Anderson, KS

Abstract Introduction: Triple negative breast carcinoma (TNBC) is a subtype of breast cancer with a paucity of therapeutic targets and a poor prognostic phenotype. In a retrospective cohort, we sought to determine the prevalence of the amplicon targeting the 9p24.1 locus, resulting in over-expression of PD-L1, PD-L2, and JAK2 (PDJ), and potentially actionable therapeutic targets. We then probed the genomic landscape of these PDJ positive tumors and identified co-occurring copy number aberrations, including focal amplifications and homozygous deletions. The presence of the PDJ amplicon and selected co-occurring aberrations provide a unique description of a clinically relevant subtype of TNBC. Methods: We evaluated fresh frozen and formalin-fixed paraffin embedded tumor samples from 64 patients with triple negative breast cancer whom underwent definitive surgical resection. Clinical annotation was available in 60 of the samples. Tumor populations (diploid, tetraploid, and aneuploidy) were sorted from each biopsy using DNA content flow cytometry. Each sorted sample was interrogated with oligonucleotide array comparative genomic hybridization (aCGH). All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 10.7. The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm. Results: We detected a high level (log2ratio greater than or equal to 2) amplicon targeting 9p24.1 in 18 of 64 patients (28%) genomic profiles with triple negative breast carcinoma. In the PDJ positive population, we detected 8 of 18 patients (44%) with co-amplification targeting myc at 8q24, 3 of 18 patients (17%) with co-amplifications targeting EGFR at 7p11, 3 of 18 patients (17%) with co-amplifications targeting PIK3CA. These co-occurring genomic events in PDJ positive tumors may provide clinically actionable targets. Other selected amplifications detected included NOTCH3, KRAS, RUNX1, TUBAL3, FGFR2, AKT1, AKT2, YPEL2, PBXL7, KIT. We detected PTEN homozygous deletion in 2 of 18 patients (11%) PDJ positive tumors. Other homozygous deletions identified in the genomic landscape included FAT1, SOX3, Park2, TNFAIP3, GPC3, RB1, and CREBBP. Conclusions: In our retrospective analysis, the amplification of chromosome 9p24.1 involving PD-L1, PD-L2, and JAK2 is present in approximately 28% of triple negative breast cancer patients. The genomic landscape of these PDJ positive TNBCs include recurring high-level focal amplifications and targeted homozygous deletions of clinically relevant genes. The clinical implications of these data are under current investigation using model systems and are in early phase clinical trials. The efficacy of immune checkpoint inhibitors including nivolumab, pembrolizumab, and JAK2 inhibitors including ruxolitinib, in PDJ positive triple negative breast carcinoma is intriguing and remains to be elucidated. Citation Format: Gawryletz CD, Anderson KS, Cunliffe HE, Northfelt DW, McCullough AE, Lenkiewicz E, Malasi S, Pockaj BA, Barrett MT. The genomic landscape of PD-L1, PD-L2, Jak2 (PDJ) amplified triple negative breast carcinoma. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-13.

Abstract Background A subset of triple negative breast cancers (TNBC) has somatic amplification of chromosome 9p24.1, encoding PD-L1, PD-L2, and JAK2 (the "PDJ" amplicon). The JAK/STAT pathway promotes malignant transformation and proliferation, and the JAK1/JAK2 inhibitor ruxolitinib is being evaluated in early phase clinical trials in breast cancer. This study was designed to measure the frequency of PDJ copy number gain in existing TNBC cell lines, and determine the impact of targeted JAK2 inhibition on cellular proliferation. Methods: Copy number alterations were measured in nine TNBC cell lines (MDA-MB-453, MDA-MB-436, BT549, MDA-MB231, MFM-223, MDA-MB-468, H5578T, MDA-MB-157, HCC1937) by array comparative genomic hybridization (aCGH). JAK2 and pSTAT3 expression was measured by immunoblot in four of the TNBC lines (HCC1937, MDA-MB-468, MDA-MB-231, MDA-MB-436) and compared with MCF10A, SK-BR3, and T47D. To selectively inhibit JAK2, lentiviral vectors encoding five different shRNA targeting JAK2 were generated. Ruxolitinib treatment was performed at 25 uM for 48 hrs and 72 hrs. Cell proliferation was measured by CellTiter-Glo. Results: All TNBC cell lines had an elevated level of baseline protein expression of JAK2 and pSTAT3 compared to SK-BR3, T47D, and MCF10A. Of the nine TNBC cell lines, only MDA-MB-436 and BT549 had copy number gain of 9p24.1 (log2ratio<1). Four independent shRNA efficiently silenced over 90% of JAK2 expression in MDA-MB-231. The inhibition of JAK2 in MDA-MB-231 was associated with a decrease in both JAK2 and pSTAT3 protein expression and reduction in cell proliferation compared to control shRNA after 96 hrs (p<0.0001). Inhibition of proliferation was also observed for both MDA-MB-231 and MDA-MB-436 after ruxolitinib treatment. Conclusion These results demonstrate that existing TNBC cell lines have varying copy number alterations of chromosome 9p24.1 encoding JAK2, and targeted JAK2 inhibition in TNBC inhibits cell proliferation. Citation Format: Chen M, Andreozzi M, Gonzalez-Malerva L, Eaton S, Pockaj B, Barrett MT, Anderson KS. JAK2 copy number and targeted JAK2 inhibition of TNBC cell lines. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-04-19.

Abstract Introduction: In a pilot study, we recently described amplification of chromosome 9p24 encoding PD-L1, PD-L2, and JAK2 (the PDJ amplicon) in 29% of early stage triple negative breast cancers (TNBC). Amplification was associated with poor DFS and OS. The impact of this amplicon on immune function is not known. Methods: Fresh frozen tumor samples from 36 subjects with newly-diagnosed TNBC (stages I-III) were evaluated for copy number aberrations using DNA-based flow cytometry to enrich nuclei based on ploidy status (tetraploidy or aneuploidy), followed by oligonucleotide CGH arrays. Targeted immune expression profiling was performed using the Nanostring PanCancer Immune Profiling Panel (n=770 genes). Results: 23 samples had measurable abnormal ploidy (evidence of sufficient tumor content) for CGH analysis; the remaining samples were omitted from analysis. High level (log2ratio >1) amplification was detected in 6/23 (26.1%) of TNBCs, and low-level copy number gain (CN log2ratio >0 and<1) was detected in 3/23 (13.0%). The remaining samples had no copy number change (n=9) or low level copy number loss (CN log2ratio>-1 and <0, n=5). Increased RNA expression of STAT1, STAT2, STAT3, and STAT6 was associated with PDJ amplification, as well as upregulation of the immune regulatory genes CD47 and IDO1. Conclusion: Amplification of chromosome 9p24.1 involving PD-L1, PD-L2, and JAK2 is present in a significant proportion of TNBCs. This amplicon is associated with altered gene expression of the tumor microenvironment. Citation Format: Anderson KS, Andreozzi M, Pockaj BA, Hopper M, McCullough AE, Barrett MT. Amplification of chromosome 9p24 targeting PD-L1 and JAK2 correlates with altered tumor microenvironment expression profiles in triple negative breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-04-02.

Abstract Abstract #6074 Objective: To analyze blood-serum biomarkers (HER2, EGFR, uPA, and TIMP-1) for prediction of response to treatment in conjunction with Study 96-32-55, a multicenter phase II trial assessing the efficacy and tolerability of two irinotecan schedules in anthracycline- or taxane-refractory MBC patients.
 Methods: MBC patients who experienced disease progression after one to three chemotherapy regimens, including at least one anthracycline- or taxane-based regimen, were randomly assigned to irinotecan in 6-week cycles comprising 100 mg/m2 weekly for 4 weeks, then a 2-week rest or 240 mg/m2 every 3 weeks. During this study the serum samples from each patient were collected at a possibility of three time points; prior to treatment, at the first occurrence of response, and at completion of or withdrawal from treatment. Response prediction was analyzed using predetermined elevated/non-elevated serum biomarker cutoffs. Percentage changes from baseline to first response and disease progression were analyzed.
 Results: In the weekly arm, the objective response (CR+PR) rate was 23% (95% CI, 13% to 37%), and in the every-3-weeks arm, the objective response rate was 14% (95% CI, 6% to 26%). Serum biomarker levels were determined for HER2, EGFR, uPA, and TIMP-1 prior to treatment for 91 patients. Of these 91 patients, 17 had serum measurements at first response, and 38 had serum measurements at their completion of study due to disease progression. Only 7 patients had serum-levels collected at all three event-points. The baseline levels of sHER2, EGFR, uPA, and TIMP-1 were not different among responders and non-responders (Fisher's Exact p=0.41, 0.26, 0.68, 0.75). sHER2 level increased by 20.6% from baseline to disease progression (p=0.01). TIMP-1 level was 15.2% lower than baseline at first response (p=0.03), 16.5% higher than baseline at disease progression (p=0.01), and for 7 patients with all three event-point measures, TIMP-1 was 21.8% lower than baseline at first response and was 22.3% higher than baseline at disease progression (p=0.02, 0.04).
 Conclusions: In this study, serum levels of HER2, EGFR, uPA, and TIMP-1 do not appear to be predictive of response. However, interpretation of the data is compromised due to limited availability of serum at all 3 points. Serum HER2 appears higher at disease progression than at baseline. Serum TIMP-1 appears to decrease from baseline to first response, and then appears to increase at disease progression. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 6074.