The effect of ginger extract on cisplatin-induced acute anorexia in rats

Cisplatin is a platinum-based chemotherapeutic agent widely used to treat various cancers. However, several side effects have been reported in treated patients. Among these, acute anorexia is one of the most severe secondary effects. In this study, a single oral administration of 100 or 500 mg/kg ginger extract (GE) significantly alleviated the cisplatin-induced decrease in food intake in rats. However, these body weight and water intake decreases were reversed in the 100 mg/kg group rats. To elucidate the underlying mechanism of action, serotonin (5-HT) and 5-HT2C, 3A, and 4 receptors in the nodose ganglion of the vagus nerve were investigated. The results showed that cisplatin-induced increases in serotonin levels in both the blood and nodose ganglion tissues were significantly decreased by100 and 500 mg/kg of GE administration. On 5-HT receptors, 5-HT3A and 4, but not 2C receptors, were affected by cisplatin, and GE 100 and 500 mg/kg succeeded in downregulating the evoked upregulated gene of these receptors. Protein expression of 5-HT3A and 4 receptors were also reduced in the 100 mg/kg group. Furthermore, the injection of 5-HT3A, and 4 receptors antagonists (palonostron, 0.1 mg/kg, i.p.; piboserod, 1 mg/kg, i.p., respectively) in cisplatin treated rats prevented the decrease in food intake. Using high-performance liquid chromatography (HPLC) analysis, [6]-gingerol and [6]-shogaol were identified and quantified as the major components of GE, comprising 4.12% and 2.15% of the GE, respectively. Although [6]-gingerol or [6]-shogaol alone failed to alleviate the evoked anorexia, when treated together, the effect was significant on the cisplatin-induced decrease in food intake. These results show that GE can be considered a treatment option to alleviate cisplatin-induced anorexia.

Response to immune checkpoint blockade improved in pre-clinical model of breast cancer after bariatric surgery

Bariatric surgery is a sustainable weight loss approach, including vertical sleeve gastrectomy (VSG). Obesity exacerbates tumor growth, while diet-induced weight loss impairs progression. It remains unknown how bariatric surgery-induced weight loss impacts cancer progression or alters response to therapy. Using a pre-clinical model of obesity followed by VSG or diet-induced weight loss, breast cancer progression and immune checkpoint blockade therapy were investigated. Weight loss by VSG or weight-matched dietary intervention before tumor engraftment protected against obesity-exacerbated tumor progression. However, VSG was not as effective as diet in reducing tumor burden despite achieving similar weight and adiposity loss. Leptin did not associate with changes in tumor burden; however, circulating IL-6 was elevated in VSG mice. Uniquely, VSG tumors displayed elevated inflammation and immune checkpoint ligand PD-L1+ myeloid and non-immune cells. VSG tumors also had reduced T lymphocytes and markers of cytolysis, suggesting an ineffective anti-tumor microenvironment which prompted investigation of immune checkpoint blockade. While obese mice were resistant to immune checkpoint blockade, anti-PD-L1 potently impaired tumor progression after VSG through improved anti-tumor immunity. Thus, in formerly obese mice, surgical weight loss followed by immunotherapy reduced breast cancer burden. Finally, we compared transcriptomic changes in adipose tissue after bariatric surgery from patients and mouse models. A conserved bariatric surgery-associated weight loss signature (BSAS) was identified which significantly associated with decreased tumor volume. Findings demonstrate conserved impacts of obesity and bariatric surgery-induced weight loss pathways associated with breast cancer progression.

As the number of people classified as obese rises globally, so do obesity-related health risks. Studies show that people diagnosed with obesity have inflammation that contributes to tumor growth and their immune system is worse at detecting cancer cells. But weight loss is not currently used as a strategy for preventing or treating cancer.

Surgical procedures for weight loss, also known as ‘bariatric surgeries’, are becoming increasingly popular. Recent studies have shown that individuals who lose weight after these treatments have a reduced risk of developing tumors. But how bariatric surgery directly impacts cancer progression has not been well studied: does it slow tumor growth or boost the anti-tumor immune response?

To answer these questions, Sipe et al. compared breast tumor growth in groups of laboratory mice that were obese due to being fed a high fat diet. The first group of mice lost weight after undergoing a bariatric surgery in which part of their stomach was removed. The second lost the same amount of weight but after receiving a restricted diet, and the third underwent a fake surgery and did not lose any weight. The experiments found that surgical weight loss cuts breast cancer tumor growth in half compared with obese mice. But mice who lost the same amount of weight through dietary restrictions had even less tumor growth than surgically treated mice.

The surgically treated mice who lost weight had more inflammation than mice in the two other groups, and had increased amounts of proteins and cells that block the immune response to tumors. Giving the surgically treated mice a drug that enhances the immune system’s ability to detect and destroy cancer cells reduced inflammation and helped shrink the mice’s tumors. Finally, Sipe et al. identified 54 genes which were turned on or off after bariatric surgery in both mice and humans, 11 of which were linked with tumor size.

These findings provide crucial new information about how bariatric surgery can impact cancer progression. Future studies could potentially use the conserved genes identified by Sipe et al. to develop new ways to stimulate the anti-cancer benefits of weight loss without surgery.

Abstract 49: Integrative genomic analysis of human papillomavirus associated head and neck squamous cell carcinoma reveals selective pressure for somatic alteration of E6 and E7 targets

Purpose: Previous studies implicated viral oncoproteins E6 and E7, of which targets include but are not limited to tumor suppressors p53 and pRb, in human papillomavirus (HPV) associated tumorigenesis. However, HPV-associated tumors must accumulate additional genomic alterations as HPV oncoproteins alone are insufficient for tumor formation in vivo.

Experimental Design: Targeted sequencing was conducted with a panel of over 800 cancer related genomic regions and genes in a novel cohort of 525 head and neck squamous cell carcinoma (HNSCC) patients, including 252 HPV(+) and 273 HPV(-) tumors. Variant calling and filtering, followed by analysis with computational tools such as MutSig for somatic mutations and DiNAMIC.Duo for recurrent copy number alterations (CNAs), defined the catalog of driver alterations that are specific to HPV(+) and HPV(-) tumors. Pathway analysis was then used to elucidate the functional role of somatic alterations in the context of previously described HNSCC perturbations and HPV pathophysiology.

Results: Integrative genomic analysis in one of the largest HPV(+) HNSCC cohorts to date revealed differential patterns of somatic mutations and CNAs in E6/E7 targets between HPV(+) and HPV(-) tumors. Specifically, EP300, an activator of p53 and target of E6, and retinoblastoma (RB) family members RB1 (pRb) and RBL2 (p130), which are known targets of E7 mediated degradation, were selected as significantly mutated by MutSig in HPV(+) samples only (EP300 & RB1 P<0.001, RBL2 P=0.01), while RBL1 (p107) was significant for both HPV(+) and HPV(-) samples (P<0.001, P=0.02 respectively). Higher fractions of mutations in HPV(+) vs. HPV(-) tumors were observed for EP300 (13% vs 6%, Fisher’s exact test P=0.006), RB1 (7% vs 3%, P=0.07), RBL2 (3% vs 1%, P=0.09), and FOXM1 (4% vs 1%, P=0.02), another cell cycle pathway target of E7, but not for RBL1 (4% vs. 3%, P=1). Lower copy numbers were detected in HPV(+) tumors compared to HPV(-) for chromosome regions containing RB1 (P=0.03), RBL1 (P=0.08), RBL2 (P<0.001), and for another inhibitory target of E6, FADD (P<0.001), which is an activator of the proapoptotic protein caspase-8. Additionally, significant copy number gains were detected in HPV(+) vs. HPV(-) tumors within the genomic region containing E2F1 (P<0.001), the transcription factor whose inhibition by RB family proteins is abrogated in the presence of E7, thus leading to abnormal cell cycle progression and proliferation.

Conclusions: Previous studies suggest HPV-associated tumors lack significant levels of somatic alterations in canonical tumor suppressor genes that are known targets of viral oncoproteins. Here, we show additional selective pressure exists for somatic alteration of E6/E7 target genes in at least a subset of HPV(+) HNSCCs, which further deregulate cell cycle and apoptosis pathways in these tumors.

Citation Format: Jeremiah Holt, Heejoon Jo, Xiaobei Zhao, Hyo Young Choi, Vonn Walter, Paul Little, Benjamin Wahle, Angela Mazul, Jose P. Zevallos, David Neil Hayes. Integrative genomic analysis of human papillomavirus associated head and neck squamous cell carcinoma reveals selective pressure for somatic alteration of E6 and E7 targets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 49.

OP0027 ASSOCIATION BETWEEN BASELINE CARDIOVASCULAR RISK AND INCIDENCE RATES OF MAJOR ADVERSE CARDIOVASCULAR EVENTS AND MALIGNANCIES IN PATIENTS WITH PSORIATIC ARTHRITIS AND PSORIASIS RECEIVING TOFACITINIB

Background

Common comorbidities of psoriatic arthritis (PsA) and psoriasis (PsO) are cardiovascular (CV) disease and metabolic syndrome (MetS).1,2 Risk of CV disease may be associated with increased risk of future malignancies.3 Tofacitinib is a JAK inhibitor for treatment of PsA and has been investigated for treatment of PsO.

Objectives

To examine baseline (BL) CV risk and its association with incidence rates (IRs) of major adverse CV events (MACE) and malignancies in tofacitinib-treated patients (pts) with PsA and PsO.

Methods

Analysis included data from 3 (Phase [P]3/long-term extension [LTE]) trials of pts with PsA and 7 (P2/3/LTE) trials of pts with PsO receiving ≥1 dose of tofacitinib (5 or 10 mg twice daily). IRs (pts with events/100 pt-yrs) for MACE and malignancies (excluding non-melanoma skin cancer) were stratified by: history of coronary artery disease (HxCAD [≥1 of myocardial infarction, coronary heart disease, coronary artery procedure or stable angina pectoris]); BL 10-yr atherosclerotic CV disease (ASCVD) risk (ASCVD-pooled cohort equations calculator [only in pts without HxCAD]); and BL MetS (≥3 of hypertension, raised triglycerides, reduced high-density lipoprotein cholesterol, high waist circumference or high fasting glucose levels).

Results

Of 783 and 3663 pts with PsA and PsO, total tofacitinib exposure was 2038 and 8950 pt-yrs, and median duration of exposure was 3.0 and 2.4 yrs, respectively. In pts with PsA and PsO, 5.0% and 2.5% had HxCAD, respectively; in those without HxCAD, >20% had intermediate/high BL 10-yr ASCVD risk (Figure 1). At BL, 40.9% and 32.7% of pts with PsA and PsO had MetS, respectively. IRs of MACE were greatest in pts with PsA and PsO who had HxCAD/high BL 10-yr ASCVD risk (Table 1). In the PsA cohort, 5/6 pts with MACE had BL MetS. IRs of malignancies in pts with PsA were greatest in those with intermediate/high BL 10-yr ASCVD risk; 8/9 pts with malignancies in these risk categories had BL MetS (Table 1). In the PsO cohort, IR of malignancies was notably greater in those with high vs low/intermediate BL 10-yr ASCVD risk (Table 1).

Table 1.

IRs of MACE and malignancies in pts with PsA and PsO receiving tofacitinib, stratified by HxCAD, BL 10-yr ASCVD risk and BL MetS

MACEMalignanciesPsAPsOPsAPsOn/N[n1]IR (95% CI)n/N[n1]IR (95% CI)n/N[n1]IR (95% CI)n/N[n1]IR (95% CI)HxCADYes1/39[0]0.97 (0.02, 5.38)3/93[0]1.49 (0.31, 4.36)0/39[0]0.00 (0.00, 3.52)0/93[0]0.00 (0.00, 1.83)No5/744[5]0.25 (0.08, 0.59)20/3570[10]0.22 (0.13, 0.34)15/744[10]0.75 (0.42, 1.24)60/3570[26]0.66 (0.51, 0.85)BL 10-yr ASCVD risk categoryHigh risk (≥20%)1/35[1]1.26 (0.03, 7.01)7/179[4]1.67 (0.67, 3.43)1/35[1]1.26 (0.03, 7.03)15/179[10]3.57 (2.00, 5.89)Intermediate risk(≥7.5–<20%)2/121[2]0.62 (0.07, 2.23)9/716[6]0.50 (0.23, 0.95)8/121[7]2.46 (1.06, 4.86)23/716[9]1.28 (0.81, 1.92)Borderline risk(≥5–<7.5%)1/91[1]0.42 (0.01, 2.32)2/400[0]0.19 (0.02, 0.67)2/91[1]0.83 (0.10, 3.01)5/400[1]0.47 (0.15, 1.09)Low risk (<5%)1/487[1]0.08 (0.00, 0.42)2/2241[0]0.03 (0.00, 0.13)4/487[1]0.30 (0.08, 0.77)17/2241[6]0.30 (0.17, 0.47)BL MetSYes5/3200.60 (0.20, 1.40)10/11970.34 (0.16, 0.63)10/3201.20 (0.58, 2.21)26/11970.89 (0.58, 1.31)No1/4630.08 (0.00, 0.44)13/24660.20 (0.11, 0.35)5/4630.40 (0.13, 0.92)34/24660.54 (0.37, 0.75)

Follow-up time calculated up to the day of the first event and subject to risk period of 28 days beyond the last dose of study drug.

CI, confidence interval; N, total pts; n, pts with MACE/malignancies; n1, pts with MACE/malignancies and BL MetS.

Conclusion

In tofacitinib-treated pts with PsA and PsO, raised CV risk and MetS at BL were potentially associated with higher IRs of MACE and malignancies. Our findings support assessing CV risk in pts with PsA and PsO and enhanced monitoring for malignancies in those with raised CV risk.

References

[1]Karmacharya et al. Ther Adv Musculoskel Dis 2021; 13: 1-15.

[2]Garshick et al. J Am Coll Cardiol 2021; 77: 1670-1680.

[3]Lau et al. JACC CardioOncol 2021; 3: 48-58.

Acknowledgements

Study sponsored by Pfizer Inc. Medical writing support was provided by Emma Mitchell, CMC Connect, and funded by Pfizer Inc.

Disclosure of Interests

Lars Erik Kristensen Speakers bureau: AbbVie, Amgen, Biogen, Bristol-Myers Squibb, Eli Lilly, Janssen, MSD, Novartis, Pfizer Inc and UCB, Grant/research support from: Biogen, Janssen, Novartis and UCB, Bruce Strober Speakers bureau: AbbVie, Amgen, Eli Lilly, Janssen and Ortho Dermatologics, Consultant of: AbbVie, Almirall, Amgen, Arcutis, Arena, Aristea, Boehringer Ingelheim, Bristol-Myers Squibb, Cara, Celgene, Dermavant, Dermira, Eli Lilly, GlaxoSmithKline, Janssen, Leo, Meiji Seika Pharma, Novartis, Ortho Dermatologics, Pfizer Inc, Regeneron, Sanofi-Genzyme, Sun Pharma and UCB, Denis Poddubnyy Speakers bureau: AbbVie, Bristol-Myers Squibb, Eli Lilly, MSD, Novartis, Pfizer Inc and UCB, Consultant of: AbbVie, BIOCAD, Gilead Sciences, GlaxoSmithKline, Eli Lilly, MSD, Novartis, Pfizer Inc, Samsung Bioepis and UCB, Grant/research support from: AbbVie, MSD, Novartis and Pfizer, Ying Ying Leung Consultant of: AbbVie, Eli Lilly, Janssen and Novartis, Hyejin Jo Consultant of: Pfizer Inc, Employee of: Syneos Health, Kenneth Kwok Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Ivana Vranic Shareholder of: Pfizer Inc, Employee of: Pfizer Ltd, Dona Fleishaker Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Lara Fallon Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Arne Yndestad Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Dafna D Gladman Consultant of: AbbVie, Amgen, Celgene, Eli Lilly, Galapagos, Gilead Sciences, Janssen, Novartis, Pfizer Inc and UCB.

UNMASC: tumor-only variant calling with unmatched normal controls

Despite years of progress, mutation detection in cancer samples continues to require significant manual review as a final step. Expert review is particularly challenging in cases where tumors are sequenced without matched normal control DNA. Attempts have been made to call somatic point mutations without a matched normal sample by removing well-known germline variants, utilizing unmatched normal controls, and constructing decision rules to classify sequencing errors and private germline variants. With budgetary constraints related to computational and sequencing costs, finding the appropriate number of controls is a crucial step to identifying somatic variants. Our approach utilizes public databases for canonical somatic variants as well as germline variants and leverages information gathered about nearby positions in the normal controls. Drawing from our cohort of targeted capture panel sequencing of tumor and normal samples with varying tumortypes and demographics, these served as a benchmark for our tumor-only variant calling pipeline to observe the relationship between our ability to correctly classify variants against a number of unmatched normals. With our benchmarked samples, approximately ten normal controls were needed to maintain 94% sensitivity, 99% specificity and 76% positive predictive value, far outperforming comparable methods. Our approach, called UNMASC, also serves as a supplement to traditional tumor with matched normal variant calling workflows and can potentially extend to other concerns arising from analyzing next generation sequencing data.

Correlation of alterations in the KEAP1/CUL3/NFE2L2 pathway with radiation failure in larynx squamous cell carcinoma

OBJECTIVES

Patients with laryngeal squamous cell carcinoma (LSCC) often fail radiation therapy (RT), when received as monotherapy or in combination with other treatment modalities. Mechanisms for RT failure are poorly understood. We hypothesized that tumors failing RT would have increased rates of somatic mutations in genes associated with radiation resistance, particularly in genes associated with the NFE2L2 oxidative stress pathway. Using targeted exome sequencing on pretreated LSCC tumors, we retrospectively compared somatic mutation profile with clinical data and response to treatment.

METHODS

Tumors were classified as either radiation-resistant (RR) or radiation-sensitive (RS). RR was defined as persistent or recurrent disease within 2 years of receiving full-dose RT. Early stage (ES) LSCC was defined as Stage I or II tumors without lymph node involvement. Eight genes associated with radiation resistance were prioritized for analysis. RT-qPCR was performed on five NFE2L2 pathway genes.

RESULTS

Twenty LSCC tumors were included and classified as either RR (n = 8) or RS (n = 12). No differences in individual rates of somatic mutations by genes associated with radiation resistance were identified. Higher rates of total mutational burden (TMB) and increased alterations associated with the NFE2L2 pathway was observed in RR vs RS tumors (P < .05). In an analysis of only ES-LSCC patients (RR, n = 3 and RS, n = 3), RR tumors had increased NFE2L2 somatic pathway mutations (P = .014) and increased NQO1 mRNA expression (P = .05).

CONCLUSION

Increased TMB and NFE2L2 pathway alterations were associated with radiation resistance in LSCC. NQO1 mRNA expression may serve as a biomarker for RT response in ES-LSCC.Level of Evidence: II1.

Immune checkpoint blockade reprograms systemic immune landscape and tumor microenvironment in obesity-associated breast cancer

Immune checkpoint blockade (ICB) has improved outcomes in some cancers. A major limitation of ICB is that most patients fail to respond, which is partly attributable to immunosuppression. Obesity appears to improve immune checkpoint therapies in some cancers, but impacts on breast cancer (BC) remain unknown. In lean and obese mice, tumor progression and immune reprogramming were quantified in BC tumors treated with anti-programmed death-1 (PD-1) or control. Obesity augments tumor incidence and progression. Anti-PD-1 induces regression in lean mice and potently abrogates progression in obese mice. BC primes systemic immunity to be highly responsive to obesity, leading to greater immunosuppression, which may explain greater anti-PD-1 efficacy. Anti-PD-1 significantly reinvigorates antitumor immunity despite persistent obesity. Laminin subunit beta-2 (Lamb2), downregulated by anti-PD-1, significantly predicts patient survival. Lastly, a microbial signature associated with anti-PD-1 efficacy is identified. Thus, anti-PD-1 is highly efficacious in obese mice by reinvigorating durable antitumor immunity. VIDEO ABSTRACT.

AB0248 INFLUENZA ADVERSE EVENTS IN PATIENTS WITH RHEUMATOID ARTHRITIS IN THE TOFACITINIB CLINICAL PROGRAMME

Background:

Patients (pts) with rheumatoid arthritis (RA) have an increased susceptibility to seasonal influenza and its complications.1 In light of the COVID-19 pandemic, there is a need to better understand acute respiratory viral RNA infections, such as influenza, in pts with RA.

Objectives:

To present a comprehensive summary of data on influenza adverse events (AEs) occurring in the tofacitinib RA clinical programme.

Methods:

Influenza AEs were evaluated in pts with RA from 21 Phase (P)1–3b/4 trials and two open-label, long-term extension (LTE) studies from 2005–2019. These were analysed as two cohorts: P2–3b/4 cohort (pts who received tofacitinib 5 or 10 mg twice daily [BID] as monotherapy or with conventional synthetic [cs]DMARDs, adalimumab, methotrexate or placebo, in P2–3b/4 controlled studies) and Overall cohort (pts who received ≥1 tofacitinib dose, as monotherapy or with csDMARDs, in P1–3b/4 and LTE studies; data were summarised by average tofacitinib dose [average tofacitinib 5 or 10 mg BID based on average total daily dose of <15 or ≥15 mg, respectively]). Incidence rates (IRs; unique pts with events/100 pt-years of exposure; censored at day of first event or up to last dose +28 days) were evaluated for influenza AEs, influenza complication AEs, influenza-like illness (all composites of several MedDRA preferred/verbatim terms) and overall influenza AEs (composite of all preferred/verbatim terms included under influenza AEs, influenza complication AEs and influenza-like illness). In the Overall cohort, the incidence of serious non-influenza AEs within 28 days of the start of an overall influenza AE and time taken to resolution of overall influenza AEs by action taken were summarised descriptively.

Results:

In total, 7964 pts were included; 517 (6.5%) pts reported overall influenza AEs, three of which occurred outside the risk period. In the P2–3b/4 cohort (N=6690), IRs for influenza AEs, influenza-like illness and overall influenza AEs generally appeared similar across treatment arms (Figure 1a). In the Overall cohort, IRs for influenza AEs and influenza-like illness were similar between tofacitinib doses (Figure 1b), and IRs for overall influenza AEs were similar between tofacitinib doses and pt age groups (Figure 1c). No influenza complication AEs (eg pneumonia/encephalitis influenzal) were reported in either cohort. Among pts with overall influenza AEs, nine (1.7%) had serious overall influenza AEs (average tofacitinib 5 mg BID, n=6; average tofacitinib 10 mg BID, n=3). Of these pts, eight (1.5%) were hospitalised (average tofacitinib 5 mg BID, n=6; average tofacitinib 10 mg BID, n=2) and two (0.4%) died (average tofacitinib 5 mg BID, n=1; average tofacitinib 10 mg BID, n=1). Both deaths occurred in pts with H1N1 Influenza A. Twelve (2.3%) pts had a serious non-influenza AE within 28 days of the start of the overall influenza AE (average tofacitinib 5 mg BID, n=6; average tofacitinib 10 mg BID, n=6). The most common serious non-influenza AEs (one event each in average tofacitinib 5 and 10 mg BID groups) were acute respiratory distress syndrome and pneumonia. In most pts with overall influenza AEs, no change to tofacitinib treatment was made (70.2%, n=363) or treatment was stopped temporarily (28.2%, n=146) for a mean duration of 11.0 days. The mean number of days to resolution of overall influenza AEs was numerically similar, ranging from 10.4–11.8 days across tofacitinib doses, irrespective of these actions.

Conclusion:

This post hoc analysis of influenza AEs across the tofacitinib RA clinical programme, over 14–15 influenza seasons, showed generally similar rates between treatment groups, and between tofacitinib doses and pt age groups. Limitations include varying exposure across treatment arms in the P2–3b/4 cohort. Most influenza AEs were non-serious (98.3%), and were not associated with changes to tofacitinib treatment.

References:

[1]Blumentals et al. BMC Musculoskelet Disord 2012; 13: 158.

Acknowledgements:

Study sponsored by Pfizer Inc. Medical writing support was provided by Kirsten Woollcott, CMC Connect, and funded by Pfizer Inc.

Disclosure of Interests:

Kevin Winthrop Grant/research support from: AbbVie, Bristol-Myers Squibb, Eli Lilly, Galapagos, Gilead Sciences, Pfizer Inc, Roche, UCB, Arne Yndestad Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Dan Henrohn Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Hyejin Jo Consultant of: Pfizer Inc, Employee of: Syneos Health, Sara Marsal Shareholder of: IMIDomics, Consultant of: AbbVie, Celgene, Galapagos, Gilead Sciences, Pfizer Inc, Sandoz, Sanofi, Grant/research support from: AbbVie, Bristol-Myers Squibb, Celgene, Jansen-Cilag, MSD, Novartis, Pfizer Inc, Roche, Sandoz, Sanofi, UCB, María Galindo-Izquierdo Grant/research support from: AbbVie, Eli Lilly, GSK, Janssen-Cilag, Annette Diehl Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Andrea Shapiro Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Stanley B. Cohen Consultant of: AbbVie, Eli Lilly, Genentech, Gilead Sciences, Pfizer Inc, Grant/research support from: AbbVie, Eli Lilly, Genentech, Gilead Sciences, Pfizer Inc

Genomic profiling of endometrial cancer and relationship with volume of endometrial cancer disease spread

OBJECTIVES

Lymph node (LN) metastasis and genomic profiles are important prognostic factors in endometrial cancer (EMCA). However, the prognostic significance of low volume metastasis found in sentinel lymph nodes (SLN) is unknown. We sought to determine if genomic mutations were associated with metastatic volume.

METHODS

Surgically staged women with EC who were enrolled in both a SLN clinical trial and tumor sequencing protocol were eligible. Relevant targets were enriched by a custom designed Agilent SureSelect hybrid capture enrichment library using standard protocols. Three specific gene mutations were evaluated, TP53, PTEN and PIK3CA in the primary tumor of patients with LN negative, LN positive and ITC disease.

RESULTS

42 patients were eligible; of these, 7 (16.7%) had ITC only and 7 (16.7%) had micrometastatic or macrometastatic (LN positive) disease. No differences were seen in TP53, PIK3CA or PTEN between groups. All ITC patients with TP53 mutations were of non-endometrioid histology (2/7). Deeper myometrial invasion and lymph vascular space invasion were more likely to occur in the LN positive group (p < 0.01 for both). No patients with ITC had a recurrence in a median 67.7 months of follow-up since surgery.

CONCLUSIONS

This pilot investigation did not identify differences between frequency of PIK3CA, PTEN or TP53 mutations in tumors and volume of LN metastasis. Low number of ITC limited the ability to detect genomic differences, however mutations appeared to align with expected histology. More work is needed to define the relationship between genomic mutations, histology, ITC, and prognosis.

Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell

Established in vitro models for SARS-CoV-2 infection are limited and include cell lines of non-human origin and those engineered to overexpress ACE2, the cognate host cell receptor. We identified human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of ACE2. Infection of H522 cells required the SARS-CoV-2 spike protein, though in contrast to ACE2-dependent models, spike alone was not sufficient for H522 infection. Temporally resolved transcriptomic and proteomic profiling revealed alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type-I interferon signaling. Focused chemical screens point to important roles for clathrin-mediated endocytosis and endosomal cathepsins in SARS-CoV-2 infection of H522 cells. These findings imply the utilization of an alternative SARS-CoV-2 host cell receptor which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.

Abstract PS17-04: Immune checkpoint blockade reprograms tumor microenvironment and systemic immune landscape in obesity associated triple negative breast cancer

Few targeted therapies exist for triple negative breast cancer (TNBC), an aggressive and deadly subtype. Obesity exacerbates poor outcomes in TNBC due to elevated invasion and metastasis leading to increased mortality. Obesity has paradoxically been shown to improve immune checkpoint therapies in other cancers, yet the underlying mechanisms are unclear. Despite being an inflammatory state, obesity increases immune checkpoint ligands PD-1 and PD-L1 which drives immunosuppression. Thus, we tested the hypothesis that obesity-driven changes to the immune milieu will improve ICB efficacy in TNBC. Syngeneic tumors were generated via orthotopic engraftment of E0771 basal-like TNBC cell line into age-matched immune-competent C57BL/6J female littermates on obesogenic or low fat diets. Mice were treated with anti-mouse anti-PD-1 or isotype control (IgG2a) every 3rd day until sacrifice. Obese mice gained almost 2-fold great body weight and 3.6-fold greater adiposity compared to lean mice and immunotherapy did not impact weights or body composition. Obesity led to immunosuppression systemically in bone marrow and spleen in tumor-free mice, which was exacerbated in tumor-bearing mice. Obese mice had significantly greater tumor progression and fewer regressed tumors at endpoint vs. lean mice. Anti-PD-1 significantly reduced tumor progression in obese mice with 4.2-fold reduction in volume and 5.7-fold reduction in tumor weights in obese mice vs. isotype controls. Anti PD-1 significantly reduced immunosuppressive cells including M2-like tumor associated macrophages and monocytic and granulocytic myeloid derived suppressor cells (MDSC) and raised anti-tumor M1-like macrophages, cytotoxic CD8+ T cells, and dendritic cells. Last, the microbiome has potent effects on responses to anti-tumor therapies such as chemotherapy and immune checkpoint blockade. Obesity is a major regulator of the gut microbiome. We found that beneficial bacteria belonging to genus Bifidobacterium was higher in lean compared to obese mice, which could limit tumor progression and lead to greater regression through robust anti-tumor immunity. In obese mice, beneficial bacteria belonging to genus Ruminococcus, Adlercreutzia, Corpococcus that promote anti-tumor immunity increased with anti PD-1 immunotherapy. In sum, we show for the first time that obesity-induced systemic and microenvironmental immunosuppression augmented tumor incidence and tumor progression. Furthermore, anti-PD-1 immune checkpoint blockade successfully reduced tumor progression in obese mice through reprogramming not only the TME but systemic immune milieu as well. Immunosuppressive targets unique to the obese TME could be targeted in concert with checkpoint inhibitors in future interventions to enhance durable anti-tumor immunity.

Citation Format: Ajeeth K Pingili, Mehdi Chaib, Laura M Sipe, Emily J Miller, Bin Teng, Rahul Sharma, Qusai AI Abdallah, Deidra Daria, Radhika Sekhri, Heejoon Jo, Mims S Tahliyah, D. Neil Hayes, Joseph F Pierre, Liza Makowski. Immune checkpoint blockade reprograms tumor microenvironment and systemic immune landscape in obesity associated triple negative breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS17-04.

SCISSOR: a framework for identifying structural changes in RNA transcripts

High-throughput sequencing protocols such as RNA-seq have made it possible to interrogate the sequence, structure and abundance of RNA transcripts at higher resolution than previous microarray and other molecular techniques. While many computational tools have been proposed for identifying mRNA variation through differential splicing/alternative exon usage, challenges in its analysis remain. Here, we propose a framework for unbiased and robust discovery of aberrant RNA transcript structures using short read sequencing data based on shape changes in an RNA-seq coverage profile. Shape changes in selecting sample outliers in RNA-seq, SCISSOR, is a series of procedures for transforming and normalizing base-level RNA sequencing coverage data in a transcript independent manner, followed by a statistical framework for its analysis ( https://github.com/hyochoi/SCISSOR ). The resulting high dimensional object is amenable to unsupervised screening of structural alterations across RNA-seq cohorts with nearly no assumption on the mutational mechanisms underlying abnormalities. This enables SCISSOR to independently recapture known variants such as splice site mutations in tumor suppressor genes as well as novel variants that are previously unrecognized or difficult to identify by any existing methods including recurrent alternate transcription start sites and recurrent complex deletions in 3' UTRs.

Integrative Analysis of miRNAs Identifies Clinically Relevant Epithelial and Stromal Subtypes of Head and Neck Squamous Cell Carcinoma

PURPOSE

The objective of this study is to characterize the role of miRNAs in the classification of head and neck squamous cell carcinoma (HNSCC).

EXPERIMENTAL DESIGN

Here, we analyzed 562 HNSCC samples, 88 from a novel cohort and 474 from The Cancer Genome Atlas, using miRNA microarray and miRNA sequencing, respectively. Using an integrative correlations method followed by miRNA expression-based hierarchical clustering, we validated miRNA clusters across cohorts. Evaluation of clusters by logistic regression and gene ontology approaches revealed subtype-based clinical and biological characteristics.

RESULTS

We identified two independently validated and statistically significant (P < 0.01) tumor subtypes and named them "epithelial" and "stromal" based on associations with functional target gene ontology relating to differing stages of epithelial cell differentiation. miRNA-based subtypes were correlated with individual gene expression targets based on miRNA seed sequences, as well as with miRNA families and clusters including the miR-17 and miR-200 families. These correlated genes defined pathways relevant to normal squamous cell function and pathophysiology. miRNA clusters statistically associated with differential mutation patterns including higher proportions of TP53 mutations in the stromal class and higher NSD1 and HRAS mutation frequencies in the epithelial class. miRNA classes correlated with previously reported gene expression subtypes, clinical characteristics, and clinical outcomes in a multivariate Cox proportional hazards model with stromal patients demonstrating worse prognoses (HR, 1.5646; P = 0.006).

CONCLUSIONS

We report a reproducible classification of HNSCC based on miRNA that associates with known pathologically altered pathways and mutations of squamous tumors and is clinically relevant.

Abstract 5448: Integrative analysis of microRNA expression identifies two biologically distinct and clinically relevant subtypes of head and neck squamous cell carcinoma

Purpose: The objective of this study is to investigate the potential role of microRNAs (miRNA) as molecular markers of tumor heterogeneity in head and neck squamous cell carcinoma (HNSCC).

Experimental Design: Here, we analyzed 562 HNSCC samples, 88 from a novel cohort and 474 from The Cancer Genome Atlas (TCGA), using miRNA-microarray and miRNA-seq, respectively. Using an integrative correlations method followed by miRNA expression-based hierarchical clustering, we validated miRNA clusters across cohorts, and evaluation of clusters by logistic regression and gene ontology approaches revealed subtype-based clinical and biological characteristics.

Results: We identified two statistically significant tumor subtypes and named them ‘epithelial' and ‘stromal' based on correlations with functional target gene ontology in relation to differing stages of epithelial cell differentiation. Each subtype demonstrated significant differences in terms of mRNA signature (p &lt; 0.001), primary tumor sites (p &lt; 0.001) and HPV status (p &lt; 0.001), and multivariate analysis associated the stromal subtype with a worse prognosis (HR = 1.5646, p = 0.006). We also observed several dysregulated miRNA families and clusters that function as regulators of subtype-specific gene expression networks in HNSCC.

Conclusion: Our findings suggest miRNAs determine HNSCC subclassifications through coordinating growth and differentiation programs in epithelial cells. These results delineate developmental miRNA signatures characterizing the phenotypic diversity between HNSCC subtypes, providing an expanded framework for the pathogenesis and personalized treatment of HNSCC.

Citation Format: Jeremiah R. Holt, Heejoon Jo, Vonn Walter, Xiaobei Zhao, David Neil Hayes, Yoon Ho Ko. Integrative analysis of microRNA expression identifies two biologically distinct and clinically relevant subtypes of head and neck squamous cell carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5448.

Abstract 2091: DeepBTS: Prediction of recurrence-free survival of non-small cell lung cancer using time-binned deep neural network

Introduction: Accurate prediction of non-small cell lung cancer (NSCLC) prognosis after surgery is still challenging. Cox proportional hazard model is widely used, but there are some limitations like proportional hazard assumption, computational complexity, and unspecified time component. In this study, we developed the novel neural network models using 30 clinicopathological features of surgically resected NSCLC patients.

Materials and Methods: We analyzed a dataset of training cohorts of 1,034 patients and external validation cohort of 303 patients, and compared the novel neural network model and Cox PH model to predict 3-year recurrence of the patient.

Results: We developed deep neural network for binned time survival analysis (DeepBTS) algorithm, which use root-mean-squared error (supervised learning model, s- DeepBTS) or negative log-likelihood (semi-unsupervised learning model, su- DeepBTS) as loss function. The su-DeepBTS algorithm showed the improved performance (C-index, 0.7166; AUC, 0.7606) compared to other models (Cox PH: 0.6861 and 0.7185; s-DeepBTS: 0.6926 and 0.7250, respectively). Top 10 features was selected from su-DeepBTS model and su-DeepBTS selector pair: the number of lymph node metastasis, tumor size, histologic subtype, vascular invasion, R0 resection, neoadjuvant /adjuvant treatment, and performance status of patients. These features distinguished low and high-risk group in the training cohort (p = 4.25×10-5) and the validation cohort (p = 1.07×10-11).

Conclusions: The su-DeepBTS model using 10 selected features can predict the prognosis of resected NSCLC patients. We plan to diversify the input features by radiologic, pathological imaging and genomic data to integrate multimodal medical information and enhance the performance of this model using deep neural network.

Citation Format: Ho Jung An, Bora Lee, Sang Hoon Chun, Ji Hyung Hong, In Sook Woo, Seoree Kim, Joon Won Jeong, Jae Jun Kim, Hyun Woo Lee, Sungsoo Park, Heejoon Jo, Yoon Ho Ko. DeepBTS: Prediction of recurrence-free survival of non-small cell lung cancer using time-binned deep neural network [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2091.

Abstract PR01: HPV structure and functional alterations impact prognosis in HPV (+) oropharyngeal squamous cell carcinoma

Background: Over the last two decades, there has been a sharp increase in the incidence of oropharyngeal squamous cell carcinoma (OPSCC) linked to human papillomavirus (HPV). Compared to tobacco-associated, HPV (-) cancers, HPV (+) tumors are generally less aggressive and more likely to respond to new deintensified treatment regimens. However, there is a subset of HPV (+) OPSCC patients with poor oncologic outcomes, and an understanding of underlying molecular characteristics of HPV (+) OPSCC with poor prognosis is lacking. In this study, we sought to determine the impact of HPV-tumor genomic interactions and their impact on prognosis. We define novel, quantifiable, sequencing-based metrics of HPV structure and function with prognostic significance.

Methods: We performed targeted DNA sequencing of 770 cancer-associated genes and the full-length HPV genome on 259 HPV (+) OPSCC cases derived from four cohorts. Sequencing data were routed through automated pipelines for DNA, including 1) somatic variant detection, 2) structural variations, and 3) quantitative and qualitative characterization of full-length HPV sequencing. Patients were assigned as either “high” or “low” based on the inherent binomial distribution of E6 and E7 normalized sequenced read counts across the cohort. Patient outcomes were assessed using the hazard ratio from the Cox proportional hazards regression adjusting for known and suspected confounders of outcome including stage, age, and smoking status defined as greater than 10 pack years.

Results: We demonstrate that both HPV viral read count and HPV structure significantly impact prognosis in HPV (+) OPSCC. In addition to integrated and episomal structure, we define a novel viral structural subtype in 15% of cases characterized by simple or complex rearrangement composed of single or multiple breakpoints within the viral genome. Furthermore, we demonstrate that patients with the lowest HPV viral loads had a 30% greater hazard of death compared to patients with high viral loads. When we considered the impact of HPV counts and HPV structure taken together, we note that Integrated cases with low viral load were associated with outcomes much lower than expected for HPV-positive oropharyngeal cancer (5-year overall survival: 56.8%). These results were unaffected by smoking status measured by ever/never smoking or pack-year status.

Conclusions: In the largest sequenced HPV (+) OPSCC cohort to date, we identify a quantifiable measure of HPV structure and function with prognostic significance. We define a novel rearranged viral structure and define integrated low viral count cases as associated with dismal survival. These findings highlight the molecular heterogeneity of HPV (+) OPSCC and provide a framework for future clinical trials based on molecular viral characterization.

Citation Format: Jose P. Zevallos, Angela L. Mazul, Xiaobei Zhao, Heejoon Jo, Cherie-Ann Nathan, Andrew F. Olshan, Bhishamjit S. Chera, D. Neil Hayes. HPV structure and functional alterations impact prognosis in HPV (+) oropharyngeal squamous cell carcinoma [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; 2019 Apr 29-30; Austin, TX. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_2):Abstract nr PR01.

Prognostic implications of stromal hyaluronic acid protein expression in resected oropharyngeal and oral cavity cancers

BACKGROUND/AIMS

Hyaluronic acid (HA) regulates cell adhesion, migration and proliferation in various cancers. The clinical implications of HA in resected head and neck squamous cell carcinoma have not been elucidated. We investigated the clinical significance and prognostic value of the expression of tumoral and stromal HA and its related proteins in oropharyngeal and oral cavity cancer.

METHODS

Resected tissues from oropharyngeal or oral cavity cancer patients undergoing surgery were analysed in tissue microarrays divided into stroma and cancer panels. The expression levels of HA, HA synthases and hyaluronidases were also assessed by immunohistochemistry.

RESULTS

A total of 160 resected oropharyngeal or oral cavity cancer tissues were analysed. Stromal HA expression was observed more frequently in human papilloma virus (HPV)-negative tumors, but other clinicopathological characteristics did not differ. In patients with HPV-negative oral cavity cancers, high stromal HA expression was associated with significantly shorter recurrence-free survival and overall survival compared with low stromal HA expression. The expression of HA in both tumors and stroma was significantly correlated with poorer outcomes than other combinations in patients with HPV-negative oral cavity cancers. However, these prognostic roles of HA were not observed in patients with HPV-negative oropharyngeal cancers. In the HPV-stratified multivariate analysis, high stromal HA expression remained an independent indicator of poor prognosis in terms of recurrence-free survival.

CONCLUSION

High stromal HA and expression of HA in both tumors and stroma were correlated with poor prognosis in HPV-negative oral cavity cancer, but not in HPV-negative oropharyngeal cancers.

The Prognostic Significance of Low-Frequency Somatic Mutations in Metastatic Cutaneous Melanoma

Background: Little is known about the prognostic significance of somatically mutated genes in metastatic melanoma (MM). We have employed a combined clinical and bioinformatics approach on tumor samples from cutaneous melanoma (SKCM) as part of The Cancer Genome Atlas project (TCGA) to identify mutated genes with potential clinical relevance. Methods: After limiting our DNA sequencing analysis to MM samples (n = 356) and to the CANCER CENSUS gene list, we filtered out mutations with low functional significance (snpEFF). We performed Cox analysis on 53 genes that were mutated in ≥3% of samples, and had ≥50% difference in incidence of mutations in deceased subjects versus alive subjects. Results: Four genes were potentially prognostic [RAC1, FGFR1, CARD11, CIITA; false discovery rate (FDR) < 0.2]. We identified 18 additional genes (e.g., SPEN, PDGFRB, GNAS, MAP2K1, EGFR, TSC2) that were less likely to have prognostic value (FDR < 0.4). Most somatic mutations in these 22 genes were infrequent (< 10%), associated with high somatic mutation burden, and were evenly distributed across all exons, except for RAC1 and MAP2K1. Mutations in only 9 of these 22 genes were also identified by RNA sequencing in >75% of the samples that exhibited corresponding DNA mutations. The low frequency, UV signature type and RNA expression of the 22 genes in MM samples were confirmed in a separate multi-institution validation cohort (n = 413). An underpowered analysis within a subset of this validation cohort with available patient follow-up (n = 224) showed that somatic mutations in SPEN and RAC1 reached borderline prognostic significance [log-rank favorable (p = 0.09) and adverse (p = 0.07), respectively]. Somatic mutations in SPEN, and to a lesser extent RAC1, were not associated with definite gene copy number or RNA expression alterations. High (>2+) nuclear plus cytoplasmic expression intensity for SPEN was associated with longer melanoma-specific overall survival (OS) compared to lower (≤ 2+) nuclear intensity (p = 0.048). We conclude that expressed somatic mutations in infrequently mutated genes beyond the well-characterized ones (e.g., BRAF, RAS, CDKN2A, PTEN, TP53), such as RAC1 and SPEN, may have prognostic significance in MM.

The Integrated Genomic Landscape of Thymic Epithelial Tumors

Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy.

Prognostic implication of ERCC1 protein expression in resected oropharynx and oral cavity cancer

BACKGROUND

Excision repair cross complement group 1 (ERCC1) expression is a predictive biomarker for platinum-containing treatment in squamous cell carcinoma of head and neck (SCCHN). However, the prognostic significance after surgical resection is not well understood.

METHODS

Oropharynx (n=143) or oral cavity (n=61) SCCHN patients undergoing surgery were included. ERCC1 protein expression and HPV status were assessed by ERCC1 and p16 immunohistochemistry.

RESULTS

The ERCC1, over-expressed in 66.7% of patients, was associated with oral cavity cancer (P<0.001), well differentiation (P=0.036), and HPV negativity (P<0.001). In TCGA database, ERCC1 mRNA upregulation was enriched in HPV-negative and oral cavity cancers, and associated with HRAS mutation (P<0.001). The prognostic role of ERCC1 was not different according to HPV status. High ERCC1 expression showed a trend toward poor prognosis in patients with an advanced stage (P=0.079) with marginal significance.

CONCLUSIONS

The ERCC1 expression was not prognostic in surgically resected oropharynx/oral cavity SCCHN, irrespective of HPV status. However, it could provide additional prognostic information for advanced stage patients.

LCCC 1025: Phase II study of everolimus, trastuzumab, and vinorelbine for HER2+ breast cancer brain metastases (BCBM)

1011

Background: HER2+ BC is an aggressive subset of BC with high rates of BM and poor survival. Two-thirds of BCBM demonstrate activation of the PI3K/mTOR pathway driving resistance to anti-HER2 therapy (Rx). This phase II study evaluated everolimus (E), a brain permeable mTOR inhibitor, added to trastuzumab (T) and vinorelbine (V) in patients (pts) with HER2+ BCBM. Methods: Eligible pts had progressing HER2+ BCBM. Pts received E (5mg PO QD), T (2mg/kg IV weekly) and V (25mg/m2 IV d1, 8 of 21d cycle). The primary endpoint was intracranial response rate (RR [CR+PR], modified RECIST); secondary objectives (CNS clinical benefit rate [CBR, CR+PR+SD], extracranial RR, time to progression (TTP), overall survival (OS), and correlative studies). Targeted DNA sequencing of 20 tissues from 18 pts was performed. We used a two-stage design to distinguish ORR of 5% vs 20%. Results: 32 pts were evaluable for toxicity; 26 for efficacy. Median age was 53 (28–70 yrs). 31/32 pts had prior radiation: 13 (42%) WBRT, 8 (26%) radiosurgery, 9 (29%) both. Median prior lines of metastatic Rx was 2 (0–7). 30 (94%) received anti-HER2 Rx: 91% T, 69% lapatinib, 38% pertuzumab, 25% TDM1. Intracranial RR was 4% (1 PR, 6 SD > 6 mos, 10 SD > 3 mos, 9 PD). CNS CBR (6 mos) was 27%; CNS CBR (3 mos) was 65%. Extracranial RR was 46%. Median TTP was 4 mos (95% CI, 2.2 –5). OS was 12.2 mos (95% CI, 0.6 – 20.2). Grade 3-4 toxicities included neutropenia (41%), anemia (16%), and stomatitis (16%). DNA sequencing showed heterogeneous HER2 copy number amplification (CN amp): only 11/20 show HER2 CN amp (median 40X v 0.7X; 5/11 BC, 4/4 BCBM, 1/2 liver mets, 1/3 LN). BCBM exhibited high-level HER2 CN amp (median 49X) vs other sites (16X). While 11/20 show both HER2 CN amp and PI3K pathway mutation, this was not associated TTP; RAD21 CN amp was associated with TTP < 3 mos. Lack of HER2 CN amp plus a HER2 Tyr-kinase domain mutation was seen in a pt with nonresponse and short OS. Conclusions: While intracranial RR to ETV was low in pts with HER2+ BCBM, a substantial proportion had CNS CBR; OS was 1 year for this pt population. No new toxicity signals were observed. Further evaluation of DNA heterogeneity, including degree of HER2 CN amp in HER2+ BCBM, and association with outcome is warranted. Clinical trial information: NCT01305941.

Extracellular ATP Induces Calcium Signaling in Odontoblasts

Odontoblasts form dentin at the outermost surface of tooth pulp. An increasing level of evidence in recent years, along with their locational advantage, implicates odontoblasts as a secondary role as sensory or immune cells. Extracellular adenosine triphosphate (ATP) is a well-characterized signaling molecule in the neuronal and immune systems, and its potential involvement in interodontoblast communications was recently demonstrated. In an effort to elaborate the ATP-mediated signaling pathway in odontoblasts, the current study performed single-cell reverse transcription polymerase chain reaction (RT-PCR) and immunofluorescent detection to investigate the expression of ATP receptors related to calcium signal in odontoblasts from incisal teeth of 8- to 10-wk-old rats, and demonstrated an in vitro response to ATP application via calcium imaging experiments. While whole tissue RT-PCR analysis detected P2Y₂, P2Y₄, and all 7 subtypes (P2X₁ to P2X₇) in tooth pulp, single-cell RT-PCR analysis of acutely isolated rat odontoblasts revealed P2Y₂, P2Y₄, P2X₂, P2X₄, P2X₆, and P2X₇ expression in only a subset (23% to 47%) of cells tested, with no evidence for P2X₁, P2X₃, and P2X₅ expression. An increase of intracellular Ca²⁺ concentration in response to 100μM ATP, which was repeated after pretreatment of thapsigargin or under the Ca²⁺-free condition, suggested function of both ionotropic and metabotropic ATP receptors in odontoblasts. The enhancement of ATP-induced calcium response by ivermectin and inhibition by 5-(3-bromophenyl)-1,3-dihydro-2H-benzofuro[3,2-e]-1,4-diazepin-2-one (5-BDBD) confirmed a functional P2X₄ subtype in odontoblasts. Positive calcium response to 2',3'-O-(benzoyl-4-benzoyl)-ATP (BzATP) and negative response to α,β-methylene ATP suggested P2X₂, P2X₄, and P2X₇ as functional subunits in rat odontoblasts. Single-cell RT-PCR analysis of the cells with confirmed calcium response and immunofluorescent detection further corroborated the expression of P2X₄ and P2X₇ in odontoblasts. Overall, this study demonstrated heterogeneous expression of calcium-related ATP receptor subtypes in subsets of individual odontoblasts, suggesting extracellular ATP as a potential signal mediator for odontoblastic functions.

Abstract 4499: Integration of targeted RNA sequencing to targeted DNA sequencing for the characterization of clinically relevant variants in a population of thousands of patients treated on clinical trial

Background: Targeted sequencing has become common in the care of some patients with cancer, both for the detection of standard of care clinical mutations as well as in the care of patients with advanced disease who are looking for clinical trials or other non-standard therapies. Many patients have mutations detected, although many variants are of unknown significance, and many patients have no mutations at all. We added RNA targeted sequencing along with DNA targeted sequencing to add utility of targeted sequencing strategy in cancer genomics and assessed the performances of RNA sequencing analysis.

Methods: Genomic sequencing of investigative biomarkers was prospectively offered to selected patients. DNA and RNA libraries were prepared separately from a retrieved archival FFPE tumor sample or a fresh frozen tumor sample from each patient. Relevant targets were enriched by custom designed Agilent SureSelect hybrid capture baits using standard protocols. Samples were sequenced on Illumina HiSeq 2000/2500 platforms. We compared somatic variants detected by DNA alone to those detected by DNA plus RNA using the UNCeqR algorithm and software.

Results: From a population of 2200 patients consented as part of LCCC1108 (NCT01457196), a subset of 300 patients was selected at random for RNA profiling. Selected patients were 7 to 83 years old (median, 54) and the cases included more than 20 cancer types including uterus, breast, ovary, and thyroid etc. And stages of cancers were as follows; I, 34.6%, II, 16.8%, III, 25.2%, and IV, 23.4% respectively. Sequencing of RNA was successful in 90% of specimens using 2.5 ug of RNA. RNA sequencing could detect 97.5% of sequence variants called by DNA sequencing and detect 20% more variants than DNA sequencing. Also 97.9% of variants showed higher mutant allele fraction (MAF) in RNA sequencing than DNA sequencing. We further interrogated the impact of certain classes of mutations on transcript structure and abundance. Specifically, we observed that splice site mutations and indels were associated with detectable alterations in the full length transcripts of their respective genes as well as overall gene abundance, with nonsense and frameshift mutations associated with decreased relative expression of the transcript relative to controls. We also observed that gene amplification of EGFR and ERBB2 was reflected in the RNA sequencing as increased gene expression with statistical significance by Fishers’ exact test (P &lt; 0.05), which suggests that RNA can be used as a surrogate for known protein and nucleic quantitative assays.

Conclusion: Using clinical samples, including relatively small quantities, we were able to confirm that nucleotide variants detected at DNA level leads to significant alteration at the transcription level and to have additional information potentially helpful for better management of cancer patients.

Citation Format: Woochang Lee, Heejoon Jo, Xiaoying Yin, David A. Eberhard, Nirali M. Patel, Michele C. Hayward, Ashley H. Salazar, Joel S. Parker, William Y. Kim, Henry S. Earp, Norman E. Sharpless, David N. Hayes. Integration of targeted RNA sequencing to targeted DNA sequencing for the characterization of clinically relevant variants in a population of thousands of patients treated on clinical trial. [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 4499.

Multi-threading the generation of Burrows-Wheeler Alignment

Along with recent progress in next-generation sequencing technology, it has become easier to process larger amounts of genome sequencing data at a lower cost. The most time-consuming step of next-generation sequencing data analysis involves the mapping of read data into a reference genome. Although the Burrows-Wheeler Alignment (BWA) tool is one of the most widely used open-source software tools for aligning read sequences, it still has a limitation in that it does not fully support a multi-thread mechanism during the alignment generation step. In this article, we propose a BWA-MT tool based on BWA that supports multi-thread mechanisms for processing alignment generation. To evaluate BWA-MT, we used an evaluation system equipped with 24 cores and 128 GB of memory. As workloads, we used the hg19 human genome reference sequence and sequences of various read sizes from the 1 to 40 M spots. In our evaluation, BWA-MT showed a maximum of 3.66-times better performance, and generated the same Sequence Alignment/Map result file as that of BWA. Although the ability to speed up the procedure might be dependent on computing resources, we confirmed that BWA-MT is a highly effective and fast alignment tool.

Inorganic phosphate induces mammalian growth plate chondrocyte apoptosis in a mitochondrial pathway involving nitric oxide and JNK MAP kinase

Chondrocytes in the hypertrophic zone of the growth plate undergo apoptosis during endochondral bone development via mechanisms that involve inorganic phosphate (Pi) and nitric oxide (NO). Recent evidence suggests that Pi-dependent NO production plays a role in apoptosis of cells in the resting zone as well. This study examined the mechanism by which Pi induces NO production and the signaling pathways by which NO mediates its effects on apoptosis in these cells. Pi decreased the number of viable cells based on MTT activity; the number of TUNEL-positive cells and the level of DNA fragmentation were increased, indicating an increase in apoptosis. Blocking NO production using the NO synthase (NOS) inhibitor L: -NAME or cells from eNOS(-/-) mice blocked Pi-induced chondrocyte apoptosis, indicating that NO production is necessary. NO donors NOC-18 and SNOG both induced chondrocyte apoptosis. SNOG also upregulated p53 expression, the Bax/Bcl-2 expression ratio, and cytochrome c release from mitochondria, as well as caspase-3 activity, indicating that NO induces apoptosis via a mitochondrial pathway. Inhibition of JNK, but not of p38 or ERK1/2, MAP kinase was able to block NO-induced apoptosis, indicating that JNK is necessary in this pathway. Pi elevates NO production via eNOS in resting zone chondrocytes, which leads to a mitochondrial apoptosis pathway dependent on JNK.

Molecular characterization of the human ABO blood group orthologus system in pigs

The selection and use of animals with blood group 0 in the process of transplanting pig organs or tissues into humans can positively contribute to the control of acute immune rejection due to differences in blood groups. Exon-specific PCRs for the porcine blood group A transferase gene against genomic DNA from either blood group A or 0 animals resulted in the amplification failure of the A0 blood group gene exon 8 from blood group 0 animals. To characterize the genetic abnormality in the genome of blood group 0 animals, we screened bacterial artificial chromosome (BAC) clones from a Korean native pig BAC library which had the blood group 0 allele, and carried out shotgun sequencing. The analysis showed that the 0 allele has a large deletion between exon 7 of the A0 blood group gene and the neighbouring SURF6. We also showed that the ABO blood group antigens in humans and the A0 blood group antigens in pigs are coded by mutations within the orthologous glycosyltransferase gene. In addition, we developed a multiplex genotyping method for the porcine A0 blood group gene.