The Role of Weak Interactions in the Phase Transition and Distinct Mechanical Behavior of Two Structurally Similar Caffeine Co-crystal Polymorphs Studied by Nanoindentation

Although weak interactions, such as C-H center dot center dot center dot O and pi-stacking, are generally considered to be insignificant, it is their reorganization that holds the key for many a solid-state phenomenon, such as phase transitions, plastic deformation, elastic flexibility, and mechanochromic luminescence in solid-state fluorophores. Despite this, the role of weak interactions in these dynamic phenomena is poorly understood. In this study, we investigate two co-crystal polymorphs of caffeine:4-chloro-3-nitrobenzoic acid, which have close structural similarity (2D layered structures), but surprisingly show distinct mechanical behavior. Form I is brittle, but shows shear-induced phase instability and, upon grinding, converts to Form II, which is soft and plastically shearable. This observation is in contrast to those reported in earlier studies on aspirin, wherein the metastable drug forms are softer and convert to stable and harder forms upon stressing To establish a molecular level understanding, have investigated the two co-crystal polymorphs I and II by single crystal X-ray diffraction, nanoindentation to quantify mechanical properties, and theoretical calculations. The lower hardness (from nanoindentation) and smooth potential surfaces (from theoretical studies) for shearing of layers in Form II allowed us to rationalize the role of stronger intralayer (sp(2))C-H center dot center dot center dot O and nonspecific interlayer pi-stacking interactions in the structure of II. Although the Form I also possesses the same type of interactions, its strength is clearly opposite, that is, weaker intralayer (sp(3))C-H center dot center dot center dot O and specific interlayer pi-stacking interactions. Hence, Form I is harder than Form IL Theoretical calculations and indentation on (111) of Form I suggested the low resistance of this face to mechanical stress; thus, Form I converts to II upon mechanical action. Hence, our approach demonstrates the usefulness of multiple techniques for establishing the role of weak noncovalent interactions in solid-state dynamic phenomena, such as stress induced phase transformation, and hence is important in the context of solid-state pharmaceutical chemistry and crystal engineering.

Structure-specific nuclease activity of RAGs is modulated by sequence, length and phase position of flanking double-stranded DNA

RAGs (recombination activating genes) are responsible for the generation of antigen receptor diversity through the process of combinatorial joining of different V (variable), D (diversity) and J (joining) gene segments. In addition to its physiological property, wherein RAG functions as a sequence-specific nuclease, it can also act as a structure-specific nuclease leading to genomic instability and cancer. In the present study, we investigate the factors that regulate RAG cleavage on non-B DNA structures. We find that RAG binding and cleavage on heteroduplex DNA is dependent on the length of the double-stranded flanking region. Besides, the immediate flanking double-stranded region regulates RAG activity in a sequence-dependent manner. Interestingly, the cleavage efficiency of RAGs at the heteroduplex region is influenced by the phasing of DNA. Thus, our results suggest that sequence, length and phase positions of the DNA can affect the efficiency of RAG cleavage when it acts as a structure-specific nuclease. These findings provide novel insights on the regulation of the pathological functions of RAGs.

DNA Double-Strand Break Repair Inhibitors as Cancer Therapeutics

Among DNA damages, double-strand breaks (DSBs) are one of the most harmful lesions to a cell. Failure in DSB repair could lead to genomic instability and cancer. Homologous recombination (HR) and nonhomologous end joining (NHEJ) are major DSB repair pathways in higher eukaryotes. It is known that expression of DSB repair genes is altered in various cancers. Activation of DSB repair genes is one of the reasons for chemo-and radioresistance. Therefore, targeting DSB repair is an attractive strategy to eliminate cancer. Besides, therapeutic agents introduce breaks in the genome as an intermediate. Therefore, blocking the residual repair using inhibitors can potentiate the efficacy of cancer treatment. In this review, we discuss the importance of targeting DSB repair pathways for the treatment of cancer. Recent advances in the development of DSB repair inhibitors and their clinical relevance are also addressed.

Detection of G-Quadruplex DNA Using Primer Extension as a Tool

DNA sequence and structure play a key role in imparting fragility to different regions of the genome. Recent studies have shown that non-B DNA structures play a key role in causing genomic instability, apart from their physiological roles at telomeres and promoters. Structures such as G-quadruplexes, cruciforms, and triplexes have been implicated in making DNA susceptible to breakage, resulting in genomic rearrangements. Hence, techniques that aid in the easy identification of such non-B DNA motifs will prove to be very useful in determining factors responsible for genomic instability. In this study, we provide evidence for the use of primer extension as a sensitive and specific tool to detect such altered DNA structures. We have used the G-quadruplex motif, recently characterized at the BCL2 major breakpoint region as a proof of principle to demonstrate the advantages of the technique. Our results show that pause sites corresponding to the non-B DNA are specific, since they are absent when the G-quadruplex motif is mutated and their positions change in tandem with that of the primers. The efficiency of primer extension pause sites varied according to the concentration of monovalant cations tested, which support G-quadruplex formation. Overall, our results demonstrate that primer extension is a strong in vitro tool to detect non-B DNA structures such as G-quadruplex on a plasmid DNA, which can be further adapted to identify non-B DNA structures, even at the genomic level.

A longitudinal study of epigenetic variation in twins.

DNA methylation is a key epigenetic mechanism involved in the developmental regulation of gene expression. Alterations in DNA methylation are established contributors to inter-individual phenotypic variation and have been associated with disease susceptibility. The degree to which changes in loci-specific DNA methylation are under the influence of heritable and environmental factors is largely unknown. In this study, we quantitatively measured DNA methylation across the promoter regions of the dopamine receptor 4 gene (DRD4), the serotonin transporter gene (SLC6A4/SERT) and the X-linked monoamine oxidase A gene (MAOA) using DNA sampled at both ages 5 and 10 years in 46 MZ twin-pairs and 45 DZ twin-pairs (total n=182). Our data suggest that DNA methylation differences are apparent already in early childhood, even between genetically identical individuals, and that individual differences in methylation are not stable over time. Our longitudinal-developmental study suggests that environmental influences are important factors accounting for interindividual DNA methylation differences, and that these influences differ across the genome. The observation of dynamic changes in DNA methylation over time highlights the importance of longitudinal research designs for epigenetic research.

Human Papillomavirus Type 16 E6 and E7 Cause Polyploidy in Human Keratinocytes and Up-Regulation of G2-M-phase Proteins

Human papillomavirus type 16 proteins E6 and E7 have been shown to cause centrosome amplification and lagging chromosomes during mitosis. These abnormalities during mitosis can result in missegregation of the chromosomes, leading to chromosomal instability. Genomic instability is thought to be an essential part of the conversion of a normal cell to a cancer cell. We now show that E6 and E7 together cause polyploidy in primary human keratinocytes soon after these genes are introduced into the cells. Polyploidy seems to result from a spindle checkpoint failure arising from abrogation of the normal functions of p53 and retinoblastoma family members by E6 and E7, respectively. In addition, E6 and E7 cause deregulation of cellular genes such as Plk1, Aurora-A, cdk1, and Nek2, which are known to control the G2-M-phase transition and the ordered progression through mitosis.

New advances in radiation biology.

Current understanding of risk associated with low-dose radiation exposure has for many years been embedded in the linear-no-threshold (LNT) approach, based on simple extrapolation from the Japanese atomic bomb survivors. Radiation biology research has supported the LNT approach although much of this has been limited to relatively high-dose studies. Recently, with new advances for studying effects of low-dose exposure in experimental models and advances in molecular and cellular biology, a range of new effects of biological responses to radiation has been observed. These include genomic instability, adaptive responses and bystander effects. Most have one feature in common in that they are observed at low doses and suggest significant non-linear responses. These new observations pose a significant challenge to our understanding of low-dose exposure and require further study to elucidate mechanisms and determine their relevance.

The Delta Np63 Proteins Are Key Allies of BRCA1 in the Prevention of Basal-Like Breast Cancer

Little is known about the origin of basal-like breast cancers, an aggressive disease that is highly similar to BRCA1-mutant breast cancers. p63 family proteins that are structurally related to the p53 suppressor protein are known to function in stem cell regulation and stratified epithelia development in multiple tissues, and p63 expression may be a marker of basal-like breast cancers. Here we report that Delta Np63 isoforms of p63 are transcriptional targets for positive regulation by BRCA1. Our analyses of breast cancer tissue microarrays and BRCA1-modulated breast cancer cell lines do not support earlier reports that p63 is a marker of basal-like or BRCA1 mutant cancers. Nevertheless, we found that BRCA1 interacts with the specific p63 isoform Delta Np63 gamma along with transcription factor isoforms AP-2 alpha and AP-2 gamma. BRCA1 required Delta Np63 gamma and AP-2 gamma to localize to an intronic enhancer region within the p63 gene to upregulate transcription of the Delta Np63 isoforms. In mammary stem/progenitor cells, siRNA- mediated knockdown of Delta Np63 expression resulted in genomic instability, increased cell proliferation, loss of DNA damage checkpoint control, and impaired growth control. Together, our findings establish that transcriptional upregulation of Delta Np63 proteins is critical for BRCA1 suppressor function and that defects in BRCA1-Delta Np63 signaling are key events in the pathogenesis of basal-like breast cancer. Cancer Res; 71( 5); 1933-44. (c) 2011 AACR.

Elevated expression of Runx2 as a key parameter in the etiology of osteosarcoma

To understand the molecular etiology of osteosarcoma, we isolated and characterized a human osteosarcoma cell line (OS1). OS1 cells have high osteogenic potential in differentiation induction media. Molecular analysis reveals OS1 cells express the pocket protein pRB and the runt-related transcription factor Runx2. Strikingly, Runx2 is expressed at higher levels in OS1 cells than in human fetal osteoblasts. Both pRB and Runx2 have growth suppressive potential in osteoblasts and are key factors controlling competency for osteoblast differentiation. The high levels of Runx2 clearly suggest osteosarcomas may form from committed osteoblasts that have bypassed growth restrictions normally imposed by Runx2. Interestingly, OS1 cells do not exhibit p53 expression and thus lack a functional p53/p21 DNA damage response pathway as has been observed for other osteosarcoma cell types. Absence of this pathway predicts genomic instability and/or vulnerability to secondary mutations that may counteract the anti-proliferative activity of Runx2 that is normally observed in osteoblasts. We conclude OS1 cells provide a valuable cell culture model to examine molecular events that are responsible for the pathologic conversion of phenotypically normal osteoblast precursors into osteosarcoma cells.

The epigenome as a therapeutic target in prostate cancer

During cancer development and progression, tumor cells undergo abnormal epigenetic modifications, including DNA methylation, histone deacetylation and nucleosome remodeling. Collectively, these aberrations promote genomic instability and lead to silencing of tumor-suppressor genes and reactivation of oncogenic retroviruses. Epigenetic modifications, therefore, provide exciting new avenues for prostate cancer research. Promoter hypermethylation is widespread during neoplastic transformation of prostate cells, which suggests that restoration of a 'normal' epigenome through treatment with inhibitors of the enzymes involved could be clinically beneficial. Global patterns of histone modifications are also being defined and have been associated with clinical and pathologic predictors of prostate cancer outcome. Although treatment for localized prostate cancer can be curative, the development of successful therapies for the management of castration-resistant metastatic disease is urgently needed. Reactivation of tumor-suppressor genes by demethylating agents and histone deacetylase inhibitors could be a potential treatment option for patients with advanced disease.

DNA mismatch repair and the transition to hormone independence in breast and prostate cancer

The molecular basis for the progression of breast and prostate cancer from hormone dependent to hormone independent disease remains a critical issue in the management of these two cancers. The DNA mismatch repair system is integral to the maintenance of genomic stability and suppression of tumorigenesis. No firm consensus exists regarding the implications of mismatch repair (MMR) deficiencies in the development of breast or prostate cancer. However, recent studies have reported an association between mismatch repair deficiency and loss of specific hormone receptors, inferring a potential role for mismatch repair deficiency in this transition. An updated review of the experimental data supporting or contradicting the involvement of MMR defects in the development and progression of breast and prostate cancer will be provided with particular emphasis on their implications in the transition to hormone independence.

AURKA overexpression accompanies dysregulation of DNA-damage response genes in invasive urothelial cell carcinoma

Invasive urothelial cell carcinoma (UCC) is characterized by increased chromosomal instability and follows an aggressive clinical course in contrast to non-invasive disease. To identify molecular processes that confer and maintain an aggressive malignant phenotype, we used a high-throughput genome-wide approach to interrogate a cohort of high and low clinical risk UCC tumors. Differential expression analyses highlighted cohesive dysregulation of critical genes involved in the G(2)/M checkpoint in aggressive UCC. Hierarchical clustering based on DNA Damage Response (DDR) genes separated tumors according to a pre-defined clinical risk phenotype. Using array-comparative genomic hybridization, we confirmed that the DDR was disrupted in tumors displaying high genomic instability. We identified DNA copy number gains at 20q13.2-q13.3 (AURKA locus) and determined that overexpression of AURKA accompanied dysregulation of DDR genes in high risk tumors. We postulated that DDR-deficient UCC tumors are advantaged by a selective pressure for AURKA associated override of M phase barriers and confirmed this in an independent tissue microarray series. This mechanism that enables cancer cells to maintain an aggressive phenotype forms a rationale for targeting AURKA as a therapeutic strategy in advanced stage UCC.

Clinical Application of Poly(ADP-Ribose) Polymerase Inhibitors in High-Grade Serous Ovarian Cancer

: High-grade serous ovarian cancer is characterized by genomic instability, with one half of all tumors displaying defects in the important DNA repair pathway of homologous recombination. Given the action of poly(ADP-ribose) polymerase (PARP) inhibitors in targeting tumors with deficiencies in this repair pathway by loss of BRCA1/2, ovarian tumors could be an attractive population for clinical application of this therapy. PARP inhibitors have moved into clinical practice in the past few years, with approval from the Food and Drug Administration (FDA) and European Medicines Agency (EMA) within the past 2 years. The U.S. FDA approval of olaparib applies to fourth line treatment in germline BRCA-mutant ovarian cancer, and European EMA approval to olaparib maintenance in both germline and somatic BRCA-mutant platinum-sensitive ovarian cancer. In order to widen the ovarian cancer patient population that would benefit from PARP inhibitors, predictive biomarkers based on a clear understanding of the mechanism of action are required. Additionally, a better understanding of the toxicity profile is needed if PARP inhibitors are to be used in the curative, rather than the palliative, setting. We reviewed the development of PARP inhibitors in phase I-III clinical trials, including combination trials of PARP inhibitors and chemotherapy/antiangiogenics, the approval for these agents, the mechanisms of resistance, and the outstanding issues, including the development of biomarkers and the rate of long-term hematologic toxicities with these agents.

IMPLICATIONS FOR PRACTICE: The poly(ADP-ribose) polymerase (PARP) inhibitor olaparib has recently received approval from the Food and Drug Administration (FDA) and European Medicines Agency (EMA), with a second agent (rucaparib) likely to be approved in the near future. However, the patient population with potential benefit from PARP inhibitors is likely wider than that of germline BRCA mutation-associated disease, and biomarkers are in development to enable the selection of patients with the potential for clinical benefit from these agents. Questions remain regarding the toxicities of PARP inhibitors, limiting the use of these agents in the prophylactic or adjuvant setting until more information is available. The indications for olaparib as indicated by the FDA and EMA are reviewed.

Avaliação do efeito de metais pesados na fertilidade do ratinho

A infertilidade é um problema actual que afecta cerca de 8 a 12% dos casais em idade fértil, sendo 50% dos casos atribuídos ao factor masculino. A exposição ocupacional e/ou ambiental a metais pesados representa uma das suas principais causas. O chumbo, o cádmio e o crómio são metais com elevada utilização industrial e muito persistentes no ambiente, sendo motivo de grande preocupação devido aos seus efeitos na saúde reprodutiva dos trabalhadores e da população em geral. Neste trabalho estudaram-se os efeitos do cloreto de chumbo (PbCl2), cloreto de cádmio (CdCl2) e cromato de potássio (K2CrO4) na fertilidade, usando como modelo ratinhos machos ICR-CD1. Os ratinhos foram injectados subcutaneamente com 74 e 100 mg de PbCl2/kg pc ou com 5 e 10 mg de K2CrO4/kg pc, respectivamente, durante 4 dias consecutivos ou com 1, 2 e 3 mg de CdCl2/kg pc numa única injecção. Nos ensaios com PbCl2 e K2CrO4 os animais foram sacrificados 5 e 35 dias após o início da exposição, enquanto que nos ensaios com CdCl2 os animais foram sacrificados após 24 horas e 35 dias. O cloreto de chumbo não alterou a histologia do testículo nem do epidídimo, mas induziu um aumento da percentagem de células em fase S no testículo. O cloreto de chumbo alterou também alguns parâmetros dos espermatozóides, tais como a motilidade, morfologia e integridade do acrossoma. Contudo, não foram observados efeitos na integridade do DNA ou na estrutura da cromatina. O cloreto de cádmio induziu lesões severas e não reversíveis nos testículos que, após 35 dias, reverteram em necrose testicular. O cloreto de cádmio alterou ainda as subpopulações de células testiculares após 24 horas e induziu IMS no testículo após 35 dias. Em consequência das lesões no testículo, a densidade espermática foi severamente afectada após 35 dias. A exposição ao cloreto de cádmio afectou também a morfologia, a motilidade e a integridade acrossómica nos espermatozóides. O cloreto de cádmio induziu ainda fragmentação do DNA nestas células após 35 dias. O cromato de potássio alterou a morfologia dos espermatozóides e a integridade do acrossoma, sobretudo nos animais sacrificados após 35 dias. Verificou-se ainda uma redução da motilidade dos espermatozóides. Não foram detectados efeitos genotóxicos nos espermatozóides, devido à acção do K2CrO4 nas doses testadas. Dos parâmetros avaliados neste trabalho, destacam-se duas novas abordagens, nomeadamente o programa informático Snakes e a análise do conteúdo em DNA de células de testículo, a partir de material incluído em parafina. O Snakes permitiu fazer medições rigorosas do diâmetro dos tubos seminíferos, enquanto que a fixação de amostras de testículo de ratinhos em formol tamponado e inclusão em parafina resultou numa boa preservação do DNA, possibilitando assim a quantificação das subpopulações de células testiculares por citometria de fluxo. Os resultados obtidos para os diferentes parâmetros testados indicam que a motilidade dos espermatozóides e a integridade do acrossoma sejam parâmetros sensíveis à toxicidade de metais. O acrossoma aparenta ser um dos principais alvos da toxicidade dos metais e cuja reacção acrossómica prematura pode reduzir a capacidade do espermatozóide para fertilizar o oócito. Assim, este trabalho representa uma contribuição para uma melhor compreensão dos efeitos do chumbo, cádmio e crómio na fertilidade masculina.