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Glatiramer acetate (GA) therapy induces a focused, oligoclonal CD8+ T-cell repertoire in multiple sclerosis.

We have demonstrated that GA therapy induces a differential upregulation of GA-specific, cytotoxic/suppressor CD8+ T-cell responses in MS patients. We utilized a novel combination of flow sorting and anchored PCR to analyze the evolving clonal composition of GA-specific CD4+ and CD8+ T-cells. TCRbeta chain analysis revealed the development of an oligoclonal GA-specific CD8+ repertoire with persistence of dominant clones over long periods. Interestingly, some sequences resembled published oligoclonal CD8+ TCR sequences from MS lesions. In contrast, GA-specific CD4+ responses were polyclonal and showed continual evolution of their repertoire. This clonotypic and functional analysis provides mechanistic insights into GA therapy.

Adult↗

Physiology of immunity in the water flea Daphnia magna: environmental and genetic aspects of phenoloxidase activity.

In an attempt to understand the ecological correlates of immunocompetence in Daphnia magna (Crustacea, Cladocera), we tested for variation in immune function in relation to feeding conditions, host conditions, and host genotype. We investigated both phenotypic (environmental dependent and condition dependent) as well as genotypic aspects of the prophenoloxidase activating system (Pro-POAS), which has been described as a key factor in invertebrate immunity. Daphnia magna is an ideal study system to disentangle phenotypic and genetic variation because females can reproduce clonally. Well-fed Daphnia showed higher phenoloxidase (PO) activity than Daphnia kept at a low food level. Wounding provoked a higher level of PO activity, indicating that the Pro-POAS was condition dependent. Further, we found clonal variation in PO activity among four clones of D. magna isolated from four different populations. The same four clones were tested for their resistance to the bacterial pathogen Pasteuria ramosa. High resistance corresponded to high PO activity. Our results suggest adaptive variation in PO activity and suggest that its expression is costly. These costs may influence the evolution of the PO activity level and the maintenance of its genotypic variation.

Animals↗

Recombination in adenovirus. I. Analysis of recombinant viruses under non-selective conditions.

A method is described, based on an approach previously employed for the mapping of adenovirus ts mutants (Grodzicker et al. 1975), for the identification of recombinant viruses in the progeny of mixed infections of human HeLa cells with wild-type adenovirus types 2 and 5 under non-selective conditions. Differences in restriction enzyme sites for the endonuclease HpaI could be used to detect new recombinant DNA fragments in a yield of 3 to 6% after single mixed infections and yields up to 25% following three successive mixed infections. The recombinant nature of the new fragments was proved by the clonal isolation of recombinant viruses in similar yields. Analysis of one cloned recombinant pointed to the occurrence of multiple crossover events at different sites along the virus chromosome. The results are discussed in terms of a biochemical approach towards the study of the mechanism of general genetic recombination in human cells as well as with respect to the evolution of adenoviruses.

Adenoviruses, Human↗

MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction.

Mitochondrial (MT) mutations serve as natural genetic markers for inferring clonal relationships using single cell sequencing data. However, the fundamental challenge of MT mutation-based lineage tracing is automated identification of informative MT mutations. Here, we introduced an open-source computational algorithm called "MitoTracer", which accurately identified clonally informative MT mutations and inferred evolutionary lineage from scRNA-seq or scATAC-seq samples. We benchmarked MitoTracer using the ground-truth experimental lineage sequencing data and demonstrated its superior performance over the existing methods measured by high sensitivity and specificity. MitoTracer is compatible with multiple single cell sequencing platforms. Its application to a cancer evolution dataset revealed the genes related to primary BRAF-inhibitor resistance from scRNA-seq data of BRAF-mutated cancer cells. Overall, our work provided a valuable tool for capturing real informative MT mutations and tracing the lineages among cells.

Journal Article↗

MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction.

Mitochondrial (MT) mutations serve as natural genetic markers for inferring clonal relationships using single cell sequencing data. However, the fundamental challenge of MT mutation-based lineage tracing is automated identification of informative MT mutations. Here, we introduced an open-source computational algorithm called "MitoTracer", which accurately identified clonally informative MT mutations and inferred evolutionary lineage from scRNA-seq or scATAC-seq samples. We benchmarked MitoTracer using the ground-truth experimental lineage sequencing data and demonstrated its superior performance over the existing methods measured by high sensitivity and specificity. MitoTracer is compatible with multiple single cell sequencing platforms. Its application to a cancer evolution dataset revealed the genes related to primary BRAF-inhibitor resistance from scRNA-seq data of BRAF-mutated cancer cells. Overall, our work provided a valuable tool for capturing real informative MT mutations and tracing the lineages among cells.

Humans↗

Evolution of Hepatitis B virus in an acute hepatitis B patient co-infected with genotypes B and C.

The interactions between different genotypes of Hepatitis B virus (HBV) in co-infected patients remain largely unknown, especially in acute infection. Here, the evolution of HBV strains was studied in an acute, self-limited hepatitis B patient co-infected with genotypes Ba (B2) and C. Virological analyses were performed at four time points after admission: T1 (5 days), T2 (11 days), T3 (22 days) and T4 (260 days). A dominant-genotype change from genotype C to Ba was found after anti-HBV e antigen (anti-HBe) seroconversion. Further clonal and phylogenetic analyses of the pre-S and pre-core/core regions of HBV were carried out to clarify the interactions between genotypes Ba and C. All clones propagated from T1 and T2 were of genotype C. In contrast, clones propagated from T3 (after anti-HBe seroconversion) were of genotype Ba, C and/or recombinant within the pre-S region. At T4, all clones were of genotype Ba with a 123 bp (from nt 3147 of the pre-S1 region to nt 54 of the pre-S2 region) in-frame pre-S deletion and had lost the start codon of the middle envelope protein and the nucleocapsid-binding site. Phylogenetic analysis showed that genetic distance was greater at T3 after seroconversion to anti-HBe. By using SimPlot, the breakpoint of one pre-S recombinant was located at nt 3069-3100 and the other two at nt 49-87. In conclusion, HBV genotype Ba may overtake genotype C as the predominant strain after anti-HBe seroconversion in acute hepatitis B. Recombination within the pre-S region emerged transiently and the pre-S deletion mutant was finally cleared.

Acute Disease↗

Evolutionary aspects of human cancer.

Evolutionary aspects of human cancer can be dealt with at two levels--on the one hand long-term evolution involving hereditary effects between generations; and on the other hand evolutionary processes operating within the organisms between tissues, cells and cell constituents, which also comprise genetic alterations, selection and adaptation. These two levels of evolution can be designated as phylogenetic and ontogenetic evolution, respectively. Concerning phylogenetic evolution there must have been a strong selection against neoplastic diseases occurring at reproductive age and a variety of protective mechanisms against carcinogenic agents have been developed. Cancer is therefore primarily a disease of old age, which does not constitute a significant risk in natural populations for the simple reason that the life length is too short. The development of an individual comprises selection forces between cells and tissues, which are particularly striking for the multistage development of tumours. The accumulation of several genetic alterations in the same cells, as illustrated by the analysis of colorectal tumours, must require a pronounced clonal expansion between each event. Such selective growth effect has recently been demonstrated for the tumour suppressor gene p53 in brain tumours. Cancer often implies a break down of between balanced systems antagonistic forces, such as oncogenes and suppressors of oncogenes. Examples of this are provided by the genetic regulation of metastasis, involving metalloproteinase as well as the inhibitor of metalloproteinase. The immortalization of cells by transformation points to the fact that programmed cell death and the balance between suicide genes and suppressors of such suicide genes is affected.

Apoptosis↗

Molecular evolution perspectives on intraspecific lateral DNA transfer of topoisomerase and gyrase loci in Streptococcus pneumoniae, with implications for fluoroquinolone resistance development and spread.

Fluoroquinolones are an important class of antibiotics for the treatment of infections arising from the gram-positive respiratory pathogen Streptococcus pneumoniae. Although there is evidence supporting interspecific lateral DNA transfer of fluoroquinolone target loci, no studies have specifically been designed to assess the role of intraspecific lateral transfer of these genes in the spread of fluoroquinolone resistance. This study involves a comparative evolutionary perspective, in which the evolutionary history of a diverse set of S. pneumoniae clinical isolates is reconstructed from an expanded multilocus sequence typing data set, with putative recombinants excluded. This control history is then assessed against networks of each of the four fluoroquinolone target loci from the same isolates. The results indicate that although the majority of fluoroquinolone target loci from this set of 60 isolates are consistent with a clonal dissemination hypothesis, 3 to 10% of the sequences are consistent with an intraspecific lateral transfer hypothesis. Also evident were examples of interspecific transfer, with two isolates possessing a parE-parC gene region arising from viridans group streptococci. The Spain 23F-1 clone is the most dominant fluoroquinolone-nonsusceptible clone in this set of isolates, and the analysis suggests that its members act as frequent donors of fluoroquinolone-nonsusceptible loci. Although the majority of fluoroquinolone target gene sequences in this set of isolates can be explained on the basis of clonal dissemination, a significant number are more parsimoniously explained by intraspecific lateral DNA transfer, and in situations of high S. pneumoniae population density, such events could be an important means of resistance spread.

Amino Acid Sequence↗

Initial clonal acute lymphoblastic transformation of chronic lymphocytic leukemia with (11;14) and (8;12) chromosome translocations and acquired homozygosity.

A 69-year-old woman presented with chronic lymphocytic leukemia (CLL) diagnosed after bone marrow recovery following intensive chemotherapy for acute lymphoblastic leukemia. The retrospective diagnosis of initial blastic transformation of CLL was made. The patient eventually died, 5 months after initial blastic phase, from a blastic relapse of her CLL. Immunologic and karyotypic studies of the lymphoid cells at different times during the evolution of the disease provided evidence that both the small lymphocytes and the large blastic cells originated from the same clone since they carried the same surface markers and the same (11;14) (q13;q32) translocation. A subpopulation of cells carried in addition a t(8;12) (q24;q22) together with the loss of the normal chromosome 8 and homozygosity for the abnormal der(8). The possibility that this second population might correspond to the blast cells and that the occurrence of the t(8;12) with homozygosity might be linked to blastic transformation of the CLL is discussed.

Aged↗

Selective inactivation of p53 facilitates mouse epithelial tumor progression without chromosomal instability.

We examined the selective pressure for, and the impact of, p53 inactivation during epithelial tumor evolution in a transgenic brain tumor model. In TgT(121) mice, cell-specific inactivation of the pRb pathway in brain choroid plexus epithelium initiates tumorigenesis and induces p53-dependent apoptosis. We previously showed that p53 deficiency accelerates tumor growth due to diminished apoptosis. Here we show that in a p53(+/-) background, slow-growing dysplastic tissue undergoes clonal progression to solid angiogenic tumors in all animals. p53 is inactivated in all progressed tumors, with loss of the wild-type allele occurring in 90% of tumors. Moreover, similar progression occurs in 38% of TgT(121)p53(+/+) mice, also with loss of at least one p53 allele and inactivation of p53. Thus, the selective pressure for p53 inactivation, likely based on its apoptotic function, is high. Yet, in all cases, p53 inactivation correlates with progression beyond apoptosis reduction, from dysplasia to solid vascularized tumors. Hence, p53 suppresses tumor progression in this tissue by multiple mechanisms. Previous studies of fibroblasts and hematopoietic cells show that p53 deficiency can be associated with chromosomal instability, a mechanism that may drive tumor progression. To determine whether genomic gains or losses are present in tumors that progress in the absence of p53, we performed comparative genomic hybridization analysis. Surprisingly, the only detectable chromosomal imbalance was partial or complete loss of chromosome 11, which harbors the p53 gene and is thus the selected event. Flow cytometry confirmed that the majority of tumor cells were diploid. These studies indicate that loss of p53 function is frequent under natural selective pressures and furthermore that p53 loss can facilitate epithelial tumor progression by a mechanism in addition to apoptosis reduction and distinct from chromosomal instability.

Animals↗

A clonal selection based timecourse model for antibody responses to killed vaccine, with applications to foot and mouth disease.

Published models for the timecourse of the immune response are reviewed for their applicability to data from animals that have been injected with killed vaccine. Simple models are required so that statistical fitting procedures become straightforward. A class of models that incorporates the concept of clonal selection has been found useful. Immune memory is described in terms of persistence of mean antibody affinity when the overall concentration of antibody has declined towards background. The model is demonstrated on multipoint affinity distributions and initial negative exponential densities, from which conditions for boundedness can be developed. Predictions are made that are consistent with experiments on the evolution of immunoassay data using foot and mouth disease vaccine.

Animals↗

Generation and regulation of developing immortalized neural cell lines.

The genetic and environmental signals that regulate progressive lineage elaboration in the mammalian brain are poorly understood. In addition, characterization of the developmental profiles of early central nervous system (CNS) stem/ progenitor cells and analysis of the mechanisms involved in their clonal expansion, lineage restriction, and cellular maturation have been fragmentary and elusive. These seminal neurodevelopmental issues have been examined using a series of clonally derived neural stem/progenitor cell lines established by retroviral transduction of embryonic (E16.5-E17.5) murine hippocampal and cerebellar cells using temperature-sensitive alleles (A58/U19) of the simian virus (SV) 40 large tumor (T) antigen. Under conditions permissive for T-antigen expression (33 degrees C), single neural stem cells exhibited self-renewal, clonal expansion, and both symmetric and asymmetric modes of cell division. By contrast, at the nonpermissive temperature for T-antigen expression (39 degrees C), specific sets of cytokines potentiated the progressive elaboration of neuronal, oligodendroglial, and astroglial lineage species. These observations demonstrate that a spectrum of genetic and epigenetic signals and distinct cellular processes are involved in orchestrating the evolution of individual neural lineages from regional CNS stem/progenitor species. Further, the availability of conditionally immortalized neural cell lines that can be transplanted back into the mammalian brain may represent an important experimental resource for the detailed characterization of cellular and molecular mechanisms involved in the developmental sculpting, plasticity, and regeneration of the mammalian CNS.

3T3 Cells↗

The immune system evolved to discriminate infectious nonself from noninfectious self.

Here, Charles Janeway argues that the requirement for two signals to initiate the adaptive immune response may reflect the evolutionary history of host defences. Early phases of host defence involve receptors and ligands that may have controlled immune responses prior to the development of clonally-distributed receptors encoded in rearranging genes. The former receptors persist in contemporary vertebrates both to trigger innate or nonclonal responses and to signal to lymphocytes that a particular antigen is associated with a microorganism.

Animals↗

Genetic diversity and reproductive biology in ecotypes of the facultative apomict Hypericum perforatum L.

Apomixis is a mode of asexual reproduction through seed. Progeny produced by apomixis are clonal replicas of a mother plant. The essential feature of apomixis is that embryo sacs and embryos are produced in ovules without meiotic reduction or egg cell fertilisation. Thus, apomixis fixes successful gene combinations and propagates high fitness genotypes across generations. A more profound knowledge of the mechanisms that regulate reproductive events in plants would contribute fundamentally to understanding the evolution and genetic control of apomixis. Molecular markers were used to determine levels of genetic variation within and relationship among ecotypes of the facultative apomict Hypericum perforatum L. (2n = 4x = 32). All ecotypes were polyclonal, being not dominated by a single genotype, and characterised by different levels of differentiation among multilocus genotypes. Flow cytometric analysis of seeds indicated that all ecotypes were facultatively apomictic, with varying degrees of apomixis and sexuality. Seeds set by haploid parthenogenesis and/or by fertilisation of aposporic egg cells were detected in most populations. The occurrence of both dihaploids and hexaploids indicates that apospory and parthenogenesis may be developmentally uncoupled and supports two distinct genetic factors controlling apospory and parthenogenesis in this species. Cyto-embryological analysis showed that meiotic and aposporic processes do initiate within the same ovule: the aposporic initial often appeared evident at the time of megaspore mother cell differentiation. Our observations suggest that the egg cell exists in an active metabolic state before pollination, and that its parthenogenetic activation leading to embryo formation may occur before fertilisation and endosperm initiation.

DNA Primers↗

A novel Leu153Ser mutation of the Fanconi anemia FANCD2 gene is associated with severe chemotherapy toxicity in a pediatric T-cell acute lymphoblastic leukemia.

Fanconi anemia (FA) is an autosomal recessive disease characterized by pancitopenia, congenital malformations, predisposition to cancers and chromosomal instability. We report the clinical and molecular features of a patient initially identified as a potential FA case only because of chemotherapy toxicity during the treatment of a T-lineage acute lymphoblastic leukemia (ALL). Cells from this patient showed a moderate chromosomal instability, increasing sensitivity to DNA crosslinking agents but normal response to ionizing radiation. The analysis of FA proteins demonstrated a marked reduction of FANCD2 (>95%), but normal levels of FANCA or FANCG. Interestingly, this defect was associated with a homozygous missense mutation of FANCD2, resulting in a novel amino-acid substitution (Leu153Ser) at residue Leu153, which is highly conserved through evolution. The FANCD2(L153S) protein, whose reduced expression was not due to impaired transcription, was detected also in its monoubiquitinated form in the nucleus, suggesting that the mutation does not affect post-translation modifications or subcellular localization but rather the stability of FANCD2. Therefore, the hypomorphic Leu153Ser mutation represents the first example of a FANCD2 defect that might promote clonal progression of tumors, such as T-ALL, and severe chemotherapy toxicity in patients without any clinical manifestations typical of FA.

Amino Acid Substitution↗

Cryptic sex and many-to-one coevolution in the fungus-growing ant symbiosis.

The fungus-growing ants have long provided a spectacular example of coevolutionary integration. Their ecological success is thought to depend largely on the evolutionary alignment of reproductive interests between ants and fungi after vertical transmission and the ancient suppression of fungal sexuality. In the present study we test these assumptions and provide the first evidence of recombination in attine cultivars, contradicting widely held perceptions of obligate clonality. In addition, we document long-distance horizontal transmission of symbionts between leaf-cutter ant species on mainland Central America and South America and those endemic to Cuba, suggesting both lack of pairwise coevolutionary specificity in ant/cultivar interactions and dispersal of symbionts independent of their ant hosts. The coevolution between leaf-cutters and their fungal symbionts is thus not reciprocally pairwise. Rather, a single widespread and sexual fungal symbiont species is engaged in multiple interactions with divergent ant lineages. Strict fungal clonality and vertical transmission evidently have not played a critical role in the long-term evolutionary or ecological success of this well known mutualism.

Agaricales↗

Acute panmyelosis with myelofibrosis.

Acute panmyelosis with myelofibrosis (APMF) is an ill-defined disorder that may either evolve as a clonal hematopoietic condition or as a sequel of toxic exposure to the bone marrow (BM). Therefore, controversy and discussion continues as to whether APMF may be considered as a hyperfibrotic (de novo) myelodysplastic syndrome (MDS), as acute myeloid leukemia (AML) or as a severe toxic myelopathy with accompanying myelofibrosis. In this context scant knowledge exists about BM findings, but especially evolution of this disorder according to sequential examinations. Clinically patients present with pancytopenia, a very few blasts in the peripheral blood and no or little splenomegaly. Initially BM histopathology is characterized by different degrees of reticulin-collagen fibrosis and wide ranges of cellularity with a prominent left-shifted and often macrocytic erythropoiesis associated with a reduction and maturation defects of the neutrophil series. Most conspicuous are abnormalities of the megakaryocytes including loose clustering, dislocation towards the endosteal border and appearance of atypical microforms with compact nuclei. Moreover, besides myelofibrosis in a number of patients the interstitial compartment displays a remarkable inflammatory reaction with lymphoid nodules, abundant iron-laden macrophages, perivascular plasmacytosis and increase in microvessels. Repeatedly performed BM biopsies reveal an accumulation of dispersed or clustered CD34+ and lysozyme-expressing blasts in keeping with the insidious transformation into acute leukemia. Prognosis is unfavorable with a median survival of less than 1 year. In conclusion, APMF has to be regarded as a condition that shows considerable overlappings with primary hyperfibrotic MDS, AML and toxic myelopathy (secondary MDS) with accompanying myelofibrosis and therefore can not be considered as a definite clinical entity.

Acute Disease↗

Extensive acronecrosis as a manifestation of mixed cryoglobulinaemia: a case report.

Cryoglobulinaemia is a systemic disorder characterized by circulating antibodies that precipitate in the cold and resolve on rewarming. Three different types have been described, distinct in the class of immunoglobulins and their clonality. The clinical expression varies from purpura and arthralgia to progressive renal failure and even acronecrosis (1-3). Associated conditions are lymphoproliferative disorders, auto-immune diseases and chronic infections, but several cases occur in the absence of identifyable other disease states. The present communication reports on a case of mixed cryoglobulinaemia. Of particular interest are the rapidly progressive clinical evolution to acronecrosis of the four limbs, necessitating amputation, the presence of spurious leucocytosis and the absence of other systemic symptoms.

Aged↗