Quantitative phosphoproteomics reveals GSK3A substrate network is involved in the cryodamage of sperm motility

During sperm cryopreservation, the most significant phenotype of cryodamage is the decrease of sperm motility. Several proteomic studies have already been performed to search for key regulators at the protein level. However, sperm functions are known to be highly regulated by phosphorylation signaling. Here, we constructed a quantitative phosphoproteome to investigate the expression change of phosphorylated sites during sperm cryopreservation. A total of 3167 phosphorylated sites are identified and 848 of them are found to be significantly differentially expressed. Bioinformatics analysis showed that the corresponding genes of these regulated sites are highly associated with sperm motility, providing a connection between the molecular basis and the phenotype of cryodamage. We then performed kinase enrichment analysis and successfully identified GSK3A as the key kinase that may play an important role in the regulation of sperm motility. We further constructed a GSK3A centric network that could help us better understand the molecular mechanism of cryodamage in sperm motility. Finally, we also verified that GSK3A was abnormally activated during this process. The presented phosphoproteome and functional associations provide abundant research resources for us to learn the regulation of sperm functions, as well as to optimize the cryoprotectant for sperm cryopreservation.

Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data

Phosphoproteomic experiments routinely observe thousands of phosphorylation sites. To understand the intracellular signaling processes that generated this data, one or more causal protein kinases must be assigned to each phosphosite. However, limited knowledge of kinase specificity typically restricts assignments to a small subset of a kinome. Utilizing simple machine-learning methods on data from high-throughput, in vitro kinase-substrate assays, I have developed an approach to high-coverage, multi-label kinase-substrate assignment called IV-KAPhE (“In vivo-Kinase Assignment for Phosphorylation Evidence”). Tested on human data, IV-KAPhE outperforms other methods of similar scope. Such computational methods generally predict a densely connected kinase-substrate network, with most sites targeted by multiple kinases, pointing either to unaccounted-for biochemical constraints or significant cross-talk and signaling redundancy. Finally, I show that such predictions can potentially identify biased kinase-site misannotations within families of closely related kinase isoforms.

Admission Control for 5G Network Slicing based on (Deep) Reinforcement Learning

Network Slicing is a promising technology for providing customized logical and virtualized networks for the industry’s vertical segments.This paper proposes SARA and DSARA for the performance of admission control and resource allocation for network slice requests of eMBB, URLLC, and MIoT type in the 5G core network. SARA introduced a Q-learning based algorithm and DSARA a DQN-based algorithm to select the most profitable requests from a set that arrived in given time windows. These algorithms are model-free, meaning they do not make assumptions about the substrate network as do optimization based approaches.

Admission Control for 5G Network Slicing based on (Deep) Reinforcement Learning

Network Slicing is a promising technology for providing customized logical and virtualized networks for the industry’s vertical segments.This paper proposes SARA and DSARA for the performance of admission control and resource allocation for network slice requests of eMBB, URLLC, and MIoT type in the 5G core network. SARA introduced a Q-learning based algorithm and DSARA a DQN-based algorithm to select the most profitable requests from a set that arrived in given time windows. These algorithms are model-free, meaning they do not make assumptions about the substrate network as do optimization based approaches.

System-wide hematopoietic and immune signaling aberrations in COVID-19 revealed by deep proteome and phosphoproteome analysis

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has become a global crisis. To gain systems-level insights into its pathogenesis, we compared the blood proteome and phosphoproteome of ICU patients with or without SARS-CoV-2 infection, and healthy control subjects by quantitative mass spectrometry. We find that COVID-19 is marked with hyperactive T cell and B cell signaling, compromised innate immune response, and dysregulated inflammation, coagulation, metabolism, RNA splicing, transcription and translation pathways. SARS-CoV-2 infection causes global reprogramming of the kinome and kinase-substrate network, resulting in defective antiviral defense via the CK2-OPN-IL-12/IFN-I axis, lymphocyte cell death via aberrant JAK/STAT signaling, and inactivation of innate immune cells via inhibitory SIRPA, SIGLEC and SLAM family receptor signaling. Our work identifies CK2, SYK, JAK3, TYK2 and IL-12 as potential targets for immunomodulatory treatment of severe COVID-19 and provides a valuable approach and resource for deciphering the mechanism of pathogen-host interactions.

System-wide hematopoietic and immune signaling aberrations in COVID-19 revealed by deep proteome and phosphoproteome analysis

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has become a global crisis. To gain systems-level insights into its pathogenesis, we compared the blood proteome and phosphoproteome of ICU patients with or without SARS-CoV-2 infection, and healthy control subjects by quantitative mass spectrometry. We find that COVID-19 is marked with hyperactive T cell and B cell signaling, compromised innate immune response, and dysregulated inflammation, coagulation, metabolism, RNA splicing, transcription and translation pathways. SARS-CoV-2 infection causes global reprogramming of the kinome and kinase-substrate network, resulting in defective antiviral defense via the CK2-OPN-IL-12/IFN-I axis, lymphocyte cell death via aberrant JAK/STAT signaling, and inactivation of innate immune cells via inhibitory SIRPA, SIGLEC and SLAM family receptor signaling. Our work identifies CK2, SYK, JAK3, TYK2 and IL-12 as potential targets for immunomodulatory treatment of severe COVID-19 and provides a valuable approach and resource for deciphering the mechanism of pathogen-host interactions.

Molecular Contribution to Embryonic Aneuploidy and Genotypic Complexity During Initial Cleavage Divisions of Mammalian Development

ABSTRACTEmbryonic aneuploidy is highly complex, often leading to developmental arrest, implantation failure, or spontaneous miscarriage in both natural and assisted reproduction. Despite our knowledge of mitotic mis-segregation in somatic cells, the molecular pathways regulating chromosome fidelity during the error-prone cleavage-stage of mammalian embryogenesis remain largely undefined. Using bovine embryos and live-cell fluorescent imaging, we observed frequent micro-/multi-nucleation of anaphase lagging or mis-segregated chromosomes in initial mitotic divisions that underwent unilateral inheritance, re-fused with the primary nucleus, or formed a chromatin bridge with neighboring cells. A correlation between a lack of maternal and paternal pronuclei fusion (syngamy), multipolar cytokinesis, and uniparental genome segregation was also revealed and single-cell DNA-seq showed propagation of primarily non-reciprocal mitotic errors in embryonic blastomeres. Depletion of the mitotic checkpoint protein, BUB1B/BUBR1, resulted in micro-/multi-nuclei formation, atypical cytokinesis, chaotic aneuploidy, and disruption of the kinase-substrate network regulating mitotic progression and exit, culminating in embryo arrest prior to genome activation. This demonstrates that embryonic micronuclei sustain multiple fates, provides a mechanism for blastomeres with uniparental origins, and substantiates the contribution of defective checkpoint signaling and/or the inheritance of other maternally-derived factors to the high genotypic complexity afflicting preimplantation development in higher-order mammals.

Phosphoproteomics Reveals AMPK Substrate Network in Response to DNA Damage and Histone Acetylation

AMPK is a conservative energy sensor that plays roles in diverse biologic processes via direct phosphorylation on various substrates. Emerging studies have demonstrated the regulatory roles of AMPK in DNA repair, but the underlying mechanisms remain to be fully understood. Herein, using mass spectrometry-based proteomic technologies, we systematically investigate the regulatory network of AMPK in DNA damage response. Our system-wide phosphoproteome study uncovers a variety of newly-identified potential substrates involved in diverse biologic processes, whereas our system-wide histone modification analysis reveals a linkage between AMPK and histone acetylation. Together with these findings, we discover that AMPK promotes apoptosis by phosphorylating ASPP2 in irradiation-dependent way and regulates histone acetylation by phosphorylating HDAC9 in irradiation-independent way. Besides, we reveal that disturbing the histone acetylation by the bromodomain BRD4 inhibitor JQ-1 enhanced the sensitivity of AMPK-deficient cells to irradiation. Therefore, our studies provided a source to study the phosphorylation and histone acetylation underlying the regulatory network of AMPK, which could be beneficial to understand the exact role of AMPK in DNA damage response.