Honors & Awards

  • Postdoctoral Fellowship, American Cancer Society (2016)
  • Postdoctoral Enrichment Award, Burroughs Wellcome Fund (2014-2017)
  • Tumor Biology Training Grant, NIH Institutional Grant/Stanford University (2013-2015)
  • Dean's Postdoctoral Fellow, Stanford University (2013)

Professional Education

  • Bachelor of Science, University of Arkansas Fayetteville (2005)
  • Master of Science, University of Arkansas Fayetteville (2007)
  • Doctor of Philosophy, Ohio State University (2013)

Stanford Advisors

Lab Affiliations

All Publications

  • The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nature reviews. Molecular cell biology Saldivar, J. C., Cortez, D., Cimprich, K. A. 2017; 18 (10): 622–36


    One way to preserve a rare book is to lock it away from all potential sources of damage. Of course, an inaccessible book is also of little use, and the paper and ink will continue to degrade with age in any case. Like a book, the information stored in our DNA needs to be read, but it is also subject to continuous assault and therefore needs to be protected. In this Review, we examine how the replication stress response that is controlled by the kinase ataxia telangiectasia and Rad3-related (ATR) senses and resolves threats to DNA integrity so that the DNA remains available to read in all of our cells. We discuss the multiple data that have revealed an elegant yet increasingly complex mechanism of ATR activation. This involves a core set of components that recruit ATR to stressed replication forks, stimulate kinase activity and amplify ATR signalling. We focus on the activities of ATR in the control of cell cycle checkpoints, origin firing and replication fork stability, and on how proper regulation of these processes is crucial to ensure faithful duplication of a challenging genome.

    View details for DOI 10.1038/nrm.2017.67

    View details for PubMedID 28811666

  • Exome-wide single-base substitutions in tissues and derived cell lines of the constitutive Fhit knockout mouse. Cancer science Paisie, C. A., Schrock, M. S., Karras, J. R., Zhang, J., Miuma, S., Ouda, I. M., Waters, C. E., Saldivar, J. C., Druck, T., Huebner, K. 2016; 107 (4): 528-535


    Loss of expression of Fhit, a tumor suppressor and genome caretaker, occurs in preneoplastic lesions during development of many human cancers. Furthermore, Fhit-deficient mouse models are exquisitely susceptible to carcinogen induction of cancers of the lung and forestomach. Due to absence of Fhit genome caretaker function, cultured cells and tissues of the constitutive Fhit knockout strain develop chromosome aneuploidy and allele copy number gains and losses and we hypothesized that Fhit-deficient cells would also develop point mutations. On analysis of whole exome sequences of Fhit-deficient tissues and cultured cells, we found 300 to >1000 single-base substitutions associated with Fhit loss in the 2% of the genome included in exomes, relative to the C57Bl6 reference genome. The mutation signature is characterized by increased C>T and T>C mutations, similar to the "age at diagnosis" signature identified in human cancers. The Fhit-deficiency mutation signature also resembles a C>T and T>C mutation signature reported for human papillary kidney cancers and a similar signature recently reported for esophageal and bladder cancers, cancers that are frequently Fhit deficient. The increase in T>C mutations in -/- exomes may be due to dNTP imbalance, particularly in thymidine triphosphate, resulting from decreased expression of thymidine kinase 1 in Fhit-deficient cells. Fhit-deficient kidney cells that survived in vitro dimethylbenz(a)anthracene treatment additionally showed increased T>A mutations, a signature generated by treatment with this carcinogen, suggesting that these T>A transversions may be evidence of carcinogen-induced preneoplastic changes.

    View details for DOI 10.1111/cas.12887

    View details for PubMedID 26782170

    View details for PubMedCentralID PMC4832848

  • DNA replication stress underlies renal phenotypes in CEP290-associated Joubert syndrome JOURNAL OF CLINICAL INVESTIGATION Slaats, G. G., Saldivar, J. C., Bacal, J., Zeman, M. K., Kile, A. C., Hynes, A. M., Srivastava, S., Nazmutdinova, J., den Ouden, K., Zagers, M. S., Foletto, V., Verhaar, M. C., Miles, C., Sayer, J. A., Cimprich, K. A., Giles, R. H. 2015; 125 (9): 3657-3666

    View details for DOI 10.1172/JCI80657

    View details for Web of Science ID 000362303600038

  • FHIT loss-induced DNA damage creates optimal APOBEC substrates: Insights into APOBEC-mediated mutagenesis ONCOTARGET Waters, C. E., Saldivar, J. C., Amin, Z. A., Schrock, M. S., Huebner, K. 2015; 6 (5): 3409-3419


    APOBEC cytidine deaminase activity is a major source of hypermutation in cancer. But previous studies have shown that the TC context signature of these enzymes is not observed in sizable fractions of cancers with overexpression of APOBEC, suggesting that cooperating factors that contribute to this mutagenesis should be identified. The fragile histidine triad protein (Fhit) is a tumor suppressor and DNA caretaker that is deleted or silenced in >50% of cancers. Loss of Fhit protein activity causes replication stress through reduced Thymidine Kinase 1 expression, increased DNA breaks, and global genome instability in normal and cancer cells. Using data from The Cancer Genome Atlas (TCGA), we show that FHIT-low/APOBEC3B-high expressing lung adenocarcinomas display significantly increased numbers of APOBEC signature mutations. Tumor samples in this cohort with normal FHIT expression do not exhibit APOBEC hypermutation, despite having high APOBEC3B expression. In vitro, silencing Fhit expression elevates APOBEC3B-directed C > T mutations in the TP53 gene. Furthermore, inhibition of Fhit loss-induced DNA damage via thymidine supplementation decreases the TP53 mutation burden in FHIT-low/APOBEC3B-high cells. We conclude that APOBEC3B overexpression and Fhit-loss induced DNA damage are independent events that, when occurring together, result in a significantly increased frequency of APOBEC-induced mutations that drive cancer progression.

    View details for Web of Science ID 000352694400064

    View details for PubMedID 25401976

  • Initiation of Genome Instability and Preneoplastic Processes through Loss of Fhit Expression PLOS GENETICS Saldivar, J. C., Miuma, S., Bene, J., Hosseini, S. A., Shibata, H., Sun, J., Wheeler, L. J., Mathews, C. K., Huebner, K. 2012; 8 (11)


    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.

    View details for DOI 10.1371/journal.pgen.1003077

    View details for Web of Science ID 000311891600058

    View details for PubMedID 23209436