Abstract 339: Identification of novel covalent inhibitors of K-Ras G12C that are efficacious in a xenograft model of NSCLC

KRAS is the frequently mutated isoform in RAS driven cancers. The G12C mutation is more predominantly associated with various tumor types over other changes in K-Ras. Although direct targeting of RAS is very challenging, it is possible to selectively target G12C mutant K-Ras using a covalent approach. Mutant specific covalent inhibitors with high selectivity against wild type K-Ras and other GTPases are expected to lead to efficacy with a very high degree of tolerability. Here, we report identification of lead compounds from two distinct chemical series that selectively target K-Ras G12C. Molecular modeling based on the reported crystal structures aided in the identification of these compounds. Covalent binding of the lead compounds to K-Ras G12C was demonstrated by MALDI-TOF. Lead compounds were potent in selectively inhibiting proliferation of cell lines with K-Ras G12C mutation but not with wild type K-Ras. The anti-proliferative activity of the lead compounds correlated well with their potency in a cellular mechanistic assay. Lead compounds from both series exhibited excellent drug-like properties including solubility, metabolic stability, permeability lack of CYP inhibition and desired exposure in pharmacokinetic studies. In a xenograft model of NSCLC, the lead compound demonstrated dose-dependent tumor growth inhibition with excellent tolerability upon oral dosing. In summary, we have identified a novel, potent and selective K-Ras G12C inhibitor with optimized drug-like properties including oral bioavailability and efficacy in a NSCLC derived xenograft model. Toxicity evaluation is ongoing towards progressing the lead compound to the clinic.

Citation Format: Leena Khare Satyam, Dinesh Chikkanna, Aswani K. G, Vinayak V. Khairnar, Sreekanth Reddy, Vakkapatla Durgaprasad, Kowju Radhakrishna, Sunil K. Panigrahi, Anuradha Ramanathan, Kumari Mahasweta, Anirudha Lakshminarasimhan, Narasimha R. K, Vinutha R, Sreevalsam Gopinath, Suryakant Kumar, Mubarak H. Shah, Raghuveer Ramachandra, Kiran A. B, Chetan Pandit, Murali Ramachandra. Identification of novel covalent inhibitors of K-Ras G12C that are efficacious in a xenograft model of NSCLC. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 339.

Abdominal Wall Transplantation: Skin as a Sentinel Marker for Rejection

Abdominal wall transplantation (AWTX) has revolutionized difficult abdominal closure after intestinal transplantation (ITX). More important, the skin of the transplanted abdominal wall (AW) may serve as an immunological tool for differential diagnosis of bowel dysfunction after transplant. Between August 2008 and October 2014, 29 small bowel transplantations were performed in 28 patients (16 male, 12 female; aged 41 ± 13 years). Two groups were identified: the solid organ transplant (SOT) group (n = 15; 12 ITX and 3 modified multivisceral transplantation [MMVTX]) and the SOT-AWTX group (n = 14; 12 ITX and 2 MMVTX), with the latter including one ITX-AWTX retransplantation. Two doses of alemtuzumab were used for induction (30 mg, 6 and 24 h after reperfusion), and tacrolimus (trough levels 8-12 ng/mL) was used for maintenance immunosuppression. Patient survival was similar in both groups (67% vs. 61%); however, the SOT-AWTX group showed faster posttransplant recovery, better intestinal graft survival (79% vs. 60%), a lower intestinal rejection rate (7% vs. 27%) and a lower rate of misdiagnoses in which viral infection was mistaken and treated as rejection (14% vs. 33%). The skin component of the AW may serve as an immune modulator and sentinel marker for immunological activity in the host. This can be a vital tool for timely prevention of intestinal graft rejection and, more important, avoidance of overimmunosuppression in cases of bowel dysfunction not related to graft rejection.

Abstract P4-09-19: Comprehensive multiplatform molecular profiling identifies potentially targetable biomarkers in malignant phyllodes tumors of the breast

Introduction: Malignant phyllodes tumors are rare breast malignancies (0.1% of all breast tumors) with limited effective treatment options for recurrent and metastatic disease. Recent trials indicated a potential for anti-angiogenic therapy in soft tissue sarcomas, which led us to investigate these pathways.

Materials and Methods: Thirty-five malignant phyllodes tumors (including two cases with matched primary and metastatic tumors) were profiled using gene sequencing (Next-generation and Sanger), gene copy number analysis (in-situ hybridization), whole genome RNA expression, and protein expression (immunohistochemical assay).

Results: RNA microarray assay showed consistent over-expression of genes involved in angiogenesis including VEGFA, Angiopoietin2, VCAM1, PDGFRA, PTTG1, and CYP3A5 in all cases analyzed (n=5). No mutations in KDR (VEGFR2) were detected (0/26). EGFR protein overexpression was observed in 25/26 (96%) of cases with amplification of the EGFR gene in 8 cases (33%). EGFR gene mutations were identified in 2 cases (8%) including one case with presumed pathogenic V774M mutation and one case with EGFRvIII mutation. The most common mutations included those of TP53 (50%) and PIK3CA (15%) while other mutations (BRCA1, BRCA2, RET, CDH1, MLH1, ATM) were rare affecting single phyllodes cases. Two cases with matched primary and metastatic cancers harbored the same mutations in both sites (PIK3CA/KRAS and RB1 gene mutations, respectively).

Conclusions: Comprehensive multiplatform profiling approach to phyllodes tumors identifies various molecular alterations of which some are potentially actionable. Our data suggests that anti-angiogenic therapy may also be effective in patients with malignant phyllodes tumor. Evaluation of EGFR pathway discovered consistent protein over-expression but rare activating mutations, which necessitates refinement in patient selection targeting these pathways.

Citation Format: Gatalica Z, Vranic S, Ghazalpour A, Xiu J, Ocal I, McGill J, Bender R, Discianno E, Sanati S, Reddy S, Pockaj B. Comprehensive multiplatform molecular profiling identifies potentially targetable biomarkers in malignant phyllodes tumors 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 P4-09-19.

Abstract P3-07-30: Molecular profiling comparison of BRCA1/2-mutated and BRCA1/2 non-mutated triple-negative breast cancer (TNBC)

Background: Triple-negative breast cancer (TNBC) is one type of breast cancer that remains challenging because of its aggressive nature and the lack of effective targeted therapy for it. Molecular profiling has revealed different subtypes, indicating a potential for promising targeted therapy such as androgen blockade and PARP inhibition in some TNBCs. The purpose of this study is to identify differences in BRCA1/2 mutated and non-mutated TNBC to shed light on potential therapeutic options in both subtypes, utilizing a multiplatform approach.

Methods: A cohort of 386 triple-negative breast cancer specimens were tested via a multiplatform profiling service (Caris Life Sciences, Phoenix, AZ) consisting of gene sequencing (next generation sequencing [NGS]), protein expression (immunohistochemistry [IHC]) and gene amplification (fluorescence or chromogenic in situ hybridization [FISH or CISH]). Primary and metastatic specimens were evaluated. Tumor specimens with any BRCA1 and/or BRCA2 mutation (i.e. pathogenic or variant of unknown significance) were categorized as "BRCA1/2-mutated", while all others were considered "BRCA1/2 non-mutated".

Results: In our cohort, 16.3% (63/386) of specimens were BRCA1/2-mutated while 83.7% (323/386) had no BRCA1/2 alteration detected. Amongst the highest rates of protein expression in BRCA1/2-mutated and non-mutated specimens were biomarkers like TOPO1 (63.5% and 63.4%), EGFR (65.2% and 67.4%), and the immune checkpoint biomarker, PD-1 (65.1% and 61.9%), with non-statistically significant differences. Differences noted between BRCA1/2-mutated and non-mutated specimens were detected by IHC in AR (11.1% versus 22.0%, p=0.0585) and PTEN (47.6% versus 59.6%, p=0.0941), with both trending but not achieving statistical significance. The highest overall mutation rate in both BRCA1/2-mutated and non-mutated were TP53 (80.6% and 73.1%, p=0.2659). Differences were also noted between BRCA1/2-mutated and non-mutated specimens by NGS in APC (6.3% versus 1.9%, p = 0.0644) and PIK3CA (11.1% versus 25.8%, p = 0.0137), with PIK3CA being statistically significant.

Conclusion: Multiplatform tumor profiling identified differences in molecular profiles between BRCA1/2 mutated and BRCA1/2 non-mutated TNBC. Our findings raise the possibility for future investigation of potential combination therapeutic targeted therapy. Increased AR overexpression in BRCA1/2 non-mutated specimens is consistent with reports from other institutions. Further studies utilizing tumor profiling to elucidate the biological differences in in TNBC subtypes are warranted, to optimally include patients on clinical trials with specific targeted therapy and possibly improve treatment options.

Citation Format: Arguello D, Abbott B, Reddy S, Gatalica Z, Obeid E, Goldstein L. Molecular profiling comparison of BRCA1/2-mutated and BRCA1/2 non-mutated triple-negative breast cancer (TNBC). [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 P3-07-30.

Abstract P3-07-26: Biomarker comparison between androgen receptor – Positive-triple-negative breast cancer (AR+ TNBC) and quadruple-negative breast cancer (QNBC)

Background: Quadruple-negative breast cancer (QNBC) is a subgroup of triple-negative breast cancer (TNBC) that lacks androgen receptor (AR) expression. While TNBC patients with AR expression have shown a promising response to AR-targeted therapies, QNBC patients' treatment options remain limited, with no targeted therapy We investigated the biomarker profiles of large cohorts of AR+TNBC and QNBC to identify their molecular differences.

Method: TNBC tumors (defined as negative by IHC for ER, PR, Her2 and ISH for Her2) referred to Caris Life Sciences (Phoenix, AZ) between 2009 and 2015 were evaluated by board-certified pathologists with a combination of immunohistochemistry (AR, cKIT, cMET, EGFR, ER, ERCC1, Her2, MGMT, PD-1, PD-L1, PGP, PR, PTEN, RRM1, SPARC, TLE3, TOPO2A, TOPO1, TS and TUBB3), fluorescent/chromogenic in-situ hybridization (cMET, EGFR, Her2, TOP2A), and sequencing (Next-generation and Sanger). Tumors evaluated included a mix of primary tumors and metastases. QNBC tumors were defined as TNBC tumors that showed negative AR expression (<10% of cells staining).

Results: Among 2,071 TNBC tumors identified, 1,952 tumors had AR IHC performed, out of which 1,612 (83%) were QNBC and 340 (17%) were AR+ TNBC tumors. Tumor expression of PD-L1 (Ab: SP142, Spring Bioscience/130021, R&D Systems, cutoff used: 2+, 5%) was significantly higher in QNBC compared to AR+TNBC tumors (18% vs. 8%, p=0.01), while PD-1 (Ab: NAT105, Ventana) expression on tumor-infiltrating lymphocytes was comparable between the two cohorts (60% vs. 62%). QNBC tumors were significantly more likely to express proteins of cKIT (26% vs. 15%, p=0.01), EGFR (69% vs. 56%, p=0.03), TS (49% vs. 33%, p<0.0001) and TOPO2A (85% vs. 65%, p<0.0001) compared to AR+TNBC. TLE3 expression was significantly higher in AR+TNBC cohorts (48% vs. 32%, p<0.0001). Sequencing reveals that QNBC tumors carried significantly higher mutation rate of TP53 (71% vs. 55%, p<0.0001) while AR+TNBC tumors showed significantly higher mutation rates of PIK3CA (42% vs. 12%, p<0.0001), AKT1 (13% vs. 1%, p<0.0001) as well as ERBB2 (5% vs. 1%, p=0.0003).

Conclusion:

Biomarker comparisons between two molecular subgroups of the TNBC tumors confirm the molecular heterogeneity of this aggressive type of breast cancer. Our biomarker results suggests that for AR+TNBC tumors, future clinical trial design can consider fluoropyrimidines, taxanes, and agents targeting PI3K/AKT/mTOR pathway as well as pan-HER inhibitors, and those agents may be combined with anti-androgen therapies. On the other hand, clinical trials for immune checkpoint inhibitors, TOP2A inhibitors, as well as agents that target cKIT and EGFR should be considered for QNBC tumors. Our findings highlight the molecular differences that should be considered in the design of future clinical trial strategies, warranting further investigation for improving targeted therapy and outcomes in TNBC.

Citation Format: Xiu J, Obeid E, Gatalica Z, Reddy S, Goldstein LJ, Link J, Waisman J. Biomarker comparison between androgen receptor – Positive-triple-negative breast cancer (AR+ TNBC) and quadruple-negative breast cancer (QNBC). [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 P3-07-26.

Abstract P3-07-27: Distinct biomarker features in triple-negative breast cancer metastases to the brain, liver and bone

Background: Triple-negative breast cancer (TNBC) is characterized by its aggressive nature and accounts for a disproportionate number of metastatic disease cases and breast cancer-related deaths. Despite recent improvements, TNBC patients who develop metastatic diseases have limited treatment options. We investigated biomarkers from brain, liver and bone metastases collected from TNBC patients to identify therapeutic options and to examine molecular differences between the metastatic sites.

Method: Triple-negative breast cancer tumors referred to Caris Life Sciences (Phoenix, AZ) between 2009 and 2015 were tested with a combination of immunohistochemistry, fluorescent/chromogenic in-situ hybridization and sequencing (Next-generation and Sanger).

Result: 1570 TNBC tumors were analyzed, including 1297 tumors taken from breast, 54 from brain, 172 from liver and 47 from bone. Select biomarker frequencies of protein overexpression (IHC), gene amplification (ISH) and mutations (SEQ) are summarized in Table 1. Brain metastases showed the highest protein expression of TOPO2A and PDL1; liver metastases showed the highest expression of AR and SPARC, as well as the highest mutation rate of PIK3CA. Bone metastases showed the lowest expression of TS, RRM1 and ERCC1. BRCA1 and BRCA2 mutation rates ranged from 0-11% in various specimen sites.

Table 1Biomarker and MethodBreast Metastases (%)Brain Metastases (%)Liver Metastases (%)Bone Metastases (%)p value[pound]TOP2A IHC76100[sect]7339<0.0001PDL1 IHC1540[sect]8170.03AR IHC151036[sect]260.0005SPARC IHC173040[sect]150.0027PIK3CA SEQ165.329[sect]250.036TS IHC[dagger]49542415[sect]<0.0001RRM1 IHC[dagger]39433216[sect]0.006ERCC1 IHC[dagger]35554816[sect]0.002BRCA1 SEQ708n/ansBRCA2 SEQ11114n/ans[sect]:the group with the highest frequency of actionable results; [pound]:p values are calculated from comparing the group with the highest frequency with the lowest frequency using two tailed Fisher-Exact test, further detailed statistical analysis will be presented;[dagger]:low levels predict response to associated drugs; Ns: non-significant, i.e., p >0.05; n/a: data not available due to low N

Conclusion: Distinct biomarker features identified in different metastatic sites in TNBC present the rationale to investigate differential treatment strategies. Based on biomarker results, etoposide, immune-modulatory agents may seem promising for brain metastases; anti-androgen therapies and nab-paclitaxel may be promising in treating liver metastases; while fluoropyrimidines, gemcitabine and platinum may be considered for TNBC patients with bone metastases.

Citation Format: Xiu J, Gatalica Z, Reddy S, Waisman J, Link J. Distinct biomarker features in triple-negative breast cancer metastases to the brain, liver and bone. [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 P3-07-27.

Abstract P3-07-47: Comprehensive profiling of metaplastic breast carcinoma reveals frequent over-expression of PD-L1

Background: Metaplastic breast carcinoma (MBC) is a rare subtype of breast carcinoma less responsive to conventional chemotherapy relative to usual breast carcinomas (UBCs) such as ductal and lobular subtype. In molecular terms MBC usually clusters with triple negative breast cancer (TNBC), but MBCs portray a worse prognosis in comparison to TNBCs. Published studies investigating MBCs for specific biomarkers of therapy response are rare and limited by the methodological approaches.

Methods: This study included 132 patients with 38 histologically confirmed MBCs and 94 UBCs. Amongst the 94 UBCSs, 44 were estrogen receptor positive, 33 were triple negative and 17 were HER2 positive. Direct sequencing analysis was performed on genomic DNA isolated from formalin-fixed paraffin-embedded tissue (FFPE) using the Illumina MiSeq Next Generation Sequencing platform (NGS). Immunohistochemistry for PD-L1 (SP142, Spring Bioscience), PD-1 (NAT105, Ventana) and EGFR (31G7, Life Technologies) was performed using automated procedures. Additionally, mutation analysis for EGFRvIII was performed on RNA extracted from FFPE tissue.

Results: At the genomic level, numerous cases of MBC had multiple genomic alterations with the most frequent genetic mutation in TP53 gene (14/24), similar to the TNBC controls (17/33). BRCA1 mutations were detected in 2/10 cases. Potentially actionable mutations were rare and included PIK3CA gene. Importantly, PD-L1 expression on cancer cells was detected in significantly higher proportion of MBCs (37%) than in the UBC cohort (6%) or TNBC control (14%) (p=3.7x10-5 and p=0.03, respectively). PD-1 positive tumors infiltrating lymphocytes (TILS) varied greatly in MBC (0 to >50/mm2). Over-expression of EGFR was frequent in MBCs (62%); however no mutations in the gene including EGFRvIII were detected.

Conclusion: Comprehensive profiling of a large cohort of this rare carcinoma highlighted predominance of TP53 mutations, wild type EGFR gene expression, a distinct increase in proportion of PD-L1 expression in carcinoma cells, and PD-1 expression in TILS. The latter properties can be exploited in clinical trials utilizing immune check point inhibitors.

Citation Format: Gatalica Z, Joneja U, Ghazalpour A, Swensen J, Feldman R, Cai F, Chen W, Xiao N, Reddy S, Palazzo J. Comprehensive profiling of metaplastic breast carcinoma reveals frequent over-expression of PD-L1. [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 P3-07-47.

Identification of high-risk Listeria monocytogenes serotypes in lineage I (serotype 1/2a, 1/2c, 3a and 3c) using multiplex PCR

AIMS

Using molecular subtyping techniques, Listeria monocytogenes is divided into three major phylogenetic lineages, and a multiplex PCR method can differentiate five L. monocytogenes subgroups: 1/2a-3a, 1/2c-3c, 1/2b-3b-7, 4b-4d-4e and 4a-4c. In this study, we conducted genome comparisons and evaluated serotype-associated genes for their utility as a multiplex PCR-based method for distinguishing high-risk serotypes 1/2a and 1/2c in lineage I from low-risk serotypes 3a and 3c.

METHODS AND RESULTS

Primer sets were developed that are specific for serotype 1/2c (LMOSLCC2372_0308) and serotype 3a (LMLG_0742). These primers were then tested in a multiplex format with primers specific for serotype 1/2a (flaA) to separate serotypes 1/2a, 1/2c, 3a and 3c using 25 strains of lineage I L. monocytogenes.

CONCLUSIONS

Here, for the first time, we report primers specific for L. monocytogenes serotype 1/2c and serotype 3a, and we demonstrate a multiplex PCR method for separating the four serotypes of lineage I L. monocytogenes.

SIGNIFICANCE AND IMPACT OF THE STUDY

The described multiplex PCR assay consistently showed successful separation of 1/2a and 1/2c strains from 3a and 3c strains. PCR is routinely performed in many diagnostic and epidemiologic investigations for L. monocytogenes, and these primers should increase the feasibility and accessibility of L. monocytogenes serotyping.

Effect of changing NAVA levels on peak inspiratory pressures and electrical activity of the diaphragm in premature neonates

BACKGROUND

Neurally adjusted ventilator assist (NAVA) uses electrical activity of the diaphragm (Edi) to provide patient-directed ventilatory support. The NAVA level determines the proportional amount of ventilatory support. Systematically increasing NAVA level initially increases peak inspiratory pressure (PIP) while maintaining a constant Edi until a breakpoint (BrP) is reached. Further increases in NAVA level reduce the Edi, while the PIP plateaus. This study was performed to establish whether premature neonates have intact neural feedback systems allowing them to have a BrP.

METHOD

NAVA level was increased by 0.5 cm H2O μV(-1) every 3 min from 0.5 to 4.0 cm H2O μV(-1). PIP, Edi, mean blood pressure, heart rate, respiratory rate, oxygen saturation and FIO2 were recorded. Statistics: Non-linear regression was done for PIP and Edi. Linear regression was done for the other variables. The data from the trials were combined by normalizing to NAVA levels above and below the BrP.

RESULT

Nine neonates were studied on NAVA and 12 on non-invasive NAVA. PIP increased until the BrP was reached and then remained unchanged. Edi decreased after the BrP was reached. All other variables remained unchanged.

CONCLUSION

Neonates demonstrated a BrP suggesting intact neural feedback mechanisms that may protect lungs from over distention with NAVA ventilation.

Focal segmental glomerulosclerosis in renal allografts: Is it possible to diagnose the etiology?

Recurrence of FSGS in renal allo grafts is a major cause of graft loss. In this context, we tried to diagnose and classify FSGS in renal allografts. Indications for biopsy included graft dysfunction and/or proteinuria. Three hundred and sixty-three graft biopsies were studied over a period of 2 years. We classified FSGS into recurrent FSGS, new-onset primary FSGS and FSGS secondary to chronic humoral rejection, calcineurin inhibitor toxicity, and nephron loss and hyperfiltration injury. Twenty-four cases were diagnosed as FSGS, constituting 6.6%. Secondary FSGS was the most common FSGS in grafts in our study. Incidence of recurrent FSGS may not be accurate as pretransplant biopsy is available in very few cases.