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PubMed1999

Systematic biology of gymnotiform and mormyriform electric fishes: phylogenetic relationships, molecular clocks and rates of evolution in the mitochondrial rRNA genes

The phylogenetic relationships of both African and South American electric fish orders are reviewed at their intra-ordinal level taking into consideration recent studies in which cladistic principles have been employed. Several concordant topologies emerge from the different data sets, but some unsettled issues still remain. From the studies available, a consensus topology has been suggested for the Mormyriformes and for the Gymnotiformes. Subsequently, the evolutionary relationships of these two electric fish clades are considered within each respective superorder, i.e. in relation to the other osteoglossomorph and ostariophysan orders. The inter-ordinal phylogenies are used as a framework to test the molecular clock hypothesis with two gene fragments of the mitochondrial genome. Gymnotiformes, Siluriformes and Characiformes are accumulating mutations at the same pace in relation to their respective outgroups, but for all the other combinations of sister clades tested the molecular clock can be statistically rejected. Fossil records are then surveyed and used to calibrate absolute rates of genetic differentiation for each main lineage (orders) of both osteoglossomorphs and ostariophysans. The most conserved regions (stems) of the 12S and 16S gene fragments used are evolving at an average rate of 0.123 % 10(6 )years-1 for the osteoglossomorphs and 0.137 % 10(6 )years-1 for the ostariophysans, with no significant difference between these two values. The rate of mutation in the loops, the faster-evolving segments, estimated for closely related electric fish taxa is 0.82 % 10(6 )years-1 for four Brienomyrus species and 1.01 % 10(6 )years-1 for the four eigenmanniid genera. When the entire molecule (loops + stems) is considered, the rate of mutation in both mormyriforms and gymnotiforms converges to a rounded value of 0.23 % 10(6 )years-1.

Journal Article↗
PubMed2005

Cell delivery system: a novel strategy to improve the efficacy of cancer immunotherapy by manipulation of immune cell trafficking and biodistribution.

Tumor cells that generally accumulate mutations in the genome express molecules different both qualitatively and quantitatively from normal cells. An immunosurveillance system for these molecules, known as the tumor-associated antigens (TAAs), plays an important role in the elimination of cancer cells during the initial stage. Although cancer immunotherapy targeting TAAs has progressed steadily with the development of various vaccine strategies, satisfactory efficacy, such as marked tumor regression and complete response, has not been previously reported in a clinical setting. To improve the therapeutic effects of cancer immunotherapy, the application of chemokine-chemokine receptor coupling, which controls the trafficking and biodistribution of immune cells in the living body, is an attractive potential approach. This review introduces our novel "cell delivery system," which employs an Arg-Gly-Asp (RGD) fiber-mutant adenovirus vector encoding the chemokine or chemokine receptor gene in cancer immunotherapy.

Animals↗
PubMed2006

Emergence of protein fold families through rational design.

Diverse proteins with similar structures are grouped into families of homologs and analogs, if their sequence similarity is higher or lower, respectively, than 20%-30%. It was suggested that protein homologs and analogs originate from a common ancestor and diverge in their distinct evolutionary time scales, emerging as a consequence of the physical properties of the protein sequence space. Although a number of studies have determined key signatures of protein family organization, the sequence-structure factors that differentiate the two evolution-related protein families remain unknown. Here, we stipulate that subtle structural changes, which appear due to accumulating mutations in the homologous families, lead to distinct packing of the protein core and, thus, novel compositions of core residues. The latter process leads to the formation of distinct families of homologs. We propose that such differentiation results in the formation of analogous families. To test our postulate, we developed a molecular modeling and design toolkit, Medusa, to computationally design protein sequences that correspond to the same fold family. We find that analogous proteins emerge when a backbone structure deviates only 1-2 angstroms root-mean-square deviation from the original structure. For close homologs, core residues are highly conserved. However, when the overall sequence similarity drops to approximately 25%-30%, the composition of core residues starts to diverge, thereby forming novel families of protein homologs. This direct observation of the formation of protein homologs within a specific fold family supports our hypothesis. The conservation of amino acids in designed sequences recapitulates that of the naturally occurring sequences, thereby validating our computational design methodology.

Computational Biology↗
PubMed2005

Leukemic stem cells: where do they come from?

Leukemias can now be viewed as aberrant hematopoietic processes initiated by rare cancer stem cells, or leukemic stem cells (LSCs) that have maintained or reacquired the capacity for indefinite proliferation through accumulated mutations and/or epigenetic changes. Yet, despite their critical importance, much remains to be learned about the developmental origin of LSCs and the mechanisms responsible for their emergence in the course of the disease. Mouse models of human leukemias have provided a unique system to study the mechanisms influencing LSC generation and function, and were recently used to demonstrate that LSCs can arise from both self-renewing hematopoietic stem cells (HSCs) and committed progenitor populations. This striking finding indicates that LSC identity is largely dictated by the nature of the oncogenic events and by how these events perturb essential processes such as self-renewal, proliferation, differentiation, and survival. Such approaches in the mouse are essential for the basic understanding of leukemogenesis and for the conceptual design of novel therapeutic strategies that could lead to improved treatments for human leukemias.

Animals↗
PubMed2005

Stem cells and mammary cancer in mice.

I have used the paradigm of mammary cancer induction by the mouse mammary tumor virus (MMTV) to illustrate the body of evidence that supports the hypothesis that mammary epithelial stem/progenitor cells represent targets for oncogenic transformation. Further, it is argued that this is not a special case applicable only to MMTV-induced mammary cancer, because MMTV acts as an environmental mutagen producing random interruptions in the somatic DNA of infected cells by insertion of proviral DNA copies. In addition to disrupting the host genome, the proviral DNA also influences gene expression through its associated enhancer sequences over significant inter-genome distances. Genes commonly affected by MMTV insertion in multiple individual tumors include the Wnt genes, the fibroblast growth factor (FGF) gene family, and the Notch gene family. All of these gene families are known to play essential roles in stem cell maintenance and behavior in a variety of organs. The MMTV-induced mutations accumulate in cells that are long-lived and possess the properties of stem cells, namely, self-renewal and the capacity to produce divergent epithelial progeny through asymmetric division. The evidence shows that epithelial cells with these properties are present in normal mammary glands, may be infected with MMTV, and become transformed to produce epithelial hyperplasia through MMTV-induced mutagenesis and progress to frank mammary malignancy. Retroviral marking via MMTV proviral insertion demonstrates that this process progresses from a single mammary epithelial cell that possesses all the features ascribed to tissue-specific stem cells.

Animals↗
PubMed2005

Quantitative trait loci with age-specific effects on fecundity in Drosophila melanogaster.

Life-history theory and evolutionary theories of aging assume the existence of alleles with age-specific effects on fitness. While various studies have documented age-related changes in the genetic contribution to variation in fitness components, we know very little about the underlying genetic architecture of such changes. We used a set of recombinant inbred lines to map and characterize the effects of quantitative trait loci (QTL) affecting fecundity of Drosophila melanogaster females at 1 and 4 weeks of age. We identified one QTL on the second chromosome and one or two QTL affecting fecundity on the third chromosome, but these QTL affected fecundity only at 1 week of age. There was more genetic variation for fecundity at 4 weeks of age than at 1 week of age and there was no genetic correlation between early and late-age fecundity. These results suggest that different loci contribute to the variation in fecundity as the organism ages. Our data provide support for the mutation accumulation theory of aging as applied to reproductive senescence. Comparing the results from this study with our previous work on life-span QTL, we also find evidence that antagonistic pleiotropy may contribute to the genetic basis of senescence in these lines as well.

Aging↗
PubMed2006

The genetic architecture of life span and mortality rates: gender and species differences in inbreeding load of two seed-feeding beetles.

We examine the inbreeding load for adult life span and mortality rates of two seed beetle species, Callosobruchus maculatus and Stator limbatus. Inbreeding load differs substantially between males and females in both study populations of C. maculatus--life span of inbred females was 9-13% shorter than the life span of outbred females, whereas the life span of inbred males did not differ from the life span of outbred males. The effect of inbreeding on female life span was largely due to an increase in the slope of the mortality curve. In contrast, inbreeding had only a small effect on the life span of S. limbatus--life spans of inbred beetles were approximately 5% shorter than those of outbred beetles, and there was no difference in inbreeding load between the sexes. The inbreeding load for mean life span was approximately 0.4-0.6 lethal equivalents per haploid gamete for female C. maculatus and approximately 0.2-0.3 for both males and females of S. limbatus, all within the range of estimates commonly obtained for Drosophila. However, contrary to the predictions of mutation-accumulation models, inbreeding load for loci affecting mortality rates did not increase with age in either species, despite an effect of inbreeding on the initial rate of increase in mortality. This was because mortality rates decelerated with age and converged to a mortality plateau for both outbred and inbred beetles.

Animals↗
PubMed2006

Genomewide evolutionary rates in laboratory and wild yeast.

As wild organisms adapt to the laboratory environment, they become less relevant as biological models. It has been suggested that a commonly used S. cerevisiae strain has rapidly accumulated mutations in the lab. We report a low-to-intermediate rate of protein evolution in this strain relative to wild isolates.

Evolution, Molecular↗
PubMed1997

Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor.

From a database containing the published nuclear hormone receptor (NR) sequences I constructed an alignment of the C, D and E domains of these molecules. Using this alignment, I have performed tree reconstruction using both distance matrix and parsimony analysis. The robustness of each branch was estimated using bootstrap resampling methods. The trees constructed by these two methods gave congruent topologies. From these analyses I defined six NR subfamilies: (i) a large one clustering thyroid hormone receptors (TRs), retinoic acid receptors (RARs), peroxisome proliferator-activated receptors (PPARs), vitamin D receptors (VDRs) and ecdysone receptors (EcRs) as well as numerous orphan receptors such as RORs or Rev-erbs; (ii) one containing retinoid X receptors (RXRs) together with COUP, HNF4, tailless, TR2 and TR4 orphan receptors; (iii) one containing steroid receptors; (iv) one containing the NGFIB orphan receptors; (v) one containing FTZ-F1 orphan receptors; and finally (vi) one containing to date only one gene, the GCNF1 orphan receptor. The relationships between the six subfamilies are not known except for subfamilies I and IV which appear to be related. Interestingly, most of the liganded receptors appear to be derived when compared with orphan receptors. This suggests that the ligand-binding ability of NRs has been gained by orphan receptors during the course of evolution to give rise to the presently known receptors. The distribution into six subfamilies correlates with the known abilities of the various NRs to bind to DNA as homo- or heterodimers. For example, receptors heterodimerizing efficiently with RXR belong to the first or the fourth subfamilies. I suggest that the ability to heterodimerize evolved once, just before the separation of subfamilies I and IV and that the first NR was able to bind to DNA as a homodimer. From the study of NR sequences existing in vertebrates, arthropods and nematodes, I define two major steps of NR diversification: one that took place very early, probably during the multicellularization event leading to all the metazoan phyla, and a second occurring later on, corresponding to the advent of vertebrates. Finally, I show that in vertebrate species the various groups of NRs accumulated mutations at very different rates.

Animals↗
PubMed2001

Novel paracellin-1 mutations in 25 families with familial hypomagnesemia with hypercalciuria and nephrocalcinosis.

Familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) is an autosomal recessive tubular disorder that is frequently associated with progressive renal failure. The primary defect is related to impaired tubular reabsorption of magnesium and calcium in the thick ascending limb of Henle's loop. Mutations in PCLN-1, which encodes the renal tight junction protein paracellin-1 (claudin-16), were identified as the underlying genetic defects. Comprehensive clinical data and the results of PCLN-1 mutation analysis of 25 FHHNC families with 33 affected individuals are presented. Patients presented mainly with urinary tract infections, polyuria, and hematuria at a median age of 3.5 yr. At the time of diagnosis, the GFR was already decreased to <60 ml/min per 1.73 m(2) for 11 patients. Twelve patients exhibited progression to end-stage renal disease, at a median age of 14.5 yr. Treatment with magnesium salts and thiazides seemed to have no effect on the progression of the disease. Genotype analysis revealed PCLN-1 mutations in all except three mutant alleles (94%). Fifteen different mutations were observed, including eight novel mutations. The accumulation of mutations affecting the first extracellular loop was striking, with 48% of all mutant alleles exhibiting a Leu151Phe exchange. Haplotype analysis strongly suggested a founder effect among patients with FHHNC who originated from Germany or eastern European countries. In 13 of 23 families, hypercalciuria and/or nephrolithiasis were observed in otherwise unaffected family members, indicating a possible role of heterozygous PCLN-1 mutations in yielding hypercalciuric stone-forming conditions.

Adolescent↗
PubMed2001

Detecting rare mutations associated with cancer risk.

For more than a decade, investigators have been searching for a means of determining the risk of individuals developing cancer by detecting rare oncogenic mutations. The accumulation of mutations and the clonal evolvement of tumors provide opportunities for monitoring disease development and intervening prior to the presentation of clinical symptoms, or determining the risk of disease relapse during remission. A number of techniques, mostly polymerase chain reaction (PCR)-based, have been developed that enable the detection of rare oncogenic mutations within the range of 10(-2) to 10(-4) wild-type cells. Only a handful of procedures enable the detection of intragenic single base mutations at one mutant in 10-6 or better. These ultra-sensitive mutation detection techniques have produced some interesting results regarding single base mutation spectra and frequencies in p53, Harvey-ras, N-ras, and other reporter genes and DNA sequences in human tissues. Although there is evidence that some individuals may harbor cells or clones expressing genomic instability, the connection with the processes of carcinogenesis is still tenuous. There remains a need for rigorous epidemiological studies employing these ultra-sensitive mutation detection procedures. Since genomic instability is considered key to tumor development, the relevance of the detection of hypermutable clones in individuals is discussed in the context of cancer risk.

Body Fluids↗
PubMed2004

Structural determinants and molecular mechanisms for the resistance of HIV-1 RT to nucleoside analogues.

The reverse transcriptase (RT) of human immunodeficiency virus type-1 (HIV-1) is an RNA- and DNA-dependent DNA polymerase capable of copying the viral genome before it gets integrated into the human host DNA. Hence, HIV-1 RT plays a major role in viral replication and represents a key target for anti-AIDS treatments. Amongst the eleven licensed drugs that inhibit RT, eight are chain-terminating nucleoside analogues (NRTIs) that compete with their natural counterparts during the DNA polymerization process. Unfortunately, under therapeutic pressure, the HIV-1 inevitably develops resistance to these inhibitors by accumulating mutations in the viral pol gene encoding RT. Mechanisms for this resistance can be sorted in two categories, depending on the nature of the drug and the selected mutations. The first category includes mutations involving a specific alteration of the discrimination between natural nucleotides and NRTIs. The second category includes mutations able to promote the removal of the incorporated NRTI and thus repair the nascent DNA chain. This review summarizes the modes of inhibition of HIV-1 RT with NRTIs, and describes the mechanisms of resistance to these drugs, based on enzymatic data correlated to crystal structures and molecular models involving HIV-1 RT. We also give insights into different aspects of resistance such as antagonistic mutations, replication capacity, and the implications for a rational, structure-based drug design.

Animals↗
PubMed1997

Molecular pathways in low grade B-cell lymphoma.

Low grade B-cell non-Hodgkin's lymphomas (B-NHL) represent a markedly heterogeneous group of lymphoproliferative disorders, including B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma (B-CCL/SLL), lymphoplasmacytoid lymphoma (LPL), follicular lymphoma (FL), mucosa-associated lymphoid tissue lymphoma (MALTL), and splenic lymphoma with villous lymphocytes (SLVL). The molecular pathogenesis of low grade B-NHL is characterized by distinct genetic pathways which selectively associate with each clinicopathologic category. At diagnosis, B-CLL/SLL frequently display deletions of 13q14 and trisomy 12, whereas evolution to Richter's syndrome associates with disruption of p53. LPL carries t(9;14)(p13;q32) in 40-50% of the cases, leading to the deregulated expression of the PAX-5 gene. FL consistently harbors rearrangements of BCL-2 independent of the cytologic variant. With time, a fraction of FL cases accumulates mutations of p53 and evolves into a high grade B-NHL. Low grade MALTL are characterized by the frequent occurrence of trisomy 3 and, occasionally, by p53 mutations. SLVL carries p53 mutations in a fraction of cases. The identification of distinct genetic categories among low grade B-NHL may help in the therapeutic stratification of these disorders. In addition, genetic lesions of low grade B-NHL have proved to be a useful molecular marker for monitoring minimal residual disease.

Antigens, CD↗
PubMed2006

Complementary analysis of microsatellite tumor profile and mismatch repair defects in colorectal carcinomas.

Microsatellite instability (MSI) is a prognostic factor and a marker of deficient mismatch repair (MMR) in colorectal adenocarcinomas (CRC). However, a proper application of this marker requires understanding the following: (1) The MSI concept: The PCR approach must amplify the correct locus and accurately identify the microsatellite pattern in the patient's normal tissue. MSI is demonstrated when the length of DNA sequences in a tumor differs from that of nontumor tissue. Any anomalous expansion or reduction of tandem repeats results in extra-bands normally located in the expected size range (100 bp, above or below the expected product), differ from the germline pattern by some multiple of the repeating unit, and must show appropriate stutter. (2) MSI mechanisms: MMR gene inactivation (by either mutation or protein down-regulation as frequently present in deep CRC compartments) leads to mutation accumulation in a cell with every cellular division, resulting in malignant transformation. These mechanisms can express tumor progression and result in a decreased prevalence of aneuploid cells and loss of the physiologic cell kinetic correlations in the deep CRC compartments. MSI molecular mechanisms are not necessarily independent from chromosomal instability and may coexist in a given CRC. (3) Because of intratumoural heterogeneity, at least two samples from each CRC should be screened, preferably from the superficial (tumor cells above the muscularis propria) and deep (tumor cells infiltrating the muscularis propria) CRC compartments to cover the topographic tumor heterogeneity. (4) Pathologists play a critical role in identifying microsatellite-unstable CRC, such as occur in young patients with synchronous or metachronous tumors or with tumors showing classic histologic features. In these cases, MSI testing and/or MMR immunohistochemistry are advisable, along with gene sequencing and genetic counseling if appropriate. MSI is an excellent functional and prognostically useful marker, whereas MMR immunohistochemistry can guide gene sequencing.

Adenocarcinoma↗
PubMed2000

Effects of cyclin D1 polymorphism on age of onset of hereditary nonpolyposis colorectal cancer.

A common polymorphism in the cyclin D1 gene enhances the gene's alternate splicing. The alternatively spliced product encodes an altered protein that does not contain sequences involved in the turnover of the protein. We found that hereditary nonpolyposis colorectal carcinoma patients who were homozygous or heterozygous for the mutant allele developed colorectal cancer an average of 11 years earlier than patients who were homozygous for the normal alleles. This is the first report indicating that the cyclin D1 polymorphism influences age of onset of cancer. Because cyclin D1 plays an important role in the G1 to S phase transition of the cell cycle, our findings suggest that cells with the mutant allele accumulate mutations as a result of defective mismatch repair and may also bypass the G1-S checkpoint of the cell cycle more easily than in cells not carrying the polymorphism. The polymorphism has a dominant phenotype.

Adaptor Proteins, Signal Transducing↗
PubMed2000

Molecular pathophysiology of indolent lymphoma.

Indolent lymphomas are a markedly heterogeneous group of lymphoproliferative disorders including B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma, lymphoplasmacytoid lymphoma, follicular lymphoma, mantle cell lymphoma and mucosa-associated lymphoid tissue (MALT) lymphoma. The molecular pathophysiology of indolent lymphoma is characterized by distinct genetic pathways which selectively associate with different clinico-pathologic categories of the disease. At diagnosis, B-cell chronic lymphocytic leukemia frequently display deletions of 13q14, trisomy 12 and alterations of the ATM gene, whereas evolution to Richter's syndrome is associated with disruption of p53. Lymphoplasmacytoid lymphoma carries t(9;14) (p13;q32) in approximately 50% of cases, leading to the deregulated expression of the PAX-5 gene. Follicular lymphoma consistently harbors rearrangement of BCL-2. With time, a fraction of follicular lymphoma accumulates mutations of p53 and of p16 and evolves into a high grade lymphoma. MALT-lymphoma frequently associates with alterations of API2/MLT and, in some cases, of p53, BCL-6 and BCL-10. Studies of genotypic and phenotypic markers of histogenesis have shown that mantle cell lymphoma and a fraction of B-CLL/SLL derive from naive B-cells, whereas follicular lymphoma, lymphoplasmacytoid lymphoma and MALT-lymphoma originate from germinal center (GC) or post-GC B-cells. The identification of distinct genetic categories of indolent lymphoma may help in the therapeutic stratification of these disorders. In addition, genetic lesions of indolent lymphoma provide useful molecular markers for disease monitoring by high sensitivity techniques.

Chromosome Aberrations↗
PubMed2000

Mutational analysis of RET/GDNF/NTN genes in children with total colonic aganglionosis with small bowel involvement.

Hirschsprung disease (HSCR) is characterized by the absence of intramural ganglion cells in the distal gut, resulting in bowel obstruction shortly after birth. Aganglionosis usually affects the distal colon, but may also extensively involve the entire colon and, rarely, the more proximal bowel. Recently, germline mutations of RET, GDNF, and NTN genes have been reported in HSCR. Here we describe the results of mutational analysis of these genes in 15 Japanese child patients with total colonic aganglionosis with small bowel involvement. DNA sequences of all the RET/GDNF/NTN coding regions were determined by the direct dyedeoxy terminator cycle method. Eight different RET mutations were identified in exons 1, 7, 10, 12, 15, and 17 in 10 of the 15 patients. Of these eight mutations, five were found in the tyrosine kinase domain. No GDNF or NTN mutation was found. Compared with typical HSCR, this patient group appeared to exhibit a higher percentage of RET mutations and accumulation of mutations in the tyrosine kinase domain. A homozygous (or hemizygous) RET mutation was found in a male baby with total intestinal aganglionosis, while the heterozygosity of the same mutation resulted in a less severe type of aganglionosis. In familial cases, all heterozygous for the same mutation, aganglionosis was more severe in male than in female siblings. These results also urge us to examine if the RET germline mutation may cause critical alteration of the GDNF/NTN-Ret signal transduction more severely in homo(hemi)zygosity and in male fetuses during organogenesis.

Child↗
PubMed2001

Neurovirulence of Sabin 1-derived polioviruses isolated from an immunodeficient patient with prolonged viral excretion.

We have analysed the neurovirulence of Sabin 1-derived isolates which persisted more than nine years in an immunodeficient patient in the U.S.A. Samples were collected from stool specimens at days 11 (St1), 23 (St2), 48 (St3), 126 (St5), and 200 (St7) after the onset of paralysis. Critical nucleotides associated with the reversion of virulence were examined. All the isolates had the substitutions at nucleotide positions 480 (G to A) in the 5'-non-coding region (NCR), 2438 (A to U) in VP3, 2795 (A to G) in VP1, and 6203 (C to U) in 3D. Serially diluted samples were injected intracerebrally to transgenic mice harbouring the human poliovirus receptor gene. Samples St2, 3, 5 and 7 showed typical virulent characters in transgenic mice, whereas the sample ST1 showed intermediate neurovirulence. It seemed that there were two variant viruses providing for a major (M) and a minor (m) populations. After disappearance of the m-variant, samples obtained at the later stages showed neurovirulence almost equivalent to that of the Mahoney strain. Thus, the Sabin 1 strain evolved towards full neuropathogenicity after long-term replication in humans by accumulating mutations. Therefore, OPV-vaccination of immunodeficient persons should be avoided.

Animals↗