Program Affiliations

Stanford Advisors

All Publications

  • Chemical constituents from the whole herbs of Peperomia tetraphylla and their chemotaxonomic significance BIOCHEMICAL SYSTEMATICS AND ECOLOGY Wang, S., De Souza, C., Wang, L., Zhou, H. 2021; 96
  • Effect of the p53 P72R Polymorphism on Mutant TP53 Allele Selection in Human Cancer. Journal of the National Cancer Institute De Souza, C., Madden, J., Koestler, D. C., Minn, D., Montoya, D. J., Minn, K., Raetz, A. G., Zhu, Z., Xiao, W., Tahmassebi, N., Reddy, H., Nelson, N., Karnezis, A. N., Chien, J. 2021


    BACKGROUND: TP53mutations occur in more than 50% of cancers. We sought to determine the effect of the intragenic P72R SNP (rs1042522) on the oncogenic properties of mutantp53.METHODS: P72R allelic selection in tumors was determined from genotype calls and a Gaussian distributed mixture model. The SNP effect on mutant p53 was determined in p53-negative cancer cell lines. RNA-sequencing, chromatin immunoprecipitation, and survival analysis were performed to describe the SNP effect. All statistical tests were 2-sided.RESULTS: Among 409 patients with germline heterozygous P72R SNP who harbored somatic mutations inTP53, we observed a selection bias against missenseTP53mutants encoding the P72 SNP (P=1.64 x 10-13). Exogenously expressed hotspotp53mutants with the P72 SNP were negatively selected in cancer cells. Gene expression analyses showed the enrichment of p53 pathway genes and inflammatory genes in cancer cells transduced with mutants encoding P72 SNP. Immune gene signature is enriched in patients harboring missense TP53 mutations with homozygous P72 SNP. These patients have improved overall survival as compared to those with the R72 SNP (P=0.04).CONCLUSION: This is the largest study demonstrating a selection against the P72 SNP. Missense p53 mutants with the P72 SNP retain partial wild type tumor-suppressive functions, which may explain the selection bias against P72 SNP across cancer types. Ovarian cancer patients with the P72 SNP have a better prognosis than with the R72 SNP. Our study describes a previously unknown role through which thers1042522SNP modifies tumor suppressor activities of mutantp53in patients.

    View details for DOI 10.1093/jnci/djab019

    View details for PubMedID 33555293

  • Long non-coding RNA signatures as predictors of prognosis in thyroid cancer: a narrative review. Annals of translational medicine Zhao, H., De Souza, C., Kumar, V. E., Nambiar, R., Hao, D., Zhu, X., Luo, Y., Liu, S., Zhang, L., Zhu, J. 2021; 9 (4): 359


    Thyroid cancer (TC) is the most common endocrine malignancy, with high incidence rates in recent decades. Most TC cases have good prognoses, but a high risk of recurrence and metastases poses challenges, especially for patients with high-risk factors. Currently used prognostic markers for TC involve a combination of genetic factors and overexpressed proteins. Long non-coding RNAs (lncRNAs) regulate several integral biologic processes by playing key roles in the transcription of several downstream targets maintaining cellular behavior. Prior studies have revealed that lncRNAs promote tumor cell proliferation, invasion, metastasis, and angiogenesis, making them important targets for therapeutic intervention in cancer. While the exact molecular mechanisms underlying the role of lncRNAs in modulating TC progression and recurrence is still unclear, it is important to note that some lncRNAs are upregulated in certain cancers, while others are downregulated. In the present study, we review several key lncRNAs, their association with cancer progression, and the important roles they may play as tumor suppressors or tumor promoters in tumorigenesis. We discuss the potential mechanisms of lncRNA-mediated pathogenesis that can be targeted for the treatment of TC, the existing and potential benefits of using lncRNAs as diagnostic and prognostic measures for cancer detection, and tumor burden in patients.

    View details for DOI 10.21037/atm-20-8191

    View details for PubMedID 33708986