Karen Vasquez - Academia.edu (original) (raw)

Papers by Karen Vasquez

Chromosomal breakpoints and translocation hotspots in human cancers are often found near sites of... more Chromosomal breakpoints and translocation hotspots in human cancers are often found near sites of aberrant DNA methylation. DNA hypomethylation can lead to illegitimate recombination events and can stimulate V(D)J recombination in the immunoglobulin genes. However, this co-localization of chromosomal breakage cannot be explained by previously proposed mechanisms of CpG hypermethylation-induced genetic instability, e.g., deamination-induced point mutation, or epigenetic gene silencing, because these events should not lead directly to DNA double-strand breaks. In this study, we determined the effect of cytosine methylation on the stability of CpG-rich sequences in mammalian cells and on chromosomes in mice, without altering the global genome-wide DNA methylation status. We found that methylation of specific CpG repeats induced higher frequencies of deletions and rearrangements within and surrounding the methylated repeats than that found with unmethylated CpG repeats. In addition, we found that those mutations induced by the methylated CpG repeats had a broader size distribution than that found with unmethylated CpG repeats. In an effort to elucidate the mechanism of hypermethylation-induced genetic instability, we discovered that unusual structural features of the methylated CpG sequences precluded local nucleosome assembly, leading to an increase in mutations. Thus, we propose a novel process of DNA methylation-induced genetic instability in mammals in which methylation of CpG-rich sequences can alter both DNA and chromatin structures, leading to DNA double-strand breaks. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 153.

Cancer Research, Apr 1, 2004

Psoralen is a bifunctional crosslinking agent that can form DNA interstrand crosslinks (ICLs) fol... more Psoralen is a bifunctional crosslinking agent that can form DNA interstrand crosslinks (ICLs) following exposure to UVA irradiation. ICLs present a formidable block to DNA metabolism and must be repaired for cell survival. Crosslinking agents are both beneficial and ...

Nature Cell Biology, Jul 1, 2022

Regulation of Z-DNA levels in the germ line. To detect Z-DNA in prospermatogonia globally, we car... more Regulation of Z-DNA levels in the germ line. To detect Z-DNA in prospermatogonia globally, we carried out immunostaining of mouse foetal testis samples using a monoclonal anti Z-DNA antibody, Z22 (ref. 10). Z-DNA staining declines as a function of gestational age (Fig. 1a). This reduction was found in the PGC7-positive germ cells in the testicular cords at 15.5 days post coitum (dpc) but not in somatic cells of the testis (Fig. 1b,c). This finding reveals the existence of a process that reduces Z-DNA levels specifically in the germ cells at the time of major epigenome remodelling in foetal mouse germ cells 11-14. Zbtb43 RNA is highly expressed in prospermatogonia. To understand the epigenome remodelling processes that take place in foetal male germ cells (MGCs) at 15.5 dpc, we focused on genes encoding transcription factors and epigenome remodellers. According to our RNA-seq data 14 in purified foetal germ cells 15 (Extended Data Fig. 1a), the transcription of Zbtb43 was by far the highest among all Zbtbs in prospermatogonia at 15.5 dpc (Extended Data Fig. 1b). Zbtb43 transcript levels were at over 1,300 reads per 1 kb, per million reads (RPKM) in MGCs, but 10-20-fold lower in the female germ cells (FGC) and somatic cells of the foetal gonads. Zbtb43 was one of the most highly expressed genes in MGC, among important genes that carry out germ cell functions, such as Dppa3, Mael, Dnmt3l, Pou5f1, Piwil2, Piwil4, Asz1 and Dazl (Extended Data Fig. 1c). Notably, in adult and foetal mouse organs the transcript level of Zbtb43 is below 6 RPKM, many orders of magnitude lower than in MGC (Extended Data Fig. 1d). These data suggested that the ZBTB43 protein may carry out an important role in prospermatogonia.

DNA

Genetic instability can result from increases in DNA damage and/or alterations in DNA repair prot... more Genetic instability can result from increases in DNA damage and/or alterations in DNA repair proteins and can contribute to disease development. Both exogenous and endogenous sources of DNA damage and/or alterations in DNA structure (e.g., non-B DNA) can impact genome stability. Multiple repair mechanisms exist to counteract DNA damage. One key DNA repair protein complex is ERCC1-XPF, a structure-specific endonuclease that participates in a variety of DNA repair processes. ERCC1-XPF is involved in nucleotide excision repair (NER), repair of DNA interstrand crosslinks (ICLs), and DNA double-strand break (DSB) repair via homologous recombination. In addition, ERCC1-XPF contributes to the processing of various alternative (i.e., non-B) DNA structures. This review will focus on the processing of alternative DNA structures by ERCC1-XPF.

Life Sciences, 2020

Despite the recent scientific advances made in cancer diagnositics and therapeutics, cancer still... more Despite the recent scientific advances made in cancer diagnositics and therapeutics, cancer still remains the second leading cause of death worldwide. Thus, there is a need to identify new potential biomarkers/molecular targets to improve the diagnosis and treatment of cancer patients. In this regard, long non-coding RNAs (lncRNAs), a type of non-coding RNA molecule, have been found to play important roles in diverse biological processes, including tumorigenesis, and may provide new biomarkers and/or molecular targets for the improved detection of treatment of cancer. For example, one lncRNA, tissue differentiation-inducing non-protein coding RNA (TINCR) has been found to be significantly dysregulated in many cancers, and has an impact on tumor development and progression through targeting pivotal molecules in cancer-associated signaling pathways. Hence, based on recent discoveries, herein, we discuss the regulatory functions and the underlying mechanisms of how TINCR regulates signaling pathways attributed to cancer hallmarks associated with the pathogenesis of various human cancers. We also highlight studies assessing its potential clinical utility as a biomarker/target for early detection, cancer risk stratification, and personalized cancer therapies.

Translational Oncology, 2020

Based on epidemiological data provided by the World Health Organization (2018), cancer is the sec... more Based on epidemiological data provided by the World Health Organization (2018), cancer is the second most prevalent cause of death worldwide. Several factors are thought to contribute to the high mortality rate in cancer patients, including less-than-optimal diagnostic and therapeutic strategies. Thus, there is an urgent need to identify accurate biomarkers with diagnostic, prognostic, and potential therapeutic applications. In this regard, long noncoding RNAs (lncRNAs) hold immense potential due to their regulatory roles in cancer development and associated cancer hallmarks. Recently, CASC9 transcripts have attracted significant attention due to their altered expression during the pathogenesis of cancer and their apparent contributions to various cancer-associated phenotypes involving a broad spectrum of molecular mechanisms. Here, we have provided an in-depth review describing the known functions of the lncRNA CASC9 in cancer development and progression.

Cancer Research, 2020

Chromatin-associated architectural proteins are part of a fundamental support system for cellular... more Chromatin-associated architectural proteins are part of a fundamental support system for cellular DNA-dependent processes and can maintain/modulate the efficiency of DNA replication, transcription, and DNA repair. Interestingly, prognostic outcomes of many cancer types have been linked with the expression levels of several of these architectural proteins. The high mobility group box (HMGB) architectural protein family has been well studied in this regard. The differential expression levels of HMGB proteins and/or mRNAs and their implications in cancer etiology and prognosis present the potential of novel targets that can be explored to increase the efficacy of existing cancer therapies. HMGB1, the most studied member of the HMGB protein family, has pleiotropic roles in cells including an association with nucleotide excision repair, base excision repair, mismatch repair, and DNA double-strand break repair. Moreover, the HMGB proteins have been identified in regulating DNA damage resp...

Frontiers in Oncology, 2019

Limitations in current diagnostic procedures warrant identification of new methodologies to impro... more Limitations in current diagnostic procedures warrant identification of new methodologies to improve diagnoses of cancer patients. In this context, long non-coding RNAs (lncRNAs) have emerged as stable biomarkers which are expressed abundantly in tumors. Importantly, these can be detected at all stages of tumor development, and thus may provide potential biomarkers and/or therapeutic targets. Recently, we suggested that aberrant levels of lncRNAs can be used to determine the invasive and metastatic potential of tumor cells. Further, direct correlations of lncRNAs with cancer-derived inflammation, metastasis, epithelial-to-mesenchymal transition, and other hallmarks of cancer indicate their potential as biomarkers and targets for cancer. Thus, in this review we have discussed the importance of small nucleolar RNA host gene 12 (SNHG12), a lncRNA, as a potential biomarker for a variety of cancers. A meta-analysis of a large cohort of cancer patients revealed that SNHG12 may also serve as a potential target for cancer-directed interventions due to its involvement in unfolded protein responses, which many tumor cells exploit to both evade immune-mediated attack and enhance the polarization of effector immune cells (e.g., macrophages and T cells). Thus, we propose that SNHG12 may serve as both a biomarker and a druggable therapeutic target with promising clinical potential.

Cancer Research, 2018

Many anticancer chemotherapeutic agents induce DNA interstrand crosslinks (ICLs) and DNA double-s... more Many anticancer chemotherapeutic agents induce DNA interstrand crosslinks (ICLs) and DNA double-strand breaks (DSBs) leading to cytotoxicity; however, the mechanisms involved in processing such damage is not completely understood. Thus, a better understanding of the processing of ICLs and DSBs will assist in the identification of novel pharmacological targets, and improved drug design, particularly in chemo-resistant populations. We discovered that the High Mobility Group Box proteins (HMGBs), a family of non-histone architectural proteins, modulate DNA lesion processing in human cancer cells and significantly alter cell survival. We have shown that one of the HMGB family members, HMGB1, binds with high affinity to ICLs targeted to specific sites using triplex-forming oligonucleotides (TFOs), and modulates the repair of ICLs as a co-factor of the nucleotide excision repair (NER) mechanism. We found that other HMGB family members, HMGB2 and HMGB3, which share sequence and structural ...

Biochimie, 2019

The five-year survival rate of esophageal cancer patients is less than 20%. This may be due to in... more The five-year survival rate of esophageal cancer patients is less than 20%. This may be due to increased resistance (acquired or intrinsic) of tumor cells to chemo/radiotherapies, often caused by aberrant cell cycle, deregulated apoptosis, increases in growth factor signaling pathways, and/or changes in the proteome network. In addition, deregulation in non-coding RNA-mediated signaling pathways may contribute to resistance to therapies. At the molecular level, these resistance factors have now been linked to various microRNA (miRNAs), which have recently been shown to control cell development, differentiation and neoplasia. The increased stability and dysregulated expression of miRNAs have been associated with increased resistance to various therapies in several cancers, including esophageal cancer. Therefore, miRNAs represent the next generation of molecules with tremendous potential as biomarkers and therapeutic targets. Yet, a detailed studies on miRNA-based therapeutic intervention is still in its infancy. Hence, in this review, we have summarized the current status of microRNAs in dictating the resistance/sensitivity of tumor cells against chemotherapy and radiotherapy. In addition, we have discussed various strategies to increase radiosensitivity, including targeted therapy, and the use of miRNAs as radiosensitive/radioresistance biomarkers for esophageal cancer in the clinical setting.

Methods in Enzymology, 1999

High mobility group box protein 1 (HMGB1) is a highly versatile, abundant, and ubiquitously expre... more High mobility group box protein 1 (HMGB1) is a highly versatile, abundant, and ubiquitously expressed, nonhistone chromosomal protein, which belongs to the HMGB family of proteins. These proteins form an integral part of the architectural protein repertoire to support chromatin structure in the nucleus. In the nucleus, the role of HMGB1 is attributed to its ability to bind to undamaged DNA, damaged DNA, and alternative (i.e. non-B) DNA structures with high affinity and subsequently induce bending of the DNA substrates. Due to its binding to DNA, HMGB1 has been implicated in critical biological processes, such as DNA transcription, replication, repair, and recombination. In addition to its intracellular functions, HMGB1 can also be released in the extracellular space where it elicits immunological responses. HMGB1 associates with many different molecules, including DNA, RNA, proteins, and lipopolysaccharides to modulate a variety of processes in both DNA metabolism and in innate immunity. In this review, we will focus on the implications of the interactions of HMGB1 with nucleic acids in DNA repair and immune responses. We report on the roles of HMGB1 in nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR) and DNA double-strand break repair (DSBR). We also report on its roles in immune responses via its potential effects on antigen receptor diversity generation [V(D)J recombination] and interactions with foreign and self-nucleic acids. HMGB1 expression is altered in a variety of cancers and immunological disorders. However, due to the diversity and complexity of the biological processes influenced by HMGB1 (and its family members), a detailed understanding of the intracellular and extracellular roles of HMGB1 in DNA damage repair and immune responses is warranted to ensure the development of effective HMGB1-related therapies.

Toxicology and Applied Pharmacology, 2012

Sulfur mustard [bis(2-chloroethyl)sulfide, SM] is a well-known DNA-damaging agent that has been u... more Sulfur mustard [bis(2-chloroethyl)sulfide, SM] is a well-known DNA-damaging agent that has been used in chemical warfare since World War I, and is a weapon that could potentially be used in a terrorist attack on a civilian population. Dermal exposure to high concentrations of SM produces severe, long-lasting burns. Topical exposure to high concentrations of 2-(chloroethyl) ethyl sulfide (CEES), a monofunctional analog of SM, also produces severe skin lesions in mice. Utilizing a genetically engineered mouse strain, Big Blue, that allows measurement of mutation frequencies in mouse tissues, we now show that topical treatment with much lower concentrations of CEES induces significant dose-and time-dependent increases in mutation frequency in mouse skin; the mutagenic exposures produce minimal toxicity as determined by standard histopathology and immunohistochemical analysis for cytokeratin 6 and the DNA-damage induced phosphorylation of histone H2AX (γ-H2AX). We attempted to develop a therapeutic that would inhibit the CEES-induced increase in mutation frequency in the skin. We observe that multi-dose, topical treatment with 2,6-dithiopurine (DTP), a known chemical scavenger of CEES, beginning 1 hour post-exposure to CEES, completely abolishes the CEES-induced increase in mutation frequency. These findings suggest the possibility that DTP, previously shown to be non-toxic in mice, may be useful as a therapeutic agent in accidental or malicious human exposures to SM.

Genes, Mar 5, 2014

Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by wh... more Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs). Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS) and other endogenous or exogenous electron-abstracting molecules.

Biochemistry, Jul 29, 2010

Naturally occurring poly(purine•pyrimidine) rich regions in the human genome are prone to adopt n... more Naturally occurring poly(purine•pyrimidine) rich regions in the human genome are prone to adopt non-canonical DNA structures such as intramolecular triplexes (i.e. H-DNA). Such structureforming sequences are abundant and can regulate the expression of several diseases-linked genes. In addition, the use of triplex-forming oligonucleotides (TFOs) to modulate gene structure and function has potential as an approach to targeted gene therapy. Previously, we found that endogenous H-DNA structures can induce DNA double-strand breaks and promote genomic rearrangements. Herein, we find that the DHX9 helicase co-immunoprecipitates with triplex DNA structures in mammalian cells, suggesting a role in the maintenance of genome stability. We tested this postulate by assessing the helicase activity of purified human DHX9 on various duplex and triplex DNA substrates in vitro. DHX9 displaced the third strand from a specific triplex DNA structure and catalyzed the unwinding with a 3′→5′ polarity with respect to the displaced third strand. Helicase activity required a 3′-single-stranded overhang on the third strand and was dependent on ATP hydrolysis. The reaction kinetics consisted of a pre-steady-state burst phase followed by a linear, steady-state pseudo-zero-order-reaction. In contrast, very little, if any helicase activity was detected on blunt triplexes, triplexes with 5′-overhangs, blunt duplexes, duplexes with overhangs, or forked duplex substrates. Thus, triplex structures containing a 3′overhang represent preferred substrates for DHX9, where it removes the strand with Hoogsteen hydrogen-bonded bases. Our results suggest the involvement of DHX9 in maintaining genome integrity by unwinding mutagenic triplex DNA structures. Alternative DNA conformations (i.e. non-B DNA), in addition to the canonical form of DNA consisting of a right-handed double helix (B-DNA), can form at repetitive DNA motifs, including left-handed Z-DNA adopted by alternating purine•pyrimidine sequences, cruciforms and hairpin/loops extruded from inverted and direct repeats, respectively, and multistranded triplex and quadruplex conformations assembled from poly(purine•pyrimidine) tracts with mirror repeat symmetry and G-rich sequences, respectively (1-7). ☟ Funding was provided by NIH/NCI grants to K.M.V. (CA097175 and CA093729). Facility Core services were supported in part by the NIH/NIEHS Center Grant (ES007784) and M. D. Anderson's Cancer Center Support Grant (CA016672).

Cellular and Molecular Life Sciences, Sep 1, 2009

Repetitive DNA motifs are abundant in the genomes of various species and have the capacity to ado... more Repetitive DNA motifs are abundant in the genomes of various species and have the capacity to adopt non-canonical (i.e. non-B) DNA structures. Several non-B DNA structures, including cruciforms, slipped structures, triplexes, G-quadruplexes, and Z-DNA, have been shown to cause mutations, such as deletions, expansions, and translocations in both prokaryotes and eukaryotes. Their distributions in genomes are not random and often co-localize with sites of chromosomal breakage associated with genetic diseases. Current genome-wide sequence analyses suggest that the genomic instabilities induced by non-B DNA structure-forming sequences not only result in predisposition to disease, but also contribute to rapid evolutionary changes, particularly in genes associated with development and regulatory functions. In this review, we describe the occurrence of non-B DNA-forming sequences in various species, the classes of genes enriched in non-B DNA-forming sequences, and recent mechanistic studies on DNA structure-induced genomic instability to highlight their importance in genomes.

Elsevier eBooks, 2013

The term non-B-DNA refers to all secondary structures that the canonical, antiparallel right-hand... more The term non-B-DNA refers to all secondary structures that the canonical, antiparallel right-handed double helix (B-DNA) can adopt, including left-handed duplexes and three- and four-stranded helices. Bioinformatic studies indicate that the number of sequences with the potential to form DNA secondary structures in the human genome is greater than expected by chance and probing in vivo supports the conclusion that a fraction of such sequences adopts non-B conformations. Non-B-DNA is found to elicit both physiological and pathological effects, including the regulation of transcription, telomere function, protein function, and the induction of genomic instability leading to human genetic disease.

Nucleic Acids Research, Apr 20, 2015

Single base substitutions (SBSs) and insertions/deletions are critical for generating population ... more Single base substitutions (SBSs) and insertions/deletions are critical for generating population diversity and can lead both to inherited disease and cancer. Whereas on a genome-wide scale SBSs are influenced by cellular factors, on a fine scale SBSs are influenced by the local DNA sequence-context, although the role of flanking sequence is often unclear. Herein, we used bioinformatics, molecular dynamics and hybrid quantum mechanics/molecular mechanics to analyze sequence context-dependent mutagenesis at mononucleotide repeats (A-tracts and G-tracts) in human population variation and in cancer genomes. SBSs and insertions/deletions occur predominantly at the first and last base-pairs of A-tracts, whereas they are concentrated at the second and third basepairs in G-tracts. These positions correspond to the most flexible sites along A-tracts, and to sites where a 'hole', generated by the loss of an electron through oxidation, is most likely to be localized in G-tracts. For A-tracts, most SBSs occur in the direction of the base-pair flanking the tracts. We conclude that intrinsic features of local DNA structure, i.e. basepair flexibility and charge transfer, render specific nucleotides along mononucleotide runs susceptible to base modification, which then yields mutations. Thus, local DNA dynamics contributes to phenotypic variation and disease in the human population.

Nucleic Acids Research, Sep 17, 2013

Sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures in the human ge... more Sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures in the human genome have been implicated in stimulating genomic instability. Previously, we found that a naturally occurring intra-molecular triplex (H-DNA) caused genetic instability in mammals largely in the form of DNA double-strand breaks. Thus, it is of interest to determine the mechanism(s) involved in processing H-DNA. Recently, we demonstrated that human DHX9 helicase preferentially unwinds inter-molecular triplex DNA in vitro. Herein, we used a mutation-reporter system containing H-DNA to examine the relevance of DHX9 activity on naturally occurring H-DNA structures in human cells. We found that H-DNA significantly increased mutagenesis in small-interfering siRNA-treated, DHX9-depleted cells, affecting mostly deletions. Moreover, DHX9 associated with H-DNA in the context of supercoiled plasmids. To further investigate the role of DHX9 in the recognition/processing of H-DNA, we performed binding assays in vitro and chromatin immunoprecipitation assays in U2OS cells. DHX9 recognized H-DNA, as evidenced by its binding to the H-DNA structure and enrichment at the H-DNA region compared with a control region in human cells. These composite data implicate DHX9 in processing H-DNA structures in vivo and support its role in the overall maintenance of genomic stability at sites of alternatively structured DNA.