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Non-Fc receptor-binding humanized anti-CD3 antibodies induce apoptosis of activated human T cells.

Human trials in organ allografts have demonstrated that murine anti-CD3 mAbs are immunosuppressive. By mimicking Ag, anti-CD3 can produce T cell activation, anergy, or death. Activation of resting T cells in vivo results in dose-limiting cytokine release and is caused by Ab-mediated cross-linking of T cells and Fcgamma receptor (FcR)-bearing cells. With the goal of minimizing cytokine-induced toxicity, anti-CD3 have been engineered to lower Fc binding avidity. Preclinical murine studies have indicated that non-FcR-binding anti-CD3 can induce apoptosis of Ag-activated T cells. Since induction of T cell apoptosis may be an important mechanism of immunosuppression by anti-CD3, we tested whether Fc mutations affect the ability of anti-human CD3 to induce apoptosis of activated T cells. We compared wild-type murine anti-CD3, M291, and OKT3 and their humanized, FcR- and non-FcR-binding structural variants in quantitative assays of T cell apoptosis. Non-FcR-binding variants produced more sustainable phosphorylation of extracellular signal-regulated kinase-2, greater release of IFN-gamma, and more effectively caused activation-dependent T cell apoptosis. Non-FcR-binding variants dissociated more quickly from the T cell surface and caused less internalization of the TCR, which then remained available in greater abundance on the cell surface for signaling. Cross-linking of non-FcR-binding variants by antiglobulin enhanced TCR internalization and minimized induction of T cell apoptosis. We conclude that non-FcR-binding, humanized anti-CD3 have improved ability to induce apoptosis of activated T cells, presumably by allowing durable expression of the TCR and sustained signaling.

Adult↗

Relaxed DM requirements during class II peptide loading and CD4+ T cell maturation in BALB/c mice.

Current ideas about DM actions have been strongly influenced by studies of mutant strains expressing the H-2(b) haplotype. To evaluate DM contributions to class II activities in BALB/c mice, we generated a novel mutation at the DMa locus via embryonic stem cell technology. Unlike long-lived A(b)/class II-associated invariant chain-derived peptide (CLIP) complexes, mature A(d) and E(d) molecules are loosely occupied by class II-associated invariant chain-derived peptide and are SDS unstable. BALB/c DM mutants weakly express BP107 conformational epitopes and toxic shock syndrome toxin-1 superantigen-binding capabilities, consistent with partial occupancy by wild-type ligands. Near normal numbers of mature CD4(+) T cells fail to undergo superantigen-mediated negative selection, as judged by TCR Vbeta usage. Ag presentation assays reveal consistent differences for A(d)- and E(d)-restricted T cells. Indeed, the mutation leads to decreased peptide capture by A(d) molecules, and in striking contrast causes enhanced peptide loading by E(d) molecules. Thus, DM requirements differ for class II structural variants coexpressed under physiological conditions in the intact animal.

Alleles↗

RAG-mediated structural variation and its impact on relapse risk in acute lymphoblastic leukemia.

Relapse during treatment of B-cell acute lymphoblastic leukemia (B-ALL) is a harbinger of poor outcomes. Identifying biomarkers for subsequent relapse risk which are detectable at B-ALL diagnosis remains a priority. Off-target recombination-activating gene (RAG)-mediated structural variants (SVs) generate genomic instability that drives leukemogenesis and may underlie treatment resistance. Leveraging sequencing data in 1,496 pediatric B-ALL patients enriched for relapse status (relapse n=532; non-relapse n=964), we characterized RAG-mediated SVs across B-ALL molecular subtypes and examined their association with patient characteristics and their impact on clinical outcomes. Off-target RAG-mediated SVs were overall frequent, particularly in ETV6::RUNX1, ETV6::RUNX1-like, and Ph-like B-ALL subtypes, while increasing age-at-diagnosis was positively associated with burden of off-target RAG-mediated SVs (P<.001). Off-target RAG-mediated SVs with a recombination signal sequence (RSS) at one breakpoint, a hallmark of off-target RAG activity, were significantly more frequent at diagnosis in patients who subsequently relapsed (P=.001). This association remained significant in multivariable regression analysis (per SV odds ratio [OR]:1.08, 95%CI:1.04-1.12), in minimal residual disease (MRD)-negative patients (OR:1.09, 95%CI:1.04-1.14) and across subtypes. Excluding deletions, MRD-negative ETV6::RUNX1 patients with &#x2265;3 off-target RAG-mediated SVs had a >3-fold risk of relapse (hazard ratio:3.47, 95% CI:1.86-6.49). RAG-mediated SVs were also associated with relapse risk in T-cell ALL patients. Off-target RAG-mediated SV burden at diagnosis is a risk factor of relapse in pediatric ALL across molecular subtypes and independent of MRD status.

Journal Article↗

Population-scale detection of methylation outliers from long-read genome sequencing.

BACKGROUND: Aberrant DNA methylation can mediate the functional effects of rare genetic variation and contribute to imprinting disorders, repeat expansion diseases, and other pathogenic regulatory mechanisms. Long-read sequencing technologies now enable genome-wide detection of CpG methylation alongside genetic variation from a single assay. However, methods for systematic identification and interpretation of methylation outliers from long-read sequencing data remain limited. METHODS: We developed METAFORA, a computational workflow for detecting methylation outlier regions from PacBio and Oxford Nanopore long-read sequencing data. METAFORA constructs population-level methylation references, segments the genome into correlated CpG blocks, infers technical and biological sources of variation through hidden factor estimation, models uncertainty due to variable depth sequencing, and computes covariate-adjusted methylation outlier scores for individual samples. We applied METAFORA across large long-read sequencing cohorts and integrated methylation outliers with multi-omic data. METAFORA is implemented as a snakemake workflow available at https://github.com/tjense25/METAFORA. RESULTS: METAFORA identified methylation outlier regions associated with rare structural variants, tandem repeat expansions, and imprinting abnormalities. We found outlier regions were enriched for molecular outliers across transcriptomic and chromatin accessibility datasets, supporting their functional relevance in gene regulation. In a representative case, METAFORA identified an imprinting defect affecting the GNAS locus associated with an STX16 deletion. CONCLUSIONS: METAFORA enables scalable detection and interpretation of methylation outliers from long-read sequencing data and provides a framework for integrating epigenetic outliers with genomic and multi-omic analyses. These approaches may improve interpretation of rare regulatory variation and support discovery of clinically relevant epigenetic abnormalities in genomic medicine.

DNA methylation↗

Chondramides A approximately D, new antifungal and cytostatic depsipeptides from Chondromyces crocatus (myxobacteria). Production, physico-chemical and biological properties.

Novel depsipeptides, named chondramides were produced at levels up to 4.3 mg/liter by several myxobacteria of the genus Chondromyces. The compounds are structurally closely related to jaspamide/jasplakinolide from marine sponges of the genus Jaspis. Initially the chondramides were detected in acetone extracts of the biomass of Chondromyces crocatus, strain Cm c2. So far, four structural variants could be characterized, the chondramides A approximately D. They inhibited the growth of a few yeasts and showed high cytostatic activity against cultivated human and animal cells.

Animals↗

[Characteristics of quantitative karyotypic variability in cell line of kidney from rat kangaroo (Potorous tridactylis)].

The numerical regulations of karyotypic variability in cell line of rat kangaroo kidney, NBL-3-11, has been investigated. These regulations are similar with ones found for cell lines of the Indian muntjac skin fibroblasts (M, MT, M2). In particular the balanced karyotypic structure of cell population in vitro is determined by correlations of the structural variants of the karyotype (SVK). These correlations depend on the following regulations 1) nonrandom character of cell distribution according to the number of chromosomal deviations from MSVK; 2) specific character of deviations of each chromosome from MSVK; 3) presence of significant connections between separate chromosomes with simultaneous numeral deviations some differences in the character of significant connections between the individual chromosomes. These connections have either single directed character, mainly (+) direction, or differently directed one by deviations of each chromosome mainly in one direction in cell line NBL-3-11. At the same time single directed character of simultaneous deviations is observed in cell lines of the Indian muntjac skin fibroblasts (M, MT, M2) either in (+) or (-) direction. Represented results confirm and extend considerably the known ideas of the regulations of karyotypic variability in cell populations in vitro.

Animals↗

Primary structure of porcine pepsin. II. Amino acid sequence of two cyanogen bromide fragments, CB3 and CB4.

The amino acid sequences of two cyanogen bromide fragments from porcine pepsin have been determined. Fragment CB3 which represents the NH2-terminal 80 residues of pepsin was assembled from the peptides purified from proteolytic digests of this fragment using alpha-chymotrypsin, thermolysin, and staphylococcal protease. Two chymotryptic peptides were isolated from the NH2-terminal region of this fragment. One of these contains 2 extra residues, Ala-Leu-, at the NH2 terminus. This peptide is apparently derived from a different cleavage site of pepsinogen in its conversion to pepsin. The second cyanogen bromide fragment, CB4, contains 47 residues. The sequence was established from the peptides resulting from proteolytic digests using alpha-chymotrypsin, alpha-lytic protease, and thermolysin. An isoleucyl residue at position 29 of fragment CB4 appears to be absent in some molecules. This represents a structural variant of pepsin.

Amino Acid Sequence↗

Primary structure of porcine pepsin. III. Amino acid sequence of a cyanogen bromide fragment, CB2A, and the complete structure of porcine pepsin.

The complete amino acid sequence of porcine pepsin (EC 3.4.4.1) was constructed from the sequence of five cyanogen bromide fragments. The sequence of one of these fragments, CB2A, is reported here. The sequences of 4 other fragments are known from previous work. Porcine pepsin contains 327 residues with three structural variants. The active center aspartyl residue, which reacts with 1,2-epoxy-3-(p-nitrophenoxy)propane (Chen, K. C. S., and Tang, J. (1972) J. Biol. Chem. 247, 2566-2574), is located at residue 32. Another active site aspartyl residue, which reacts with diazo inactivators (Bayliss, R. S., Knowles, J. B., and Wybrandt, G. B. (1969) Biochem. J. 113, 377-386, IS LOCATED AT RESIDUE 215. The sequences around these 2 aspartyl residues are apparently homologous to each other. The sequences around the tryptophanyl residues at positions 39, 141, 181, and 300 are also homologous to one another. These homologous sequences could be genetic in origin. Fragment CB2A which contains 119 residues was constructed from the peptide sequences resulting from six proteolytic digestions and chemical cleavage at tryptophanyl bonds.

Amino Acid Sequence↗

Role of platelet-activating factor in reproduction: sperm function.

Since its discovery nearly thirty years ago, platelet-activating factor has emerged as one of the more important lipid mediators known. Platelet-activating factor (PAF; 1-O-alkyl-2-O-acetyl-sn-glycero-3-phosphorylcholine) exists endogenously as a mixture of molecular species with structural variants of the alkyl moiety. PAF is a novel potent signaling phospholipid that has unique pleiotropic biological properties in addition to platelet activation. PAF also plays a significant role in reproduction. PAF content in squirrel monkey sperm is significantly higher during the breeding season than the non-breeding season. PAF content in human sperm has a positive correlation with seminal parameters and pregnancy outcomes. High-fertility boars have significantly more PAF in their sperm than low-fertility boars. The enzymes (lyso-PAF-acetyltransferase and PAF-acetylhydrolase) necessary for PAF activation and deactivation are present in sperm. PAF-acetylhydrolase may act as a "decapacitation factor". Removal of this enzyme during capacitation may promote PAF synthesis increasing motility and fertilization. PAF also plays a significant role in the fertilization process, enhancing the fertilization rates of oocytes. Enhanced embryo development has also been reported in oocytes fertilized with PAF-treated sperm. PAF antagonists inhibit sperm motility, acrosome reaction, and fertilization, thus suggesting the presence of receptors for PAF. The PAF-receptor is present on sperm, with altered transcript levels and distribution patterns on abnormal cells. Whereas the exact mechanism of PAF in sperm function and reproduction is uncertain, its importance in normal fertility is substantial. The reproductive significance of PAF activity in sperm and fertility plus the role of PAF in the establishment of pregnancy requires further study.

Animals↗

[Vertebrogenic lumbosacral radiculitis unrelated to disk herniation].

A classification of changes in the inferior lumbar portion of the spine that cause radicular pain and symptoms not amenable to concervative therapy is given. In most cases the said changes can be educed through a clinico-roentgenological investigation. Anatomical data bear proof to the presence of structural variants in which, in case of an intercurrent osteochondrosis without hernia of the disc, the compression of the root becomes quite probable. The classification lists changes that should be looked for when no hernia of the disc could be detected and lays emphasis on the multiplicity of causes accounting for the emergence of vertebrogenic radiculitis.

Exostoses↗

[Comparative-anatomical study of the formation of small and large intestinal (ileocecal) valve].

The results of the comparative-anatomical investigation of the formation of ileocecal valve are presented. The study was based on the examination of the specimens obtained from 123 representatives of all vertebrate classes and 48 isolated preparations of ileocecal area of the intestine of corpses of humans aged 22-64 years. It was performed using anatomical, histological and morphometrical methods. It was shown that the formation of this closing mechanism followed the route from sphincter between small and large intestine to the development of a shutter and, eventually, of a valve. Using these concepts, the structural variants of ileocecal valve which were detected in humans were analyzed taking into consideration both its extreme variation forms (ileocecal morphological sphincter without the valve and ileocecal valve without the sphincter) and intermediate forms, which should be considered as the variants of norm.

Adult↗

[Antibody deficiency syndrome and chromosome aberrations].

Chromosome analyses were made on culture lymphozytes from peripheral blood in 37 patients with humoral and local antibody deficiency syndrome. In one child with humoral IgA-deficiency a ploidymutation of sex chromosomes - a Klinefelter-Syndrome - and a structural variante of chromosome 16 were detected - karyotype 47, XXY, 16q+. No aberrations of chromosomes 18 and 21 were found out in these phenotypic completely normal children. Patients with secret-IgA-deficiency in mucosae had normal karyotypes. Theoretical aspects of possible connection of antibody deficiency syndrome and chromosomal anomalies are discussed.

Bacterial Infections↗

[The effect of Mycoplasma contamination on the karyotypic structure of a skin fibroblast cell line from the Indian muntjac].

The karyotypic variability has been studied in a low chromosomal cell line of the Indian muntjak skin fibroblasts contaminated with Mycoplasma arginini R-16 and Acholeplasma laidlawii A. The mycoplasmal contamination exerted influence on the cell distribution for the chromosome number. The frequency of the modal class cells with 7 chromosomes, having the main structure variant of the karyotype (MSVK) 2 + 2 + 1 + 1 + 1, was seen to decrease, while the frequency of the submodal class cells with 6 chromosomes, having MSVK 2 + 2 + 1 + 1 because of the loss of Y1 chromosome from MSVK 2 + 2 + 1 + 1, to increase. The frequency of chromosomal aberrations, predominantly that of dicentrics, was higher in the contaminated variants. Dicentrics were mainly produced by chromosomes 1 and 2. They were formed by a nonrandom combination of chromosomes and their arms. Possible correlations are discussed between aneuploidy and dicentric chromosome formation in low chromosomal cell lines, and cell adaptations to culture conditions.

Acholeplasma laidlawii↗

Antithrombin-III-Stockholm: a codon 392 (Gly----Asp) mutation with normal heparin binding and impaired serine protease reactivity.

Antithrombin-III-Stockholm is a new structural variant of antithrombin-III (AT-III) with normal heparin affinity but defective serine protease inhibitory activity. The proposita, a white female born in 1966, was diagnosed to have developed a pulmonary embolus while on oral contraceptives at age 19. The proposita, as well as her father, were diagnosed to have a type 2 AT-III deficiency as they had normal levels of immunoreactive AT-III associated with decreased (approximately 60%) functional AT-III when measured with either alpha-thrombin or factor Xa as the substrate, either in the presence or absence of heparin. There was no evidence of abnormal electrophoretic mobility of AT-III from the proposita either in the presence or absence of heparin. Genomic DNA was prepared and all seven AT-III exons were polymerase chain reaction (PCR)-amplified and sequenced in both directions using nested primers. Only exon 7 provided evidence for the presence of a mutation, with the second base of codon 392 having a G----A substitution. Such a mutation would cause the substitution of aspartic acid at the site of the normally appearing glycine in the translated product. Furthermore, this mutation caused the destruction of an Hae III restriction site at this point in the AT-III gene. The absence of this Hae III site was confirmed using restriction fragment length polymorphism analysis of PCR-amplified material from the proposita. Experiments with AT-III from the proposita together with experiments with cell-free translated AT-III-Stockholm provided evidence that the mutant AT-III protein does not efficiently form a stable covalent inhibitory complex with alpha-thrombin, although it exhibits normal heparin affinity. The minimal thrombin-complexing ability of the mutant AT-III protein that was observed was accelerated by heparin, but to subnormal levels.

Adult↗

Cytogenetics of genetic counseling patients in Pelotas, Rio Grande do Sul, Brazil.

From 1986 to 2002, we examined the chromosomal composition of 916 patients attended by two genetic counseling services in the city of Pelotas, in the Brazilian State of Rio Grande do Sul, to determine the genetic causes of their disturbances. Patterns of G-banding using trypsin and Giemsa (GTG) and C-banding using barium and Giemsa (CBG) were studied using phytohemagglutinin M-stimulated lymphocytes cultured from peripheral blood. Among the patients, 110 had Down's syndrome, 7 had Edward's syndrome, 4 had Patau's syndrome, 29 had Turner's syndrome, 5 had Klinefelter's syndrome, and 3 had "cri-du-chat" syndrome. Abnormal chromosomes were observed in 29.3% of the patients. Most of these (56.3%) were numerical abnormalities, with the remaining being structural variants.

Brazil↗

Regulation of type II luteinizing hormone-releasing hormone (LHRH-II) gene expression by the processed peptide of LHRH-I, LHRH-(1-5) in endometrial cells.

Luteinizing hormone-releasing hormone (LHRH) was first isolated in the mammalian hypothalamus and shown to be the primary regulator of the reproductive system through its initiation of pituitary gonadotropin release. Since its discovery, this form of LHRH (LHRH-I) has been shown to be one of many structural variants with a variety of roles in both the brain and peripheral tissues. Enormous interest has been focused on LHRH-I, LHRH-II, and their cognate receptors as targets for designing therapies to treat cancers of the reproductive system. LHRH-I is processed by a zinc metalloendopeptidase EC 3.4.24.15 (EP24.15) that cleaves the hormone at the Tyr(5)-Gly(6) bond. We have previously reported that the autoregulation of LHRH gene expression can also be mediated by its processed peptide, LHRH-(1-5). Given its importance in the brain, we have investigated the role of the specific processed peptide of LHRH-I, LHRH-(1-5), within Ishikawa cells, a human endometrial cell line. Using real-time polymerase chain reaction, we observed that LHRH-(1-5) upregulates LHRH-II mRNA expression in Ishikawa cells but does not exert any influence on LHRH-I mRNA levels. This is in contrast to the effects of LHRH-I, which affects the expression of LHRH-I mRNA. Our findings support a potential role for LHRH-(1-5) as a processed metabolite in the endometrium. Further investigations are needed to determine the role of this processed metabolite and to identify specific pathways involved in LHRH-(1-5) signaling.

Cell Line, Tumor↗

Multiple origins of the human glycophorin Sta gene. Identification of hot spots for independent unequal homologous recombinations.

Human glycophorin Sta (HGpSta), one of the structural variants of erythrocyte membrane sialoglycoproteins, is encoded by a delta-alpha hybrid gene that arose from a single unequal crossover between the parent HGpB(delta) and HGpA(alpha) genes. We report here the identification of two new HGpSta genes (type A and type B) in four unrelated Sta heterozygotes from two ethnic groups. These Sta genes represent distinct genetic isoforms that differ from the previously reported Sta gene (type C) in the location of crossing-over sites. Comparison of nucleotide sequences among HGpB(delta), HGpA(alpha), and HGpSta type A genes revealed that the delta-alpha unequal crossover for the Sta type A gene occurred 110-246 base pairs downstream from pseudoexon III. In the crossing-over site of this Sta gene, an AT-rich sequence lying 3' to a nonameric palindrome was found to be highly similar to the lambda phage attachment site, att B, in inverted orientation. In the Sta type B gene, the delta-alpha crossing-over point was localized to an AG-rich sequence that is 302-490 base pairs downstream from pseudoexon III. Multiple lambda chi-like elements were identified at the crossover boundaries and within the breakpoint of this Sta gene. These results suggest strongly that recurrent and independent unequal recombination events have occurred in the formation of multiple Sta genes and that particular genomic sequences are important in defining the recombination sites for these homology-driven processes.

Asian People↗