All Publications


  • Multidisciplinary management of newly diagnosed pediatric large cell neuroendocrine carcinoma of the lung causing hemoptysis. Pediatric blood & cancer Marquez, C. P., Violari, E. G., Sodji, Q., Jiang, A. L., Donaldson, S. S., Josephs, S., Hiniker, S. M. 2021: e29182

    View details for DOI 10.1002/pbc.29182

    View details for PubMedID 34125484

  • Cell-free DNA concentration and fragment size as a biomarker for prostate cancer. Scientific reports Chen, E., Cario, C. L., Leong, L., Lopez, K., Marquez, C. P., Chu, C., Li, P. S., Oropeza, E., Tenggara, I., Cowan, J., Simko, J. P., Chan, J. M., Friedlander, T., Wyatt, A. W., Aggarwal, R., Paris, P. L., Carroll, P. R., Feng, F., Witte, J. S. 2021; 11 (1): 5040

    Abstract

    Prostate cancer is the most commonly diagnosed neoplasm in American men. Although existing biomarkers may detect localized prostate cancer, additional strategies are necessary for improving detection and identifying aggressive disease that may require further intervention. One promising, minimally invasive biomarker is cell-free DNA (cfDNA), which consist of short DNA fragments released into circulation by dying or lysed cells that may reflect underlying cancer. Here we investigated whether differences in cfDNA concentration and cfDNA fragment size could improve the sensitivity for detecting more advanced and aggressive prostate cancer. This study included 268 individuals: 34 healthy controls, 112 men with localized prostate cancer who underwent radical prostatectomy (RP), and 122 men with metastatic castration-resistant prostate cancer (mCRPC). Plasma cfDNA concentration and fragment size were quantified with the Qubit 3.0 and the 2100 Bioanalyzer. The potential relationship between cfDNA concentration or fragment size and localized or mCRPC prostate cancer was evaluated with descriptive statistics, logistic regression, and area under the curve analysis with cross-validation. Plasma cfDNA concentrations were elevated in mCRPC patients in comparison to localized disease (OR5ng/mL=1.34, P=0.027) or to being a control (OR5ng/mL=1.69, P=0.034). Decreased average fragment size was associated with an increased risk of localized disease compared to controls (OR5bp=0.77, P=0.0008). This study suggests that while cfDNA concentration can identify mCRPC patients, it is unable to distinguish between healthy individuals and patients with localized prostate cancer. In addition to PSA, average cfDNA fragment size may be an alternative that can differentiate between healthy individuals and those with localized disease, but the low sensitivity and specificity results in an imperfect diagnostic marker. While quantification of cfDNA may provide a quick, cost-effective approach to help guide treatment decisions in advanced disease, its use is limited in the setting of localized prostate cancer.

    View details for DOI 10.1038/s41598-021-84507-z

    View details for PubMedID 33658587

  • Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer Via Targeted, Multiregion Sequencing. JCO precision oncology Chen, E., Cario, C. L., Leong, L., Lopez, K., Marquez, C. P., Li, P. S., Oropeza, E., Tenggara, I., Cowan, J., Simko, J. P., Kageyama, R., Wells, D. K., Chan, J. M., Friedlander, T., Aggarwal, R., Paris, P. L., Feng, F., Carroll, P. R., Witte, J. S. 2021; 5

    Abstract

    Cell-free DNA (cfDNA) may allow for minimally invasive identification of biologically relevant genomic alterations and genetically distinct tumor subclones. Although existing biomarkers may detect localized prostate cancer, additional strategies interrogating genomic heterogeneity are necessary for identifying and monitoring aggressive disease. In this study, we aimed to evaluate whether circulating tumor DNA can detect genomic alterations present in multiple regions of localized prostate tumor tissue.METHODS: Low-pass whole-genome and targeted sequencing with a machine-learning guided 2.5-Mb targeted panel were used to identify single nucleotide variants, small insertions and deletions (indels), and copy-number alterations in cfDNA. The majority of this study focuses on the subset of 21 patients with localized disease, although 45 total individuals were evaluated, including 15 healthy controls and nine men with metastatic castration-resistant prostate cancer. Plasma cfDNA was barcoded with duplex unique molecular identifiers. For localized cases, matched tumor tissue was collected from multiple regions (one to nine samples per patient) for comparison.RESULTS: Somatic tumor variants present in heterogeneous tumor foci from patients with localized disease were detected in cfDNA, and cfDNA mutational burden was found to track with disease severity. Somatic tissue alterations were identified in cfDNA, including nonsynonymous variants in FOXA1, PTEN, MED12, and ATM. Detection of these overlapping variants was associated with seminal vesicle invasion (P = .019) and with the number of variants initially found in the matched tumor tissue samples (P = .0005).CONCLUSION: Our findings demonstrate the potential of targeted cfDNA sequencing to detect somatic tissue alterations in heterogeneous, localized prostate cancer, especially in a setting where matched tumor tissue may be unavailable (ie, active surveillance or treatment monitoring).

    View details for DOI 10.1200/PO.20.00428

    View details for PubMedID 34250416

  • Use of cardiac radiation therapy as bridging therapy to CAR-T for relapsed pediatric B-cell acute lymphoblastic leukemia. Pediatric blood & cancer Marquez, C. P., Montiel-Esparza, R., Hui, C., Schultz, L. M., Davis, K. L., Hoppe, R. T., Donaldson, S. S., Ramakrishna, S., Hiniker, S. M. 2020: e28870

    Abstract

    The use of radiotherapy as bridging therapy to chimeric antigen receptor T-cell therapy (CAR-T) in pre-B acute lymphoblastic leukemia (B-ALL) has been minimally explored. Here, we present a boy with B-ALL who relapsed after allogeneic bone marrow transplant with disseminated disease, including significant symptomatic cardiovascular and gastrointestinal (GI) involvement. The cardiac and GI leukemic infiltrates were successfully treated with bridging radiation therapy (BRT) prior to CAR-T infusion. Using this approach, he successfully tolerated CAR-T with no evidence of disease or sequelae on 3-month follow-up. This is the first reported case of safe and effective delivery of cardiac BRT in B-ALL.

    View details for DOI 10.1002/pbc.28870

    View details for PubMedID 33355997

  • Engineering a potent receptor superagonist or antagonist from a novel IL-6 family cytokine ligand. Proceedings of the National Academy of Sciences of the United States of America Kim, J. W., Marquez, C. P., Sperberg, R. A., Wu, J., Bae, W. G., Huang, P., Sweet-Cordero, E. A., Cochran, J. R. 2020

    Abstract

    Interleukin-6 (IL-6) family cytokines signal through multimeric receptor complexes, providing unique opportunities to create novel ligand-based therapeutics. The cardiotrophin-like cytokine factor 1 (CLCF1) ligand has been shown to play a role in cancer, osteoporosis, and atherosclerosis. Once bound to ciliary neurotrophic factor receptor (CNTFR), CLCF1 mediates interactions to coreceptors glycoprotein 130 (gp130) and leukemia inhibitory factor receptor (LIFR). By increasing CNTFR-mediated binding to these coreceptors we generated a receptor superagonist which surpassed the potency of natural CNTFR ligands in neuronal signaling. Through additional mutations, we generated a receptor antagonist with increased binding to CNTFR but lack of binding to the coreceptors that inhibited tumor progression in murine xenograft models of nonsmall cell lung cancer. These studies further validate the CLCF1-CNTFR signaling axis as a therapeutic target and highlight an approach of engineering cytokine activity through a small number of mutations.

    View details for DOI 10.1073/pnas.1922729117

    View details for PubMedID 32522868

  • Antitumor activity of an engineered decoy receptor targeting CLCF1-CNTFR signaling in lung adenocarcinoma. Nature medicine Kim, J. W., Marquez, C. P., Kostyrko, K. n., Koehne, A. L., Marini, K. n., Simpson, D. R., Lee, A. G., Leung, S. G., Sayles, L. C., Shrager, J. n., Ferrer, I. n., Paz-Ares, L. n., Gephart, M. H., Vicent, S. n., Cochran, J. R., Sweet-Cordero, E. A. 2019

    Abstract

    Proinflammatory cytokines in the tumor microenvironment can promote tumor growth, yet their value as therapeutic targets remains underexploited. We validated the functional significance of the cardiotrophin-like cytokine factor 1 (CLCF1)-ciliary neurotrophic factor receptor (CNTFR) signaling axis in lung adenocarcinoma (LUAD) and generated a high-affinity soluble receptor (eCNTFR-Fc) that sequesters CLCF1, thereby inhibiting its oncogenic effects. eCNTFR-Fc inhibits tumor growth in multiple xenograft models and in an autochthonous, highly aggressive genetically engineered mouse model of LUAD, driven by activation of oncogenic Kras and loss of Trp53. Abrogation of CLCF1 through eCNTFR-Fc appears most effective in tumors driven by oncogenic KRAS. We observed a correlation between the effectiveness of eCNTFR-Fc and the presence of KRAS mutations that retain the intrinsic capacity to hydrolyze guanosine triphosphate, suggesting that the mechanism of action may be related to altered guanosine triphosphate loading. Overall, we nominate blockade of CLCF1-CNTFR signaling as a novel therapeutic opportunity for LUAD and potentially for other tumor types in which CLCF1 is present in the tumor microenvironment.

    View details for DOI 10.1038/s41591-019-0612-2

    View details for PubMedID 31700175

  • Targeting the CLCF1-CNTFR signaling axis using directed evolution for lung cancer therapy Marquez, C., Kim, J., Giaccia, A., Cochran, J., Sweet-Cordero, A. AMER ASSOC CANCER RESEARCH. 2018
  • Using natural ligand and receptors to develop next-generation cancer therapeutics Kim, J., Marquez, C., Sweet-Cordero, A., Cochran, J. AMER CHEMICAL SOC. 2017
  • Analysis of Epithelial-Stromal Interactions and their Relevance to Lung Cancer Marquez, C., Kim, J., Giaccia, A., Cochran, J., Sweet-Corderoz, A. ELSEVIER SCIENCE INC. 2017: S828–S829