Quantum Nondemolition Measurement of a Quantum Squeezed State Beyond the 3 dB Limit

We use a reservoir engineering technique based on two-tone driving to generate and stabilize a quantum squeezed state of a micron-scale mechanical oscillator in a microwave optomechanical system. Using an independent backaction-evading measurement to directly quantify the squeezing, we observe 4.7±0.9  dB of squeezing below the zero-point level surpassing the 3 dB limit of standard parametric squeezing techniques. Our measurements also reveal evidence for an additional mechanical parametric effect. The interplay between this effect and the optomechanical interaction enhances the amount of squeezing obtained in the experiment.

Abstract P6-03-12: Comprehensive genomic profiling of clinically advanced mucinous carcinoma of the breast

Background: Mucinous carcinoma of the breast (mucBC) is generally associated with a favorable prognosis, but on occasion, may have an aggressive clinical course in which it is commonly refractory to cytotoxic chemotherapy. The low incidence of mucBC (∼2% of breast cancers) precludes the development of consensus based guidelines for management of these relapsed/refractory cases. We performed hybrid-capture based comprehensive genomic profiling (CGP) to identify potential therapy targets not routinely searched for in clinical management of metastatic mucBC.

Methods: DNA was extracted from 40 microns of FFPE sections from 22 cases of stage IV mucBC. Comprehensive genomic profiling (CGP) was performed using a hybrid-capture, adaptor ligation based next generation sequencing assay to a mean coverage depth of >550X. The results were analyzed for all classes of genomic alterations (GA) including base substitutions, insertions and deletions, select rearrangements, and copy number changes. Clinically relevant genomic alterations (CRGA) were defined as those identifying anti-cancer drugs on the market or in registered clinical trials.

Results: The median age of the 22 mucBC patients was 57 years (range 32 to 79 years). Samples were from breast (11), lymph nodes (3), chest wall (2), liver (2), soft tissue (2), bone (1) and pleura (1). Three mucBC were grade 1, 17 were grade 2 and 2 were grade 3. Twenty-one (95%) mucBC were ER+, 19 (86%) were PR+ and 4 (18%) were HER2+ by IHC and/or FISH. There were 129 GA identified on the 22 mucBC (5.9 per tumor) including 51 CRGA with a mean of 2.3 per tumor. Amplifications of FGFR1 and ZNF703 were found in 8 out of 22 cases (36%) on the same amplicon. Other most frequently altered genes were TP53 (32%), CCND1 and FGF3/4/19 often co-amplified together (27%). ERBB2/HER2 alterations were found on 5 cases (23%) including amplifications on all 4 HER2+ cases by IHC and/or FISH, and ERBB2 substitution D769Y on one additional mucBC. CRGA were found on some other 20 genes included PIK3CA (5), BRCA1 (1), TSC2 (1), STK11 (1), AKT3 (1), and ESR1 (1).

Conclusions: The subset of relapsed/refractory mucBC presents a management challenge, but comprehensive genomic profiling offers avenues for benefit from targeted therapy. MucBC relative to breast cancer is predominantly ER+, enriched for FGFR1 amplification, 36% vs 11% from TCGA ER+ breast cancer (N=601) with Fisher's test p-value <0.005. Moreover, metastatic mucBC appears more often to have ERBB2/HER2 alterations (23%) than typical mucBC cured by local treatments. Comprehensive genomic profiling uncovers a variety of genomic targets in metastatic mucBC that could facilitate the introduction of targeted therapies for patients with this challenging disease.

Citation Format: Wang K, Ali SM, Khaira D, Elvin JA, Vergilio J-A, Suh J, Yelensky R, Lipson D, Chmielecki J, Miller VA, Stephens PJ, Ross JS. Comprehensive genomic profiling of clinically advanced mucinous carcinoma of the breast. [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 P6-03-12.

Abstract P3-07-05: Non-amplification ERBB2 genomic alterations in 5,605 cases of refractory and metastatic breast cancer: An emerging opportunity for anti-HER2 targeted therapies

Background: Non-amplification ERBB2 alterations (ERBB2 mut) in advanced/metastatic breast cancer (mBC) are not detected by IHC or FISH, but when detected by DNA sequencing assays can lead to clinical responses to anti-HER2 targeted therapy. We queried a database of more than 43,000 clinical cases to uncover the frequency, type and associated genomic alterations (GA) in mBC driven by ERBB2 mut and highlight clinical responses to small molecule drug and antibody-based anti-HER2 therapeutics.

Methods: DNA was extracted from 40 microns of FFPE sections from 5,605 mBC. Comprehensive genomic profiling (CGP) was performed using a hybrid-capture, adaptor ligation based next generation sequencing assay of up to 315 genes to a mean coverage depth of >600X. The results were analyzed for base substitutions, short insertions and deletions, selected rearrangements, and copy number changes.

Results: 698 (12.5%) of 5,605 mBC featured ERBB2 alterations. 596 (10.6%) featured ERBB2 amplifications and 137 (2.4%) featured ERBB2mut. 35 (0.6%) of total mBC had both ERBB2amp and ERBB2mut, which accounted for 5.0% of all ERBB2 altered mBC. The 137 ERBB2mut mBC cases had a median age of 61 years (range 29 to 93 years) and were sequenced to a mean depth of 600X. Samples utilized for CGP included 52 (38%) from the patient's primary BC and 85 (62%) from metastatic sites including bone/soft tissue/skin (12%), liver (20%), LN (14%), serous cavities (6%), lung (4%) and miscellaneous sites (6%). 71 (52%) mBC were submitted as carcinoma NOS, 44 (32%) as IDC, 22 (16%) as ILC and 1 (1%) as mucinous mBC. Of the 137 ERBB2mut cases, 8 featured more than 1 ERBB2 mut. There were 124 (85%) ERBB2 kinase domain mutations and 15 (10%) extra-cellular domain ERBB2mut. The most common genes co-altered in ERBB2mut mBC were TP53 (49%), PIK3CA (42%), CDH1 (37%), MYC (17%), and CCND1 (16%). The enrichment of ERBB2mut in CDH1 mut mBR was significant (p=0.0006) and associated with relapsed lobular mBC. Multiple case examples of kinase domain and extra-cellular domain ERBB2mut mBC responding to a variety of anti-HER2 targeted therapies will be presented.

Conclusions: In this large series of 5,605 mBC, 20% of the total ERBB2 alterations were non-amplification ERBB2mut not detectable by standard of care IHC and FISH slide-based HER2 tests. Given the demonstration of ERBB2mut driven mBC responsive to anti-HER2 targeted therapies in this study, expansion of clinical trials designed to detect these ERBB2mut cases with CGP and optimize the targeted therapies for these patients is strongly recommended.

Citation Format: Ross JS, Wang K, Ali SM, Chumsri S, Elvin JA, Vergilio J-A, Suh J, Yelensky R, Lipson D, Chmielecki J, Miller VA, Stephens PJ. Non-amplification ERBB2 genomic alterations in 5,605 cases of refractory and metastatic breast cancer: An emerging opportunity for anti-HER2 targeted therapies. [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 P3-07-05.

Abstract A32: MCL1 gene amplification in breast cancer is associated with TNBC status and can respond to a sorafenib/vorinostat regimen

Background: MCL1 encodes the induced myeloid leukemia cell differentiation protein Mcl-1, a member of the BCL-2 family which functions to inhibit apoptosis. Mcl-1 over-expression has been associated with high tumor grade and adverse prognosis in triple negative breast cancer (TNBC) but therapies specifically leading to inhibition of MCL-1 have not been identified.

Methods: Comprehensive genomic profiling (CGP) using hybridization capture of 3,769 exons from 315 cancer-related genes and 47 introns of 19 genes commonly rearranged in cancer was applied to ≥50ng of DNA extracted from 2,824 consecutive BC and sequenced to high, uniform median coverage (>600X). The original primary BC was assayed in 44% of cases and a sample from a metastatic focus was assayed in 56% of cases.

Results: Of 2824 consecutive BC cases, 200 (7.1%) cases harbored MCL1 amplification. Of these MCL1-amplified cases, 146 (73%) were TNBC and 54 were non-TNBC (p<0.0001). Twelve of the latter cases (22%) were ERBB2 (HER2) amplified and slide-based HER2 status concordance with CGP was 99%. MCL1 amplification was also observed in the TCGA dataset for 32/123 (26%) of TNBC (p=0.008). Of the MCL1 amplified TNBC cases, 88% were high grade and 98% were stage IV at the time of CGP. Genes co-altered within MCL1 amplified TNBC included TP53 (86%), MYC (41%), MYST3 (21%), LYN (20%), CCNE1 (19%), PIK3CA (18%), and AKT3 (15%). Two MCL1 amplified TNBC patients were treated with a multi-drug regimen based on sorafenib and vorinostat and experienced significant clinical benefit.

Conclusions: MCL1 amplification is a frequent feature in advanced stage and high grade TNBC, and correspondingly such MCL1 amplified tumors very seldom harbor co-amplifications of ERBB2. Clinical observation suggests that treatment with sorafenib and vorinostat in heavily pre-treated MCL1 amplified patients may be correlated with clinical benefit, consistent with historic preclinical investigation. These preliminary findings suggest that MCL1 amplified TNBC may be able to benefit from combination targeted therapy, and warrant further systematic investigation.

Citation Format: JS Ross, K Wang, A Johnson, J Watson, C Hatzis, L Pusztai, J Chmielecki, R Yelensky, D Lipson, JA Elvin, J Vergilio, J Suh, VA Miller, K Dicke, PJ Stephens, SM Ali. MCL1 gene amplification in breast cancer is associated with TNBC status and can respond to a sorafenib/vorinostat regimen. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A32.

Comparative Studies of Crystalline Orientation and Morphology of Injection Molded Polyolefin Parts

We have studied the structural characteristics of the cross-sections of injection molded parts of various crystalline polyolefins including polyethylene (PE), isotactic polypropylene (PP), isotactic poly(butene-1) (PB1) and isotactic poly(4-methylpentene-1) (P4MP1). Polarized light microscopy, birefringence and wide angle x-ray diffraction pole figure analysis were used to investigate the samples. In most cases, high orientations were observed near the mold wall and isotropic molded part cores were found. However, highly oriented mold core regions were found in P4MP1. Significantly different types of crystalline orientation near the mold wall were observed among the various polyolefins. We represent the development of these differences through the components of a crystalline orientation tensor which represent changes in the state of orientation between melts in the mold prior to crystallization and the final crystalline molded part.