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Purpose: Devimistat (CPI-613) is a novel inhibitor of tumoral mitochondrial metabolism. We investigated the effect of devimistat in vitro and in a phase Ib clinical trial in patients with advanced biliary tract cancer (BTC). Patients and Methods: Cell viability assays of devimistat ± gemcitabine and cisplatin (GC) were performed and the effect of devimistat on mitochondrial respiration via oxygen consumption rate (OCR) was evaluated. A phase Ib/II trial was initiated in patients with untreated advanced BTC. In phase Ib, devimistat was infused over 2 hours in combination with GC on days 1 and 8 every 21 days with a primary objective to determine the recommended phase II dose (RP2D). Secondary objectives included safety, overall response rate (ORR), progression-free survival (PFS), and overall survival (OS). Results: In vitro, devimistat with GC had a synergistic effect on two cell lines. Devimistat significantly decreased OCR at higher doses and in arms with divided dosing. In the phase Ib trial, 20 patients received a median of nine cycles (range, 3–19). One DLT was observed, and the RP2D of devimistat was determined to be 2,000 mg/m2 in combination with GC. Most common grade 3 toxicities included neutropenia (n = 11, 55%), anemia (n = 4, 20%), and infection (n = 3, 15%). There were no grade 4 toxicities. After a median follow-up of 15.6 months, ORR was 45% and median PFS was 10 months (95% confidence interval, 7.1–14.9). Median OS is not yet estimable. Conclusion: Devimistat in combination with GC is well tolerated and has an acceptable safety profile in patients with untreated advanced BTC.

Genomics data

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Purpose:Devimistat (CPI-613) is a novel inhibitor of tumoral mitochondrial metabolism. We investigated the effect of devimistat in vitro and in a phase Ib clinical trial in patients with advanced biliary tract cancer (BTC).Patients and Methods:Cell viability assays of devimistat ± gemcitabine and cisplatin (GC) were performed and the effect of devimistat on mitochondrial respiration via oxygen consumption rate (OCR) was evaluated. A phase Ib/II trial was initiated in patients with untreated advanced BTC. In phase Ib, devimistat was infused over 2 hours in combination with GC on days 1 and 8 every 21 days with a primary objective to determine the recommended phase II dose (RP2D). Secondary objectives included safety, overall response rate (ORR), progression-free survival (PFS), and overall survival (OS).Results:In vitro, devimistat with GC had a synergistic effect on two cell lines. Devimistat significantly decreased OCR at higher doses and in arms with divided dosing. In the phase Ib trial, 20 patients received a median of nine cycles (range, 3–19). One DLT was observed, and the RP2D of devimistat was determined to be 2,000 mg/m2 in combination with GC. Most common grade 3 toxicities included neutropenia (n = 11, 55%), anemia (n = 4, 20%), and infection (n = 3, 15%). There were no grade 4 toxicities. After a median follow-up of 15.6 months, ORR was 45% and median PFS was 10 months (95% confidence interval, 7.1–14.9). Median OS is not yet estimable.Conclusion:Devimistat in combination with GC is well tolerated and has an acceptable safety profile in patients with untreated advanced BTC.

Loss of GBP1 expression does not impact PSaRC318 cell migration.

Prevalence of somatic DNA damage repair gene variants in Ewing cell lines included in original studies of PARP inhibition.

Ewing sarcoma is a fusion oncoprotein–driven primary bone tumor. A subset of patients (∼10%) with Ewing sarcoma are known to harbor germline variants in a growing number of genes involved in DNA damage repair. We recently reported our discovery of a germline mutation in the DNA damage repair protein BARD1 (BRCA1-associated RING domain-1) in a patient with Ewing sarcoma. BARD1 is recruited to the site of DNA double stranded breaks via the PARP protein and plays a critical role in DNA damage response pathways including homologous recombination. We thus questioned the impact of BARD1 loss on Ewing cell sensitivity to DNA damage and the Ewing sarcoma transcriptome. We demonstrate that PSaRC318 cells, a novel patient-derived cell line harboring a pathogenic BARD1 variant, are sensitive to PARP inhibition and by testing the effect of BARD1 depletion in additional Ewing sarcoma cell lines, we confirm that BARD1 loss enhances cell sensitivity to PARP inhibition plus radiation. In addition, RNA-sequencing analysis revealed that loss of BARD1 results in the upregulation of GBP1 (guanylate-binding protein 1), a protein whose expression is associated with variable response to therapy depending on the adult carcinoma subtype examined. Here, we demonstrate that GBP1 contributes to the enhanced sensitivity of BARD1-deficient Ewing cells to DNA damage. Together, our findings demonstrate the impact of loss-of function mutations in DNA damage repair genes, such as BARD1, on Ewing sarcoma treatment response.Significance:This work provides preclinical support for the inclusion of pediatric patients with advanced Ewing sarcoma and pathogenic germline variants in BARD1 in future clinical trials testing novel agents inducing DNA damage/targeting DNA damage repair.

XLSX file - 776K, Breast sample kinome compendium by RNA-Seq.

XLSX file - 613K, RNA-Seq data for matched primary pancreatic adenocarcinoma xenograft tissue, DS-08-947, and derived xenograft cell line.

XLSX file - 13K, shRNA, siRNA, and qPCR primer sequences used.

PDF file - 1133K, This file contains supplemental figures validating RNA-Seq method for measuring gene expression and nominating outlier kinases in individual cancer samples.

PDF file - 103K

XLSX file - 2238K, Complete kinome compendium of all tissue types by RNA-Seq.

PDF file - 4323K, This file contains supplemental figures providing results of additional experiments supporting sample-specific sensitivities upon targeting of outlier kinases.

Supporting information showing CTC enumeration and gene expression profiling data for CTC clusters from early stage lung cancer.

Supplementary Table 1 from Characterization of Bone Metastases from Rapid Autopsies of Prostate Cancer Patients

Supplementary Figure 2 from Characterization of Bone Metastases from Rapid Autopsies of Prostate Cancer Patients

Supplementary Table 2 from Characterization of Bone Metastases from Rapid Autopsies of Prostate Cancer Patients

Supplementary Figure and Table Legends from Characterization of Bone Metastases from Rapid Autopsies of Prostate Cancer Patients

Early detection of metastasis can be aided by circulating tumor cells (CTC), which also show potential to predict early relapse. Because of the limited CTC numbers in peripheral blood in early stages, we investigated CTCs in pulmonary vein blood accessed during surgical resection of tumors. Pulmonary vein (PV) and peripheral vein (Pe) blood specimens from patients with lung cancer were drawn during the perioperative period and assessed for CTC burden using a microfluidic device. From 108 blood samples analyzed from 36 patients, PV had significantly higher number of CTCs compared with preoperative Pe (P < 0.0001) and intraoperative Pe (P < 0.001) blood. CTC clusters with large number of CTCs were observed in 50% of patients, with PV often revealing larger clusters. Long-term surveillance indicated that presence of clusters in preoperative Pe blood predicted a trend toward poor prognosis. Gene expression analysis by RT-qPCR revealed enrichment of p53 signaling and extracellular matrix involvement in PV and Pe samples. Ki67 expression was detected in 62.5% of PV samples and 59.2% of Pe samples, with the majority (72.7%) of patients positive for Ki67 expression in PV having single CTCs as opposed to clusters. Gene ontology analysis revealed enrichment of cell migration and immune-related pathways in CTC clusters, suggesting survival advantage of clusters in circulation. Clusters display characteristics of therapeutic resistance, indicating the aggressive nature of these cells. Thus, CTCs isolated from early stages of lung cancer are predictive of poor prognosis and can be interrogated to determine biomarkers predictive of recurrence. Cancer Res; 77(18); 5194–206. ©2017 AACR.

Supplementary Figure 1 from Characterization of Bone Metastases from Rapid Autopsies of Prostate Cancer Patients

Purpose: Bone is the most common metastatic site for prostate cancer, and osseous metastases are the leading cause of morbidity from this disease. Recent autopsy studies prove that 100% of men who die of prostate cancer have bone involvement. Understanding the biology of prostate cancer and its evolution to an incurable androgen-independent phenotype requires an understanding of the genetic and cellular alterations that lead to the seeding and proliferation of tumor foci in bone, as well as the microenvironment in which these metastases arise. No intensive studies, however, have been conducted on osseous metastatic tissues from patients with metastatic prostate cancer due to lack of access to such tissues for profiling and other research.Experimental Design: We show, for the first time, a reproducible methodology to obtain high quality clinical tumor tissues metastatic to the bone. This technique allowed the procurement of viable metastatic tumor tissue from involved bones in 13 recent autopsies conducted at the University of Michigan and analyzed the gene expression of these tissues using real-time PCR and microarrays.Results: We present here the discovery of nonossified bone metastases from multiple patients with advanced prostate cancer and their subsequent characterization and comparison to nonosseous metastases from the same patients.Conclusion: This represents a versatile and practical approach that may be employed to characterize the steps in metastasis and the phenotypic characteristics of osseous metastasis of prostate cancer and to profile RNA, DNA, and cDNA from tumor samples metastatic to the bone. Clin Cancer Res; 17(12); 3924–32. ©2011 AACR.

Supplementary Table 1, Figures 1-3 from A Fluorescence In situ Hybridization Screen for E26 Transformation–Specific Aberrations: Identification of DDX5-ETV4 Fusion Protein in Prostate Cancer

Supplementary File 1 from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression

Supplementary Table 2 from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression

Bladder cancer is a common and deadly malignancy but its treatment has advanced little due to poor understanding of the factors and pathways that promote disease. ATDC/TRIM29 is a highly expressed gene in several lethal tumor types, including bladder tumors, but its role as a pathogenic driver has not been established. Here we show that overexpression of ATDC in vivo is sufficient to drive both noninvasive and invasive bladder carcinoma development in transgenic mice. ATDC-driven bladder tumors were indistinguishable from human bladder cancers, which displayed similar gene expression signatures. Clinically, ATDC was highly expressed in bladder tumors in a manner associated with invasive growth behaviors. Mechanistically, ATDC exerted its oncogenic effects by suppressing miR-29 and subsequent upregulation of DNMT3A, leading to DNA methylation and silencing of the tumor suppressor PTEN. Taken together, our findings established a role for ATDC as a robust pathogenic driver of bladder cancer development, identified downstream effector pathways, and implicated ATDC as a candidate biomarker and therapeutic target. Cancer Res; 75(23); 5155–66. ©2015 AACR.

Supplementary Methods from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression

Supplementary Table 1 from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression

Supplemental Figure 1. ATDC mRNA expression in normal littermate (N) or CAG-ATDC transgenic bladders Supplemental Figure 2. Bladder urothelial lesions in CAG-ATDC transgenic line A of 8-12 months of age. Supplemental Figure 3. ATDC mRNA levels in CAG-ATDC tumors (T) are similar to human bladder cancers (UC9 and UC14) and ~20 fold higher than normal mouse (N) or human urothelial cell (TRTHU) expression. Mean{plus minus}SE, n = 3 for each column, * p < 0.05 compared to N. Supplemental Figure 4. ATDC immunostaining in two representative human invasive urothelial carcinomas demonstrates predominantly cytoplasmic staining (A) in most samples with rare tumors showing nuclear localization (B). Supplemental Figure 5. ATDC overexpression drives invasion in UC10 bladder cancer cell line. Supplemental Figure 6. PTEN immunostaining in three representative images of normal mouse bladder, CAG-ATDC mouse bladder or CAG-ATDC mouse tumor specimens demonstrating decreased PTEN expression in ATDC transgene expressing tissues Supplemental Figure 7. PTEN Quantitative methylation specific PCR. Supplemental Figure 8. Knockdown of ATDC results in reduction in DNMT3A, but not DNMT1 or DNMT3B in UC14 cell line as measured by immunoblot. Supplemental Figure 9. ATDC overexpression up-regulates DNMT3A, �-catenin and c-MYC mRNA expression and suppresses expression of PTEN. Supplemental Figure 10. Knockdown of MYC increases miR-29A and B1 in bladder cancer cell lines. Supplemental Table 1. Summary of bladder urothelial lesions in CAG-ATDC mouse line A. Supplemental Table 2. ATDC is significantly over-expressed in human bladder cancer. Supplemental Table 3. Genes up-regulated in all three CAG-ATDC invasive bladder tumors. Supplemental Table 4. Genes up-regulated in CAG-ATDC bladder cancers show significant overlap with the top 5-10% of overexpressed genes in bladder cancer in the Oncomine database. Supplemental Table 5. Molecular concepts showing enrichment with expression signature of genes over-expressed in CAG-ATDC bladder cancers through Oncomine analysis. Supplemental Table 6. ATDC and DNMT3A IHC Expression Correlation.

Supplementary Figure Legend 1, Table Legends 1-3 from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression

Supplementary Table 3 from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression

Integrative analysis of genomic aberrations in the context of trancriptomic alterations will lead to a more comprehensive perspective on prostate cancer progression. Genome-wide copy number changes were monitored using array comparative genomic hybridization of laser-capture microdissected prostate cancer samples spanning stages of prostate cancer progression, including precursor lesions, clinically localized disease, and metastatic disease. A total of 62 specific cell populations from 38 patients were profiled. Minimal common regions (MCR) of alterations were defined for each sample type, and metastatic samples displayed the most number of alterations. Clinically localized prostate cancer samples with high Gleason grade resembled metastatic samples with respect to the size of altered regions and number of affected genes. A total of 9 out of 13 MCRs in the putative precursor lesion, high-grade prostatic intraepithelial neoplasia (PIN), showed an overlap with prostate cancer cases (amplifications in 3q29, 5q31.3-q32, 6q27, and 8q24.3 and deletions in 6q22.31, 16p12.2, 17q21.2, and 17q21.31), whereas postatrophic hyperplasia (PAH) did not exhibit this overlap. Interestingly, prostate cancers that do not overexpress ETS family members (i.e., gene fusion–negative prostate cancers) harbor differential aberrations in 1q23, 6q16, 6q21, 10q23, and 10q24. Integrative analysis with matched mRNA profiles identified genetic alterations in several proposed candidate genes implicated in prostate cancer progression. [Cancer Res 2007;67(17):8229–39]

Primary aldosteronism (PA) is the most common form of endocrine hypertension and effects one in 50 adults. PA is characterized by inappropriately elevated aldosterone production via renin-independent mechanisms. Driver somatic mutations for aldosterone excess have been found in approximately 90% of aldosterone-producing adenomas (APAs). Using next-generation sequencing, we identified recurrent in-frame deletions inSLC30A1in five APAs (p.L51_A57del, n=3; p.L49_L55del, n=2).SLC30A1encodes the ubiquitous zinc efflux transporter ZnT1 (zinc transporter 1). The identifiedSLC30A1variants are situated in close proximity of the zincbinding site (H43 and D47) in transmembrane domain II and likely cause abnormal ion transport. PA cases with the uniqueSLC30A1mutations showed male dominance and demonstrated increased aldosterone and 18-oxo-cortisol concentrations. Functional studies of the mutant SLC30A151_57delvariant in a doxycycline-inducible adrenal cell system revealed abnormal Na+conductivity caused by the mutant, which in turn led to the depolarization of the resting membrane potential, and thus to the opening of voltage-gated calcium channels. This resulted in an increase in cytosolic Ca2+activity, which stimulatedCYP11B2mRNA expression and aldosterone production. Collectively, these data implicate the first-in-field zinc transporter mutations as a dominant driver of aldosterone excess in PA.

Posterior fossa ependymomas A confer the worst prognosis among all subtypes. They demonstrate distinct epigenetic changes, which can be targeted with epigenetic modifiers like histone deacetylase inhibitors (Vorinostat). We describe a 3-year-old male diagnosed with a posterior fossa ependymoma who had a number of recurrences requiring multimodal therapy. Molecular analysis demonstrated a BCL-6 corepressor mutation, and methylation profiling matched with posterior fossa ependymomas A. He received craniospinal irradiation and focal boost with Vorinostat. Serial imaging after irradiation revealed a progressively decreasing tumor burden with nearly complete resolution of disease at 15 months. Histone deacetylase inhibitors demonstrate promise in treatment of carefully selected cases of ependymoma.