Showing papers by "Robert H. Shoemaker published in 2017"

ALK, ROS1, and NTRK Rearrangements in Metastatic Colorectal Cancer.

Abstract: Background ALK, ROS1, and NTRK fusions occur in 02% to 24% of colorectal cancers Pioneer cases of metastatic colorectal cancer (mCRC) patients bearing rearrangements who benefited from anti-ALK, ROS, and TrkA-B-C therapies have been reported previously Here we aimed at characterizing the clinical and molecular landscape of ALK, ROS1, and NTRK rearranged mCRC Methods Clinical features and molecular characteristics of 27 mCRC patients bearing ALK, ROS1, and NTRK rearranged tumors were compared with those of a cohort of 319 patients not bearing rearrangements by means of Fisher's exact, χ2 test, or Mann-Whitney test as appropriate Overall survival curves were estimated with the Kaplan-Meier method and compared using the log-rank test A Cox proportional hazard model was adopted in the multivariable analysis Deep molecular and immunophenotypic characterizations of rearranged cases, including those described in The Cancer Genome Atlas database, were performed All statistical tests were two-sided Results Closely recalling the "BRAF history," ALK, ROS1, and NTRK rearrangements more frequently occurred in elderly patients (P = 02) with right-sided tumors (P < 001) and node-spreading (P = 03), RAS wild-type (P < 001), and MSI-high (P < 001) cancers All patients bearing ALK, ROS1, and NTRK fusions had shorter overall survival (156 months, 95% confidence interval [CI] = 00 to 204 months) than negative patients (337 months, 95% CI = 283 to 421 months), both in the univariate (hazard ratio [HR] = 217, 95% CI = 103 to 457, P < 001) and multivariable models (HR = 233, 95% CI = 110 to 495, P = 02) All four evaluable patients with rearrangements showed primary resistance to anti-epidermal growth factor receptor agents Frequent association with potentially targetable RNF43 mutations was observed in MSI-high rearranged tumors Conclusions ALK, ROS1, and NTRK rearrangements define a new rare subtype of mCRC with extremely poor prognosis Primary tumor site, MSI-high, and RAS and BRAF wild-type status may help to identify patients bearing these alterations While sensitivity to available treatments is limited, targeted strategies inhibiting ALK, ROS, and TrkA-B-C provided encouraging results

Detecting Gene Rearrangements in Patient Populations Through a 2-Step Diagnostic Test Comprised of Rapid IHC Enrichment Followed by Sensitive Next-Generation Sequencing.

Abstract: Targeted therapy combined with companion diagnostics has led to the advancement of next-generation sequencing (NGS) for detection of molecular alterations. However, using a diagnostic test to identify patient populations with low prevalence molecular alterations, such as gene rearrangements, poses efficiency, and cost challenges. To address this, we have developed a 2-step diagnostic test to identify NTRK1, NTRK2, NTRK3, ROS1, and ALK rearrangements in formalin-fixed paraffin-embedded clinical specimens. This test is comprised of immunohistochemistry screening using a pan-receptor tyrosine kinase cocktail of antibodies to identify samples expressing TrkA (encoded by NTRK1), TrkB (encoded by NTRK2), TrkC (encoded by NTRK3), ROS1, and ALK followed by an RNA-based anchored multiplex polymerase chain reaction NGS assay. We demonstrate that the NGS assay is accurate and reproducible in identification of gene rearrangements. Furthermore, implementation of an RNA quality control metric to assess the presence of amplifiable nucleic acid input material enables a measure of confidence when an NGS result is negative for gene rearrangements. Finally, we demonstrate that performing a pan-receptor tyrosine kinase immunohistochemistry staining enriches detection of the patient population for gene rearrangements from 4% to 9% and has a 100% negative predictive value. Together, this 2-step assay is an efficient method for detection of gene rearrangements in both clinical testing and studies of archival formalin-fixed paraffin-embedded specimens.

Immunoprevention of KRAS-driven lung adenocarcinoma by a multipeptide vaccine

Abstract: // Jing Pan 1, * , Qi Zhang 1, * , Shizuko Sei 2 , Robert H. Shoemaker 2 , Ronald A. Lubet 2 , Yian Wang 1 and Ming You 1 1 Cancer Center and Department of Pharmacology & Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA 2 Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA * These authors have contributed equally to this work Correspondence to: Ming You, email: myou@mcw.edu Keywords: immunoprevention, KRAS, lung adenocarcinoma, peptide vaccine, MHC class II Received: December 06, 2016 Accepted: March 01, 2017 Published: August 01, 2017 ABSTRACT Lung cancer remains the leading cause of cancer death worldwide. Mutations in KRAS are detected in up to 30% of lung cancer cases. No effective therapies specifically targeting mutant KRAS have been developed. Vaccination against KRAS mutants is one of the venues of active exploration. The present study evaluated both immunogenicity and antitumor efficacy of a newly formulated multipeptide vaccine targeting multiple epitopes of the KRAS molecule. The formulated vaccine contained top four peptides, which elicited the strongest immunologic response and showed 100% sequence homology between human and mouse. The multipeptide KRAS vaccine was tested in an inducible CCSP-TetO-KRAS G12D mouse model, where the vaccine was administered prior to activating the mutant KRAS protein. The KRAS peptide vaccine exhibited striking efficacy, reducing tumor number and tumor burden by >80% when compared with adjuvant alone. Splenocytes collected from vaccinated animals showed a robust immunologic response to the immunizing peptides. Furthermore, in vitro stimulation of these splenocytes by the vaccinated peptides resulted in the secretion of cytokines indicative of Th1 responses but with minimal secretion of Th2-related cytokines. The multipeptide KRAS vaccine was immunogenic and efficacious in the primary prevention of KRAS-induced lung cancer, indicating that the approach potentially can be used to prevent other KRAS-driven cancers, either alone or in combination with other modalities.

Identification of a nucleoside analog active against adenosine kinase–expressing plasma cell malignancies

Abstract: Primary effusion lymphoma (PEL) is a largely incurable malignancy of B cell origin with plasmacytic differentiation. Here, we report the identification of a highly effective inhibitor of PEL. This compound, 6-ethylthioinosine (6-ETI), is a nucleoside analog with toxicity to PEL in vitro and in vivo, but not to other lymphoma cell lines tested. We developed and performed resistome analysis, an unbiased approach based on RNA sequencing of resistant subclones, to discover the molecular mechanisms of sensitivity. We found different adenosine kinase-inactivating (ADK-inactivating) alterations in all resistant clones and determined that ADK is required to phosphorylate and activate 6-ETI. Further, we observed that 6-ETI induces ATP depletion and cell death accompanied by S phase arrest and DNA damage only in ADK-expressing cells. Immunohistochemistry for ADK served as a biomarker approach to identify 6-ETI-sensitive tumors, which we documented for other lymphoid malignancies with plasmacytic features. Notably, multiple myeloma (MM) expresses high levels of ADK, and 6-ETI was toxic to MM cell lines and primary specimens and had a robust antitumor effect in a disseminated MM mouse model. Several nucleoside analogs are effective in treating leukemias and T cell lymphomas, and 6-ETI may fill this niche for the treatment of PEL, plasmablastic lymphoma, MM, and other ADK-expressing cancers.

Targeting "Retired Antigens" for Cancer Immunoprevention.

Abstract: Identification of immune targets for cancer immunoprevention, or immunotherapy, has historically focused on tumor-associated (self) antigens or neoantigens expressed on malignant cells. For self-antigens, overcoming tolerance can be a difficult challenge. Neoantigens do not suffer from this limitation, but the lack of recurrent mutations yielding common neoantigens that can be exploited in vaccines is a problem for many tumor types. Targeting "retired antigens," a specialized type of self-antigen, may have considerable advantages. Antigens no longer expressed in mature or aged individuals should pose reduced risk of autoimmune sequelae. Indeed, self-tolerance of these antigens may have naturally faded. Thus, when the retired antigens are highly expressed in cancer cells, it may be easier to overcome the remaining tolerance. Women who are BRCA1/2 carriers may be among the first to benefit as candidate retired antigens have been identified as highly expressed in ovarian and breast cancer cells. Although there is good preclinical data supporting this immune targeting concept, additional research is needed to understand the underlying immune phenomena and optimize the vaccine strategy. Cancer Prev Res; 10(11); 607-8. ©2017 AACRSee related article by Mazumder et al., p. 612.