Initiation of Genome Instability and Preneoplastic Processes through Loss of Fhit Expression

Genomic instability drives tumorigenesis, but how it is initiated in sporadic neoplasias is unknown. In early preneoplasias, alterations at chromosome fragile sites arise due to DNA replication stress. A frequent, perhaps earliest, genetic alteration in preneoplasias is deletion within the fragile FRA3B/FHIT locus, leading to loss of Fhit protein expression. Because common chromosome fragile sites are exquisitely sensitive to replication stress, it has been proposed that their clonal alterations in cancer cells are due to stress sensitivity rather than to a selective advantage imparted by loss of expression of fragile gene products. Here, we show in normal, transformed, and cancer-derived cell lines that Fhit-depletion causes replication stress-induced DNA double-strand breaks. Using DNA combing, we observed a defect in replication fork progression in Fhit-deficient cells that stemmed primarily from fork stalling and collapse. The likely mechanism for the role of Fhit in replication fork progression is through regulation of Thymidine kinase 1 expression and thymidine triphosphate pool levels; notably, restoration of nucleotide balance rescued DNA replication defects and suppressed DNA breakage in Fhit-deficient cells. Depletion of Fhit did not activate the DNA damage response nor cause cell cycle arrest, allowing continued cell proliferation and ongoing chromosomal instability. This finding was in accord with in vivo studies, as Fhit knockout mouse tissue showed no evidence of cell cycle arrest or senescence yet exhibited numerous somatic DNA copy number aberrations at replication stress-sensitive loci. Furthermore, cells established from Fhit knockout tissue showed rapid immortalization and selection of DNA deletions and amplifications, including amplification of the Mdm2 gene, suggesting that Fhit loss-induced genome instability facilitates transformation. We propose that loss of Fhit expression in precancerous lesions is the first step in the initiation of genomic instability, linking alterations at common fragile sites to the origin of genome instability.     

BAF180 Promotes Cohesion and Prevents Genome Instability and Aneuploidy

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Bcl-2 Expression Identifies an Early Stage of Myogenesis and Promotes Clonal Expansion of Muscle Cells

We show that Bcl-2 expression in skeletal muscle cells identifies an early stage of the myogenic pathway, inhibits apoptosis, and promotes clonal expansion. Bcl-2 expression was limited to a small proportion of the mononucleate cells in muscle cell cultures, ranging from ∼1–4% of neonatal and adult mouse muscle cells to ∼5–15% of the cells from the C2C12 muscle cell line. In rapidly growing cultures, some of the Bcl-2–positive cells coexpressed markers of early stages of myogenesis, including desmin, MyoD, and Myf-5. In contrast, Bcl-2 was not expressed in multinucleate myotubes or in those mononucleate myoblasts that expressed markers of middle or late stages of myogenesis, such as myogenin, muscle regulatory factor 4 (MRF4), and myosin. The small subset of Bcl-2–positive C2C12 cells appeared to resist staurosporine-induced apoptosis. Furthermore, though myogenic cells from genetically Bcl-2–null mice formed myotubes normally, the muscle colonies produced by cloned Bcl-2–null cells contained only about half as many cells as the colonies produced by cells from wild-type mice. This result suggests that, during clonal expansion from a muscle progenitor cell, the number of progeny obtained is greater when Bcl-2 is expressed.     

CD28 Promotes CD4+ T Cell Clonal Expansion during Infection Independently of Its YMNM and PYAP Motifs

CD28 is required for maximal proliferation of CD4(+) T cells stimulated through their TCRs. Two sites within the cytoplasmic tail of CD28, a YMNM sequence that recruits PI3K and activates NF-κB and a PYAP sequence that recruits Lck, are candidates as transducers of the signals responsible for these biological effects. We tested this proposition by tracking polyclonal peptide:MHCII-specific CD4(+) T cells in vivo in mice with mutations in these sites. Mice lacking CD28 or its cytoplasmic tail had the same number of naive T cells specific for a peptide:MHCII ligand as wild-type mice. However, the mutant cells produced one tenth as many effector and memory cells as wild-type T cells after infection with bacteria expressing the antigenic peptide. Remarkably, T cells with a mutated PI3K binding site, a mutated PYAP site, or both mutations proliferated to the same extent as wild-type T cells. The only observed defect was that T cells with a mutated PYAP or Y170F site proliferated even more weakly in response to peptide without adjuvant than wild-type T cells. These results show that CD28 enhances T cell proliferation during bacterial infection by signals emanating from undiscovered sites in the cytoplasmic tail.     

Mitochondrial Genome Mutation in Cell Death and Aging

This article reviews the concept, molecular genetics, and pathology of cell death and agingin relation to mitochondrial genome mutation. Accumulating evidence emphasizes the role ofgenetic factors in the development of naturally occurring cell death and aging. The ATPrequired for a cell's biological activity is almost exclusively produced by mitochondria. Eachmitochondrion possesses its own DNA (mtDNA) that codes essential subunits of themitochondrial energy-transducing system. Recent studies confirm that mtDNA is unexpectedly fragileto hydroxyl radical damage, hence to the oxygen stress. Cellular mtDNA easily fragmentsinto over a hundred-types of deleted mtDNA during the life of an individual. Cumulativeaccumulation of these oxygen damages and deletions in mtDNA results in a defective energytransducing system and in bioenergetic crisis. The crisis leads cells to the collapse ofmitochondrial trans-membrane potential, to the release of the apoptotic protease activating factors intocytosol, to uncontrolled cell death, to tissue degeneration and atrophy, and to aging. Thetotal base sequencing of mtDNA among individuals revealed that germ-line point mutationstransmitted from ancestors accelerate the somatic oxygen damages and mutations in mtDNAleading to phenotypic expression of premature aging and degenerative diseases. A practicalsurvey of point mutations will be useful for genetic diagnosis in predicting the life-span ofan individual.     

Causes and Consequences of Genome Instability in Psychiatric and Neurodegenerative Diseases

Molecular Biology - Each neuron has 100–10000 connections (synapses) with other neural cells, therefore genome pathologies affecting a small proportion of brain cells are capable of causing...     

The Alternative TrkAIII Splice Variant Targets the Centrosome and Promotes Genetic Instability

The hypoxia-regulated alternative TrkAIII splice variant expressed by human neuroblastomas exhibits oncogenic potential, driven by in-frame exon 6 and 7 alternative splicing, leading to omission of the receptor extracellular immunoglobulin C₁ domain and several N-glycosylation sites. Here, we show that the TrkAIII oncogene promotes genetic instability by interacting with and exhibiting catalytic activity at the centrosome. This function depends upon intracellular TrkAIII accumulation and spontaneous interphase-restricted activation, in cytoplasmic tyrosine kinase (tk) domain orientation, predominantly within structures that closely associate with the fully assembled endoplasmic reticulum intermediate compartment and Golgi network. This facilitates TrkAIII tk-mediated binding of γ-tubulin, which is regulated by endogenous protein tyrosine phosphatases and geldanamycin-sensitive interaction with Hsp90, paving the way for TrkAIII recruitment to the centrosome. At the centrosome, TrkAIII differentially phosphorylates several centrosome-associated components, increases centrosome interaction with polo kinase 4, and decreases centrosome interaction with separase, the net results of which are centrosome amplification and increased genetic instability. The data characterize TrkAIII as a novel internal membrane-associated centrosome kinase, unveiling an important alternative mechanism to “classical” cell surface oncogenic receptor tk signaling through which stress-regulated alternative TrkAIII splicing influences the oncogenic process.Alternative splicing is fundamental for differential protein expression from the same gene and not only increases the proteomic complexity of higher organisms (29) but is also involved in cancer pathogenesis, activating several oncogenes and inactivating several oncosuppressors (17).The neurotrophin receptor tropomyosin-related kinase A (TrkA) is among the proto-oncogenes activated by alternative splicing, with a novel hypoxia-regulated oncogenic alternative TrkAIII splice variant recently identified in advanced-stage human neuroblastomas (NB) and primary glioblastomas (44, 45). In contrast to wild-type TrkAI/TrkAII, the expression of which is associated with better prognosis for NB, induces NB cell differentiation, exhibits a tumor suppressor function in NB models in vivo (9, 19, 22, 30, 44, 45), and may regulate both spontaneous and therapy-induced NB regression (30), TrkAIII is expressed by more-advanced-stage NB and exhibits oncogenic activity in NB models (44, 45). This has challenged the hypothesis of an exclusively tumor-suppressing function for TrkA in NB by providing a way through which tumor-suppressing signals from TrkA can be converted to oncogenic signals from TrkAIII during tumor progression.The oncogenic potential of TrkAIII, characterized by NIH 3T3 cell transforming and NB xenograft primary and metastatic tumor-promoting activity (44, 45), is driven by in-frame alternative splicing of exons 6 and 7. This results in the omission of the receptor extracellular immunoglobulin C₁ (Ig C₁) Ig-like domain and several N-glycosylation sites important in regulating TrkA cell surface expression and preventing ligand-independent activation (2, 44, 45, 48). As a consequence, and unlike TrkAI and TrkAII, TrkAIII is not expressed at the cell surface but accumulates in the intracellular membrane compartment, within which it exhibits spontaneous tyrosine kinase (tk) and phosphoinositol-3 kinase (PI3K) activity and induces chronic signaling through PI3K/Akt/NF-κB but not Ras/mitogen-activated protein kinase (MAPK), inducing a more stress-resistant, angiogenic, and tumorigenic NB cell phenotype (44, 45). This differs from ligand-activated cell surface TrkA, which signals transiently through Ras/MAPK in NB cells to induce differentiation and a less angiogenic and tumorigenic NB cell phenotype (9, 19, 22, 30, 44, 45). This difference in signaling provides a potential basis for the opposing tumor-suppressing and oncogenic effects of alternative TrkA splice variants, which may not only depend upon the dislocation of TrkAIII from cell surface caveolae, which are the sites of TrkAI expression and Ras/MAPK signal initiation (45, 48), but also TrkAIII-associated PI3K activity below the Ras/MAPK activation threshold and/or TrkAIII-associated PI3K antagonism of Raf/MEK/extracellular signal-regulated kinase signaling (44). Signal transduction from intracellular TrkAIII bears close resemblance to the transient signaling through PI3K/Akt/NF-κB but not Ras/MAPK induced by A2a adenosine receptor/c-Src-mediated transactivation of immature TrkAI within the Golgi network (GN) (37), suggesting that the intracellular localization of TrkAIII is a critical determinant of both differential signaling and oncogenic potential.Intracellular nonnuclear membranes are separated into the endoplasmic reticulum (ER), ER-GN intermediate compartment (ERGIC), GN, and transport vesicles, which assemble around, integrate, and interact with the centrosome (38). The centrosome, comprised of two centrioles embedded within a pericentriolar matrix of over 100 proteins, including γ-tubulin, acts as the major microtubule-organizing center and orchestrates the assembly, organization, and integration of the ER, ERGIC, GN, and associated vesicles (38). The centrosome also maintains genomic integrity by duplicating once per cell cycle S phase, ensuring bipolar mitotic spindle formation, accurate chromosome segregation, and the inheritance of a single centrosome by each daughter cell (23).Centrosome duplication is tightly regulated by protein kinases Aurora-A and -B, polo kinases 1 and 4 (Plk-1 and Plk-4), Cdk2, PI3K, Zyg-1, Syk, Nek2, regulators Pin-1 and separase, and related phosphatases (11, 12, 18, 31, 42, 47, 53). The deregulation of centrosome duplication leads to centrosome amplification and subsequently to aberrant mitotic spindle formation, which promotes aneuploidy and polyploidy. These manifestations of genetic instability represent hallmarks of malignancy and drive tumor progression by promoting a more malignant phenotype (11, 12, 26, 35, 49). Centrosome amplification and subsequent genetic instability are induced by kinases that target the centrosome, the loss of centrosome-associated kinase inhibitors, altered levels of centrosome-associated regulators, and oncosuppressor inactivation (6, 7, 11, 12, 35, 40, 42, 49, 53).The localization of TrkAIII to internal membranes, as a prerequisite for oncogenic activity (44, 45), makes identification of the membrane context within which TrkAIII exhibits activity and novel substrate interactions within this environment important in elucidating how TrkAIII exerts oncogenic potential. In the present study, we unveil a novel oncogenic mechanism for TrkAIII by demonstrating that TrkAIII activation within membranes that associate closely with the assembled ER/ERGIC/GN facilitates recruitment to the centrosome, results in centrosome amplification, and promotes genetic instability.     

Replication Fork Collapse and Genome Instability in a Deoxycytidylate Deaminase Mutant

Ribonucleotide reductase (RNR) and deoxycytidylate deaminase (dCMP deaminase) are pivotal allosteric enzymes required to maintain adequate pools of deoxyribonucleoside triphosphates (dNTPs) for DNA synthesis and repair. Whereas RNR inhibition slows DNA replication and activates checkpoint responses, the effect of dCMP deaminase deficiency is largely unknown. Here, we report that deleting the Schizosaccharomyces pombe dcd1⁺ dCMP deaminase gene (SPBC2G2.13c) increases dCTP ∼30-fold and decreases dTTP ∼4-fold. In contrast to the robust growth of a Saccharomyces cerevisiae dcd1Δ mutant, fission yeast dcd1Δ cells delay cell cycle progression in early S phase and are sensitive to multiple DNA-damaging agents, indicating impaired DNA replication and repair. DNA content profiling of dcd1Δ cells differs from an RNR-deficient mutant. Dcd1 deficiency activates genome integrity checkpoints enforced by Rad3 (ATR), Cds1 (Chk2), and Chk1 and creates critical requirements for proteins involved in recovery from replication fork collapse, including the γH2AX-binding protein Brc1 and Mus81 Holliday junction resolvase. These effects correlate with increased nuclear foci of the single-stranded DNA binding protein RPA and the homologous recombination repair protein Rad52. Moreover, Brc1 suppresses spontaneous mutagenesis in dcd1Δ cells. We propose that replication forks stall and collapse in dcd1Δ cells, burdening DNA damage and checkpoint responses to maintain genome integrity.     

Correlation of Gene Expression and Genome Mutation in Single B-Cells

High-throughput measurement of gene-expression and immune receptor repertoires have recently become powerful tools in the study of adaptive immune response. However, despite their now-widespread use, both tend to discard cell identity by treating cell populations in bulk, and therefore lose the correlation between genetic variability and gene-expression at the single cell level. In order to recover this information, we developed a method to simultaneously measure gene expression profiles and genome mutations in single cells. We applied this method by quantifying the relationships between gene expression and antibody mutation in ensembles of individual B-cells from immunized mice. The results reveal correlations reflecting the manner in which information propagates between a B-cell’s antigen receptors, its gene expression, and its mutagenic machinery, and demonstrate the power of this approach to illuminate both heterogeneity and physiology in cell populations.     

Premeiotic and Meiotic Instability Generates Numerous b2 Mutation Derivatives in Ascobolus

We have studied the genetic characteristics of an unstable mutation located in the central region of the b2 gene of the fungus Ascobolus. In crosses to wild type, this spontaneous white ascospore mutation (G0 ) gives rise to a stable white spored derivative (G1) at a frequency of 5 x 10(-3). G1 is a frameshift mutation and differs from G0 by its gene conversion pattern. In self crosses, G0 gives asci with colored spore derivatives at a frequency of 1 x 10(-3). We isolated and analyzed genetically 97 independent colored derivatives ("G2" series). All but one are pseudorevertants. By the criteria of phenotype and gene conversion pattern with wild type and with G1, the pseudorevertants represent at least 13 distinct classes. Two of them are large silent deletion mutations. In crosses with wild type, some G2 derivatives, represented by G21, continue to exhibit instability, G21 yields white spored b2 mutant derivatives at a frequency of 2.6 x 10(-3). In turn, some of these "G3" mutants are themselves unstable. All the derivatives lie at the same site within the b2 locus as the parental mutation G0 . Different mutations in the G series manifest their instability at different times in the Ascobolus life cycle. Derivatives of G0 arise premeiotically (leading to two derivative meiotic products among the four), while those of G21 arise during meiosis (leading to only one derivative out of four products). The characteristics of the G instability system are similar to those of unstable mutations in other eukaryotes which are due to insertion of mobile elements.     

BAG3 蛋白Ser187磷酸化位点定点突变促进FRO细胞迁移和侵袭

Bcl-2相关抗凋亡蛋白3（Bcl-2 associated athanogene 3,BAG3）是BAG家族的重要成员,调节肿瘤细胞的黏附、迁移和侵袭,促进恶性肿瘤的复发和转移。我们的前期工作证明,PKCδ可催化BAG3的Ser187位点磷酸化。本文研究BAG3蛋白磷酸化修饰对甲状腺癌FRO 细胞迁移、侵袭的影响及其可能机制。通过定点突变的方法,将BAG3蛋白的187位丝氨酸突变为天冬氨酸（S187D）模拟磷酸化,或者将丝氨酸突变为丙氨酸（S187A）抵抗磷酸化,从而间接推测BAG3蛋白Ser187位点磷酸化对FRO细胞迁移、侵袭的影响。 FRO细胞转染野生型BAG3、模拟磷酸化型BAG3、阻碍磷酸化型BAG3,通过划痕愈合实验和Transwell转移小室实验,观察BAG3蛋白磷酸化对FRO细胞迁移、侵袭的影响。进一步通过PKC激活剂和抑制剂,研究BAG3蛋白磷酸化对FRO细胞迁移、侵袭影响的机制。 结果显示,FRO BAG3-S187D模拟磷酸化组细胞在培养24 h、48 h时,划痕愈合率分别达到35%和80%。Transwell及三维Matrigel转移小室实验显示,平均每个视野穿膜细胞数分别达到180和350个,与对照组相比,差异有统计学意义（P<0.05）。PKC激活剂TPA及抑制剂Rottelerin处理FRO WT-BAG3细胞,24 h愈合率分别为40% 和15%,48 h划痕愈合率分别为55%和18%,Transwell穿膜细胞数分别为240和70个,与对照组细胞相比,差异显著（P<0.05）。本研究提示,BAG3蛋白Ser187磷酸化修饰,可促进甲状腺癌FRO细胞迁移、侵袭,其机制可能与PKC信号通路有关。     

A P53-Independent DNA Damage Response Suppresses Oncogenic Proliferation and Genome Instability

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Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton

Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging 3-fold in genome size, namely Gossypium rotundifolium (K₂), G. arboreum (A₂), and G. raimondii (D₅), using Oxford Nanopore Technologies. Comparative genome analyses document the details of lineage-specific TE amplification contributing to the large genome size differences (K₂, 2.44 Gb; A₂, 1.62 Gb; D₅, 750.19 Mb) and indicate relatively conserved gene content and synteny relationships among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status change between active (“A”) and inactive (“B”) compartments, and TE amplification was associated with the increase of the proportion of A compartment in gene regions (∼7,000 genes) in K₂ and A₂ relative to D₅. Only 42% of topologically associating domain (TAD) boundaries were conserved among the three genomes. Our data implicate recent amplification of TEs following the formation of lineage-specific TAD boundaries. This study sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.     

Cigarette Smoke Promotes Drug Resistance and Expansion of Cancer Stem Cell-Like Side Population

It is well known that many patients continue to smoke cigarettes after being diagnosed with cancer. Although smoking cessation has typically been presumed to possess little therapeutic value for cancer, a growing body of evidence suggests that continued smoking is associated with reduced efficacy of treatment and a higher incidence of recurrence. We therefore investigated the effect of cigarette smoke condensate (CSC) on drug resistance in the lung cancer and head and neck cancer cell lines A549 and UMSCC-10B, respectively. Our results showed that CSC significantly increased the cellular efflux of doxorubicin and mitoxantrone. This was accompanied by membrane localization and increased expression of the multi-drug transporter ABCG2. The induced efflux of doxorubicin was reversed upon addition of the specific ABCG2 inhibitor Fumitremorgin C, confirming the role of ABCG2. Treatment with CSC increased the concentration of phosphorylated Akt, while addition of the PI3K inhibitor {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002 blocked doxorubicin extrusion, suggesting that Akt activation is required for CSC-induced drug efflux. In addition, CSC was found to promote resistance to doxorubicin as determined by MTS assays. This CSC-induced doxurbicin-resistance was mitigated by mecamylamine, a nicotinic acetylcholine receptor inhibitor, suggesting that nicotine is at least partially responsible for the effect of CSC. Lastly, CSC increased the size of the side population (SP), which has been linked to a cancer stem cell-like phenotype. In summary, CSC promotes chemoresistance via Akt-mediated regulation of ABCG2 activity, and may also increase the proportion of cancer stem-like cells, contributing to tumor resilience. These findings underscore the importance of smoking cessation following a diagnosis of cancer, and elucidate the mechanisms of continued smoking that may be detrimental to treatment.