Epigenetic regulation of telomeres in human cancer.

Hypomethylation of repeated elements in the genome is a common feature of human cancer, however, the direct consequences of this epigenetic defect for cancer biology are still largely unknown. Telomeres are specialized chromatin structures at the ends of eukaryotic chromosomes formed by tandem repeats of G-rich sequences and associated proteins, which have an essential role in chromosome end protection and genomic stability. Telomeric DNA repeats cannot be methylated, however, the adjacent subtelomeric DNA is heavily methylated in humans.

Affinity maturation of antibodies assisted by in silico modeling.

Rational engineering methods can be applied with reasonable success to optimize physicochemical characteristics of proteins, in particular, antibodies. Here, we describe a combined CDR3 walking randomization and rational design-based approach to enhance the affinity of the human anti-gastrin TA4 scFv. The application of this methodology to TA4 scFv, displaying only a weak overall affinity for gastrin17 (K(D) = 6 microM), resulted in a set of nine affinity-matured scFv variants with near-nanomolar affinity (K(D) = 13.

PaLS: filtering common literature, biological terms and pathway information.

Many biological experiments and their subsequent analysis yield lists of genes or proteins that can potentially be important to the prognosis or diagnosis of certain diseases (e.g. cancer).

SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data.

Background: Censored data are increasingly common in many microarray studies that attempt to relate gene expression to patient survival. Several new methods have been proposed in the last two years. Most of these methods, however, are not available to biomedical researchers, leading to many re-implementations from scratch of ad-hoc, and suboptimal, approaches with survival data.

Estrogen receptor status could modulate the genomic pattern in familial and sporadic breast cancer.

Purpose: Familial breast cancer represents 5% to 10% of all breast tumors. Mutations in the two known major breast cancer susceptibility genes, BRCA1 and BRCA2, account for a minority of familial breast cancer, whereas families without mutations in these genes (BRCAX group) account for 70% of familial breast cancer cases.

Experimental Design: To better characterize and define the genomic differences between the three classes of familial tumors and sporadic malignancies, we have analyzed 19 BRCA1, 24 BRCA2, and 31 BRCAX samples from familial breast cancer patients and 19 sporadic breast tumors using a 1-Mb resolution bacterial artificial chromosome array-based comparative genomic hybridization.

Distinct genomic aberration patterns are found in familial breast cancer associated with different immunohistochemical subtypes.

Five breast cancer subtypes have been described in sporadic breast cancer (SBC) using expression arrays: basal-like, ERBB2, normal breast-like, luminal A and B. These molecular subtypes show different genomic aberration patterns (GAPs). Recently, our group described these breast cancer subtypes in 50 non-BRCA1/2 familial tumors using immunohistochemistry assays.

GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest.

Background: Microarray data are often used for patient classification and gene selection. An appropriate tool for end users and biomedical researchers should combine user friendliness with statistical rigor, including carefully avoiding selection biases and allowing analysis of multiple solutions, together with access to additional functional information of selected genes. Methodologically, such a tool would be of greater use if it incorporates state-of-the-art computational approaches and makes source code available.

The role of activation-induced deaminase in antibody diversification and chromosome translocations.

Although B and T lymphocytes are similar in many respects including diversification of their antigen receptor genes by V(D)J recombination, 95% of all lymphomas diagnosed in the western world are of B-cell origin. Many of these are derived from mature B cells [Kuppers, R. (2005).

Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite.

Asterias (http://www.asterias.info) is an open-source, web-based, suite for the analysis of gene expression and aCGH data.

Solution structure of the endonuclease domain from the master replication initiator protein of the nanovirus faba bean necrotic yellows virus and comparison with the corresponding geminivirus and circovirus structures.

Nanoviruses are a family of plant viruses that possess a genome of multiple circular single-stranded DNA (ssDNA) components and are strikingly similar in their replication mode to the plant geminiviruses and to the circoviruses that infect birds or mammals. These viruses multiply by rolling circle replication using virus-encoded multifunctional replication initiator proteins (Rep proteins) that catalyze the initiation of replication on a double-stranded DNA (dsDNA) intermediate and the resolution of the ssDNA into circles. Here we report the solution NMR three-dimensional structure of the endonuclease domain from the master Rep (M-Rep) protein of faba bean necrotic yellows virus (FBNYV), a representative of the nanoviruses.

Genomic instability: on the birth and death of cancer.

The presence of an abnormal chromosomal content is probably the most universally conserved hallmark of cancer cells. Predicted at the beginning of the 20th century as the origin of tumours, and extensively documented thereafter, genomic instability lies at the core of neoplastic development. Regardless of this classic model, the actual impact that deficient control of genomic integrity has on human health and particularly on cancer development only started to gain attention from the scientific community two decades ago.

The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage.

Meganucleases are sequence-specific endonucleases with large cleavage sites that can be used to induce efficient homologous gene targeting in cultured cells and plants. These enzymes open novel perspectives for genome engineering in a wide range of fields, including gene therapy. A new crystal structure of the I-CreI dimer without DNA has allowed the comparison with the DNA-bound protein.

Expression, purification and crystallization of human CD5 domain III, a nano-scale crystallization example.

The human lymphocyte receptor CD5, a key regulator of immune responses, is involved in the modulation of antigen specific receptor-mediated T cell activation and differentiation signals. CD5 is a membrane glycoprotein which belongs to the group B scavenger receptor cysteine-rich (SRCR) superfamily for which no structural information is available. The most conserved membrane-proximal SRCR domain of CD5 (domain III) has been expressed in HEK-EBNA-293 cells.

Inactivation of the candidate tumor suppressor par-4 in endometrial cancer.

Recently, it has been shown that mice deficient in the proapoptotic protein prostate apoptosis response 4 (Par-4) are specifically prone to develop endometrial carcinomas. Based on this, we have examined here the possible role of Par-4 as a tumor suppressor gene in human endometrial cancer. Using cDNA arrays, quantitative reverse transcription-PCR, and immunohistochemistry, we detected Par-4 down-regulation in approximately 40% of endometrial carcinomas.

Crystal structure of the third extracellular domain of CD5 reveals the fold of a group B scavenger cysteine-rich receptor domain.

Scavenger receptor cysteine-rich (SRCR) domains are ancient protein modules widely found among cell surface and secreted proteins of the innate and adaptive immune system, where they mediate ligand binding. We have solved the crystal structure at 2.2 A of resolution of the SRCR CD5 domain III, a human lymphocyte receptor involved in the modulation of antigen specific receptor-mediated T cell activation and differentiation signals.

Molecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization.

Polo-like kinase (Plk1) is crucial for cell cycle progression through mitosis. Here we present the molecular and structural mechanisms that regulate the substrate recognition of Plk1 and influence its centrosomal localization and activity. Our work shows that Plk1 localization is controlled not only by the polo box domain (PBD); remarkably, the kinase domain is also involved in Plk1 targeting mechanism to the centrosome.

Asterias: a parallelized web-based suite for the analysis of expression and aCGH data.

The analysis of expression and CGH arrays plays a central role in the study of complex diseases, especially cancer, including finding markers for early diagnosis and prognosis, choosing an optimal therapy, or increasing our understanding of cancer development and metastasis. Asterias (http://www.asterias.

Genomic analysis of the 8p11-12 amplicon in familial breast cancer.

Amplification of 8p11-12 has been recurrently reported in sporadic breast cancer. These studies define a complex molecular structure with a set of minimal amplified regions, and different putative oncogenes that show a strong correlation between amplification and over-expression such as ZNF703/FLJ14299, SPFH2/C8orf2, BRF2 and RAB11FIP. However, none of these studies were carried out on familial breast malignancies.

Mice expressing myrAKT1 in the mammary gland develop carcinogen-induced ER-positive mammary tumors that mimic human breast cancer.

AKT1/PKB is a serine/threonine protein kinase that regulates biological processes such as proliferation, apoptosis and growth in a variety of cell types. To assess the oncogenic capability of an activated form of AKT in vivo we have generated several transgenic mouse lines that overexpress in the mammary epithelium the murine Akt1 gene modified with a myristoylation signal, which renders active this protein by localizing it to the plasma membrane. We demonstrate that expression of myristoylated AKT in the mammary glands increases the susceptibility of these mice to the induction of mammary tumors of epithelial origin by the carcinogen 9,10-dimethyl-1,2 benzanthracene (DMBA).

Normal cellular senescence and cancer susceptibility in mice genetically deficient in Ras-induced senescence-1 (Ris1).

Oncogenic Ras triggers a permanent cell-cycle arrest known as oncogene-induced senescence (OIS) that constitutes a relevant tumor suppressor mechanism. Ris1 (Ras-induced senescence-1) is a novel gene that was identified in a screen as specifically upregulated during Ras-induced senescence, and that is located at a chromosomal region, 3p21.3, frequently lost in human cancer.

Cdc45-MCM-GINS, a new power player for DNA replication.

The identity of the DNA helicase(s) involved in eukaryotic DNA replication is still a matter of debate, but the mini-chromosome maintenance (MCM) proteins are the chief candidate. Six conserved MCM proteins, Mcm2-7, are essential for the initiation and elongation stages of DNA replication, contain ATP binding pockets and can form a hexameric structure resembling that of known prokaryotic and viral helicases. However, biochemical proof of their presumed function has remained elusive.

A high-throughput loss-of-function screening identifies novel p53 regulators.

The p53 protein is a sequence-specific transcription factor that plays a crucial role in tumor suppression by inducing apoptosis or cell cycle arrest in response to cellular damage. To identify novel proteins involved in the regulation of p53 transcriptional activity we have performed a large scale RNA interference-based screen. We have identified four genes previously unknown to be involved in modulating p53 activity (GAS41, RPS6K4, RUNDC1 and CRMP-2).

Shugoshin and PP2A, shared duties at the centromere.

Sister chromatid cohesion mediated by the ring-shaped cohesin complex is essential for faithful chromosome segregation. A tight spatial and temporal control of cohesin release is observed in mitosis and meiosis, and a family of proteins known as shugoshins play a major role in this process. Shugoshin (Sgo) protects centromeric cohesin from dissociation in early mitosis and from cleavage by separase in meiosis I.

Activation-induced deaminase: light and dark sides.

Activation-induced deaminase (AID) is required for class switch recombination (CSR) and somatic hypermutation (SHM), which are responsible for secondary diversification of antibodies in germinal centers. AID initiates these processes by deamination of cytosines on the immunoglobulin (Ig) locus, a potentially mutagenic activity. AID expression is restricted to germinal-center B cells, but the mechanisms that regulate its target specificity are not completely understood.

A new mechanism of inactivation of the INK4/ARF locus.

The INK4/ARF locus encodes three tumor suppressors, p15(INK4b), p16(INK4a) and ARF, which together constitute one of the main anti-oncogenic defenses of mammalian organisms. The activity of these tumor suppressors depends mostly on the transcriptional status of the locus. Recently, we have identified a conserved DNA element with the capacity to regulate the locus in a global manner.