Using Supercomputing Resources in Genomic Research

TACC resources have proven to be critical and enabling to mine cancer genomic data, genomic variants associated with human disease and polymorphic human traits, addressing biological questions otherwise non-approachable by conventional experiments. We have developed computational scripts that we use in a parallel environment to harness the capabilities of TACC HPCs, and which we have made publicly available on GitHub. In selected peer-review publications acknowledging TACC support, we have reported the association of DNA sequences able to form alternative DNA structures (or non-B DNA) with sites of chromosomal breaks leading to gross chromosomal translocations in cancer genomes, with sites of gene duplication predisposing to Parkinson’s disease, and most recently with regions of increased polymorphism in the human population. We found an exquisite correlation between the expression of selected genes and the mutational burden in cancer patients. While solving the crystal structure of a poorly characterized exonuclease, named EXO5, TACC resources enabled the assignment of a role for EXO5 in the cellular response to DNA damage, a vital pathway used by tumors to survive and grow, along with key genes whose high expression is linked to poor survival in cancer patients. Most recently, during the discovery of a nuclear role for GRB2, an adaptor protein previously thought to act only in the cytoplasm, TACC resources enabled us to test hypotheses derived from laboratory data. We were gratified to confirm the laboratory prediction that high expression of GRB2, together with its binding partner the MRE11 nuclease, carries accurate prognostic power for poor patient survival in breast cancer patients proficient in DNA homology-directed repair. These composite findings, significantly facilitated by TACC resources, have been critical to further our understanding in biological processes relevant to human disease, and to provide knowledge for the development of more precise therapeutic tools aimed at improving human health

PRC2 is dispensable for HOTAIR-mediated transcriptional repression

Long non-coding RNAs (lncRNAs) play diverse roles in physiological and pathological processes. Several lncRNAs have been suggested to modulate gene expression by guiding chromatin-modifying complexes to specific sites in the genome. However, besides the example of Xist, clear-cut evidence demonstrating this novel mode of regulation remains sparse. Here, we focus on HOTAIR, a lncRNA that is overexpressed in several tumor types and previously proposed to play a key role in gene silencing through direct recruitment of Polycomb Repressive Complex 2 (PRC2) to defined genomic loci. Using genetic tools and a novel RNA-tethering system, we investigated the interplay between HOTAIR and PRC2 in gene silencing. Surprisingly, we observed that forced overexpression of HOTAIR in breast cancer cells leads to subtle transcriptomic changes that appear to be independent of PRC2. Mechanistically, we found that artificial tethering of HOTAIR to chromatin causes transcriptional repression, but that this effect does not require PRC2. Instead, PRC2 recruitment appears to be a consequence of gene silencing. We propose that PRC2 binding to RNA might serve functions other than chromatin targeting

Fragment- and structure-based drug discovery for developing therapeutic agents targeting the DNA Damage Response

Cancer will directly affect the lives of over one-third of the population. The DNA Damage Response (DDR) is an intricate system involving damage recognition, cell cycle regulation, DNA repair, and ultimately cell fate determination, playing a central role in cancer etiology and therapy. Two primary therapeutic approaches involving DDR targeting include: combinatorial treatments employing anticancer genotoxic agents; and synthetic lethality, exploiting a sporadic DDR defect as a mechanism for cancer-specific therapy. Whereas, many DDR proteins have proven “undruggable”, Fragment- and Structure-Based Drug Discovery (FBDD, SBDD) have advanced therapeutic agent identification and development. FBDD has led to 4 (with ∼50 more drugs under preclinical and clinical development), while SBDD is estimated to have contributed to the development of >200, FDA-approved medicines. Protein X-ray crystallography-based fragment library screening, especially for elusive or “undruggable” targets, allows for simultaneous generation of hits plus details of protein-ligand interactions and binding sites (orthosteric or allosteric) that inform chemical tractability, downstream biology, and intellectual property. Using a novel high-throughput crystallography-based fragment library screening platform, we screened five diverse proteins, yielding hit rates of ∼2–8% and crystal structures from ∼1.8 to 3.2 Å. We consider current FBDD/SBDD methods and some exemplary results of efforts to design inhibitors against the DDR nucleases meiotic recombination 11 (MRE11, a.k.a., MRE11A), apurinic/apyrimidinic endonuclease 1 (APE1, a.k.a., APEX1), and flap endonuclease 1 (FEN1)

Eliminating HIV-1 Packaging Sequences from Lentiviral Vector Proviruses Enhances Safety and Expedites Gene Transfer for Gene Therapy

Lentiviral vector genomic RNA requires sequences that partially overlap wild-type HIV-1 gag and env genes for packaging into vector particles. These HIV-1 packaging sequences constitute 19.6% of the wild-type HIV-1 genome and contain functional cis elements that potentially compromise clinical safety. Here, we describe the development of a novel lentiviral vector (LTR1) with a unique genomic structure designed to prevent transfer of HIV-1 packaging sequences to patient cells, thus reducing the total HIV-1 content to just 4.8% of the wildtype genome. This has been achieved by reconfiguring the vector to mediate reverse-transcription with a single strand transfer, instead of the usual two, and in which HIV-1 packaging sequences are not copied. We show that LTR1 vectors offer improved safety in their resistance to remobilization in HIV-1 particles and reduced frequency of splicing into human genes. Following intravenous luciferase vector administration to neonatal mice, LTR1 sustained a higher level of liver transgene expression than an equivalent dose of a standard lentivirus. LTR1 vectors produce reverse-transcription products earlier and start to express transgenes significantly quicker than standard lentiviruses after transduction. Finally, we show that LTR1 is an effective lentiviral gene therapy vector as demonstrated by correction of a mouse hemophilia B model

Alternative splicing caused by lentiviral integration in the human genome

Gene transfer vectors derived from murine oncoretroviruses or human lentiviruses are widely used in human gene therapy. Integration of these vectors in the human genome may, however, have genotoxic effects, caused by deregulation of gene expression at the transcriptional or posttranscriptional level. In particular, integration of lentiviral vectors within transcribed genes has a significant potential to affect their expression by interfering with splicing and polyadenylation of primary transcripts. Aberrant splicing is caused by the usage of both constitutive and cryptic splice sites located in the retroviral backbone as well as in the gene expression cassettes. We describe a set of simple methods that allow the identification of chimeric transcripts generated by the insertion of a lentiviral vector within genes and the evaluation of their relative abundance. Identification of the splice sites, either constitutive or cryptic, that are frequently used by the cell splicing machinery within a given vector provides a useful resource to attempt recoding of the vector with the objective of reducing its potential genotoxicity in a clinical context. © 2012 Elsevier Inc. All rights reserved

Oxoanion Binding by Guanidiniocarbonylpyrrole Cations in Water: A Combined DFT and MD Investigation

Structures and properties of non-bonding interactions involving guanidinium functionalized hosts and carboxylate substrates were investigated by the combination of ab initio and molecular dynamic approaches. The systems under study are meant on one side to be a model of the arginine – anion bond, so often observed in proteins and nucleic acids, and on the other the occasion to investigate in detail the influence of molecular structure on the formation of supramolecular complexes. DFT calculations including extended basis sets and implicit water treatment allowed to determine minimum energy structures and binding enthalpies comparing well with experimental data. Intermolecular forces were found to be mostly due to electrostatic interactions by three hydrogen bonds, one of which bifurcate, and are sufficiently strong to induce a conformational change in the ligand consisting in the rotation of about 180° around the guanidiniocarbonyl-pyrrole axis. Free binding energies of the complexes were evaluated through MD simulations performed by explicit water molecules using the MM-PBSA and LIE approaches. LIE energies were in quantitative agreement with experimental data. A detailed analysis of the MD simulations revealed that the complexes can not be described in terms of a single binding structure, but that they are characterized by a significant internal mobility responsible of several low energy metastable structures

Combinatorial co-expression of pheromone receptors, V2Rs

Basal neurons of the vomeronasal organ of the mouse express a superfamily of about 120 pheromone receptors, named V2Rs, that are grouped in four families, A, B, C, and D, according to sequence homology. Family-A, -B, and -D V2Rs are expressed as one receptor gene per cell, but we previously reported their co-expression with family-C V2Rs. Here, we show that basal neurons can be further grouped according to the combinatorial expression of different V2Rs. Altogether, these findings suggest that in each basal neuron a transcriptional program is active for expressing a combination of two compatible receptors and for excluding, at the same time, the expression of all other V2Rs. Further analyses revealed non-random combinations of co-expression between family-C V2Rs and genes of the class Ib major histocompatibility complex. Thus, each basal neuron of the vomeronasal organ represents a highly qualified sensory unit for detecting very specific combinations of pheromonal cues

Genome-wide analysis of alpharetroviral integration in human hematopoietic stem/progenitor cells

International audienceGene transfer vectors derived from gamma-retroviruses or lentiviruses are currently used for the gene therapy of genetic or acquired diseases. Retroviral vectors display a non-random integration pattern in the human genome, targeting either regulatory regions (gamma-retroviruses) or the transcribed portion of expressed genes (lentiviruses), and have the potential to deregulate gene expression at the transcriptional or post-transcriptional level. A recently developed alternative vector system derives from the avian sarcoma-leukosis alpha-retrovirus (ASLV) and shows favorable safety features compared to both gamma-retroviral and lentiviral vectors in preclinical models. We performed a high-throughput analysis of the integration pattern of self-inactivating (SIN) alpha-retroviral vectors in human CD34+ hematopoietic stem/progenitor cells (HSPCs) and compared it to previously reported gamma-retroviral and lentiviral vectors integration profiles obtained in the same experimental setting. Compared to gamma-retroviral and lentiviral vectors, the SIN-ASLV vector maintains a preference for open chromatin regions, but shows no bias for transcriptional regulatory elements or transcription units, as defined by genomic annotations and epigenetic markers (H3K4me1 and H3K4me3 histone modifications). Importantly, SIN-ASLV integrations do not cluster in hot spots and target potentially dangerous genomic loci, such as the EVI2A/B, RUNX1 and LMO2 proto-oncogenes at a virtually random frequency. These characteristics predict a safer profile for ASLV-derived vectors for clinical applications