The Search for Single-Domain Antibodies Interacting with the Receptor-Binding Domain of SARS-CoV-2 Surface Protein.

We performed a search for nanoantibodies that specifically interact with the receptor-binding domain (RBD) of the SARS-CoV-2 surface protein. The specificity of single-domain antibodies from the blood sera of a llama immunized with RBD of SARS-CoV-2 surface protein S (variant B.1.1.7 (Alpha)) was analyzed by ELISA. Recombinant trimers of the SARS-CoV-2 spike protein were used as antigens. In this work, a set of single-domain antibodies was obtained that specifically bind to the RBD of the SARS-CoV-2 virus.

shp-2 gene knockout upregulates CAR-driven cytotoxicity of YT NK cells.

In Russia, cancer is the second leading cause of death following cardiovascular diseases. Adoptive transfer of NK cells is a promising approach to fight cancer; however, for their successful use in cancer treatment, it is necessary to ensure their robust accumulation at tumor foci, provide resistance to the immunosuppressive tumor microenvironment, and to engineer them with higher cytotoxic activity. NK lymphocytes are known to kill cancer cells expressing a number of stress ligands; and the balance of signals from inhibitory and activating receptors on the surface of the NK cell determines whether a cytotoxic reaction is triggered. We hypothesized that stronger cytotoxicity of NK cells could be achieved via gene editing aimed at enhancing the activating signaling cascades and/or weakening the inhibitory ones, thereby shifting the balance of signals towards NK cell activation and target cell lysis. Here, we took advantage of the CRISPR/Cas9 system to introduce mutations in the coding sequence of the shp-2 (PTPN11) gene encoding the signaling molecule of inhibitory pathways in NK cells. These shp-2 knock-out NK cells were additionally transduced to express a chimeric antigen receptor (CAR) that selectively recognized the antigen of interest on the target cell surface and generated an activating signal. We demonstrate that the combination of shp-2 gene knockout and CAR expression increases the cytotoxicity of effector NK-like YT cells against human prostate cancer cell line Du-145 with ectopic expression of PSMA protein, which is specifically targeted by the CAR.

Engineering Chimeric Antigen Receptors.

Chimeric antigen receptors (CARs) are recombinant protein molecules that redirect cytotoxic lymphocytes toward malignant and other target cells. The high feasibility of manufacturing CAR-modified lymphocytes for the therapy of cancer has spurred the development and optimization of new CAR T cells directed against a broad range of target antigens. In this review, we describe the main structural and functional elements constituting a CAR, discuss the roles of these elements in modulating the anti-tumor activity of CAR T cells, and highlight alternative approaches to CAR engineering.

[CAR T-cell therapy: Balance of efficacy and safety].

Early results from clinical trials of autologous chimeric antigen receptor (CAR)-expressing T cells for the therapy of B-cell malignancies have encouraged extending the potency of this therapy to other cancers. However, the success of using CAR T-cells to treat patients with solid tumors has been limited. In this review, we summarize current knowledge on the design and applications of CARs for the targeted therapy of cancer. We describe existing issues that limit the widespread application of CAR T cells and discuss the optimization steps needed to further improve safety and efficacy of this therapeutic platform.

[Impact of neutron radiation on the viability of tumor cells cultured in the presence of boron-10 isotope].

Objective: To investigate the impact of a neutron beam formed with the accelerator-based epithermal neutron source designed at the G.I. Budker Institute of Nuclear Physics (INP) on the viability of human and animal tumor cells cultured in the presence of boron-10 isotope. Material and Methods: Human U251 and T98G glioma cells and Chinese hamster CHO-K1 and V-79 cells were incubated at various concentrations in the culture medium containing 10B-enriched L-boronophenylalanine. The cells were irradiated with a neuron beam using the accelerator-based epithermal neuron source. A clonogenic assay was used to evaluate the viability of the irradiated cells. The absorbed doses obtained from elastic scattering of fast neutrons by substance nuclei and the doses obtained from boron neutron capture were calculated using the NMS code. The absorbed doses of gamma-radiation were measured with a mixed radiation dosimeter. Results: The viability of boron-containing and intact human U251 and T98G cell lines and Chinese hamster CHO-K1 and V-79 cells was analyzed after neutron beam radiation. Irradiation of all four cell lines were cultured in the presence of 10B was shown to reduce their colony-forming capacity compared with the control. Elevated boron levels in the culture medium resulted in a significant decrease in the proportion of survived cells. Radiation had the most pronounced impact on the proliferative capacity of the human U251 glioma cell lines. Conclusion: The cultures of human tumor cells and mammalian cells demonstrated that the neutron beam formed with the accelerator-based epithermal neutron source designed at the INP, was effective in reducing the viability of tumor cells in the presence of 10B.

Retention of duplicated ITAM-containing transmembrane signaling subunits in the tetraploid amphibian species Xenopus laevis.

The ITAM-bearing transmembrane signaling subunits (TSS) are indispensable components of activating leukocyte receptor complexes. The TSS-encoding genes map to paralogous chromosomal regions, which are thought to arise from ancient genome tetraploidization(s). To assess a possible role of tetraploidization in the TSS evolution, we studied TSS and other functionally linked genes in the amphibian species Xenopus laevis whose genome was duplicated about 40 MYR ago. We found that X. laevis has retained a duplicated set of sixteen TSS genes, all except one being transcribed. Furthermore, duplicated TCRα loci and genes encoding TSS-coupling protein kinases have also been retained. No clear evidence for functional divergence of the TSS paralogs was obtained from gene expression and sequence analyses. We suggest that the main factor of maintenance of duplicated TSS genes in X. laevis was a protein dosage effect and that this effect might have facilitated the TSS set expansion in early vertebrates.

[Expression of human B-cell specific receptor FCRL1 in normal individuals and in patients with autoimmune diseases].

The comparative analysis of expression level of FCRL1 gene encoding human B-cell surface receptor in healthy individuals and patients with autoimmune diseases was carried out. For the expression estimation we used results of DNA dot-hybridization on the membranes, containing cDNA samples from subpopulations of blood cells of patients with autoimmune diseases. The quantitative estimation of hybridization signals showed that expression level of FCRL1 gene in peripheral blood B-lymphocytes was significantly higher in patients with a multiple sclerosis, lupus anticoagulans, Takayasu's arteritis and also in von Willebrand disease than in healthy individuals. FCRL1-specific monoclonal and polyclonal antibodies were raised. They were proven to detect FCRL1 in Western blotting, immunohistochemistry and flow cytometry. It was found that FCRL1 is expressed on the surface of CD19+ mature B-cells. In tonsil FCRL1-positive cells were located in crypt area: in mantle zone of secondary lymphoid follicles and among cells of lymphoepithelium. FCRL1-positive cells were also found in B-cell follicles of the spleen.

[Expression patterns of the human and mouse IFGP family genes].

The IFGP family is a recently identified group of human and mouse genes structurally related to the genes of leukocyte Fc-receptors. In this study we compared expression patterns of six human and four mouse IFGP genes. With the exception of mouse IFGP2, the genes of the family were found to be predominantly expressed in haemopoietic cells. Expression of human IFGP1-IFGP5 and mouse IFGP3 was B cell-specific. Mouse IFGP1 transcripts were mainly found in B cells, but this gene may be either expressed by nonlymphoid cells. Expression of the human IFGP6 was detected in CD8+ T cells and NK cells. We further demonstrated that alternative splicing of human IFGP1 and IFGP6 mRNA may generate transcripts coding for the previously unknown isoforms. The novel IFGP1 isoform lacks transmembrane domain, whereas the IFGP6 isoform has altered cytoplasmic tail. The data obtained indicate that the receptors of family may contribute to the regulation of development and/or functions of three effector types of lymphocytes, namely B cells, CD8 T cells and NK cells.

Cloning and characterization of the human FCRL2 gene.

We report cloning and characterization of FCRL2, a novel human gene that belongs to the FcR family. The gene is closely linked and structurally similar to the recently identified FCRL/FREB/FcRX gene. The encoded protein is composed of three Ig-like domains and a C-terminal mucin-like domain containing a conserved alpha-helical motif with dileucine signals. Intraexonic splicing may generate two alternative transcripts, coding for isoforms with the third and fourth domains replaced by entirely different amino acid sequences. Like FCRL, the full-length isoform of FCRL2 is expressed intracellularly in transfected 293T cells. Expression analysis revealed FCRL2 mRNA only in placenta. The gene transcripts were not detected in lymphoid tissues or in the main leukocyte subsets isolated from peripheral blood. However, we found that FCRL2 is differentially expressed by transformed B cell lines. Of interest is also the finding that the gene expression may be up-regulated in the progression of melanocytic tumors.

CD3epsilon homologues in the chondrostean fish Acipenser ruthenus.

CD3epsilon is an essential component of the T-cell receptor (TCR) complex for antigen. We report here molecular cloning and characterization of cDNAs encoding the CD3epsilon homologues in sterlet (Acipenser ruthenus), a representative of primitive chondrostean fishes. Sequence analysis of the cDNA clones demonstrated unexpectedly high CD3epsilon gene heterogeneity in this species. While some cDNAs encoded proteins with the structure typical of mammalian CD3epsilon, others coded for proteins lacking the membrane-proximal half of the extracellular domain. Two cDNAs contained in-frame stop codons in the region encoding the cytoplasmic domain. Based on genomic blot analysis and RT-PCR typing of individual spleen RNAs, we suggest that sterlet may possess two highly polymorphic CD3epsilon loci, of which one can produce alternatively spliced transcripts. The structural elements shown to be functionally important in the mammalian CD3epsilon are strongly conserved in the sterlet CD3epsilon. The cytoplasmic region contains an immunoreceptor tyrosine-based activation motif (ITAM) with YEPI and YSGL tyrosine-containing sequences that are characteristic of only this TCR subunit. The pattern of sequence conservation indicates also that strong selection pressure was imposed on a motif VYYW at the C-end of the transmembrane domain and on a CD3epsilon-specific proline-rich motif RXPPVP juxtaposed to the N-terminus of the ITAM. Weak similarity of the sterlet CD3epsilon with the chicken and Xenopus CD3gamma/delta indicates that these two TCR subunits diverged before radiation of bony fishes and tetrapods. While the role of CD3epsilon heterogeneity in sterlet remains to be elucidated, the data obtained show that the basic mechanisms of TCR signaling have ancient evolutionary origin.

Cloning of a CXCR4 homolog in chondrostean fish and characterization of the CXCR4-specific structural features.

The chemokine receptor CXCR4 and its ligand SDF-1 are essential components of hematopoiesis, organogenesis and immunomodulation in mammalian species. We cloned a cDNA encoding CXCR4 homolog of sterlet (Acipenser ruthenus), a representative of chondrostean fishes. The deduced amino acid sequence of sterlet CXCR4 is almost equally distant from mammalian and teleost CXCR4 (66-68% identical residues). Percent identity with the other chemokine receptors varies in the 30-35% range. The CXCR4 sequences from the three phylogenetically diverged lineages were compared with the sequences of the other chemokine receptors to determine the CXCR4-specific structural elements that were conserved during vertebrate evolution. The characteristic residues and/or motifs are located predominantly in the intracellular and extracellular regions and in the third, fourth and fifth transmembrane domains. The data presented may be helpful for structure-function analysis of the CXCR4 ligand binding and signal transduction.

Identification of an IL-8 homolog in lamprey (Lampetra fluviatilis): early evolutionary divergence of chemokines.

Subtractive hybridization was used to study river lamprey (Lampetra fluviatilis) leukocyte-specific cDNA. A clone representing the most abundant component (12%) of the leukocyte library subtracted with liver cDNA was isolated and characterized. The cDNA encodes a presumably secreted polypeptide of 101 residues. The 3' untranslated region of the cDNA contains motifs characteristic of the transiently expressing genes. Comparison of the deduced amino acid sequence with known protein sequences revealed its homology to the members of the chemokine superfamily. Designated as LFCA-1, the lamprey protein contains four conserved cysteines, of which the first two are separated by a residue, and a number of other CXC family characteristic residues. LFCA-1 has the highest similarity to the chicken EMF-1 (40%) and to the mammalian IL-8 (32-33%). However, it lacks the ELR motif essential for the function of the mammalian IL-8-related chemokines. Based on the phylogenetic analysis of the LFCA-1 relationship to the higher vertebrate chemokines, it is concluded that the evolutionary origin of the chemokine superfamily is ancient, and that the divergence of the CXC and CC families most likely occurred at the time or before the first vertebrates emerged.

Structure of mink immunoglobulin gamma chain cDNA.

Two cDNA clones, encoding mink Ig gamma chains were characterized. The pIGG47 clone contains a part of the leader segment, VDJ and C regions, and pIGG14 contains a part of the J and a complete C region. The clones differ by only four nucleotides in the C region, and they most probably represent allelic variants of the same gene. The V gene segment of pIGG47 was found to be highly similar to human VHIII subgroup sequences; there was 86-87% similarity for the whole V gene segment and 91% for the VHIII specific regions (codons 65-87). Southern blot analysis demonstrated that a high proportion of mink VH genes is VHIII related. The V gene segment used as a probe revealed 19-23 bands in mink DNA under stringent conditions. This is in agreement with our previous data showing that a high proportion of mink Ig contains an 'alternative' binding site for protein A, a feature common to VHIII-related molecules. According to Southern blot analysis there may be 5-7 C gamma genes at the mink IgH locus.

cDNA clones encoding mink immunoglobulin lambda chains.

Screening of a mink cDNA library with an antibody probe resulted in the isolation of clone pIGL-2 containing an Ig lambda chain coding sequence. The sequence comprised almost the entire V segment as well as J, C, and 3'-untranslated sequences. A second clone, pIGL-10, was isolated by rescreening the cDNA library with the use of pIGL-2 as a probe. pIGL-10 was found to contain a frameshift deletion of a single nucleotide in the C region. pIGL-2 and pIGL-10 were 81% homologous to each other in the FR3 of the V segment, and 95% of homology was found in their C regions. The J segments of the two clones differed in only one nucleotide position. Comparison of cloned lambda chain sequences with those of other mammals revealed that mink V lambda and C lambda genes have the highest homology with their human counterparts. The V lambda sequence of clone pIGL-2 appears to be a homologue of human subgroup III V lambda genes. Southern blot hybridization of mink DNA with the C lambda and V lambda probes derived from pIGL-2 revealed five or six hybridizing C lambda fragments and at least 11 hybridizing V lambda fragments. This suggested that the lambda genes in carnivores, like those in primates, have duplicated extensively during evolution.

Expression of immunoglobulin kappa and lambda chains in mink.

The ratio of kappa and lambda chains of immunoglobulins varies significantly from one species to another. It has previously been thought that lambda was only type expressed in mink. We tested mink immunoglobulin light chains using two monoclonal antibodies G80 and G88. It has been shown that G80 and G88 specifically recognize two antigenically different subpopulations of the light chains. Immunochemical analysis of these subpopulations separated by affinity chromatography suggested that they represent lambda and kappa types of light chains, respectively. Screening of a mink cDNA library with monoclonal antibody G88 resulted in the isolation of clone pIGK-1 containing kappa chain-encoding sequence. The cDNA insert of pIGK-1 included most of the V segment, as well as the J, C and 3' untranslated sequences. Mink V kappa sequence shown the highest homology with the human V kappa II subgroup genes (76-79%). Mink C kappa sequence was 53-63% homologous to C kappa of other species. The striking feature of mink C kappa chain is the presence of glutamine in the C-terminal position. Southern blot analysis suggested that mink haploid genome has one C kappa gene and multiple V kappa genes. The kappa:lambda chain ratio in the 12 minks studied was, on the average, 46:54. The same ratio was observed for the kappa- and lambda-producing cells in the mesenteric lymph nodes. The five previously identified mink light chain allotypes were assigned to the lambda chains, thereby confirming that lambda chains in this species are additionally subdivided into several subtypes.

Monoclonal antibodies against heavy and light chains of domestic mink IgG.

A panel of 26 monoclonal antibodies (MAbs) specific to mink IgG was produced and analyzed by ELISA, immunodiffusion assay (IDA) and immunoblotting assay. All the raised MAbs were directed against the isotypic IgG epitopes. Immunoblotting assay demonstrated that 11 MAbs reacted only with the Fc-fragments of IgG and 7 only with the light chains. Four antibodies bound to the Fab-containing fragments and failed to react with the Fc-fragments or isolated L-chains. Three MAbs did not react with IgG in IDA. Based on the results of IDA and cross-blocking assays, the MAbs were divided into 10 groups, with the MAbs of each group recognizing the same epitope. In IDA some MAbs were able to react with the epitopes which are common to the IgGs of some other representatives of Mustelidae family and also to some mammalian species remote from mink (dog, horse, pig, fox and rabbit).

Genetic polymorphism of IgG in the mink. IX. High proportion of allotype-producing lymphocytes in individuals with minor level of allotypes H3 and H4 in serum.

The levels of mink C gamma-allotypes (H3, H4, H6 and H8) were determined in sera, and the proportion of the corresponding allotype-synthesizing B cells was estimated in peripheral blood, spleen and mesenteric lymph nodes. Individual differences in H6 levels and, possibly, those in H8 were entirely dependent on the proliferation degree of the corresponding clone of B cells and also determined by the dosage of the structural gene. There was no correspondence between the great numbers of H3+, H4+ cells and low levels of H3 and H4 allotypes in the sera of the majority of minks with their minor expression. A possible cause of this discrepancy may be a blockade of the secretion of IgG by H3+, H4+ cells. There exists most likely a gene (or genes) controlling the blockade of IgG secretion. The regulation of C gamma-allotype expression is presumably effected in a manner specific to each of the allotypes.

Genetic polymorphism of IgG in the mink. VIII. A quantitative study of the expression of C gamma-allotypes (H3, H4, H6, H8) in sera.

The results of a quantitative study of the expression of mink C gamma-allotypes (H3, H4, H6, and H8) in sera are presented. H6 and H8 were found to be stably expressed, and the individual concentrations of the allotypes varied within one order of magnitude. Gene dosage effects were observed for H6 and H8: average sera allotype concentrations in homozygotes were twice those in heterozygotes. In contrast, the serum concentrations of H3 and H4 varied by three orders of magnitude, ranging from minor (2-200 micrograms/ml) to high (1-10 mg/ml). No gene dosage effects were observed for the expression of H3 and H4. Histograms for the population of H3 concentrations showed three peaks, sharply differing from those of H4, H6, and H8. There was no association between the minor expression of H3 and H4. The data obtained indicate that the expression of mink C gamma-allotypes is regulated by different allotype-specific mechanisms.

A tissue-specific puff (Balbiani ring a) in Chironomus thummi may contain a gene encoding a 67-kDa protein which exhibits non-tissue-specific expression.

A 2.3-kb genomic clone has been isolated from the region where the tissue-specific puff, Balbiani ring a (BRa), is found on chromosome IV of the special lobe of Chironomus thummi salivary gland cells. The clone was characterized by nucleotide sequence analysis. Two clusters of direct tandem repeats were identified, as well as large and small open reading frames (ORFs). The large ORF was fused to an Escherichia coli lacZ gene. Antibodies against the beta-galactosidase/ORF fusion protein reacted selectively on Western blots with a 67-kDa protein. Western-blot analysis and immunoelectron microscopy showed that this protein was distributed in the cells of all larval tissues examined. We concluded that BRa, a tissue-specific puff, whose activity correlates with the synthesis of 160-kDa secretory protein [Kolesnikov et al., Chromosoma 83 (1981) 661-677], may also contain a gene which is not expressed in a tissue-specific manner.