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1
Mulloy, Barbara, and Ten Feizi. "Tricks of the trade in glycoscience: The preparation and analysis of a blood group A-active mucin glycoprotein." Biochemist 36, no. 4 (August 1, 2014): 18–20. http://dx.doi.org/10.1042/bio03604018.
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Many aspects of glycosylation are conserved among animals, and it can be advantageous and sometimes critical to identify a readily available and abundant source of carbohydrate material that harbours a hard-to-characterize antigen or ligand of interest. The Biochemical Journal Classic paper by Morgan and King is a well-written account of serviceable methods for the extraction and quantification of a carbohydrate antigen. These methods were highly influential in subsequent studies of the blood group antigens. Some of these tricks of the trade still have a place in modern glycobiology.
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De Masi, Luigi, Maria Antonia Argenio, Deborah Giordano, and Angelo Facchiano. "Molecular Aspects of Spike–ACE2 Interaction." Encyclopedia 2, no. 1 (January 10, 2022): 96–108. http://dx.doi.org/10.3390/encyclopedia2010007.
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A new betacoronavirus (CoV-2) is responsible for the pandemic of severe acute respiratory syndrome (SARS) that began in China at the end of 2019, today known as COronaVIrus Disease 2019 (COVID-19). Subsequent studies confirmed the human angiotensin-converting enzyme 2 (hACE2) as the main cell receptor of spike trimeric glycoprotein, located on the viral envelope, mediating the CoV-2 invasion into the host cells through the receptor-binding domain (RBD) of the spike. Computational analysis of the known experimental 3D structures of spike–ACE2 complexes evidenced distinguishing features in the molecular interactions at the RBD-cell receptor binding interface between CoV-2 and previous CoV-1. The spike represents a key target for drug design as well as an optimal antigen for RNA/viral vector vaccines and monoclonal antibodies in order to maximize prevention and therapy of COVID-19.
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van der Zee, J. S., P. van Swieten, and R. C. Aalberse. "Serologic aspects of IgG4 antibodies. II. IgG4 antibodies form small, nonprecipitating immune complexes due to functional monovalency." Journal of Immunology 137, no. 11 (December 1, 1986): 3566–71. http://dx.doi.org/10.4049/jimmunol.137.11.3566.
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Abstract Human IgG4 antibodies directed against phospholipase A, the P1 antigen from Dermatophagoïdes pteronyssinus extracts, and cat albumin were found unable to cross-link antigen. Previously, it was demonstrated that IgG4 antibodies, in contrast to IgG1 antibodies, did not cross-link Sepharose-bound antigen and antigen added in solution. To eliminate the possibility that this phenomenon was caused by preferential binding of both IgG4 Fab fragments to the solid-phase-bound antigen, cross-linking of antigen was studied in a fluid-phase system. In this test, incapability of IgG4 antibodies to bridge two antigens was also found. As a result of such a phenomenon, it is expected that immune complexes formed by IgG4 antibodies will be considerably smaller than complexes formed by IgG1. This was confirmed by analysis of the molecular size profiles of IgG1- and IgG4-containing immune complexes in sucrose-density gradients. Moreover, IgG1 was able to precipitate antigen in a radioimmunoprecipitation test, whereas precipitation was not demonstrable by the same amount of IgG4 antibodies. Even 3% polyethylene glycol 8,000 did not precipitate the small IgG4-containing immune complexes efficiently. The antibodies studied were of a high-affinity type, and there was no significant difference in association constants between IgG1 and IgG4 antibodies. Therefore, we were not able to confirm observations reported in the literature that the IgG4 subclass is associated with a low-affinity antibody response; probably, the affinity of the IgG4 antibodies was underestimated by other investigators because of the polyethylene glycol precipitation technique used to separate antibody-bound and free antigen. Our findings stress the point that IgG4 antibodies take a special place in the immune response upon chronic exposure to antigen.
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Bräunlein, Eva, Gaia Lupoli, Franziska Füchsl, Esam T. Abualrous, Niklas de Andrade Krätzig, Dario Gosmann, Lukas Wietbrock, et al. "Functional analysis of peripheral and intratumoral neoantigen-specific TCRs identified in a patient with melanoma." Journal for ImmunoTherapy of Cancer 9, no. 9 (September 2021): e002754. http://dx.doi.org/10.1136/jitc-2021-002754.
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BackgroundNeoantigens derived from somatic mutations correlate with therapeutic responses mediated by treatment with immune checkpoint inhibitors. Neoantigens are therefore highly attractive targets for the development of therapeutic approaches in personalized medicine, although many aspects of their quality and associated immune responses are not yet well understood. In a case study of metastatic malignant melanoma, we aimed to perform an in-depth characterization of neoantigens and respective T-cell responses in the context of immune checkpoint modulation.MethodsThree neoantigens, which we identified either by immunopeptidomics or in silico prediction, were investigated using binding affinity analyses and structural simulations. We isolated seven T-cell receptors (TCRs) from the patient’s immune repertoire recognizing these antigens. TCRs were compared in vitro by multiparametric analyses including functional avidity, multicytokine secretion, and cross-reactivity screenings. A xenograft mouse model served to study in vivo functionality of selected TCRs. We investigated the patient’s TCR repertoire in blood and different tumor-related tissues over 3 years using TCR beta deep sequencing.ResultsSelected mutated peptide ligands with proven immunogenicity showed similar binding affinities to the human leukocyte antigen complex and comparable disparity to their wild-type counterparts in molecular dynamic simulations. Nevertheless, isolated TCRs recognizing these antigens demonstrated distinct patterns in functionality and frequency. TCRs with lower functional avidity showed at least equal antitumor immune responses in vivo. Moreover, they occurred at high frequencies and particularly demonstrated long-term persistence within tumor tissues, lymph nodes and various blood samples associated with a reduced activation pattern on primary in vitro stimulation.ConclusionsWe performed a so far unique fine characterization of neoantigen-specific T-cell responses revealing defined reactivity patterns of neoantigen-specific TCRs. Our data highlight qualitative differences of these TCRs associated with function and longevity of respective T cells. Such features need to be considered for further optimization of neoantigen targeting including adoptive T-cell therapies using TCR-transgenic T cells.
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Makhneva, Nataliya V., Yu S. Butov, and V. Yu Vasenova. "THE MOLECULAR BIOLOGICAL AND IMMUNE PATHOLOGIC CHARACTERISTICS UNDER AUTO-IMMUNE DISEASES OF SKIN." Medical Journal of the Russian Federation 23, no. 5 (October 15, 2017): 258–62. http://dx.doi.org/10.18821/0869-2106-2017-23-5-258-262.
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The skin and mucous membranes are the min barrier organs providing systemic defense from environmental effects. They actively participate in deliverance of organism from antigens of various origin due to availability of one's own elements of immune system. The failure in chain of immune defense causes deceleration of process of elimination of antigen damaging structure of one's own tissue. The article presents mechanism of elimination of immune complexes and examples of therapeutic procedures accelerating and normalizing this process. The maintenance and recovery of excretory function of skin ensure positive dynamics of clinical manifestations of various diseases, including ones of autoimmune genesis. In case of fixation of immunoglobulins in tissues, skin acts as a target-organ. At that, detected specific antibodies are diagnostic markers for a wide circle of autoimmune dermatoses. Furthermore, immunopathologic processes occurring in skin are associated with disorders of synthesis of various molecular compounds of its tissue structures. This is testified by the results of immune morphologic picture of expression of a number of molecules of adhesion, protein components of desmosomal apparatus and basal membrane of epidermis, antigens of HLA-system. Therefore, skin is a complex organized structure capable to actively participate in development of inflammatory and autoimmune reactions. The analysis of these reactions at molecular biological level permits to evaluate intensity of occurring processes, to implement testing of efficacy of applied curative activities and in a number of cases to serve as an additional diagnostic marker. Undoubtedly, implementation of molecular biological methods as a tool of cognition favors continuous broadening of information about a number of aspects of pathogenesis of skin diseases and brings to development of new methods of their treatment at the molecular genetic level.
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Buscaglia, Carlos A., Julieta Alfonso, Oscar Campetella, and Alberto C. C. Frasch. "Tandem Amino Acid Repeats From Trypanosoma cruzi Shed Antigens Increase the Half-Life of Proteins in Blood." Blood 93, no. 6 (March 15, 1999): 2025–32. http://dx.doi.org/10.1182/blood.v93.6.2025.406k19_2025_2032.
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Proteins containing amino acid repeats are widespread among protozoan parasites. It has been suggested that these repetitive structures act as immunomodulators, but other functional aspects may be of primary importance. We have recently suggested that tandem repeats present in Trypanosoma cruzi trans-sialidase stabilize the catalytic activity in blood. Because the parasite releasestrans-sialidase, this delayed clearance of the enzyme might have implications in vivo. In the present work, the ability of repetitive units from different T. cruzi molecules in stabilizing trans-sialidase activity in blood was evaluated. It is shown that repeats present on T. cruzi shed proteins (antigens 13 and Shed-Acute-Phase-Antigen [SAPA]) increase trans-sialidase half-life in blood from 7 to almost 35 hours. Conversely, those repeats present in intracellular T. cruzi proteins only increase the enzyme half-life in blood up to 15 hours. Despite these results, comparative analysis of structural and catalytic properties of both groups of chimeric enzymes show no substantial differences. Interestingly, antigens 13 and SAPA also increase the persistence in blood of chimeric glutathione S-transferases, thus suggesting that this effect is inherent to these repeats and independent of the carrier protein. Although the molecular basis of this phenomenon is still uncertain, its biotechnological potential can be envisaged.
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Udintseva, I. N., O. Ye Chechina, N. G. Zhoukova, L. V. Lukashova, N. V. Ryazantseva, A. M. Poponina, L. A. Malysheva, N. N. Bartfeld, and S. A. Pershina. "Clinical immunological aspects of tick-borne encephalitis." Bulletin of Siberian Medicine 7, no. 5-2 (December 30, 2008): 438–43. http://dx.doi.org/10.20538/1682-0363-2008-5-2-438-443.
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In this article results of the clinical-immunological analysis with different forms tick-borne encephalitis of Tomsk Region during the period from 2000 to 2008 are represented. The revealled disbalance of cytokines alongside with breach of the expressions cytokines's receptor by limphocytes's cells, can be one of the main of the reasons to inefficiency answer when introducing the infectious agent in organism and shaping the chronic form to infectious pathology, in particular, with long presence of the antigen of the virus tick-borne encephalitis in blood. The trend to increase the level sick with long presence of the antigen of the virus tick-borne encephalitis in blood, with prevalence of the persons feminine flap, mainly average and senior age for the last years is given.
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BILIC, I., M. LEBERL, and M. HESS. "Identification and molecular characterization of numerous Histomonas meleagridis proteins using a cDNA library." Parasitology 136, no. 4 (January 21, 2009): 379–91. http://dx.doi.org/10.1017/s0031182008005477.
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SUMMARYHistomonas meleagridis is a protozoan parasite of various galliform birds causing a type of enterohepatitis termed histomonosis or ‘blackhead disease’. Due to the ban of chemotherapeutic substances and an increase in free-range poultry production, histomonosis is currently a re-emerging disease. So far limited molecular knowledge is available. In the present work, mRNAs coding for antigenic proteins of H. meleagridis were identified. For this purpose, a cDNA expression library was constructed from a mono-eukaryotic culture of H. meleagridis. The library was screened with polyclonal rabbit serum raised against purified H. meleagridis trophozoites. Polyclonal rabbit serum specifically recognized the same major H. meleagridis antigens as chicken and turkey sera originating from animal trials, but displayed a significantly lower bacteria-dependent background signal. After 2 rounds of screening, a total of 95 positive clones were sequenced. Bioinformatics analyses were performed on nucleotide and deduced amino acid sequences, identifying 37 unique clones. Based on the homology to other protozoan parasites, mostly Trichomonas vaginalis, the clones were grouped according to functional aspects: structural proteins, possible surface proteins, oxygen reducing proteins, ribosomal proteins, protein kinases and various other intracellular proteins.
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Hui, Winnie W., Lisa E. Emerson, Beata Clapp, Austin E. Sheppe, Jatin Sharma, Johanna del Castillo, Mark Ou, et al. "Antigen-encapsulating host extracellular vesicles derived from Salmonella-infected cells stimulate pathogen-specific Th1-type responses in vivo." PLOS Pathogens 17, no. 5 (May 6, 2021): e1009465. http://dx.doi.org/10.1371/journal.ppat.1009465.
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Salmonella Typhimurium is a causative agent of nontyphoidal salmonellosis, for which there is a lack of a clinically approved vaccine in humans. As an intracellular pathogen, Salmonella impacts many cellular pathways. However, the intercellular communication mechanism facilitated by host-derived small extracellular vesicles (EVs), such as exosomes, is an overlooked aspect of the host responses to this infection. We used a comprehensive proteome-based network analysis of exosomes derived from Salmonella-infected macrophages to identify host molecules that are trafficked via these EVs. This analysis predicted that the host-derived small EVs generated during macrophage infection stimulate macrophages and promote activation of T helper 1 (Th1) cells. We identified that exosomes generated during infection contain Salmonella proteins, including unique antigens previously shown to stimulate protective immune responses against Salmonella in murine studies. Furthermore, we showed that host EVs formed upon infection stimulate a mucosal immune response against Salmonella infection when delivered intranasally to BALB/c mice, a route of antigen administration known to initiate mucosal immunity. Specifically, the administration of these vesicles to animals stimulated the production of anti-Salmonella IgG antibodies, such as anti-OmpA antibodies. Exosomes also stimulated antigen-specific cell-mediated immunity. In particular, splenic mononuclear cells isolated from mice administered with exosomes derived from Salmonella-infected antigen-presenting cells increased CD4+ T cells secreting Th1-type cytokines in response to Salmonella antigens. These results demonstrate that small EVs, formed during infection, contribute to Th1 cell bias in the anti-Salmonella responses. Collectively, this study helps to unravel the role of host-derived small EVs as vehicles transmitting antigens to induce Th1-type immunity against Gram-negative bacteria. Understanding the EV-mediated defense mechanisms will allow the development of future approaches to combat bacterial infections.
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Fu, Jie, Lenong Li, and Marlene Bouvier. "Modulation of MHC class I antigen presentation by the adenovirus E3-19K protein (100.8)." Journal of Immunology 186, no. 1_Supplement (April 1, 2011): 100.8. http://dx.doi.org/10.4049/jimmunol.186.supp.100.8.
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Abstract The presentation of viral antigens by MHC I to CTLs is vital for elimination of infected cells. In turn, viruses have evolved various strategies to abrogate antiviral cellular immune responses. For example, the adenovirus (Ad) E3-19K protein retains MHC I in the endoplasmic reticulum, dramatically suppressing the cell-surface presentation of viral antigens. Many aspects of how E3-19K exerts its function towards MHC I are poorly understood. This knowledge is important as the E3-19K/MHC I interaction is thought to play a role in enabling Ads to cause persistent infections. We characterized biophysically and cellularly interaction between E3-19K proteins of different Ad serotypes (Ad 7 and 35, subgroup B; Ad 2 and Ad 5, subgroup C; Ad 37, subgroup D; and Ad 4, subgroup E) and HLA-A, -B, and -C molecules. Our results show that E3-19K proteins from Ad serotypes of the same subgroup display more similar binding properties for a given MHC I than those of different subgroups. Furthermore, E3-19K proteins exhibited allele- and locus-specificity; higher avidity for HLA-A relative to -B molecules, and no interaction with HLA-C molecules. FACS analysis showed that binding affinities correlated (in a negative way) with levels of MHC I expression on infected cells. Finally, we propose the first model of interaction between E3-19K and MHC I. Overall, our studies provide novel insights into the structure/function relationship of E3-19K and the molecular cell biology of antigen presentation.
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Rao, Chinthalapally V., Altaf Mohammed, Adam S. Asch, and Naveena B. Janakiram. "Immunoprevention of Pancreatic Cancer." Current Medicinal Chemistry 25, no. 22 (July 4, 2018): 2576–84. http://dx.doi.org/10.2174/0929867324666170223153509.
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Background: Pancreatic cancer (PC) is considered an incurable disease due to late diagnosis, rapid spread and negligible response treatment methods, with a 5-year survival rate of only 7%. Hence, there is an urgency in developing novel strategies for PC prevention. This review is focused on discussing the challenges in understanding complex immune functions in tumor microenvironment and host-induced immune responses against tumors, selection of antigens for development of preventive vaccines, lessons from immunoprevention clinical trials and challenges in developing future vaccines. Methods: 65 original articles were referenced from various sources, based on immunoprevention or criteria pertaining to tumor antigens and immune responses in PC. All these articles were analyzed for the method details and results obtained, and the existing challenges were derived for successful development of clinical immunoprevention strategies. Results: The analysis of these articles and our experience with preclinical efficacy evaluations of various preventive approaches against PC helped in identifying specific tumor antigens as targets which can overcome tumor cell immune suppression. This review discussed the status of primary, secondary and tertiary preventive vaccines and reasons for failure of therapeutic vaccines. The key parameters for effective vaccination were identified, including stage of the disease for vaccination efficacy, use of appropriate animal models for development of preventive vaccines. Potential of chemopreventive agents as adjuvants in immunoprevention was discussed. This review identified new challenges for development of immunopreventive vaccines. Conclusion: This review analyzed various aspects of vaccine development for immunoprevention of PC and emphasized the challenges for development of immunoprevention strategies.
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PHAM, THO HOAN, KENJI SATOU, and TU BAO HO. "SUPPORT VECTOR MACHINES FOR PREDICTION AND ANALYSIS OF BETA AND GAMMA-TURNS IN PROTEINS." Journal of Bioinformatics and Computational Biology 03, no. 02 (April 2005): 343–58. http://dx.doi.org/10.1142/s0219720005001089.
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Tight turns have long been recognized as one of the three important features of proteins, together with α-helix and β-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are β-turns and most of the rest are γ-turns. Analysis and prediction of β-turns and γ-turns is very useful for design of new molecules such as drugs, pesticides, and antigens. In this paper we investigated two aspects of applying support vector machine (SVM), a promising machine learning method for bioinformatics, to prediction and analysis of β-turns and γ-turns. First, we developed two SVM-based methods, called BTSVM and GTSVM, which predict β-turns and γ-turns in a protein from its sequence. When compared with other methods, BTSVM has a superior performance and GTSVM is competitive. Second, we used SVMs with a linear kernel to estimate the support of amino acids for the formation of β-turns and γ-turns depending on their position in a protein. Our analysis results are more comprehensive and easier to use than the previous results in designing turns in proteins.
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Taylor, Diane E. "Helicobacter pyloriand Its Genome: Lessons from the Treasure Map." Canadian Journal of Gastroenterology 13, no. 3 (1999): 218–23. http://dx.doi.org/10.1155/1999/964025.
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The availability of the complete genome sequence ofHelicobacter pylori26695 has opened new avenues for research in the molecular biology of this gastric pathogen. The present review gives a general overview ofH pyloriobtained from the complete genome sequence and compares this with data previously obtained from cloning and functional studies ofH pylori. The cagA pathogenicity island of 40 kilobases, which encodes a type IV secretion system, is discussed. The diversity ofH pylorigenomes is well known, yet new data indicate that some aspects of the genome, particularly outer membrane protein genes, are conserved. Genes encoding proteins involved in molecular mimicry between bacterium and gastric epithelial tissue, specifically those encoding Lewis X and Lewis Y antigens, are discussed. The large number of DNA restriction and modification genes and their role inH pyloriinfection are considered. Finally, gene transfer is discussed. The availability of the complete genome sequence ofH pylori26695 and the soon to be available sequence of J99 will speed up and assist in the analysis ofH pylorigenes and their encoded proteins. The genomes of both strains will be useful as references with which otherH pylorigenomes can be compared.
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GOLDSMITH, MARK A., and ARTHUR WEISS. "Generation and Analysis of a T-Lymphocyte Somatic Mutant for Studying Molecular Aspects of Signal Transduction by the Antigen Receptor." Annals of the New York Academy of Sciences 546, no. 1 Molecular Bas (December 1988): 91–103. http://dx.doi.org/10.1111/j.1749-6632.1988.tb21623.x.
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Felix, Fabiana, Alexandre Baccaro, and Lúcio Angnes. "Disposable Voltammetric Immunosensors Integrated with Microfluidic Platforms for Biomedical, Agricultural and Food Analyses: A Review." Sensors 18, no. 12 (November 24, 2018): 4124. http://dx.doi.org/10.3390/s18124124.
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Disposable immunosensors are analytical devices used for the quantification of a broad variety of analytes in different areas such as clinical, environmental, agricultural and food quality management. They detect the analytes by means of the strong interactions between antibodies and antigens, which provide concentration-dependent signals. For the herein highlighted voltammetric immunosensors, the analytical measurements are due to changes in the electrical signals on the surface of the transducers. The possibility of using disposable and miniaturized immunoassays is a very interesting alternative for voltammetric analyses, mainly, when associated with screen-printing technologies (screen-printed electrodes, SPEs), and microfluidic platforms. The aim of this paper is to discuss a carefully selected literature about different examples of SPEs-based immunosensors associated with microfluidic technologies for diseases, food, agricultural and environmental analysis. Technological aspects of the development of the voltammetric immunoassays such as the signal amplification, construction of paper-based microfluidic platforms and the utilization of microfluidic devices for point-of-care testing will be presented as well.
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Nascimento, A. L. T. O., A. I. Ko, E. A. L. Martins, C. B. Monteiro-Vitorello, P. L. Ho, D. A. Haake, S. Verjovski-Almeida, et al. "Comparative Genomics of Two Leptospira interrogans Serovars Reveals Novel Insights into Physiology and Pathogenesis." Journal of Bacteriology 186, no. 7 (April 1, 2004): 2164–72. http://dx.doi.org/10.1128/jb.186.7.2164-2172.2004.
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ABSTRACT Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in accidental hosts, including humans. Complete genome sequencing of Leptospira interrogans serovar Copenhageni and comparative analysis with the available Leptospira interrogans serovar Lai genome reveal that despite overall genetic similarity there are significant structural differences, including a large chromosomal inversion and extensive variation in the number and distribution of insertion sequence elements. Genome sequence analysis elucidates many of the novel aspects of leptospiral physiology relating to energy metabolism, oxygen tolerance, two-component signal transduction systems, and mechanisms of pathogenesis. A broad array of transcriptional regulation proteins and two new families of afimbrial adhesins which contribute to host tissue colonization in the early steps of infection were identified. Differences in genes involved in the biosynthesis of lipopolysaccharide O side chains between the Copenhageni and Lai serovars were identified, offering an important starting point for the elucidation of the organism's complex polysaccharide surface antigens. Differences in adhesins and in lipopolysaccharide might be associated with the adaptation of serovars Copenhageni and Lai to different animal hosts. Hundreds of genes encoding surface-exposed lipoproteins and transmembrane outer membrane proteins were identified as candidates for development of vaccines for the prevention of leptospirosis.
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Schröder, Sarah K., Herdit M. Schüler, Kamilla V. Petersen, Cinzia Tesauro, Birgitta R. Knudsen, Finn S. Pedersen, Frederike Krus, et al. "Genetic and Molecular Characterization of the Immortalized Murine Hepatic Stellate Cell Line GRX." Cells 11, no. 9 (April 30, 2022): 1504. http://dx.doi.org/10.3390/cells11091504.
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The murine cell line GRX has been introduced as an experimental tool to study aspects of hepatic stellate cell biology. It was established from livers of C3H/HeN mice that were infected with cercariae of Schistosoma mansoni. Although these cells display a myofibroblast phenotype, they can accumulate intracellular lipids and acquire a fat-storing lipocyte phenotype when treated with retinol, insulin, and indomethacin. We have performed genetic characterization of GRX and established a multi-loci short tandem repeat (STR) signature for this cell line that includes 18 mouse STR markers. Karyotyping further revealed that this cell line has a complex genotype with various chromosomal aberrations. Transmission electron microscopy revealed that GRX cells produce large quantities of viral particles belonging to the gammaretroviral genus of the Retroviridae family as assessed by next generation mRNA sequencing and Western blot analysis. Rolling-circle-enhanced-enzyme-activity detection (REEAD) revealed the absence of retroviral integrase activity in cell culture supernatants, most likely as a result of tetherin-mediated trapping of viral particles at the cell surface. Furthermore, staining against schistosome gut-associated circulating anodic antigens and cercarial O- and GSL-glycans showed that the cell line lacks S. mansoni-specific glycostructures. Our findings will now help to fulfill the recommendations for cellular authentications required by many granting agencies and scientific journals when working with GRX cells. Moreover, the definition of a characteristic STR profile will increase the value of GRX cells in research and provides an important benchmark to identify intra-laboratory cell line heterogeneity, discriminate between different mouse cell lines, and to avoid misinterpretation of experimental findings by usage of misidentified or cross-contaminated cells.
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Church, Sarah, Christina Bailey, Sarah Warren, and Lisa Butterfield. "946 Standardized transcriptional profiling for optimizing cellular therapies: a multi-center PICI-NanoString collaboration." Journal for ImmunoTherapy of Cancer 9, Suppl 2 (November 2021): A995. http://dx.doi.org/10.1136/jitc-2021-sitc2021.946.
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BackgroundThe field of cellular therapy remains one of the most promising areas for the development of new cancer treatments. To further these improvements, it is imperative to broadly understand cell therapy products at the molecular level and to identify factors that contribute to their efficacy. NanoString and the Parker Institute for Cancer Immunotherapy (PICI) have established a ground-breaking collaboration to characterize up to 1,000 apheresis and cellular therapy infusion products with the primary goal to dissect and study molecular pathways that correlate with optimal cellular therapies.MethodsUsing a large and diverse sample cohort collected from eight PICI network Cell Therapy Centers the team will aim to study gene expression profiles (GEP) that correlate with optimal apheresis and downstream cellular products, identifying biomarkers and signatures for clinical response or toxicity and further explore unique cancer-specific and shared characteristics that make an optimal and effective chimeric antigen receptor (CAR) T cell. As shown here, this first of its kind study will include samples that target dozens of different antigens covering both primary and metastatic hematological and solid tumors. Samples will be characterized using the standardized set of genes included in the nCounter CAR-T Characterization Panel and will measure essential components of CAR-T including: metabolic fitness, phenotype, TCR diversity, toxicity, activation, persistence, exhaustion and cell typing along with individual transgene expression.ResultsPresented here are initial questions that will be asked as part of this study. Meta-analysis will be performed as an aggregated set of data and individual site-specific analysis. Data will further be analyzed across individual cancer types, target types, outcome and manufacturing conditions as examples. We anticipate this information will prove useful across many aspects of the development, manufacturing and clinical applications for cellular therapies and further hypothesize that these findings will promote the understanding of pathways affecting safety and efficacy that may help optimize the therapy.ConclusionsThe project is anticipated to begin Fall of 2021 with work continuing in phases through 2022 with periodic data reports to be shared through scientific conferences. All data and findings will be made publicly available to the scientific community through PICI’s Cancer Data and Evidence Library analysis platform (CANDEL).
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De Matos, Leandro Luongo, Damila Cristina Trufelli, Maria Graciela Luongo De Matos, and Maria Aparecida Da Silva Pinhal. "Immunohistochemistry as an Important Tool in Biomarkers Detection and Clinical Practice." Biomarker Insights 5 (January 2010): BMI.S2185. http://dx.doi.org/10.4137/bmi.s2185.
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The immunohistochemistry technique is used in the search for cell or tissue antigens that range from amino acids and proteins to infectious agents and specific cellular populations. The technique comprises two phases: (1) slides preparation and stages involved for the reaction; (2) interpretation and quantification of the obtained expression. Immunohistochemistry is an important tool for scientific research and also a complementary technique for the elucidation of differential diagnoses which are not determinable by conventional analysis with hematoxylin and eosin. In the last couple of decades there has been an exponential increase in publications on immunohistochemistry and immunocytochemistry techniques. This review covers the immunohistochemistry technique; its history, applications, importance, limitations, difficulties, problems and some aspects related to results interpretation and quantification. Future developments on the immunohistochemistry technique and its expression quantification should not be disseminated in two languages–-that of the pathologist and another of clinician or surgeon. The scientific, diagnostic and prognostic applications of this methodology must be explored in a bid to benefit of patient. In order to achieve this goal a collaboration and pooling of knowledge from both of these valuable medical areas is vital
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Pickard, Derek, Ana Luisa Toribio, Nicola K. Petty, Andries van Tonder, Lu Yu, David Goulding, Bart Barrell, et al. "A Conserved Acetyl Esterase Domain Targets Diverse Bacteriophages to the Vi Capsular Receptor of Salmonella enterica Serovar Typhi." Journal of Bacteriology 192, no. 21 (September 3, 2010): 5746–54. http://dx.doi.org/10.1128/jb.00659-10.
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ABSTRACT A number of bacteriophages have been identified that target the Vi capsular antigen of Salmonella enterica serovar Typhi. Here we show that these Vi phages represent a remarkably diverse set of phages belonging to three phage families, including Podoviridae and Myoviridae. Genome analysis facilitated the further classification of these phages and highlighted aspects of their independent evolution. Significantly, a conserved protein domain carrying an acetyl esterase was found to be associated with at least one tail fiber gene for all Vi phages, and the presence of this domain was confirmed in representative phage particles by mass spectrometric analysis. Thus, we provide a simple explanation and paradigm of how a diverse group of phages target a single key virulence antigen associated with this important human-restricted pathogen.
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Varma, Garima, Pratishtha Rawat, Manisha Jalan, Manjula Vinayak, and Madhulika Srivastava. "Influence of a CTCF-Dependent Insulator on Multiple Aspects of Enhancer-Mediated Chromatin Organization." Molecular and Cellular Biology 35, no. 20 (August 3, 2015): 3504–16. http://dx.doi.org/10.1128/mcb.00514-15.
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Developmental stage-specific enhancer-promoter-insulator interactions regulate the chromatin configuration necessary for transcription at various loci and additionally for VDJ recombination at antigen receptor loci that encode immunoglobulins and T-cell receptors. To investigate these regulatory interactions, we analyzed the epigenetic landscape of the murine T-cell receptor β (TCRβ) locus in the presence and absence of an ectopic CTCF-dependent enhancer-blocking insulator, H19-ICR, in genetically manipulated mice. Our analysis demonstrated the ability of the H19-ICR insulator to restrict several aspects of enhancer-based chromatin alterations that are observed during activation of the TCRβ locus for transcription and recombination. The H19-ICR insulator abrogated enhancer-promoter contact-dependent chromatin alterations and additionally prevented Eβ-mediated histone modifications that have been suggested to be independent of enhancer-promoter interaction. Observed enhancer-promoter-insulator interactions, in conjunction with the chromatin structure of the Eβ-regulated domain at the nucleosomal level, provide useful insights regarding the activity of the regulatory elements in addition to supporting the accessibility hypothesis of VDJ recombination. Analysis of H19-ICR in the heterologous context of the developmentally regulated TCRβ locus suggests that different mechanisms proposed for CTCF-dependent insulator action might be manifested simultaneously or selectively depending on the genomic context and the nature of enhancer activity being curtailed.
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Scharfstein, J., M. Schechter, M. Senna, J. M. Peralta, L. Mendonça-Previato, and M. A. Miles. "Trypanosoma cruzi: characterization and isolation of a 57/51,000 m.w. surface glycoprotein (GP57/51) expressed by epimastigotes and bloodstream trypomastigotes." Journal of Immunology 137, no. 4 (August 15, 1986): 1336–41. http://dx.doi.org/10.4049/jimmunol.137.4.1336.
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Abstract We have recently described the application of a purified glycoprotein of 25,000 Mr (GP25) of Trypanosoma cruzi in serodiagnosis of Chagas' disease. Purified GP25 lacks appreciable immunogenicity in some animal species, in spite of being generally antigenic to parasitized hosts. The underlying cause for these contrasting observations has not been determined, but it may relate to the drastic extraction conditions used in the original isolation procedure, and possible damage inflicted to the native form of this antigen. This report describes the molecular properties of a GP25-related primary antigen, and a fast performance liquid chromatographic (FPLC) procedure to attain its isolation under gentle conditions. The expression of GP25-related antigen by epimastigotes or bloodstream forms was investigated with a high-affinity monoclonal antibody to GP25, SC11G10, as well as with monospecific antisera to GP25. Immunochemical analysis of Nonidet P-40 lysates supplemented with protease inhibitors indicated that GP25 is not synthesized as such; instead, a 57,000 Mr component (GP57) was identified as the primary antigen product. Partial enzymatic conversion to GP25 was observed when inhibitors were deliberately omitted from cell extracts. Most significantly, GP57 was established as the primary biosynthetic product in [35S]-labeled bloodstream trypomastigotes after immunoprecipitation with SC11G10 antibody. This analysis when applied to metabolically labeled epimastigotes has consistently revealed a minor antigen component of 51,000 Mr (GP51), in addition to GP57. The former was identified as the antigenically related product exposed at the parasite cell surface after external radioiodination of viable trypanosomes. Access to the native form of this widely distributed surface glycoprotein should stimulate the investigation of functional and structural aspects of its immunologic activity.
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Fox, Barbara A., Alejandra Falla, Leah M. Rommereim, Tadakimi Tomita, Jason P. Gigley, Corinne Mercier, Marie-France Cesbron-Delauw, Louis M. Weiss, and David J. Bzik. "Type II Toxoplasma gondiiKU80Knockout Strains Enable Functional Analysis of Genes Required for Cyst Development and Latent Infection." Eukaryotic Cell 10, no. 9 (April 29, 2011): 1193–206. http://dx.doi.org/10.1128/ec.00297-10.
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ABSTRACTType IIToxoplasma gondiiKU80knockouts (Δku80) deficient in nonhomologous end joining were developed to delete the dominant pathway mediating random integration of targeting episomes. Gene targeting frequency in the type II Δku80Δhxgprtstrain measured at the orotate (OPRT) and the uracil (UPRT) phosphoribosyltransferase loci was highly efficient. To assess the potential of the type II Δku80Δhxgprtstrain to examine gene function affecting cyst biology and latent stages of infection, we targeted the deletion of four parasite antigen genes (GRA4,GRA6,ROP7, andtgd057) that encode characterized CD8+T cell epitopes that elicit corresponding antigen-specific CD8+T cell populations associated with control of infection. Cyst development in these type II mutant strains was not found to be strictly dependent on antigen-specific CD8+T cell host responses. In contrast, a significant biological role was revealed for the dense granule proteins GRA4 and GRA6 in cyst development since brain tissue cyst burdens were drastically reduced specifically in mutant strains withGRA4and/orGRA6deleted. Complementation of the Δgra4and Δgra6mutant strains using a functional allele of the deletedGRAcoding region placed under the control of the endogenousUPRTlocus was found to significantly restore brain cyst burdens. These results reveal that GRA proteins play a functional role in establishing cyst burdens and latent infection. Collectively, our results suggest that a type II Δku80Δhxgprtgenetic background enables a higher-throughput functional analysis of the parasite genome to reveal fundamental aspects of parasite biology controlling virulence, pathogenesis, and transmission.
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Zoure, Abdou Azaque, Henri Gautier Ouedraogo, Tani Sagna, T. Rebecca Compaore, Serge Théophile Soubeiga, Kadari Cisse, Dinanibé Kambire, et al. "Molecular diagnosis of COVID-19 in Burkina Faso: successful challenge." International Journal of Biological and Chemical Sciences 16, no. 1 (June 8, 2022): 440–63. http://dx.doi.org/10.4314/ijbcs.v16i1.37.
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COVID-19 has worsened the health situation in Burkina Faso. In fact, the country has known a peak of the second wave, which began in November, and ended around January 2021. Biological diagnosis has played a key role in the management of COVID-19. The aim of this review paper is to address the practical aspects that laboratories have faced in order to meet the challenge of SARS-CoV-2 diagnosis in Burkina Faso. According to international requirements, Burkina Faso has used real-time Reverse Transcription Polymerase Chain Reaction (rRT-PCR) as the “gold standard” for the diagnosis of COVID-19. From March 9, 2020 to July 31, 2021, in Burkina Faso, laboratories involved in COVID-19 diagnosis analyzed 226,189 samples by molecular tests and 2, 352 samples by rapid antigenic tests, whose peak was in January 2021 with 35,984 samples analyzed. The daily average rate of samples analysis was 456.02 tests. The majority of the individuals requesting COVID-19 tests were travelers (62.00%), followed by contact cases (18.42%), suspected cases (7.95%), voluntary screening (7.57%), and 4.06% of other applicants consisting of health care personnel and at-risk patients. In terms of prevention, vaccines are being administered to the general population. However, some efforts must be made to provide automated sample analysis equipment and complete sequencing of SARS-CoV-2 remains among the challenges.
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Zhang, Wei, Wenhua Xie, Jianqiang Wang, Xi Chen, Jianwen Fang, Yongsheng Chen, Jun Li, Libing Yu, Depu Chen, and Peng George Wang. "Recent Progress in Glycochemistry and Green Chemistry." Current Organic Chemistry 3, no. 3 (May 1999): 241–67. http://dx.doi.org/10.2174/1385272803666220202193253.
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Abstract: This two-part article will focus on the most recent research efforts from the Wang's group in areas of glycochemistry and green chemistry. In the first part, we wish to address the progress in synthesis, conformational analysis, and transformations of some biologically active a galactosyl oligosaccharides. Carbohydrate structures containing Gala1-3Galterminus (a-Gal epitopes) are xenoactive antigens and are considered to be the major cause for hyperacute rejection in xenotransplantation. The latest chemo-enzymatic synthesis of a-galactosyl epitopes using a recombinant a1,3-galactosyltransferase is described. Along with an efficient chemical synthesis of an a-Gal trisaccharide, these synthetic approaches provide an easy access to this important class of oligosaccharides. Conformational analysis of an a-Gal epitope using various NMR techniques and molecular modeling is discussed. These studies provide important information in structure-function relationship and binding conformation of a-Gal epitopes and their interaction with anti-Gal antibody. In another aspect, novel glycoconjugates containing receptor-specific ligands and a-Gal epitopes have been synthesized as potential immunotherapeutic agents.
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Iwamoto, Sadahiko. "Molecular aspects of Rh antigens." Legal Medicine 7, no. 4 (July 2005): 270–73. http://dx.doi.org/10.1016/j.legalmed.2004.12.002.
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Balla, Keir M., Geanncarlo Lugo-Villarino, Jan M. Spitsbergen, David L. Stachura, Yan Hu, Karina Bañuelos, Octavio Romo-Fewell, Raffi V. Aroian, and David Traver. "Eosinophils in the zebrafish: prospective isolation, characterization, and eosinophilia induction by helminth determinants." Blood 116, no. 19 (November 11, 2010): 3944–54. http://dx.doi.org/10.1182/blood-2010-03-267419.
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Abstract Eosinophils are granulocytic leukocytes implicated in numerous aspects of immunity and disease. The precise functions of eosinophils, however, remain enigmatic. Alternative models to study eosinophil biology may thus yield novel insights into their function. Eosinophilic cells have been observed in zebrafish but have not been thoroughly characterized. We used a gata2:eGFP transgenic animal to enable prospective isolation and characterization of zebrafish eosinophils, and demonstrate that all gata2hi cells in adult hematopoietic tissues are eosinophils. Although eosinophils are rare in most organs, they are readily isolated from whole kidney marrow and abundant within the peritoneal cavity. Molecular analyses demonstrate that zebrafish eosinophils express genes important for the activities of mammalian eosinophils. In addition, gata2hi cells degranulate in response to helminth extract. Chronic exposure to helminth- related allergens resulted in profound eosinophilia, demonstrating that eosinophil responses to allergens have been conserved over evolution. Importantly, infection of adult zebrafish with Pseudocapillaria tomentosa, a natural nematode pathogen of teleosts, caused marked increases in eosinophil number within the intestine. Together, these observations support a conserved role for eosinophils in the response to helminth antigens or infection and provide a new model to better understand how parasitic worms activate, co-opt, or evade the vertebrate immune response.
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Zippel, Claus, Sarah C. Ronski, Sabine Bohnet-Joschko, Frederik L. Giesel, and Klaus Kopka. "Current Status of PSMA-Radiotracers for Prostate Cancer: Data Analysis of Prospective Trials Listed on ClinicalTrials.gov." Pharmaceuticals 13, no. 1 (January 13, 2020): 12. http://dx.doi.org/10.3390/ph13010012.
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The recent development of dedicated prostate-specific membrane antigen (PSMA) targeted radioligands shows the potential to change and improve the diagnosis and therapy of prostate cancer. There is an increasing number of prospective trials to further establish these tracers in the clinical setting. We analyzed data from the ClinicalTrials.gov registry including all listed prospective trials with PSMA-ligands for prostate cancer as of October 2019 concerning the different tracers and study characteristics. We found n = 104 eligible studies with a total of n = 25 different tracers in use: most frequently [68Ga]Ga-PSMA-11 (32%), followed by [18F]DCFPyL (24%) and [177Lu]Lu-PSMA-617 (10%). 85% are single-center, 15% multi-center studies. 95% national and 5% international studies. 34% are phase-II, 24% phase-I, 13% phase-I/-II, 12% phase-II/-III and phase-III and 7% early-phase-I. The primary purpose was classified as diagnostic in 72% of cases and therapeutic in 23% of cases. Most studies were executed in the USA (70%), followed by Canada (13%) and France (6%). This quantitative descriptive registry analysis indicates the rapid and global clinical developments and current status of PSMA-radioligands with emphasis on radiopharmaceutical and organizational aspects. It will be very interesting to see which tracers will prevail in the clinical setting.
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Melarkode Vattekatte, Akhila, Nicolas Ken Shinada, Tarun J. Narwani, Floriane Noël, Olivier Bertrand, Jean-Philippe Meyniel, Alain Malpertuy, Jean-Christophe Gelly, Frédéric Cadet, and Alexandre G. de Brevern. "Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction." PeerJ 8 (March 6, 2020): e8408. http://dx.doi.org/10.7717/peerj.8408.
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Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of VHH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.
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Young, Matthew, and Michael Criscitiello. "Demonstrating the immune response of D. rerio using keyhole limpet hemocyanin (EDU1P.249)." Journal of Immunology 192, no. 1_Supplement (May 1, 2014): 49.3. http://dx.doi.org/10.4049/jimmunol.192.supp.49.3.
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Abstract In this project, immunization of a model aquatic organism is used in the classroom to facilitate understanding of molecular biology, evolution and the vertebrate adaptive immune system. Molecular immunoglobulin and T cell receptor cloning, sequencing and repertoire analysis techniques that I learned in the Criscitiello Comparative Immunogenetics Lab at Texas A&M this summer were applied to analysis of the lymphocyte antigen receptor repertoire in zebrafish. Students at A&M Consolidated High School performed experiments to quantify and qualify various aspects of the immune response of the model organism, D. rerio. Hemocytometry was used to measure leukocyte counts before and after immunization with keyhole limpet hemocyanin. Serum IgM was analyzed using ELISA. Repertoire analysis was performed using PCR and DNA sequencing. The data from these experiments was used in the classroom to discuss the evolution of vertebrate adaptive immunity, immunization techniques, and vaccination design. Furthermore, the repertoire sequence data contributed to an important phylogenetic perspective for ongoing NSF funded studies at A&M on the plasticity of B and T cell receptor immunogenetics. One goal is for high school students to earn co-authorship on journal publications from the Criscitiello lab. This was the first stage in an iterative system of teaching and research that will continue to include reciprocal pedagogical exchange and hands-on experience in comparative molecular immunology.
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Ahnaf, Ilman, Luisetto Mauro, Rafa Ahmed Yesvi, Musa Naeem, Abu Syed Md., Anan Sabit Ibtisam, and Haque Tazwan. "SARS-CoV-2 infection and phylogenetic analysis with the risk factors in human body alongside the pulmonary effects and medication." Insights in Biology and Medicine 4, no. 1 (November 6, 2020): 023–29. http://dx.doi.org/10.29328/journal.ibm.1001018.
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Related the extremely transmittable abilities of SARS-CoV-2,a harmonious virus to the bat CoV, gets transmitted by three principal processes-- the inhalation of droplets from the SARS-CoV-2 infected person, contacting to the person, and by the surfaces and materials defiled with the virus. Whereupon bat Coronavirus is mostly like the pandemic causing virus SARS-CoV-2, bats are often deliberated and figured out as a possible primary host although no intermediate has not been defined yet in the wherewithal of transmission. The Spike Glycoprotein plays an important role in the case of penetration with the assistance of the ACE2 receptor and the Receptor Binding Domain. In the human body, infiltrating the nucleic acid into host cells, SARS-CoV-2 attacks one cell and one by one into the whole human body; therefore, infected cases are found symptomatic and asymptomatic considering the immune power. Patients with cardiovascular disease or diabetes proceed with their treatment with ACE2 often; therefore, there might be a high chance of getting infected. Whereas the SARS-CoV-2 infects the blood and then lungs, Antigens improvement can be better in order to avoid high-complicated effects. Currently, no vaccination or no accurate cure and treatment has not been defined. An explanation with analysis on SARS-CoV-2 has been performed from the aspect of virology, immunology and molecular biology. Several relevant figures have been included hereby in order to a better understanding of the very concept.
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Stürzbecher, H. W., C. Addison, and J. R. Jenkins. "Characterization of mutant p53-hsp72/73 protein-protein complexes by transient expression in monkey COS cells." Molecular and Cellular Biology 8, no. 9 (September 1988): 3740–47. http://dx.doi.org/10.1128/mcb.8.9.3740-3747.1988.
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Several mutant, but not wild-type, p53 proteins form complexes with hsp72/73 heat shock-related proteins in simian virus 40-transformed monkey COS cells. We carried out a detailed biochemical and structural mapping analysis of p53 and report here that p53-hsp72/73 complex formation showed considerable structural specificity. Such complexes were remarkably stable, but unlike analogous complexes formed between p53 and simian virus 40 T antigen, they did not form in in vitro association assays. p53-hsp72/73 complex formation in vivo appears to be dependent on aspects of mutant p53 protein conformation. However, absence of the conformation-sensitive epitope recognized by monoclonal antibody PAb 246 was not reliably diagnostic of such complexes, nor was p53-hsp72173 binding reliably diagnostic of oncogenic activation.
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Wei, Eric X., Vasiliki Leventaki, John K. Choi, Susana C. Raimondi, Elizabeth M. Azzato, Sheila A. Shurtleff, Menchu G. Ong, Diana M. Veillon, James D. Cotelingam, and Rodney E. Shackelford. "γδ T-Cell Acute Lymphoblastic Leukemia/Lymphoma: Discussion of Two Pediatric Cases and Its Distinction from Other Mature γδ T-Cell Malignancies." Case Reports in Hematology 2017 (2017): 1–7. http://dx.doi.org/10.1155/2017/5873015.
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Gamma delta (γδ) T-cell antigen receptor (TCR) expression and its related T-cell differentiation are not commonly reported in T-cell acute lymphoblastic leukemia/lymphoma (T-ALL). Here we report two pediatric T-ALL cases and present their clinical features, histology, immunophenotypes, cytogenetics, and molecular diagnostic findings. The first patient is a two-year-old girl with leukocytosis, circulating lymphoblasts, and a cryptic insertion of a short-arm segment at 10p12 into the long-arm segment of 11q23 resulting in an MLL and AF10 fusion transcript, which may be the first reported in γδ T-ALL. She responded to the chemotherapy protocol poorly and had persistent diseases. Following an allogeneic bone marrow transplant, she went into remission. The second patient is an eleven-year-old boy with a normal white cell count, circulating blasts, and a normal karyotype, but without any immature cellular markers by flow cytometric analysis. He responded to the chemotherapy well and achieved a complete remission. These cases demonstrate the diverse phenotypic, cytogenetic, and molecular aspects of γδ T-ALL. Early T-precursor- (ETP-) ALL and their differential diagnosis from other mature γδ T-cell leukemia/lymphomas are also discussed.
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Kostareli, Efterpi, Tatjana Smilevska, Kostas Stamatopoulos, Anastasia Kouvatsi, and Achilles Anagnostopoulos. "Chronic lymphocytic leukaemia: An immunobiology approach." Srpski arhiv za celokupno lekarstvo 136, no. 5-6 (2008): 319–23. http://dx.doi.org/10.2298/sarh0806319k.
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B cell chronic lymphocytic leukaemia (CLL) is the most common adult leukaemia that follows an extremely variable clinical course. Several important prognostic parameters defining pathogenic and clinical subgroups of CLL have been identified and validated recently. The biological significance of immunoglobulin (Ig) heavy chain variable region gene (IgHV) mutational status and associated ZAP-70 over-expression, CD38 and chromosomal aberrations have enabled to identify patients at high risk for early disease progression and inferior survival. Moreover, studies of the B cell antigen receptor (BCR) structure and receptor signaling have been most helpful in revealing some new aspects of the biology of this disease. In particular, the analysis of IG genes has revealed that the expressed IgHV/IgKV/IgLV gene repertoires of CLL cells differ from those of normal B cells. A further unique feature of the CLL IG repertoire is the existence of subsets of cases with "stereotyped" BCRs. Accumulating molecular and phenotypic data support the notion that CLL development and evolution is not a simple scholastic event and strongly indicates a role for antigen in driving the cell of origin for at least some subsets of CLL cases.
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Havranek, Ondrej, Jingda Xu, Stefan Koehrer, Zhiqiang Wang, Justin M. Comer, Lisa Becker, Allen F. Yi, et al. "Molecular Aspects of Tonic B-Cell Receptor Signaling in Diffuse Large B-Cell Lymphoma Provide Biomarkers and Targets for Specific Inhibition." Blood 128, no. 22 (December 2, 2016): 779. http://dx.doi.org/10.1182/blood.v128.22.779.779.
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Abstract Introduction. Targeting antigen-driven B-cell receptor (BCR) signaling with the BTK inhibitor ibrutinib is clinically effective against most B-cell lymphomas, including activated B-cell diffuse large B-cell lymphoma (ABC-DLBCL), but not germinal center B-cell (GCB) DLBCL. We have formally confirmed that GCB-DLBCL cell lines utilize tonic BCR signaling, by showing: 1) sensitivity (variable) to knockout (KO) of the BCR, SYK, and CD19; 2) dependence on CD79A ITAM phosphorylation; and 3) independence from BCR antigen specificity. However, uncertainty remains about molecular events in upstream parts of tonic BCR signaling, why dependence of GCB-DLBCL cells on tonic BCR signaling is variable, and their clinical relevance. Methods. We used CRISPR/Cas9 methods to modify selected genes by KO and/or knock-in (KI) of the cDNA of a fluorescent protein (FP; e.g., GFP), with the FP serving as a marker of cells with gene KO or modification, or as a gene-fused tag for localization or quantitation. Cells expressing a membrane-targeted Forster resonance energy transfer (FRET) based AKT activity reporter (Lyn-AktAR2) were used to measure AKT activity directly by flow cytometry (FCM). Results. The effect of KI of CD79A Y188F mutation alone was similar to complete BCR KO, implying that CD79A Y188 phosphorylation is essential for tonic BCR signal transduction. Western blot analysis of GCB-DLBCL cell lines after BCR KO showed variable decreases of AKT S473 phosphorylation (frequently used as surrogate measure of AKT activity), but these did not correlate well with the variable decreases in proliferation of GCB-DLBCL cell lines caused by BCR KO. Measuring AKT activity directly (Fig. 1), or by another indirect approach (surface expression of CXCR4, a target gene of FOXO1 inhibited by AKT activity), showed high correlation between decreases in AKT activity and proliferation after BCR KO. In contrast to the variable effect of BCR KO on growth, pan-AKT KO was uniformly growth-slowing in GCB-DLBCL lines (Fig. 2). Interestingly, baseline surface density of BCR units in GCB lines, quantified by FCM using CD79A-GFP KI cells or anti-CD79B staining, correlated highly with reduction in growth or AKT activity caused by BCR KO (Fig. 3). These findings lead us to conclude that the BCR contributes to AKT activation in GCB-DLBCL cell lines, to a variable degree determined by BCR surface density. We also conclude that BCR surface density is determined by cell line-specific factors, as well as immunoglobulin heavy (IgH) and light (IgL) hypervariable region (HVR) sequences, based on measurements of BCR surface levels after exchanging endogenous HVR sequences in OCI-Ly19 and OCI-Ly7 cell lines for HVRs derived from other GCB and ABC-DLBCL cell lines. Reduction of AKT activity after BCR KO (measured by FRET reporter) and baseline BCR surface density in GCB-DLBCL cell lines also correlated well with the sensitivity of GCB-DLBCL lines to the clinically-tested SYK inhibitor (P505-15, PRT062607) or FDA-approved PI3K p110d isoform specific inhibitor (idelalisib). Interestingly, isogenic GCB-DLBCL cell lines with KO of PTEN, a negative regulator of AKT activation, were substantially more resistant to both inhibitors. A crucial role of PTEN deletion in overcoming dependence on tonic BCR signaling in GCB-DLBCL is supported by evidence from two naturally PTEN-deficient cell lines: SUDHL10, which adjusts to BCR KO and resumes normal growth, and HT, which lacks BCR expression, due to a frameshifting deletion in its IgH HVR. Re-expression of the BCR in HT, by KI to correct the IgH sequence, does not affect HT cell line growth. Conclusion. Our findings suggest a biomarker-guided therapeutic strategy in GCB-DLBCL: targeting tonic BCR signaling in BCR-high patients, by inhibiting CD79A phosphorylation, SYK, or PI3K, and downstream targeting of AKT in BCR-low and/or PTEN-deficient patients. Figure 1. Correlation of relative proliferation after BCR KO with decrease of AKT activity (as measured by FRET efficiency of AKT activity reporter) in GCB-DLBCL cell lines. Figure 1. Correlation of relative proliferation after BCR KO with decrease of AKT activity (as measured by FRET efficiency of AKT activity reporter) in GCB-DLBCL cell lines. Figure 2. Effect of BCR KO or pan-AKT KO in GCB-DLBCL cell lines. Figure 2. Effect of BCR KO or pan-AKT KO in GCB-DLBCL cell lines. Figure 3. Correlation of relative proliferation after BCR KO with baseline BCR surface density (as measured by flow cytometry of cells with CD79A-GFP fusion) in GCB-DLBCL cell lines. Figure 3. Correlation of relative proliferation after BCR KO with baseline BCR surface density (as measured by flow cytometry of cells with CD79A-GFP fusion) in GCB-DLBCL cell lines. Disclosures Burger: Pharmacyclics: Research Funding. Westin:Chugai: Membership on an entity's Board of Directors or advisory committees; Spectrum: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; ProNAi: Membership on an entity's Board of Directors or advisory committees.
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Dabelsteen, E. "Molecular Biological Aspects of Acquired Bullous Diseases." Critical Reviews in Oral Biology & Medicine 9, no. 2 (April 1998): 162–78. http://dx.doi.org/10.1177/10454411980090020201.
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Bullous diseases of the oral mucosa and skin were originally classified on the basis of clinical and histological criteria. The discovery of autoantibodies in some of these patients and the introduction of molecular biology have resulted in a new understanding of the pathological mechanisms of many of the bullous lesions. In this article, updated topics of the immune-mediated bullous lesions which involve oral mucosa and skin are reviewed. Pemphigus antigens, which are desmosomal-associated proteins and belong to the cadherin superfamily of cell adhesion proteins, have been isolated, and their genes have been cloned. The antigens which react with autoantibodies from patients with bullous pemphigoid, cicatricial pemphigoid, acquired epidermolysis bullosa, and linear IgA disease are all proteins of the hemidesmosome basement membrane complex. Interestingly, most of the antigens also appear to be the target for mutations seen in patients with the inherited type of epidermolysis bullosa in which bullous lesions are a prominent clinical feature.
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Hendrickson, Jeanne E., Nicole H. Smith, Kathryn R. Girard-Pierce, Christopher A. Tormey, Kate L. Henry, James C. Zimring, and Sean R. Stowell. "Development of a Murine Model of Weak Kel: Similarities to Weak Rh(D)." Blood 120, no. 21 (November 16, 2012): 842. http://dx.doi.org/10.1182/blood.v120.21.842.842.
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Abstract Abstract 842 Introduction: Aspects of RBC antigens that define their immunogenicity are not fully understood. Multiple studies in humans have demonstrated Rh(D) to be the most immunogenic RBC antigen, yet the same antigen present in lower copy number (weak Rh(D)) is, with rare exception, considered non-immunogenic. A better understanding of factors influencing RBC alloimmunogenicity would be helpful in predicting antibody responses in transfusion and pregnancy situations alike, as well as in managing donor RBC inventory. Herein, we describe the generation of transgenic mice with different levels of RBC specific expression of the clinically significant human KEL2 antigen, and test the hypothesis that antigen density impacts recipient immune response post-transfusion. Materials and Methods: Mice with RBC specific expression of KEL2 were generated utilizing constructs containing the human KEL2 sequence expressed behind a B-globin promoter, using a random integration approach. TER119+, CD45+, and CD41+ cells were evaluated by flow cytometry for KEL expression using monoclonal anti-Jsa and anti-Kpb, and RBC antigen density was estimated utilizing QIFIKIT beads. MuMT recipients were transfused with RBCs labeled with a lipophilic dye, and post-transfusion RBC recovery and antigen expression were evaluated by flow cytometry. To determine the immunogenicity of KEL2 or weak KEL2 RBCs, RBCs were transfused into C57BL/6 recipients every 2–3 weeks in the presence or absence of poly (I:C) pre-treatment. Recipient serum was analyzed by flow cytometric crossmatch with KEL2 or C57BL/6 RBC targets, using IgM or IgG secondary antibodies. To determine the effect of recipient RBC expression of weak KEL2 on the immunogenicity of KEL2 RBCs, weak KEL2 animals were transfused with KEL2 RBCs, the clearance of lipophilic labeled RBCs was tracked, and anti-KEL was evaluated on the transfused RBCs and also in the serum. Results: KEL2 RBCs have approximately 1200 antigenic sites per cell, whereas weak KEL2 RBCs have fewer than 200 sites; flow cytometric studies of TER 119+, CD45+, and CD41+ cells suggest both strains have RBC specific KEL expression. Transfusion of KEL2 or weak KEL2 RBCs into muMT animals resulted in stable post-transfusion RBC recovery and antigen expression. In 3/3 experiments (n=30 animals), all C57BL/6 recipients of KEL2 RBCs generated detectable anti-KEL IgM and IgG, which boosted with subsequent transfusions and which was enhanced in the presence of recipient inflammation with poly (I:C). However, in 2/2 experiments (n=20 animals), weak KEL RBCs led to no detectable antibody (IgM or IgG) in C57BL/6 recipients following 3 transfusions, even in the presence of recipient pre-treatment with poly (I:C). Furthermore, weak KEL2 recipients of KEL2 RBCs generated no detectable IgG and demonstrated no clearance of KEL2 RBCs, though low levels of anti-KEL IgM were detectable on the transfused RBCs and in the serum from approximately 5–12 days post-transfusion. Discussion: As hypothesized, antigen density significantly impacts the immunogenicity of KEL RBCs in this reductionist murine alloimmunization model. C57BL/6 recipients, like Rh(D) negative recipients, lack the human antigen in question (KEL2 in this case), and recipient antibody responses to weak KEL2 are, like most recipient responses to weak Rh(D), undetectable. Strengths of the KEL2 and weak KEL2 system include the fact that these animals are, to the best of our knowledge, genetically identical except for RBC KEL antigen copy number. Thus, this system allows for detailed analyses of the immune response to KEL RBCs with different antigen densities, on both the donor and recipient side of the equation, without confounding factors encountered in human studies (such as HLA presentation issues or considerations of the molecular basis of a particular type of weak Rh(D)). A better understanding of primary, secondary, and other immune responses in the KEL2 and weak KEL2 system may lay the groundwork for strategies to induce non-responsiveness to RBCs in humans, not only in the setting of transfusion medicine but also potentially in the setting of hemolytic disease of the fetus and newborn. Furthermore, translation of these and future findings in the KEL and weak KEL systems to Rh(D), weak Rh(D), and other human antigen systems may ultimately allow for creative solutions in blood inventory management. Disclosures: No relevant conflicts of interest to declare.
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Barreto, Leidy Viviana, George Emílio Barreto, Ludis Morales, Orlando Emilio Acevedo, and Janneth González Santos. "Proteína LIC10494 de Leptospira interrogans serovar Copenhageni: modelo estructural y regiones funcionales asociadas." Universitas Scientiarum 17, no. 1 (January 1, 2012): 16. http://dx.doi.org/10.11144/javeriana.sc17-1.plol.
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<p><strong>Objective</strong>. Predict by computational means the 3D structure of the antigenic protein LIC10494 and report associated important functional regions for its pathogenicity and immunogenicity. <strong>Materials and methods</strong>. We performed a computational analysis of the primary structure of LIC10494 using the servers BLAST, PROTPARAM, PROTSCALE, DAS, SOSUI, TOPPRED, TMAP, TMpred, SPLIT4, PHDHTM, TMHMM2, HMMTOP2, GLOBPLOT and PROSITE. The secondary structure was obtained by consensus of the algorithms SOPM, PREDATOR GOR4, DPM and DSC. The approach to the tertiary structure was obtained using the algorithm MUSTER. The energy minimization was done using the AMBER94 force field of the Schrodinger suite of molecular analysis, and the stereochemistry and energy model validation was performed by the RAMPAGE server. The final model was visualized using PyMol V.0,98. <strong>Results</strong>. This study proposes a computational model that describes the 3D structure of the hypothetical lipoprotein LIC10494 and agrees with previous experimental reports; thus, our study demonstrates the existence of patterns that could play an important role in the pathogenicity and protection of the bacteria against the host immune system; the presence of a disorganized region between amino acids 80 and 140, and of a transmembrane segment between amino acids 8 and 22. <strong>Conclusion</strong>. The coincidence between structural and functional segments suggests that our model can be used to predict certain aspects of the biological behaviour of the protein according to the pathogenic and immunogenic characteristics of the bacteria.</p><p><br /><strong>Key word</strong>s: Antigen, Bacteria Leptospirosis, LIC10494, Outer membrane protein.</p><p> </p>
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Ballard, Jimmy D., R. John Collier, and Michael N. Starnbach. "Anthrax Toxin as a Molecular Tool for Stimulation of Cytotoxic T Lymphocytes: Disulfide-Linked Epitopes, Multiple Injections, and Role of CD4+ Cells." Infection and Immunity 66, no. 10 (October 1, 1998): 4696–99. http://dx.doi.org/10.1128/iai.66.10.4696-4699.1998.
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ABSTRACT We have previously demonstrated that anthrax toxin-derived proteins, protective antigen (PA) and the amino-terminal portion of lethal factor (LFn), can be used in combination to deliver heterologous molecules to the cytosol of mammalian cells. In this study we examined the ability of an LFn-peptide disulfide-linked heterodimer to prime cytotoxic T lymphocytes (CTL) in the presence of PA. A mutant of LFn that contains a carboxy-terminal reactive cysteine was generated. This form of LFn could be oxidized with a synthetic cysteine containing peptide to form a heterodimer of the protein and peptide. Mice injected with the heterodimer plus PA mounted a peptide-specific CTL response, indicating that this molecule functioned similarly to the genetically fused forms used previously. We also report the results of an analysis of two aspects of this system important for the development of experimental vaccines. First, CD4 knockout mice were unable to generate a CTL response when treated with PA plus an LFn-epitope fusion protein, suggesting that CD4+ helper responses are essential for stimulating specific CTL with the PA-LFn system. Second, we now show that primary injection with this system does not generate any detectable antibody response to the vaccine components and that prior immunization has no effect on priming a CTL response to an unrelated epitope upon subsequent injection.
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Oltz, E. M., F. W. Alt, W. C. Lin, J. Chen, G. Taccioli, S. Desiderio, and G. Rathbun. "A V(D)J recombinase-inducible B-cell line: role of transcriptional enhancer elements in directing V(D)J recombination." Molecular and Cellular Biology 13, no. 10 (October 1993): 6223–30. http://dx.doi.org/10.1128/mcb.13.10.6223-6230.1993.
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Rapid analysis of mechanisms that regulate V(D)J recombination has been hampered by the lack of appropriate cell systems that reproduce aspects of normal prelymphocyte physiology in which the recombinase is activated, accessible antigen receptor loci are rearranged, and rearrangement status is fixed by termination of recombinase expression. To generate such a system, we introduced heat shock-inducible V(D)J recombination-activating genes (RAG) 1 and 2 into a recombinationally inert B-cell line. Heat shock treatment of these cells rapidly induced high levels of RAG transcripts and RAG proteins that were accompanied by a parallel induction of V(D)J recombinase activity, strongly suggesting that RAG proteins have a primary role in V(D)J recombination. Within hours after induction, these cells began to rearrange chromosomally integrated V(D)J recombination substrates but only if the substrates contained an active transcriptional enhancer; substrates lacking an enhancer were not efficiently rearranged. Activities necessary to target integrated substrates for rearrangement were provided by two separate lymphoid-specific transcriptional enhancers, as well as an active nonlymphoid enhancer, unequivocally demonstrating that such elements enhance both transcription and V(D)J recombinational accessibility.
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Horvat-Switzer, Regina D., and Alexis A. Thompson. "Stromal Contact Inhibits Effects of Phorbol Esters but Does Not Inhibit Staurosporine Induced Megakaryocytic Differentiation in K562 Cells." Blood 106, no. 11 (November 16, 2005): 4315. http://dx.doi.org/10.1182/blood.v106.11.4315.4315.
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Abstract Development of human megakaryocytes is modulated at least in part by direct contact with stromal cells, however, the mechanisms that control this process have not been fully elucidated. Stromal contact is not needed for lineage commitment and direct contact of human progenitor cells with marrow stroma negatively influences megakaryocytic development. The K562 human erythroleukemia cell line has been extensively used as a model to study molecular aspects of megakaryocytic differentiation. Treatment of K562 with either phorbol-12 myristate-13 acetate (PMA), a PKC activator, or staurosporine (STSP) a PKC inhibitor, induces K562 cells to undergo differentiation to a megakaryocytic phenotype. Treated cells undergo growth arrest, changes in cellular morphology as well as increased expression of megakaryocytic/platelet-specific antigens, such as CD61. We have demonstrated that PMA-induced differentiation of K562 cells is inhibited by co-culture on the bone marrow stromal cell line, OP9. These cells remained small, continued to proliferate, and had less than 10% CD61 surface expression, similar to untreated K562. In contrast, K562 cells co-cultured on OP9 cells and treated with STSP retained the ability to differentiate. They were significantly larger than unstimulated K562 cells, exhibited megakaryocytic morphology, and had increased CD61 surface expression from 3.5±2.4% at baseline to 81±2.4%. These data suggest that while STSP and PMA recapitulate certain aspects of megakaryocytic differentiation, divergent signaling pathways may regulate the effects of stromal inhibition. Since stromal inhibition of differentiation plays an important role in the maintenance of hematopoietic progenitors in normal marrow, we investigated the molecular mechanisms involved in STSP induced differentiation. PMA induced megakaryocytic differentiation is dependent on sustained activation of ERK/MAPK, and stromal inhibition is associated with a loss of sustained Rap1 activation. The mechanism of action for STSP induced megakaryocytic differentiation has not been studied. Therefore we sought to investigate the ERK/MAPK signaling pathway during STSP induced differentiation. Using western blot analysis we found the small G protein c-RAF was phosphorylated at Ser338 when K562 cells were treated with either PMA or STSP, suggesting both agents activate c-RAF. In turn both led to a dramatic increase in ERK and p90RSK phosphorylation. We next examined the ERK signaling cascade during stromal inhibition. K562 cells co-cultured on OP9 cells and treated with PMA showed only a slight increase in c-RAF phosphorylation and no significant ERK or p90RSK phosphorylation, consistent with previous stromal inhibition data. However, STSP treatment of K562 co-cultured cells led to the robust phosphorylation of c-RAF and ERK. P90RSK was not significantly phosphorylated. Taken together these data suggest STSP treatment leads to activation of the ERK/MAPK pathway and that this activation may be Rap1 independent. Understanding the mechanisms involved in stromal inhibition and the divergent signaling pathways involved in megakaryocytic differentiation may bring to light novel functions of marrow stroma during normal and leukemic cell expansion.
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Morozov, Giora, Huaying Zhao, Michael Mage, Lisa Boyd, Peter Schuck, Kannan Natarajan, and David Margulies. "Tapasin-related protein TAPBPR interacts directly with peptide-free MHC-I/β2-microgolbulin complexes (APP3P.101)." Journal of Immunology 192, no. 1_Supplement (May 1, 2014): 111.2. http://dx.doi.org/10.4049/jimmunol.192.supp.111.2.
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Abstract The molecular mechanism by which MHC-I molecules are loaded with peptides is crucial to fundamental aspects of antigen presentation relating to self-tolerance and CD8 T cell activation. To gain insight into the mechanism of MHC-I peptide loading we have studied human TAPBPR (TAP binding protein-related) protein, which is 22% identical to tapasin in amino acid sequence, widely expressed and IFN-γ inducible, but is not part of the peptide-loading complex (PLC). To understand the interaction of TAPBPR with MHC-I, we produced recombinant soluble TAPBPR and evaluated its interactions with MHC-I/β2m complexes in vitro. Using recombinant MHC-I molecules refolded with photolabile peptides, we show, by gel-shift analysis, size exclusion chromatography, and analytical ultracentrifugation that TAPBPR binds MHC-I/β2m after photolysis of the bound peptide, in a 1:1 molar ratio. MHC-I molecules loaded with low-affinity peptides also bind TAPBPR. The TAPBPR/MHC interaction is reversed by exposure to high-affinity peptides known to bind the MHC-I molecule, indicating a role of TAPBPR in stabilizing a peptide-receptive form of the MHC-I/β2m complex. Because of the predicted structural similarity of TAPBPR to tapasin, this system not only provides insight into the molecular details of TAPBPR/MHC-I binding, but may also elucidate tapasin interactions in the PLC that have previously eluded experimental interrogation.
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Stover, D. G., A. M. Cushman-Vokoun, C. L. Vnencak-Jones, and J. Berlin. "Analysis of BRAF and KRAS mutations in colorectal cancer and rectal carcinogenesis via fluorescent allele-specific PCR." Journal of Clinical Oncology 29, no. 4_suppl (February 1, 2011): 436. http://dx.doi.org/10.1200/jco.2011.29.4_suppl.436.
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436 Background: Molecular analysis has become increasingly relevant in the evaluation of colorectal carcinomas. Mutations in Ras-MAPK pathway proteins KRAS (present in 30-40% of colorectal cancer) and BRAF (10-14% of colorectal cancer) or mismatch repair (MMR) enzymes can impact response to therapy and/or can assist in defining hereditary predisposition. High frequency microsatellite instability (MSI) in colorectal cancer is associated with improved outcomes. Targeted therapies against BRAF and other components of the Ras-MAPK signaling pathway are becoming important aspects of treatment in colorectal and other cancers. Methods: A retrospective study was performed on 111 paraffin-embedded tumor specimens submitted between 1/07 and 3/09 for MSI testing based on family history and/or histologic features. DNA samples were screened for the BRAF V600E mutation and 7 KRAS mutations in codons 12 and 13 using fluorescent allele specific PCR with capillary electrophoresis. Clinical data was collected via chart review. Results: 58 males and 53 females were studied. The incidence of KRAS and BRAF mutations among the 111 samples was 49.5% and 6.3%, respectively. KRAS G12D and G12V were the most common mutations, representing 57% of total KRAS mutations. Dually positive KRAS and MSI tumors exclusively demonstrated G12D and G13D mutations. KRAS and BRAF mutations were mutually exclusive. Rectal cancers did not show evidence of BRAF V600E mutation (p=0.04). KRAS, BRAF, and MSI status did not correlate with survival, however pre-operative and post-operative carcinoembryonic antigen (CEA) levels were significantly associated with survival both in univariate and multivariate analyses. Conclusions: We demonstrate that BRAF V600E mutation is significantly associated with colon cancer and not rectal cancer, suggesting that BRAF mutations are not relevant in rectal carcinogenesis. Correlation between specific KRAS mutation and outcome may require larger populations. No significant financial relationships to disclose.
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Slavkovic, Bojana, Marija Guc-Scekic, Gordana Bunjevacki, S. Djuricic, Aleksandra Krstic, D. Micic, Dragana Vujic, M. Kuzmanovic, and Nada Rasovic-Gvozdenovic. "Acute leukemia of childhood: A single institution's experience." Archives of Biological Sciences 57, no. 1 (2005): 11–17. http://dx.doi.org/10.2298/abs0501011s.
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The aim of this study was to investigate distribution of immunophenotypic and cytogenetic features of childhood acute leukemia (AL) in the cohort of 239 newly diagnosed patients registered at the leading pediatric oncohematology center in the country during a six-year period (1996-2002). With approximately 60-70% of all childhood AL cases in Serbia and Montenegro being diagnosed and treated in this institution the used data represent a valid research sample to draw conclusions for entire country. On the basis of five phenotypic markers, the distribution of immunological subtypes was as follows: 169 (70.7%) expressed B-cell marker CD19 (137 were CD10 positive and 32 CD10 negative), 37 (15.5%) belonged to T-lineage acute lymphoblastic leukemia (T-ALL) (cyCD3 positive), and 33 (13.8%) were acute myeloblastic leukemia (AML) (CD13 positive and/or CD33 positive in the absence of lymphoid-associated antigens). The ratio of males and females was 1.5:1. Most of the cases were between the ages of 2 and 4, and were predominantly B-lineage acute lymphoblastic leukemia (B-ALL) cases. Another peak of age distribution was observed at the age of 7. The frequency of T-ALL (18% of ALL) was similar to that reported for Mediterranean countries: France (19.4%), Greece (28.1%), Southern Italy (28.3%), and Bulgaria (28.0%). Cytogenetic analyses were performed in 193 patients: 164 ALL and 29 AML. Normal karyotype was found in 57% of ALL and in 55% of AML patients, while cytogenetic abnormalities including structural, numerical, and complex chromosomal rearrangements were found in 43% of ALL and in 45% of AML patients. Our results represent a contribution to epidemiological aspects of childhood leukemia studies.
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Inman, R. D. "Immunogenetic aspects of host immune response." Canadian Journal of Microbiology 34, no. 3 (March 1, 1988): 319–22. http://dx.doi.org/10.1139/m88-058.
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The central role of histocompatibility leukocyte antigens (HLA) class II molecules in antigen presentation has received great attention in recent years, yet class I molecules have been defined as primarily functioning as a restriction element for cytotoxic T cell killing of virus-infected cells. Extensive clinical evidence, however, indicates that the HLA class I genes are strongly associated with nonseptic complications of enteric and genitourinary bacterial infections. Ninety percent of patients with Reiter's syndrome and reactive arthritis are positive for HLA-B27, yet the mechanism of disease susceptibility conferred by this gene remains obscure. Hypotheses concerning this interaction include (i) class I antigens functioning as receptors for microbial antigens; (ii) class I antigens expressing determinants that cross-react with microbial antigens; and (iii) class I genes controlling immunoregulatory functions that dictate qualitative differences in immune response to pathogenic organisms. These hypotheses await formal testing and hold great promise for understanding immunogenetic control of immune responses in general.
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Greslehner, Gregor P. "The vaccinologist’s “dirty little secret”: a better understanding of structure-function relationships of viral immunogens might advance rational HIV vaccine design." Archives of Virology 166, no. 5 (February 19, 2021): 1297–303. http://dx.doi.org/10.1007/s00705-021-04982-7.
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AbstractI will offer a conceptual analysis of different notions of structure and function of viral immunogens and of different structure-function relationships. My focus will then be on the mechanisms by which the desired immune response is induced and why strategies based on three-dimensional molecular antigen structures and their rational design are limited in their ability to induce the desired immunogenicity. I will look at the mechanisms of action of adjuvants (thus the wordplay with Janeway’s “immunologist’s dirty little secret”). Strategies involving adjuvants and other (more successful) vaccination strategies rely on taking into account activities and functions (“what is going on”), and not just the structures involved (“who is there”), in binding in a “lock and key” fashion. Functional patterns as well as other organizational and temporal patterns, I will argue, are crucial for inducing the desired immune response and immunogenicity. The 3D structural approach by itself has its benefits – and its limits, which I want to highlight by this philosophical analysis, pointing out the importance of structure-function relationships. Different functional aspects such as antigenicity, immunogenicity, and immunity need to be kept separate and cannot be reduced to three-dimensional structures of vaccines. Taking into account different notions of structure and function and their relationships might thus advance our understanding of the immune system and rational HIV vaccine design, to which end philosophy can provide useful tools.
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Pershing, Nicole L., Aurélie Kapusta, Shannon Nielsen, Hillary Crandall, E. Kent Korgenski, Carrie L. Byington, Krow Ampofo, and Anne J. Blaschke. "#64: An odyssey Beyond the Capsule: Genetic Determinants of Pediatric Invasive Streptococcus pneumoniae Empyema." Journal of the Pediatric Infectious Diseases Society 10, Supplement_1 (March 1, 2021): S7. http://dx.doi.org/10.1093/jpids/piaa170.021.
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Abstract Background Streptococcus pneumoniae is among the most common causes of invasive bacterial infections in children, including pneumonia, bacteremia, and meningitis. Over 90 different serotypes (ST) of pneumococcus exist, with enrichment of some ST within specific invasive phenotypes. Other than capsular genes, molecular determinants of particular invasive phenotypes remain largely unknown. Although vaccination targeting especially invasive ST capsular antigens has successfully decreased the incidence of invasive pneumococcal disease (IPD), new ST have emerged, suggesting methods to target other aspects of pneumococcal invasiveness are needed. Methods Pneumococcal isolates from IPD were collected from children presenting to Primary Children’s Hospital from 1996–2018. All viable isolates underwent next-generation sequencing (Illumina), quality control filtering for contamination and low coverage, de novo genome assembly with SPADES, and annotation with PROKKA. Clinical phenotypes were manually validated with physician chart review. Isolates were serotyped via Quelling and in silico using SeroBA. ROARY was used for pan-genome assembly, and SCOARY for microbial genome-wide association studies. RAxML was used for phylogenetic analysis. Results A total of 354 viable pneumococcal isolates were available for genomic analysis including a spectrum of invasive phenotypes: pneumonia (n = 138, of which 54 were complicated by empyema), CNS infection (n = 50), SSTI/bone infections (n = 42), and isolated bacteremia (n = 68). Thirteen samples were censored for poor coverage or genetic contamination. Invasive isolates spanned 37 capsular ST. The pneumococcal pan-genome comprised 6462 genes, of which only 23% were shared by at least 99% of samples. Phylogenetic relatedness resulted in clustering of some ST (e.g., ST1, ST3), whereas others (eg ST19A) were more broadly distributed. Empyema and meningitis phenotypes were distributed across the phylogenetic tree, but enriched in distinct clusters that crossed ST clusters. Genes involved in empyemagenic pneumococcal capsule production, and those implicated in sensing of preferred sugars or non-preferred sugar metabolism were statistically correlated with the empyema phenotype. Conclusion There is marked genetic diversity among invasive pneumococcal isolates, potentially contributing to the variability of disease phenotypes observed. Clustering of invasive phenotypes across ST suggests a genetic signature for invasive phenotypes other than capsule genes alone, further supported by enrichment of specific genes associated with alternative sugar metabolism in empyema isolates. Critical determinants of invasive phenotypes will inform future efforts at disease prevention and treatment.
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Tanji, Takahiro, Kenji Nishikori, Hirohisa Shiraishi, Masatomo Maeda, and Ayako Ohashi-Kobayashi. "Co-operative function and mutual stabilization of the half ATP-binding cassette transporters HAF-4 and HAF-9 in Caenorhabditis elegans." Biochemical Journal 452, no. 3 (May 31, 2013): 467–75. http://dx.doi.org/10.1042/bj20130115.
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Caenorhabditis elegans HAF-4 and HAF-9 are half ABC (ATP-binding-cassette) transporters that are highly homologous to the human lysosomal peptide transporter TAPL [TAP (transporter associated with antigen processing)-like; ABCB9]. We reported previously that both HAF-4 and HAF-9 localize to the membrane of a subset of intestinal organelles, and are required for the formation of these organelles and other physiological aspects. In the present paper, we report the genetic and physical interactions between HAF-4 and HAF-9. Overexpression of HAF-4 and HAF-9 did not rescue the intestinal organelle defect of the haf-9 and haf-4 deletion mutants respectively, indicating that they cannot substitute for each other. Double haf-4 and haf-9 mutants do not exhibit more severe phenotypes than the single mutants, suggesting their co-operative function. Immunoprecipitation experiments demonstrated their physical interaction. The results of the present study suggest that HAF-4 and HAF-9 form a heterodimer. Furthermore, Western blot analysis of the deletion mutants and RNAi (RNA interference) knockdown experiments in GFP (green fluorescent protein)-tagged HAF-4 or HAF-9 transgenic worms suggest that HAF-4–HAF-9 heterodimer formation is required for their stabilization. The findings provide a clue as to how ABC transporters adopt a stable functional form.
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Ndam, Nicaise Tuikue, and Philippe Deloron. "Molecular Aspects ofPlasmodium falciparumInfection during Pregnancy." Journal of Biomedicine and Biotechnology 2007 (2007): 1–13. http://dx.doi.org/10.1155/2007/43785.
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Cytoadherence ofPlasmodium-falciparum-parasitized red blood cells (PRBCs) to host receptors is the key phenomenon in the pathological process of the malaria disease. Some of these interactions can originate poor outcomes responsible for 1 to 3 million annual deaths mostly occurring among children in sub-Saharan Africa. Pregnancy-associated malaria (PAM) represents an important exception of the disease occurring at adulthood in malaria endemic settings. Consequences of this are shared between the mother (maternal anemia) and the baby (low birth weight and infant mortality). Demonstrating that parasites causing PAM express specific variant surface antigens (VSAPAM), including theP. falciparumerythrocyte membrane protein 1 (PfEMP1) variant VAR2CSA, that are targets for protective immunity has strengthened the possibility for the development of PAM-specific vaccine. In this paper, we review the molecular basis of malaria pathogenesis attributable to the erythrocyte stages of the parasites, and findings supporting potential anti-PAM vaccine components evidenced in PAM.
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Shaw, M. W., N. H. Arden, and H. F. Maassab. "New aspects of influenza viruses." Clinical Microbiology Reviews 5, no. 1 (January 1992): 74–92. http://dx.doi.org/10.1128/cmr.5.1.74.
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Influenza virus infections continue to cause substantial morbidity and mortality with a worldwide social and economic impact. The past five years have seen dramatic advances in our understanding of viral replication, evolution, and antigenic variation. Genetic analyses have clarified relationships between human and animal influenza virus strains, demonstrating the potential for the appearance of new pandemic reassortants as hemagglutinin and neuraminidase genes are exchanged in an intermediate host. Clinical trials of candidate live attenuated influenza virus vaccines have shown the cold-adapted reassortants to be a promising alternative to the currently available inactivated virus preparations. Modern molecular techniques have allowed serious consideration of new approaches to the development of antiviral agents and vaccines as the functions of the viral genes and proteins are further elucidated. The development of techniques whereby the genes of influenza viruses can be specifically altered to investigate those functions will undoubtedly accelerate the pace at which our knowledge expands.