Biology subjects

Reyes-Ruiz, J. M.

Publications and source records attributed to Reyes-Ruiz, J. M..

4 recordsLinked to original sources

bioRxiv2026

The diversity of disease-associated natural human antibody specificities declines dramatically in Alzheimers disease.

Alzheimers disease (AD) is the leading cause of dementia and administration of monoclonal antibodies against A{beta} amyloid are associated with disease modifying effects leading to FDA approval for some antibodies. Naturally-occurring human antibodies (NAbs) are believed to be the front line of defense against a variety of diseases, so we investigated the specificity of NAbs in AD and cognitively normal (NC) individuals using epitomic profiling (EP). We found that the diversity of antibody-specific peptide epitope segments (ES) declines dramatically (26-fold) in the AD compared to NC populations. Many of these differentially expressed ES (DEES) map to amyloid sequences that accumulate in AD, such as A{beta}, tau, -synuclein, TDP43 and TMEM106b. NAbs that target amino terminal A{beta} epitopes are elevated in AD (residues 1-6 and 18-21) and NAbs that target different A{beta} epitopes are elevated in NC (residues 5-10 and 35-41). DEES that map to 2N4R tau are highly cross correlated in the population implying that that the antibodies may be polyspecific or that a set of antibodies are coordinately regulated. We used weighted gene correlation network analysis (WGCNA) to identify co-expressed DEES and UMAP to embed DEES in both AD and NC populations that bind to the same antibody or co-expressed set of antibodies. An average of approximately 25 DEES cluster in each WGCNA group. A major WGCNA cluster associated with AD contains 3 groups of overlapping DEES that assemble into longer linear epitopes. One of these 3 groups contain sequences that map to the amino terminus of A{beta}. DEES elevated in AD may be useful blood biomarkers for AD. The DEES clusters elevated in NC may be associated with protection against misfolded protein amyloid seeding and propagation and maintaining the resilience of neuronal populations.

neuroscience↗

bioRxiv2020

Epitomic analysis of the specificity of conformation-dependent, anti-aβ amyloid monoclonal antibodies

Antibodies against A{beta} amyloid are indispensable research tools and potential therapeutics for Alzheimers Disease, but display several unusual properties, such as specificity for aggregated forms of the peptide, ability to distinguish polymorphic aggregate structures and ability to recognize generic aggregation-related epitopes formed by unrelated amyloid sequences. Understanding the mechanisms underlying these unusual properties of anti-amyloid antibodies and the structures of their corresponding epitopes is crucial for the understanding why antibodies display different therapeutic activities and for the development of more effective therapeutic agents. Here we employed a novel "epitomic" approach to map the fine structure of the epitopes of 28 monoclonal antibodies against amyloid-beta using immunoselection of random sequences from a phage display library, deep sequencing and pattern analysis to define the critical sequence elements recognized by the antibodies. Although most of the antibodies map to major linear epitopes in the amino terminal 1-14 residues of A{beta}, the antibodies display differences in the target sequence residues that are critical for binding and in their individual preferences for non-target residues, indicating that the antibodies bind to alternative conformations of the sequence by different mechanisms. Epitomic analysis also identifies more discontinuous, non-overlapping sequence A{beta} segments than peptide array approaches that may constitute the conformational epitopes that underlie the aggregation specificity of antibodies. Aggregation specific antibodies recognize sequences that display a significantly higher predicted propensity for forming amyloid than antibodies that recognize monomer, indicating that the ability of random sequences to aggregate into amyloid is a critical element of their binding mechanism.

neuroscience↗

bioRxiv2018

Ezetimibe inhibits Dengue virus infection in Huh 7 cells by blocking the cholesterol transporter Niemann-Pick C1 like 1 receptor

Despite the importance of Dengue virus (DENV) infection in human health, there is not a fully effective vaccine or antiviral treatment against the infection. Since lipids such as cholesterol are required during DENV infection, its uptake and synthesis are increased in infected cells. Ezetimibe is an FDA-approved drug that reduces cholesterol uptake in humans by inhibiting the endocytosis through Niemman-Pick C1-Like 1 (NPC1L1) receptor, expressed on the membrane of enterocytes and hepatocytes. Our results indicate that an increase in the amount of NPC1L1 occurs on the surface of Huh-7 cells during DENV infection, which correlates with an increase in cholesterol levels. Blockage of NPC1L1 with ezetimibe in concentrations up to 50 M does not reduce cell viability but diminished total cellular cholesterol, the percentage of infected cells, viral yield, viral RNA and protein synthesis without affecting DENV binding and/or entry to Huh-7 cells. Moreover, ezetimibe inhibited DENV replicative complex formation and lipid droplets accumulation. All these results indicate that ezetimibe is an excellent drug to inhibit DENV infection and confirm that cholesterol is a key target to inhibit viral infection.

microbiology↗

bioRxiv2018

The Nonstructural Proteins 3 And 5 From Flavivirus Modulate Nuclear-Cytoplasmic Transport And Innate Immune Response Targeting Nuclear Proteins

Viruses hijack cellular proteins and components to be replicated in the host cell and to evade the immune response. Although flaviviruses have a cytoplasmic replicative cycle, some viral proteins such as the capsid (C) and the RNA dependent RNA polymerase, NS5, can reach the nucleus of the infected cells. Considering the important roles of NS5 in viral replication and in the control of the immune response, and its striking presence in the nucleus, the possible functions of this protein in some mechanisms orchestrated by the nucleus was analyzed. We isolated and identified nuclear proteins that interact with NS5; one of them, the DEAD-box RNA helicase DDX5 is relocated to the cytoplasm and degraded during infection with DENV, which correlates with its function in IFN dependent response. Since DDX5 and many other proteins are relocated from the nucleus to the cytoplasm during flavivirus infection, the integrity and function of the main regulator of the nuclear-cytoplasmic transport, the nuclear pore complex (NPC) was evaluated. We found that during DENV and ZIKV infection nucleoporins (NUPs) such as TPR, Nup153, Nup98, and Nup62 were cleavaged/degraded. The protease NS2B-NS3 induces NUPs degradation and it causes a dramatic inhibition of mature mRNAs export to the cytoplasm but not the export of DDX5 protein, which is dependent on NS5. Here we describe for the first time that the NS3 and NS5 proteins from flavivirus play novel functions hijacking the NPC and some nuclear proteins relevant in triggering immune response pathways, inducing a favorable environment for viral replication.\n\nIMPORTANCEViruses, as intracellular obligate parasites, hijack cellular components to enter and replicate in infected cells. Remarkably, in many cases, viruses hijack molecules with crucial functions for the cells. Here it is described how RNA viruses such as DENV and ZIKV, with a cytoplasmic replicative cycle, use NS3 and NS5, two of their unique non-structural proteins with enzymatic activity, to modulate nuclear-cytoplasmic transport. We found that NS3 disrupts the nuclear pore complex, the main regulator in nuclear-cytoplasmic transport, causing a strong reduction in the amount of mature mRNAs in the cytoplasm and an inhibition in innate immune response. Additionally, NS5 induces the relocation of nuclear proteins to the cytoplasm such as DDX5, involved in immune response, which is later degraded by NS3. These findings allow the understanding of crucial mechanisms that viruses use to deal with the control of the immune response to grant the production of new viral particles.

molecular biology↗