Yi-Mi Wu

The protein tyrosine kinase family of the human genome

As the sequencing of the human genome is completed by the Human Genome Project, the analysis of this rich source of information will illuminate many areas in medicine and biology. The protein tyrosine kinases are a large multigene family with particular relevance to many human diseases, including cancer. A search of the human genome for tyrosine kinase coding elements identified several novel genes and enabled the creation of a nonredundant catalog of tyrosine kinase genes. Ninety unique kinase genes can be identified in the human genome, along with five pseudogenes. Of the 90 tyrosine kinases, 58 are receptor type, distributed into 20 subfamilies. The 32 nonreceptor tyrosine kinases can be placed in 10 subfamilies. Additionally, mouse orthologs can be identified for nearly all the human tyrosine kinases. The completion of the human tyrosine kinase family tree provides a framework for further advances in biomedical science.

DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer

BACKGROUND Prostate cancer is a heterogeneous disease, but current treatments are not based on molecular stratification. We hypothesized that metastatic, castration-resistant prostate cancers with DNA-repair defects would respond to poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibition with olaparib. METHODS We conducted a phase 2 trial in which patients with metastatic, castration-resistant prostate cancer were treated with olaparib tablets at a dose of 400 mg twice a day. The primary end point was the response rate, defined either as an objective response according to Response Evaluation Criteria in Solid Tumors, version 1.1, or as a reduction of at least 50% in the prostate-specific antigen level or a confirmed reduction in the circulating tumor-cell count from 5 or more cells per 7.5 ml of blood to less than 5 cells per 7.5 ml. Targeted next-generation sequencing, exome and transcriptome analysis, and digital polymerase-chain-reaction testing were performed on samples from mandated tumor biopsies. RESULTS Overall, 50 patients were enrolled; all had received prior treatment with docetaxel, 49 (98%) had received abiraterone or enzalutamide, and 29 (58%) had received cabazitaxel. Sixteen of 49 patients who could be evaluated had a response (33%; 95% confidence interval, 20 to 48), with 12 patients receiving the study treatment for more than 6 months. Next-generation sequencing identified homozygous deletions, deleterious mutations, or both in DNA-repair genes--including BRCA1/2, ATM, Fanconis anemia genes, and CHEK2--in 16 of 49 patients who could be evaluated (33%). Of these 16 patients, 14 (88%) had a response to olaparib, including all 7 patients with BRCA2 loss (4 with biallelic somatic loss, and 3 with germline mutations) and 4 of 5 with ATM aberrations. The specificity of the biomarker suite was 94%. Anemia (in 10 of the 50 patients [20%]) and fatigue (in 6 [12%]) were the most common grade 3 or 4 adverse events, findings that are consistent with previous studies of olaparib. CONCLUSIONS Treatment with the PARP inhibitor olaparib in patients whose prostate cancers were no longer responding to standard treatments and who had defects in DNA-repair genes led to a high response rate. (Funded by Cancer Research UK and others; ClinicalTrials.gov number, NCT01682772; Cancer Research UK number, CRUK/11/029.).

Targeting the MLL complex in castration resistant prostate cancer

Resistance to androgen deprivation therapies and increased androgen receptor (AR) activity are major drivers of castration-resistant prostate cancer (CRPC). Although prior work has focused on targeting AR directly, co-activators of AR signaling, which may represent new therapeutic targets, are relatively underexplored. Here we demonstrate that the mixed-lineage leukemia protein (MLL) complex, a well-known driver of MLL fusion–positive leukemia, acts as a co-activator of AR signaling. AR directly interacts with the MLL complex via the menin–MLL subunit. Menin expression is higher in CRPC than in both hormone-naive prostate cancer and benign prostate tissue, and high menin expression correlates with poor overall survival of individuals diagnosed with prostate cancer. Treatment with a small-molecule inhibitor of menin–MLL interaction blocks AR signaling and inhibits the growth of castration-resistant tumors in vivo in mice. Taken together, this work identifies the MLL complex as a crucial co-activator of AR and a potential therapeutic target in advanced prostate cancer.

Prostate cancer cell-stromal cell crosstalk via FGFR1 mediates antitumor activity of dovitinib in bone metastases.

Dovitinib is therapeutically active in a subset of patients with prostate cancer bone metastases, partly due to blockade of FGFR-mediated stromal-epithelial interactions in the bone microenvironment. Effective to the Bone Bone is the most common site of metastatic spread for prostate cancer, and tumors that have spread to the bone are usually very difficult to treat. Dovitinib is a recently developed drug that inhibits the fibroblast growth factor receptor. Now, Wan et al. have demonstrated that dovitinib is effective for some patients with prostate cancer that has spread to bone. The authors also identified an explanation for some of the observed antitumor effects by showing that the drug interferes with interactions between the prostate cancer cells and surrounding stromal cells in the bone microenvironment. Bone is the most common site of prostate cancer (PCa) progression to a therapy-resistant, lethal phenotype. We found that blockade of fibroblast growth factor receptors (FGFRs) with the receptor tyrosine kinase inhibitor dovitinib has clinical activity in a subset of men with castration-resistant PCa and bone metastases. Our integrated analyses suggest that FGF signaling mediates a positive feedback loop between PCa cells and bone cells and that blockade of FGFR1 in osteoblasts partially mediates the antitumor activity of dovitinib by improving bone quality and by blocking PCa cell–bone cell interaction. These findings account for clinical observations such as reductions in lesion size and intensity on bone scans, lymph node size, and tumor-specific symptoms without proportional declines in serum prostate-specific antigen concentration. Our findings suggest that targeting FGFR has therapeutic activity in advanced PCa and provide direction for the development of therapies with FGFR inhibitors.

Clinical validation of the Tempus xO assay

We have developed a clinically validated NGS assay that includes tumor, germline and RNA sequencing. We apply this assay to clinical specimens and cell lines, and we demonstrate a clinical sensitivity of 98.4% and positive predictive value of 100% for the clinically actionable variants measured by the assay. We also demonstrate highly accurate copy number measurements and gene rearrangement identification.

Integration of Germline Pharmacogenetics Into a Tumor Sequencing Program

Purpose Evidence-based guidelines inform treatment decisions for patients for whom germline genetic information is available. Our real-time tumor sequencing program, which makes precision treatment decisions for patients with cancer, produces matched germline information, providing a unique opportunity to efficiently implement pharmacogenetics and benefit patients. Methods The germline genetic database from the Michigan Oncology Sequencing (MI-Oncoseq) program was searched for 21 clinically actionable polymorphisms in five cancer-relevant genes: TPMT, DPYD, CYP2C19, CYP3A5, and UGT1A1. Residual germ line DNA was sent to an external Clinical Laboratory Improvement Amendments-approved laboratory for confirmatory genotyping. The medical records of MI-Oncoseq patients with actionable phenotypes were searched for receipt of relevant drugs and to determine whether having genetic information at the time of treatment would have led to a treatment recommendation. Results All nine variants in TPMT, DPYD, and CYP2C19 that were detected in MI-Oncoseq were confirmed by external genotyping. Genotype determinations could not be made for CYP3A5*3, UGT1A1*28, or UGT1A1*80. On the basis of retrospective assessment of 115 adult and pediatric patient records, 4.3% (n = 5) had a potentially clinically actionable phenotype for TPMT, DPYD, or CYP2C19 and received a relevant medication. After accounting for differences in adult and pediatric recommendations, three of these patients could have received a treatment recommendation at the time of prescribing. Conclusion Germline genotype determinations for TPMT, DPYD, and CYP2C19 can be used to make evidence-based treatment recommendations in MI-Oncoseq patients. Although the proportion of patients for whom recommendations can be made is small, this added value to MI-Oncoseq and patient care comes at no additional genotyping cost. Pharmacogenetic assessment should be integrated into tumor sequencing programs that genotype matched germline DNA; however, the complexity and additional cost of implementing pharmacogenetics remain challenging.

Clinically Integrated Sequencing Alters Therapy in Children and Young Adults With High-Risk Glial Brain Tumors

Purpose Brain tumors have become the leading cause of cancer-related mortality in young patients. Novel effective therapies on the basis of the unique biology of each tumor are urgently needed. The goal of this study was to evaluate the feasibility, utility, and clinical impact of integrative clinical sequencing and genetic counseling in children and young adults with high-risk brain tumors. Patients and Methods Fifty-two children and young adults with brain tumors designated by the treating neuro-oncologist to be high risk (> 25% chance for treatment failure; mean age, 10.2 years; range, 0 to 39 years) were enrolled in a prospective, observational, consecutive case series, in which participants underwent integrative clinical exome (tumor and germline DNA) and transcriptome (tumor RNA) sequencing and genetic counseling. Results were discussed in a multi-institutional brain tumor precision medicine teleconference. Results Sequencing revealed a potentially actionable germline or tumor alteration in 25 (63%) of 40 tumors with adequate tissue, of which 21 (53%) resulted in an impact on treatment or change of diagnosis. Platelet-derived growth factor receptor or fibroblast growth factor receptor pathway alterations were seen in nine of 20 (45%) glial tumors. Eight (20%) sequenced tumors harbored an oncogenic fusion isolated on RNA sequencing. Seventeen of 20 patients (85%) with glial tumors were found to have a potentially actionable result, which resulted in change of therapy in 14 (70%) patients. Patients with recurrent brain tumors receiving targeted therapy had a median progression-free survival (from time on therapy) of 4 months. Conclusion Selection of personalized agents for children and young adults with highrisk brain tumors on the basis of integrative clinical sequencing is feasible and resulted in a change in therapy in more than two thirds of children and young adults with high-risk glial tumors.

Identification of novel MECOM gene fusion and personalized therapeutic targets through integrative clinical sequencing in secondary acute myeloid leukemia in a patient with severe congenital neutropenia: a case report and literature review

Severe congenital neutropenia (SCN) is a rare hematologic disorder characterized by defective myelopoiesis and a high incidence of malignant transformation to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). SCN patients who develop MDS/AML have excessive toxicities to traditional chemotherapy, and safer therapies are needed to improve overall survival in this population. In this report, we outline the use of a prospective integrative clinical sequencing trial (PEDS-MIONCOSEQ) in a patient with SCN and AML to help identify oncogenic targets for less toxic agents. Integrative sequencing identified two somatic cis-mutations in the colony stimulating factor 3 receptor (CSF3R) gene, a p.T640N mutation in the transmembrane region and a p.Q768* truncation mutation in the cytoplasmic domain. A somatic mutation p.H105Y, in the runt homology domain (RHD) of runt-related transcription factor 1 (RUNX1), was also identified. In addition, sequencing discovered a unique in-frame EIF4A2-MECOM (MDS1 and ectopic viral integration site 1 complex) chromosomal translocation with high MECOM expression. His mutations in CSF3R served as potential targets for tyrosine kinase inhibition and therefore provided an avenue to avoid more harmful therapy. This study highlights the utility of integrative clinical sequencing in SCN patients who develop leukemia and outlines a strategy on how to approach these patients in a future clinical sequencing trial to improve historically poor outcomes. A thorough review of leukemia in SCN and the role of CSF3R mutations in oncologic therapy are provided to support a new strategy on how to approach MDS/AML in SCN.

Genomic Landscape and Clinical Features of Triple-Negative Myelofibrosis

S268 Background: The prevalence of myeloproliferative neoplasms (MPNs) is higher among females but males have overall worse outcomes. Given that the age at presentation and the molecular characteristics influence the presenting phenotype and disease progression, the exact impact of gender remains unclear. Patients and Methods: We performed a retrospective analysis of 630 patients with MPNs evaluated at Johns Hopkins Hospital between 20052015. We used Fisher analysis to compare the incidence of different phenotypes. Univariate and multiple linear regression analysis were used to predict the initial phenotype based on gender, age and molecular characteristics. Results: The incidence of primary myelofibrosis (PMF) at diagnosis is higher among males (P<.001) and incidence of essential thrombocytosis (ET) (P<.001) is higher among females. These differences remained statistically significant in the JAK2V617F-positive subgroup. JAK2V617F-negative males presented with higher incidence of primary PMF but the difference did not reach statistical significance (P1⁄40.055). After stratifying patients by age, males <40 and >60 presented more frequently with primary PMF (P1⁄40.014 and P1⁄40.021) and females 40-60 and >60 presented more frequently with ET (P1⁄40.020 and P1⁄40.013). In the high-risk group of 183 patients who died during 2005-2015, males still presented more frequently with primary PMF (P1⁄4<.001), a difference that remained significant in both JAK2V617F-positive (P1⁄40.023) and JAK2V617F-negative (P1⁄40.018) subgroups. 275 JAK2V617F-positive patients who had both variant allele frequency (VAF) in neutrophils and CD34+ cells within 5 years from diagnosis were included in regression analysis. Univariate regression analysis showed that age, gender, JAK2V617F VAF in neutrophils and CD34+ cells can predict the phenotype at presentation but multiple regression analysis showed that only gender is an independent predictor (P<.001). Conclusions: Our data suggest that males with MPNs present more frequently with primary PMF while females present more frequently with ET. This observation seems to be independent of age, driver mutation and JAK2V617F burden for JAK2V617-positive disease. We conclude that the male CONTEXT informs disease presentation and progression, and places males at higher risk than females independently of other risk factors.

Abstract B15: The landscape of immune infiltration and mechanisms of immune escape across 500 metastatic cancers

Background: The prognostic value of tumor infiltrating lymphocytes (TILs) has been extensively reported in several primary cancers. The broad prognostic utility of TIL profiling in primary solid tumors was further demonstrated by a number of retrospective large-scale meta-analyses. These studies were enabled by in silico methods to assess leukocyte infiltration and T-cell clonality from transcriptome data. However, in contrast to primary cancers, the landscape of immune infiltration within metastases is largely unknown. This represents a significant gap in knowledge as immune evasion is widely recognized as a hallmark of metastatic cancer. To identify genetic and functional mechanisms that enable immune escape of individual tumors and to better understand tumor-host immune interactions in metastasis we characterize immune infiltration across 500 metastatic cancer patients. Methods: We obtained integrative molecular data, comprising whole-exome and transcriptome sequencing, for metastatic cancer patients enrolled under the MI-Oncoseq program. We utilized existing and novel computational methods to quantify the level of immune infiltration (TIL-score) and the predicted composition of the infiltrate within each sample. Further, to identify facets of tumor-host immune interactions we characterized the joint expression profiles of immune receptors, ligands, cytokines, and HLA molecules. Results: Application of TIL-scores revealed a large heterogeneity of lymphocyte infiltration levels, both within and across cancer types. Consistent with data from primary tumors, the highest levels of immune infiltration were observed in melanoma and kidney cancer, but highly infiltrated samples were observed for most cancers. However, multiple lines of evidence suggest that over 50% of tumors lack significant T-cell infiltration and that HLA expression is almost completely lost in lymph node metastases for several cancer types. Based on the breakdown of immune cells, cancers were most strongly typified by the ratios of M2 to M0 macrophages and CD8+ to CD4+ T-cells. Unsupervised analysis revealed coherent expression of immune ligands and their cognate receptors (CD80/CD86 and CD28), but anticorrelation between stimulatory (CD80/CD86) and suppressive (PD-L1/PD-L2) ligands. Conclusions: To develop the most effective immunotherapeutic strategies for metastatic cancer, it is essential to dissect the specifics of immune evasion in each tumor, determine the regulatory network that links these mechanisms, and identify biomarkers that predict sensitivity to specific immune therapies. This study highlights the heterogeneity of metastatic immune infiltration and represents the first step in the development of immunophenotypic biomarkers in metastatic cancer. Citation Format: Marcin P. Cieslik, Yi-Mi Wu, Lisha Wang, Xuhong Cao, Dan Robinson, Arul M. Chinnaiyan. The landscape of immune infiltration and mechanisms of immune escape across 500 metastatic cancers. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr B15.