specific DNA sequences and directly induces transcription of anti-inflammatory genes that contribute to cytokine repression, frequently in cooperation with NF-kB. Whether inflammatory repression also occurs through local interactions between GR and inflammatory gene regulatory elements remains controversial. Here, using Global Run-on Sequencing (GRO-seq) in human airway epithelial cells, we show that glucocorticoid signaling represses transcription within 10 minutes. Many repressed regulatory regions reside within hyper-ChIPable genomic regions that are subject to non-specific interactions with some antibodies. When this was accounted for, we determined that transcriptional repression occurs without local GR occupancy. Instead, widespread transcriptional induction through canonical GR binding sites is associated with reciprocal repression of distal TNF-regulated enhancers through a chromatin-dependent process, as evidenced by chromatin accessibility and enhancer-reporter assays. Simultaneously, transcriptional induction of key anti-inflammatory effectors is decoupled from primary repression through cooperation between GR and NF-kB at a subset of regulatory regions. Thus, glucocorticoids exert bimodal restraints on inflammation characterized by rapid primary transcriptional repression without local GR occupancy and secondary anti-inflammatory effects resulting from transcriptional cooperation between GR and NF-kB.

molecular biology↗

bioRxiv2019

Rice annexin OsANN4 interacting with OsCDPK24, reduces root aerenchyma formation by modulating H2O2 under ABA treatment

Plant annexins are calcium- and lipid-binding proteins that have multiple functions, and a significant amount of research on plant annexins has been reported in recent years. However, the functions of annexins in diverse biological processes in rice are largely unclear. Herein, we report that OsANN4, a calcium-binding rice annexin protein, is a substrate for OsCDPK24, and the OsANN4 phosphorylation site is the 13th serine, which is a key site for phosphorylation. Most strikingly, abscisic acid (ABA) promotes the interaction between OsANN4 and OsCDPK24. Moreover, knocking down OsANN4 by RNA interference resulted in visible and invisible phenotypes with exogenous ABA treatment, such as shorter shoots of seedlings, less lateral roots, earlier root aerenchyma formation and so on. The further analyzed results showed that decreased superoxide dismutase (SOD) and catalase (CAT) activity of the RNAi lines, which control H2O2 accumulation for redox homeostasis, and further promoted earlier aerenchyma formation of the root. These results suggest that a proposed molecular mechanism exists between OsANN4 and H2O2 production to response ABA.\n\nHighlightOsANN4 enhances SOD and CAT activities to scavenge H2O2 to alleviate the formation of aerenchyma under ABA treatment. OsCDPK24 interacts with and phosphorylates OsANN4, this interaction strengthened under ABA treatment.

plant biology↗

bioRxiv2018

Whole-Genome Genomics Correlates of Response To Anti-PD1 Therapy in Relapsed/Refractory Natural Killer/T Cell Lymphoma

AbstractThis study aims to identify recurrent genetic alterations in relapsed or refractory (RR) natural-killer/T-cell lymphoma (NKTL) patients who have achieved complete response (CR) with programmed cell death 1 (PD-1) blockade therapy. Seven of the eleven patients treated with pembrolizumab achieved CR while the remaining four had progressive disease (PD). Using whole genome sequencing (WGS), we found recurrent clonal structural rearrangements (SR) of the PD-L1 gene in four of the seven (57%) CR patients pretreated tumors. These PD-L1 SRs consist of inter-chromosomal translocations, tandem duplication and micro-inversion that disrupted the suppressive function of PD-L1 3UTR. Interestingly, recurrent JAK3-activating (p.A573V) mutations were also validated in two CR patients tumors that did not harbor the PD-L1 SR. Importantly, these mutations were absent in the four PD cases. With immunohistochemistry (IHC), PD-L1 positivity could not discriminate patients who archived CR (range: 6%-100%) from patients who had PD (range: 35%-90%). PD-1 blockade with pembrolizumab is a potent strategy for RR NKTL patients and genomic screening could potentially accompany PD-L1 IHC positivity to better select patients for anti-PD-1 therapy.

genomics↗

bioRxiv2018

Mitogen-Activated Protein Kinase-Dependent Fiber-Type Regulation in Skeletal Muscle

Mitogen-activated protein kinases (MAPK) are conserved protein kinases that regulate a diverse array of cellular activities. Stress or mitogenic signals activate three primary branches of the greater MAPK cascade, each of which consists of a phosphorylation-dependent array of successively acting kinases. The extracellular signal-regulated kinase 1/2 (ERK1/2) branch is regulated by growth factory signaling at the cell membrane, leading to phosphorylation of the dual-specificity kinase MEK1, which is dedicated to ERK1/2 phosphorylation. Previous studies have established a link between MAPK activation and endurance exercise, but whether a single MAPK is responsible for establishing muscle metabolic fate is unclear. Using mouse genetics we observed that muscle-specific expression of a constitutively active MEK1 promotes greater ERK1/2 signaling that mediates fiber-type switching in mouse skeletal muscle to a slow, oxidative phenotype with type I myosin heavy chain expression. Induced expression of the activated MEK1 mutant using either a MyoD-Cre or myosin light chain-Cre strategy equally increased the number of type I fibers in skeletal muscle with significantly reduced size compared to controls. Moreover, activation of MEK1 in mature myofibers of an adult mouse using a transgene containing a tamoxifen inducible MerCreMer cDNA under the control of a skeletal -actin promoter produced a similar phenotype of switching towards a slow-oxidative program. Physiologic assessment of mice with greater skeletal muscle slow-oxidative fibers showed enhanced metabolic activity and oxygen consumption with greater fatigue resistance of individual muscles. In summary, these results show that sustained MEK1-ERK1/2 activity in skeletal muscle produces a fast-to-slow fiber-type switch, suggesting that modulation of this signaling pathway may represent a therapeutic approach to enhance the long-term metabolic effectiveness of muscle in vivo.

developmental biology↗

bioRxiv2018

Krüppel like factor 2 - deficient myeloid cells promote skeletal muscle regeneration after injury

Regeneration of adult skeletal muscle after injury is coordinated by complex interactions between the injured muscle and the innate immune system. Myeloid lineage cells predominate in this process. This study examined the role of Kruppel - like factor 2 (KLF2), a zinc-finger transcription factor that regulates myeloid cell activation state, in muscle regeneration. Gastrocnemius muscles of wild-type and myeKlf2-/- mice, which lack KLF2 in all myeloid cells, were subjected to cardiotoxin injury and followed for 21 days. Injured muscles of myeKlf2-/- contained more infiltrating, inflammatory Ly6C+ monocytes, with elevated expression of inflammatory mediators. Infiltrating monocytes matured earlier into pro-inflammatory macrophages with phenotype Ly6C+, CD11b+, F4/80+. Inflammation resolved earlier and progressed to myogenesis, marked by an earlier decline of Ly6C+ macrophages and their replacement with anti-inflammatory Ly6C- populations, in association with elevated expression of factors that resolve inflammation and promote myogenesis. Overall, regeneration was completed earlier. These findings identify myeloid KLF2 as a central regulator of the innate immune response to acute skeletal muscle injury. Manipulating myeloid KLF2 levels may be a useful strategy for accelerating regeneration.\n\nO_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY SynopsisThe zinc-finger transcription factor, KLF2, is a central regulator of the innate immune response to skeletal muscle injury. Targeted deletion of KLF2 in myeloid lineage cells of mice (myeKlf2-/-) enhances the immune response and, notably, accelerates muscle repair. O_LIInjured muscles of myeKlf2-/- mice recruit greater numbers of Ly6C+ (inflammatory) monocytes from the circulation.\nC_LIO_LIThese mature in situ into pro-inflammatory macrophages which phagocytose necrotic tissue and prepare the environment for muscle regeneration.\nC_LIO_LISubsequently, Ly6C+ macrophages decline and are replaced by anti-inflammatory (Ly6C-) macrophages that promote myogenesis of new fibers.\nC_LIO_LIInjured muscles of myeKlf2-/- mice complete regeneration earlier, with phenotypically adult fibers.\nC_LI\n\nC_FIG_DISPLAY

immunology↗

bioRxiv2018

Efficient genome editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 system for analyzing magnetotactic behavior

Magnetotactic bacteria are a diverse group of microorganisms with the ability to use geomagnetic fields for direction sensing. This magnetotactic behavior can help microorganisms move towards favorable habitats for optimal growth and reproduction. Highly efficient genomic editing is very useful for a comprehensive understanding of the magnetotactic mechanism at the molecular level. In this study, we adapted an engineered CRISPR-cas9 system for efficient inactivation of gene in a widely used magnetotactic bacteria model strain, Magnetospirillum magneticum AMB-1. By combining an engineered nuclease-deficient Cas9 and single-guide RNA, a CRISPR interference system was successfully developed to silence amb0994 expression. More importantly, we succeeded in the construction of a single amb0994 gene deletion mutant using CRISPR-Cas9 with approximate 60-fold high efficiency compared to classical homology double-crossing replacement procedure. This mutant synthesized normally the magnetosomes, but reacted quicker and with less time than the wild-type strain to abrupt magnetic field reversals. A dynamics simulation by modeling M. magneticum AMB-1 cell as an ellipsoid showed that the difference of the motions between wild and{Delta} amb0994 is due to flagellar influence. The behavior observation being consistent with dynamics simulation indicated that Amb0994 is involved in the cellular response to magnetic torque change via controlling flagella. Besides the contribution to a better understanding of the magnetotaxis mechanism, this study demonstrates the CRISPR system as a useful genetic toolbox for high-efficiency genome editing in magnetotactic bacteria.

microbiology↗