Global Identification of Small Ubiquitin-related Modifier (SUMO) Substrates Reveals Crosstalk between SUMOylation and Phosphorylation Promotes Cell Migration.

Proteomics studies have revealed that SUMOylation is a widely used post-translational modification (PTM) in eukaryotes. However, how SUMO E1/2/3 complexes use different SUMO isoforms and recognize substrates remains largely unknown. Using a human proteome microarray-based activity screen, we identified over 2500 proteins that undergo SUMO E3-dependent SUMOylation. We next constructed a SUMO isoform- and E3 ligase-dependent enzyme-substrate relationship network. Protein kinases were significantly enriched among SUMOylation substrates, suggesting crosstalk between phosphorylation and SUMOylation. Cell-based analyses of tyrosine kinase, PYK2, revealed that SUMOylation at four lysine residues promoted PYK2 autophosphorylation at tyrosine 402, which in turn enhanced its interaction with SRC and full activation of the SRC-PYK2 complex. SUMOylation on WT but not the 4KR mutant of PYK2 further elevated phosphorylation of the downstream components in the focal adhesion pathway, such as paxillin and Erk1/2, leading to significantly enhanced cell migration during wound healing. These studies illustrate how our SUMO E3 ligase-substrate network can be used to explore crosstalk between SUMOylation and other PTMs in many biological processes.

Global Analysis of SUMO-Binding Proteins Identifies SUMOylation as a Key Regulator of the INO80 Chromatin Remodeling Complex.

SUMOylation is a critical regulator of a broad range of cellular processes, and is thought to do so in part by modulation of protein interaction. To comprehensively identify human proteins whose interaction is modulated by SUMOylation, we developed an in vitro binding assay using human proteome microarrays to identify targets of SUMO1 and SUMO2. We then integrated these results with protein SUMOylation and protein-protein interaction data to perform network motif analysis. We focused on a single network motif we termed a SUMOmodPPI (SUMO-modulated Protein-Protein Interaction) that included the INO80 chromatin remodeling complex subunits TFPT and INO80E. We validated the SUMO-binding activity of INO80E, and showed that TFPT is a SUMO substrate both in vitro and in vivo We then demonstrated a key role for SUMOylation in mediating the interaction between these two proteins, both in vitro and in vivo By demonstrating a key role for SUMOylation in regulating the INO80 chromatin remodeling complex, this work illustrates the power of bioinformatics analysis of large data sets in predicting novel biological phenomena.

Concurrent management of HIV and malaria: A comprehensive review of strategies to enhance quality of life.

The co-occurrence of human immunodeficiency virus and malaria presents a complex medical scenario, significantly impacting the quality of life for affected individuals. This comprehensive review synthesizes current knowledge, challenges, and strategies concerning the concurrent management of these infections to improve overall well-being. Epidemiological insights reveal the prevalence and demographic trends, highlighting geographical areas of concern and socioeconomic factors contributing to the burden of co-infection. Pathophysiological interactions elucidate the compounding effects, altering disease progression and treatment outcomes. Healthcare challenges underscore the necessity for integrated care models, evaluating existing healthcare frameworks and their efficacy in addressing dual infections. In-depth analysis of interventions explores pharmacological, behavioral, and preventive measures, evaluating their efficacy and safety in co-infected individuals. Additionally, the review assesses psychosocial support mechanisms, emphasizing community-based interventions and peer networks in enhancing holistic care. Consideration is given to the role of antiretroviral therapy, malaria prevention strategies, and the evolving landscape of healthcare delivery in optimizing outcomes for this vulnerable population. The paper concludes by emphasizing the significance of multidisciplinary approaches and integrated care models, stressing the need for continued research and collaborative efforts to advance interventions and improve the quality of life for those navigating the complexities of human immunodeficiency virus and malaria co-infection.

Gene expression of Aurora kinases in prostate cancer and nodular hyperplasia tissues.

OBJECTIVE: To measure the transcript levels of Aurora kinases and compare them to their immunoreactivity patterns in prostate tumors. MATERIALS AND METHODS: A total of 26 cases of prostate cancer (PCa) and 38 cases of benign nodular hyperplasia (BPH) were sampled from archived formalin-fixed paraffin-embedded tissues. Tissue sections were lysed, total RNA extracted and cDNA made by random hexamer priming while slide sections were immunostained for the kinases. Normalized relative quantitation was performed for all the kinases using real-time PCR on TaqMan chemistry. RESULTS: The immunoreactivity profile showed 15.4, 53.8 and 30.7% positivity for Aurora kinases A, B and C in PCa cases, respectively, while the positivity was 76.3, 73.7 and 84.2% for the same kinases in BPH cases. The immunoreactivity was preponderant on epithelial tissue compared to stromal component. CONCLUSION: Aurora kinases were significantly overexpressed in BPH cases compared to PCa cases. At the transcript level, there was no significant differential expression in the kinases between PCa and BPH cases.

A possible model for estimating birth length of babies from common parental variables using a sample of families in Lagos, Nigeria.

BACKGROUND: Length at birth is important for evaluating childhood growth and development. It is of interest in Pediatrics because of its implications for perinatal and postnatal morbidity and mortality. Predicting birth length will be useful in anticipating and managing possible complications associated with pregnancy and birth of babies with abnormal birth length. OBJECTIVE: The aim was to identify easily accessible parental determinants of baby's birth length in Lagos, Nigeria, using a sample of patients attending a government hospital. METHODS: Parental anthropometrics and other data were obtained from 250 couples by actual measurements, oral interviews and questionnaires. Baby's birth length was measured immediately after delivery by qualified, a well-trained obstetric nurse, and association between parental and offspring parameters were assessed. RESULTS: Weight gain, maternal weight, parity and mid-parental height were the significant parental explanatory variables of offspring birth length. They were the most suitable variables for a generated model for predicting babies' birth length from parental variables in the study. CONCLUSION: A model that might be useful for predicting babies' birth length from easily accessible parental variables was produced. This model may complement ultrasonographic data for predicting baby's birth length with a view to achieving better perinatal and postnatal care.

Allium sativum aqueous extract does not have chemo-protective effect on etoposide induced therapy-related DNA damage leading to Acute Myeloid Leukemia in albino-wistar rats.

BACKGROUND: Therapy-related acute myeloid leukemia (t-AML) is a well-recognized clinical syndrome occurring in a significant fraction of patients who have undergone previous chemotherapy for a solid tumour. OBJECTIVES: We aim to evaluate the effect of aqueous extract of fresh Allium sativum cloves on haematological parameters, bone marrow and DNA of etoposide treated albino wistar rats. Decoction method was used to prepare plant extracts and the rats were weighed and divided into experimental and control groups. Blood and bone marrow sample were analysed and DNA fragment analysis was carried out. RESULTS: There was progressive increase in the weight of animals that received distilled water only for the duration of the experiment while those that received etoposide only showed a sharp decrease in weight by the end of week 3. There was no significant difference in the mean of the haematological parameters in the test and control groups except for platelet count. The bone marrow smears showed no prevention of erythroblast fragmentation by the extract, in the same vein, DNA damage was not abated. CONCLUSION: Aqueous extract of fresh Allium sativum cloves may not be the option for the prevention of etoposide induced acute myeloid leukemia.

Distinct pattern of lymphoid neoplasms characterizations according to the WHO classification (2016) and prevalence of associated Epstein-Barr virus infection in Nigeria population.

BACKGROUND: The present study aimed to classify lymphoid neoplasms according to the latest World Health Organization (WHO) classification and outlining the distribution in Nigeria of different entities. Additionally, the study describes the prevalence of lymphoid neoplasms associated with Epstein-Barr virus (EBV) infection in the Nigerian population. METHODS: We collected 152 formalin-fixed paraffin-embedded (FFPE) tissues diagnosed as lymphoma from 2008 to 2018, coming from three different institutions located within three geopolitical zone in Nigeria. These institutions included the University College Hospital (UCH), Ibadan, Oyo State, the Enugu State University of Science and Technology Teaching Hospital (ESUTH), Enugu, Enugu State, and the Meena Histopathology and Cytology Laboratory (MHCL), Jos, Plateau State. RESULTS: From the total 152 cases retrieved, 50 were excluded due to insufficient tissue materials or inconclusive antigen reactivity. We confirmed 66 (64.7%) cases as lymphomas out of the remaining 102 FFPE with a male to female ratio of 2:1 and a mean age of 44.4 years. Ten entities were identified, and of these, chronic lymphocytic leukemia (CLL) was the most prevalent category (34.8%). For the diffuse large B-cell lymphomas not otherwise specified (DLBCL, NOS), the germinal centre B-cell type was the most common (71.4%). Ten lymphoma cases (15.2%) were positive for Epstein-Barr virus (EBV), most of which were Hodgkin lymphoma (HL). CLL was common in the Hausa ethnic group, HL in the Yoruba ethnic group, while the Igbo ethnic group had an equal distribution of CLL, HL, and DLBCL diagnosis. CONCLUSION: Although the distribution of lymphomas in Nigeria shares some similarities with those of other countries, we described distinct features of some subtypes of lymphomas. Also, the study underscores the need for a more precise diagnosis and classification of lymphoid neoplasms in Nigeria using the latest WHO classification.

Gab2-mediated signaling promotes melanoma metastasis.

Metastatic melanoma is a disease with a poor prognosis that currently lacks effective treatments. Critical biological features of metastasis include acquisition of migratory competence, growth factor independence, and invasive potential. In an attempt to identify genes that contribute to melanoma pathogenesis, a genome-wide search using bacterial artificial chromosome array comparative genomic hybridization and single nucleotide polymorphism arrays in a series of 64 metastatic melanoma samples and 20 melanoma cell lines identified increased copy numbers of Gab2 located on 11q14.1. Gab2 is an adaptor protein that potentiates the activation of the Ras-Erk and PI3K-Akt pathways and has recently been implicated in human cancer; however, its role in melanoma has not been explored. In this study, we found that Gab2 was either amplified (approximately 11%) and/or overexpressed (approximately 50%) in melanoma. Gab2 protein expression correlated with clinical melanoma progression, and higher levels of expression were seen in metastatic melanomas compared with primary melanoma and melanocytic nevi. We found that overexpression of Gab2 potentiates, whereas silencing of Gab2 reduces, migration and invasion of melanoma cells. Gab2 mediated the hyperactivation of Akt signaling in the absence of growth factors, whereas inhibition of the PI3K-Akt pathway decreased Gab2-mediated tumor cell migration and invasive potential. Gab2 overexpression resulted in enhanced tumor growth and metastatic potential in vivo. These studies demonstrate a previously undefined role for Gab2 in melanoma tumor progression and metastasis.

Mitigating the Impact of Antibacterial Drug Resistance through Host-Directed Therapies: Current Progress, Outlook, and Challenges.

Increasing incidences of multidrug resistance in pathogenic bacteria threaten our ability to treat and manage bacterial infection. The development and FDA approval of novel antibiotics have slowed over the past decade; therefore, the adoption and improvement of alternative therapeutic strategies are critical for addressing the threat posed by multidrug-resistant bacteria. Host-directed therapies utilize small-molecule drugs and proteins to alter the host response to pathogen infection. Here, we highlight strategies for modulating the host inflammatory response to enhance bacterial clearance, small-molecule potentiation of innate immunity, and targeting of host factors that are exploited by pathogen virulence factors. Application of state-of-the-art "omic" technologies, including proteomics, transcriptomics, and image-omics (image-based high-throughput phenotypic screening), combined with powerful bioinformatics tools will enable the modeling of key signaling pathways in the host-pathogen interplay and aid in the identification of host proteins for therapeutic targeting and the discovery of host-directed small molecules that will regulate bacterial infection. We conclude with an outlook on research needed to overcome the challenges associated with transitioning host-directed therapies into a clinical setting.

Posttranslational Modification Assays on Functional Protein Microarrays.

Protein microarray technology provides a straightforward yet powerful strategy for identifying substrates of posttranslational modifications (PTMs) and studying the specificity of the enzymes that catalyze these reactions. Protein microarray assays can be designed for individual enzymes or a mixture to establish connections between enzymes and substrates. Assays for four well-known PTMs-phosphorylation, acetylation, ubiquitylation, and SUMOylation-have been developed and are described here for use on functional protein microarrays. Phosphorylation and acetylation require a single enzyme and are easily adapted for use on an array. The ubiquitylation and SUMOylation cascades are very similar, and the combination of the E1, E2, and E3 enzymes plus ubiquitin or SUMO protein and ATP is sufficient for in vitro modification of many substrates.

Protein Microarrays: Flexible Tools for Scientific Innovation.

Protein microarrays have emerged as a powerful tool for the scientific community, and their greatest advantage lies in the fact that thousands of reactions can be performed in a parallel and unbiased manner. The first high-density protein microarray, dubbed the "yeast proteome array," consisted of approximately 5800 full-length yeast proteins and was initially used to identify protein-lipid interactions. Further assays were subsequently developed to allow measurement of protein-DNA, protein-RNA, and protein-protein interactions, as well as four well-known posttranslational modifications: phosphorylation, acetylation, ubiquitylation, and SUMOylation. In this introduction, we describe the advent of high-density protein microarrays, as well as current methods for assessing a wide variety of protein interactions and posttranslational modifications.

Identification of SUMO E3 ligase-specific substrates using the HuProt human proteome microarray.

The functional protein microarray is a powerful and versatile systems biology and proteomics tool that allows the rapid activity profiling of thousands of proteins in parallel. We have recently developed a human proteome array, the HuProt array, which includes ~80 % of all the full-length proteins of the human proteome. In one recent application of the HuProt array, we identified numerous SUMO E3 ligase-dependent SUMOylation substrates. For many SUMO E3 ligases, only a small number of substrates have been identified and the target specificities of these ligases therefore remain poorly defined. In this protocol, we outline a method we developed using the HuProt array to screen the human proteome to identify novel SUMO E3 ligase substrates recognized by specific E3 ligases.

A reverse-phase protein microarray-based screen identifies host signaling dynamics upon Burkholderia spp. infection.

Burkholderia is a diverse genus of gram-negative bacteria that causes high mortality rate in humans, equines and cattle. The lack of effective therapeutic treatments poses serious public health threats. Developing insights toward host-Burkholderia spp. interaction is critical for understanding the pathogenesis of infection as well as identifying therapeutic targets for drug development. Reverse-phase protein microarray technology was previously proven to identify and characterize novel biomarkers and molecular signatures associated with infectious disease and cancer. In the present study, this technology was utilized to interrogate changes in host protein expression and phosphorylation events in macrophages infected with a collection of geographically diverse strains of Burkholderia spp. The expression or phosphorylation state of 25 proteins was altered during Burkholderia spp. infections of which eight proteins were selected for further characterization by immunoblotting. Increased phosphorylation of AMPK-α1, Src, and GSK3ß suggested the importance of their roles in regulating Burkholderia spp. mediated innate immune response. Modulating the inflammatory response by perturbing their activities may provide therapeutic routes for future treatments.

Characterization of the SUMO-binding activity of the myeloproliferative and mental retardation (MYM)-type zinc fingers in ZNF261 and ZNF198.

SUMO-binding proteins interact with SUMO modified proteins to mediate a wide range of functional consequences. Here, we report the identification of a new SUMO-binding protein, ZNF261. Four human proteins including ZNF261, ZNF198, ZNF262, and ZNF258 contain a stretch of tandem zinc fingers called myeloproliferative and mental retardation (MYM)-type zinc fingers. We demonstrated that MYM-type zinc fingers from ZNF261 and ZNF198 are necessary and sufficient for SUMO-binding and that individual MYM-type zinc fingers function as SUMO-interacting motifs (SIMs). Our binding studies revealed that the MYM-type zinc fingers from ZNF261 and ZNF198 interact with the same surface on SUMO-2 recognized by the archetypal consensus SIM. We also present evidence that MYM-type zinc fingers in ZNF261 contain zinc, but that zinc is not required for SUMO-binding. Immunofluorescence microscopy studies using truncated fragments of ZNF198 revealed that MYM-type zinc fingers of ZNF198 are necessary for localization to PML-nuclear bodies (PML-NBs). In summary, our studies have identified and characterized the SUMO-binding activity of the MYM-type zinc fingers in ZNF261 and ZNF198.

Interactome mapping: using protein microarray technology to reconstruct diverse protein networks.

A major focus of systems biology is to characterize interactions between cellular components, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protein microarrays have greatly contributed to advances in proteomics and are becoming an important platform for systems biology. Protein microarrays are highly flexible, ranging from large-scale proteome microarrays to smaller customizable microarrays, making the technology amenable for detection of a broad spectrum of biochemical properties of proteins. In this article, we will focus on the numerous studies that have utilized protein microarrays to reconstruct biological networks including protein-DNA interactions, posttranslational protein modifications (PTMs), lectin-glycan recognition, pathogen-host interactions and hierarchical signaling cascades. The diversity in applications allows for integration of interaction data from numerous molecular classes and cellular states, providing insight into the structure of complex biological systems. We will also discuss emerging applications and future directions of protein microarray technology in the global frontier.