Abstract 1496: Paired, single-cell profiling of circulating tumor cell-derived xenograft models of small cell lung cancer reveals intratumoral heterogeneity and emergence of new cell clusters following treatment relapse

Small cell lung cancer (SCLC), the most aggressive form of lung cancer, is notable for early dissemination and impressive, yet transient, responses to frontline chemotherapy that are rapidly undone by refractory relapses. To gain a better understanding of resistance mechanisms, we generated circulating tumor cell-derived xenograft (CDX) models from liquid biopsies of SCLC patients and treated them with chemotherapy or targeted agents. As expected, CDXs demonstrate similar chemotherapy response to the patient from whom they were derived. We have previously established that baseline chemosensitive CDXs are molecularly homogeneous at the single cell level, while chemoresistant CDXs exhibit increased intratumoral heterogeneity (ITH) with distinct variations in gene expression between cancer cell populations. We hypothesize that paired analyses of chemosensitive CDXs will demonstrate increased ITH after developing acquired resistance and are likely to offer more specific insights into resistance mechanisms than prior work with unrelated CDX models. Platinum-sensitive CDXs were treated with cisplatin or DNA damage response targeted therapies (PARP inhibitor or CHK inhibitor) continuously until tumor progression was observed. To identify transcriptional changes associated with onset of resistance, single-cell RNAseq analysis was performed on vehicle-treated and relapsed CDX tumors. We found globally increased ITH including heterogeneous expression of therapeutic targets and potential resistance pathways, such as EMT, between cellular subpopulations following treatment-resistance. Relapse was consistently associated with increased ITH score (P<0.001) and cell cluster number. To determine whether transcriptional diversity in either therapeutic targets (ex., MYC, DLL3, TOP2A, PARP1, CHEK1, EZH2, etc.) or EMT genes (ex., ZEB1, ZEB2, TWIST1, VIM, AXL) was detectable between the paired tumors after onset of resistance, we compared transcriptional differences between clusters present in vehicle-treated versus cisplatin or targeted therapy-treated tumors. We discovered the emergence of new cell clusters in relapsed tumors in all CDX models (4 CDXs, 3 distinct treatments), including clusters expressing EMT or NOTCH signaling genes. These data suggest that, in response to treatment, SCLC develops increasing transcriptional ITH marked by concurrent, diverse resistant cell clusters. Clinically, these data underscore the importance of maximizing and maintaining the initial response in platinum-sensitive SCLC tumors and highlight the intrinsic transcriptional fluidity underlying SCLC's profound treatment resistance following initial therapy.

Citation Format: C. Allison Stewart, Carl M. Gay, Yuanxin Xi, Santhosh Sivajothi, Junya Fujimoto, Patrice M. Hartsfield, Hai Tran, Stephen G. Swisher, Jack A. Roth, Jianjun Zhang, Bonnie Glisson, John V. Heymach, Ignacio Wistuba, Paul Robson, Jing Wang, Lauren A. Byers. Paired, single-cell profiling of circulating tumor cell-derived xenograft models of small cell lung cancer reveals intratumoral heterogeneity and emergence of new cell clusters following treatment relapse [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 1496.

Abstract 557: Novel targeted combination therapies active in KRAS mutant non-small cell lung cancer (NSCLC) identified using patient-derived xenografts (PDX)

PDXs recapitulate histologic features, gene expression patterns, and genomic alterations in human primary tumors, and thus have emerged as robust preclinical models for drug development, molecular characterization of cancers, identification of biomarkers, and strategic development of precision therapy. We tested multiple combinations of small molecule targeted drugs selected on the basis of known NSCLC vulnerabilities for efficacy in NSCLC PDXs with known genotypes. We determined in vivo treatment responses to single agent and combination therapies for pathway targeted therapeutic agents, including the MEK inhibitor trametinib, the MDM2 inhibitor KRT-232, the BCL2/BCL-XL inhibitor navitoclax, and their combinations in 8-23 molecularly annotated NSCLC PDX models. Mice (n=3-5/group) were enrolled into treatment individually when tumors reached 200 mm3 in size, and were treated 5 days/week for 3 weeks. Tumor growth was monitored 2-3 times/week. We used the following criteria to determine treatment responses: 1) Tumor Regression (or partial response): tumor regression ≥ -30% based on tumor volume changes calculated by AUC0-21day or at day 21 after treatment start when compared with baseline (beginning of treatment at day 0); 2) Tumor Growth Inhibition (or stable disease): Tumor growth was significantly suppressed when compared with control (P < 0.05), but no tumor regression was observed, or tumor regression was less than -30% based on tumor volume changes calculated by AUC0-21day or at day 21 after treatment start when compared with baseline; 3) Resistance: Tumor volume changes calculated by AUC0-21day was not significantly different from control group (P>0.05). Our results showed that KRT-232 alone resulted in 15.8% (3/19) tumor regression and 26.3% (5/19) tumor growth inhibition, all in TP53 wild type PDXs. Trametinib alone induced 10% (2/20) tumor regression and 50% (10/20) growth inhibition, respectively. 80% (8/10) of KRAS mutant PDXs responded to trametinib treatment with tumor regression (1/10) or growth inhibition (7/10). Combination therapies of trametinib plus KRT-232 and trametinib plus navitoclax led to improved in vivo anticancer activity over single agent activity in a subset PDX models with KRAS mutations. Tumor regression was observed in 26% (6/23) and 50% (5/10) of trametinib plus KRT-232 and trametinib plus navitoclax treatment groups, respectively. Navitoclax alone did not induce tumor regression in 8 PDX models tested, and navitoclax plus KRT-232 did not lead to significant improvement in activity over single agents in 11 PDXs. Our results show that combination therapies of trametinib plus KRT-232 or navitoclax result in improved efficacy in a subgroup of NSCLC PDX models with KRAS mutations. Clinical trials with these targeted drug combinations in NSCLC are warranted.

Citation Format: Xiaoshan Zhang, Ran Zhang, Huiqin Chen, Li Wang, Chenghui Ren, Shuhong Wu, Min Jin Ha, Jeffrey Morris, Yuanxin Xi, Jing Wang, Don L. Gibbons, John V. Heymach, Funda Meric-Bernstam, John Minna, Stephen G. Swisher, Jack A. Roth, Bingliang Fang. Novel targeted combination therapies active in KRAS mutant non-small cell lung cancer (NSCLC) identified using patient-derived xenografts (PDX) [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 557.

Metabolomic profiling of goslings with visceral gout reveals a distinct metabolic signature

1.The objective of the experiment was to analyse serum profiles of goslings with visceral gout and compare them with those of healthy individuals to identify differentially-abundant metabolites as potential biomarkers. 2.Untargeted gas chromatography and time-of-flight mass spectrometry (GC-TOF-MS) metabolomic profiling was used to compare the serum metabolome of 15 goslings (Anser cygnoides) with gout and 15 healthy goslings (control). 3.Goslings with gout had a metabolic profile distinct from that of the controls, with 45 metabolite levels differing significantly (VIP > 1; P < 0.05) between both groups. Nine metabolites (hydrocortisone, glucose, trans-4-hydroxy-L-proline, galactose, 2-deoxy-D-galactose, beta-mannosylglycerate, d-glucoheptose, zymosterol, and hypoxanthine) were selected through receiver operating characteristics (ROC) analysis (area under curve (AUC) score ≥0.85) as potential biomarkers. Pathway analysis revealed that metabolites with differing levels were mainly involved in galactose, arginine and proline and purine metabolisms. 4.These results provided new insights into the pathogenesis of gout. Increased xanthine and hypoxanthine with decreased hydrocortisone provide promising biomarkers for gosling gout diagnosis. The findings suggested that hepatic metabolic disorders frequently occur in the development of avian gout.

Single-cell analyses reveal increased intratumoral heterogeneity after the onset of therapy resistance in small-cell lung cancer

The natural history of small cell lung cancer (SCLC) includes rapid evolution from chemosensitivity to chemoresistance, although mechanisms underlying this evolution remain obscure due to scarcity of post-relapse tissue samples. We generated circulating tumor cell (CTC)-derived xenografts (CDXs) from SCLC patients to study intratumoral heterogeneity (ITH) via single-cell RNAseq of chemo-sensitive and -resistant CDXs and patient CTCs. We found globally increased ITH including heterogeneous expression of therapeutic targets and potential resistance pathways, such as EMT, between cellular subpopulations following treatment-resistance. Similarly, serial profiling of patient CTCs directly from blood confirmed increased ITH post-relapse. These data suggest that treatment-resistance in SCLC is characterized by coexisting subpopulations of cells with heterogeneous gene expression leading to multiple, concurrent resistance mechanisms. These findings emphasize the need for clinical efforts to focus on rational combination therapies for treatment-naïve SCLC tumors to maximize initial responses and counteract the emergence of ITH and diverse resistance mechanisms.

Effect of imatinib on DOCA-induced myocardial fibrosis in rats through P38 MAPK signaling pathway

OBJECTIVE

To explore the role of imatinib in desoxycorticosterone acetate (DOCA)-induced myocardial fibrosis in rats by the p38 mitogen-activated protein kinase (MAPK) signaling pathway.

MATERIALS AND METHODS

Normal group (n=20), DOCA induction group (n=20), and imatinib treatment group (treatment group, n=20) were set up. Then, the cardiac function was examined via magnetic resonance imaging (MRI) and echocardiography (ECG) on the 21st d after modeling. Alkaline phosphatase (ALP) and myocardial function index creatine kinase-MB (CK-MB) were detected. The enzyme-linked immunosorbent assay (ELISA) was performed to measure tumor necrosis factor-gamma (TNF-γ) and interleukin-6 (IL-6). Hematoxylin-eosin (HE) staining assay was carried out to observe the pathological changes in myocardial tissues. Quantitative Polymerase Chain Reaction (qPCR) and Western blotting were employed to measure the expression levels of important myocardial fibrosis-related genes [checkpoint kinase 1 (Chek1) and alpha-smooth muscle actin (α-SMA)], as well as genes and proteins of the p38 MAPK signaling pathway.

RESULTS

In comparison with the normal group, DOCA induction group had significantly lowered fractional shortening (FS, %) and ejection fraction (EF, %), but overtly increased left ventricular end-diastolic dimension (LVEDd) and left ventricular end-systolic dimension (LVESd), as well as levels of serum ALP, alanine aminotransferase (ALT), and CK-MB. Besides, the levels of TNF-γ, IL-6, and IL-1β were notably raised in the DOCA induction group. HE staining results showed that myocardial injury was more severe in DOCA induction group. The results of the gene detection revealed that the expression levels of Chek1, α-SMA, p38 MAPK, and JNK were evidently higher in DOCA induction group than those in the imatinib treatment group (p<0.05), and the expression of p38 MAPK protein in the rat myocardial tissues was remarkably lower in the treatment group than that in the DOCA induction group (p<0.05).

CONCLUSIONS

Imatinib can regulate the repair of myocardial injury caused by DOCA-induced myocardial fibrosis in rats by repressing the p38 MAPK signaling pathway.

[Clinical assessment and related intervention of neonatal upper airway obstruction]

Objective:To discuss the diagnosis and evaluation of upper airway obstruction in neonates, classify the possible causes of neonatal upper airway obstruction, establish a standardized diagnosis and treatment procedure to improve the of treatment efficacy. Method:Clinical data of 71 cases with upper airway obstruction history were retrospective analyzed, 38 cases were treated by combined medical and surgical treatment, 17 cases underwent medical treatment, 16 cases abandonment the treatment. The effectiveness of fibrolaryngoscope, CT, neck ultrasound, MRI and other results was evaluated, and to analyze the prognosis of the treatment, the outcomes and risk factors were also analysed, to evaluate risk factors associated with upper airway obstruction. Result:Fifty-five cases were cured or improved. The mortality rate of 16 children who gave up treatment and left hospital automatically was 81.25%（13/16）. The accuracy rate of flexible laryngoscope in detecting the level of upper airway obstruction was 100%, the coincidence rate of B-ultrasound for upper airway cystic occupation was 100%. Etiological order from high to low was congenital space-occupying lesions, congenital upper airway malformation, vocal cord paralysis, Pierre-Robin syndrome. The site of obstruction has a significant influence on the severity of upper airway obstruction（P<0.05）. The cure rate of the non-endotracheal intubation group was higher than that of the endotracheal intubation group（P<0.05）. Conclusion:The obstruction site of upper airway significantly affects the outcome and the severity of the disease. Upper airway space occupying lesions are the primary causes of upper airway obstruction in neonates. Early assessment and timely treatment can improve the cure rate and improve the prognosis. Internal medicine combined with surgical treatment is effective in relieving upper airway obstruction.

Evaluation of giant cell tumors by diffusion weighted imaging-fractional ADC analysis

BACKGROUND

A single ADC value is used in clinical practice on multi b-value acquisitions. Low b-value acquisitions are affected by intravoxel incoherent motion, which is dependent on perfusion. Giant cell tumors (GCTs) are known to exhibit early arterial enhancement and low ADC values. Mean, minimum and fractional ADC characteristics of osseous and tenosynovial GCTs are systematically evaluated.

METHODS

Tenosynovial and osseous GCTs were included. Each lesion was evaluated on conventional MRI and DWI by two musculoskeletal radiologists. ADC was measured by placing an ROI on the most confluent enhancing portion of the lesion. Fractional and best fit ADC calculations were performed using MATLAB software.

RESULTS

No statistically significant difference was found between tenosynovial and osseous lesions' ADC values. Mean ADC for all lesions was 1.0 × 10^-3 mm²/s (SD = 0.2 × 10^-3 mm²/s) and minimum ADC was 0.5 × 10^-3 mm²/s (SD = 0.3 × 10^-3 mm²/s). Average mean ADC value obtained from B50-B400 slope was 1.1 × 10^-3 mm²/s (SD = 0.2 × 10^-3 mm²/s), and the average mean ADC value obtained from B400-B800 slope was 0.8 × 10^-3 mm²/s (SD = 0.1 × 10^-3 mm²/s) [p-value <0.01].

CONCLUSION

Tenosynovial and osseous GCTs demonstrate similar and low ADC values, which become even lower when using high b-value pairs. Our study also supports the theory of intravoxel incoherent motion that becomes apparent at low b values as related to giant cell tumors, which are known to be hyperperfused.

[Advances of studies on the occurrence of the upper respiratory disease correlative with immunity and tobacco]

SummaryTobacco smoke exposure has obvious and complex effects on the immune system of the human upper respiratory tract, including pro-inflammatory and anti-immune effects. Exposure to tobacco smoke is closely related to the occurrence and development of allergic rhinitis, the common rhinitis and sinusitis. The innate immune system is influenced by tobacco smoking through its effects on the respiratory mucosa and its adjuncts, natural killer cells, dendritic cells, neutrophils and innate immune receptors. Cigarette smoke can also affect the humoral immunity and cellular immunity, altering the acquired immune condition of the upper respiratory tract. Tobacco smoke exposure promotes the occurrence and development of the upper respiratory tract infectious diseases and allergic diseases by changing the composition of microflora in the upper respiratory tract.

Initial experience of CT-guided pulsed radiofrequency ablation of the pudendal nerve for chronic recalcitrant pelvic pain

AIM

To evaluate initial experience with computed tomography (CT)-guided pulsed radiofrequency ablation (pRFA) of the pudendal nerve in cases of recalcitrant neuropathic pelvic pain. Endpoints include technical feasibility, safety, and efficacy of therapy.

MATERIALS AND METHODS

Ten patients who underwent pRFA ablation for neuropathic pudendal nerve pain during the trial period were followed for response to treatment for 6 months. Each patient was treated with pRFA under CT-guidance with concurrent perineural injection of anaesthetic and/or corticosteroid. Pain scores were then measured using a numeric rating scale at fixed intervals up to 6 months.

RESULTS

All procedures were considered technically successful with no immediate complications. pRFA demonstrated improved duration of pain improvement compared to the most recent perineural injection (p=0.0195), but not compared to the initial injection (p=0.64). Reported pain scores were lower with pRFA than with both the first and most recent injection but this did not reach statistical significance (p=0.1094 and p=0.7539, respectively).

CONCLUSION

Overall, pRFA of the pudendal nerve using CT-guidance can be a safe and effective therapy. This technique provides direct visualisation of the nerve to maximise safety and efficacy while offering a novel form of therapy for patients with chronic, recalcitrant pelvic pain.

The genomic landscape of estrogen receptor α binding sites in mouse mammary gland

Estrogen receptor α (ERα) is the major driving transcription factor in the mammary gland development as well as breast cancer initiation and progression. However, the genomic landscape of ERα binding sites in the normal mouse mammary gland has not been completely elucidated. Here, we mapped genome-wide ERα binding events by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) in the mouse mammary gland in response to estradiol. We identified 6237 high confidence ERα binding sites in two biological replicates and showed that many of these were located at distal enhancer regions. Furthermore, we discovered 3686 unique genes in the mouse genome that recruit ER in response to estradiol. Interrogation of ER-DNA binding sites in ER-positive luminal epithelial cells showed that the ERE, PAX2, SF1, and AP1 motifs were highly enriched at distal enhancer regions. In addition, comprehensive transcriptome analysis by RNA-seq revealed that 493 genes are differentially regulated by acute treatment with estradiol in the mouse mammary gland in vivo. Through integration of RNA-seq and ERα ChIP-seq data, we uncovered a novel ERα targetome in mouse mammary epithelial cells. Taken together, our study has identified the genomic landscape of ERα binding events in mouse mammary epithelial cells. Furthermore, our study also highlights the cis-regulatory elements and cofactors that are involved in estrogen signaling and may contribute to ductal elongation in the normal mouse mammary gland.

Abstract 3772: Inter- and intra-tumoral variations in ASCL1, NEUROD1, and POU2F3 transcriptional programs underlie three distinct molecular subtypes of small cell lung cancers

Accounting for 15% of all lung cancer diagnoses, small cell lung cancer (SCLC) is an aggressive malignancy with dismal clinical outcomes, due in part to failure to define SCLC molecular subsets and identify the unique, targetable vulnerabilities therein. Recent data has begun to delineate these subsets by uncovering inter-tumoral heterogeneity in features such as DNA damage response, EMT, and neuroendocrine (NE) status. An integrated analysis of clinical samples to determine the implications of this heterogeneity broadly on SCLC classification has not yet been performed. Using RNAseq data from 81 SCLC tumor samples, we applied non-negative matrix factorization (NMF) which identified three clusters, each enriched for unique transcriptional programs driven by ASCL1 (30/81), NEUROD1 (24/81), or POU2F3 (27/81). These three genes encode transcription factors which define mutually exclusive NE-high, NE-low, and novel tuft cell variants of SCLC. Bulk RNAseq analyses of SCLC CTC-derived xenograft (CDX) models validated the clustering analysis in vivo. However, single-cell RNAseq from these same models reveals subtle evidence of intra-tumoral and intra-cellular heterogeneity in transcriptional programs that appear mutually exclusive in bulk analyses, suggesting plasticity among these variants. Guided by our NMF results, we performed RNAseq-based supervised clustering to classify each of 60 SCLC cell lines into ASCL1-driven, NEUROD1-driven, and POU2F3-driven clusters. Then, using reverse phase protein array data for these lines, we derived proteomic signatures for each cluster as follows: ASCL1-driven: E-cadherinhigh/TTF-1high/cMYClow, NEUROD1-driven: E-cadherinlow/TTF-1low/cMYChigh, and POU2F3-driven: E-cadherinhigh/TTF-1low/cMYChigh (ANOVA p&lt;0.001 for each). Other targetable proteins vary significantly among these clusters including BCL-2 (lower in NEUROD1-driven; p&lt;0.001) and PD-L1 (higher in ASCL1-driven; p=0.04). Correlating these clusters with IC50 values for over 500 drugs we find unique vulnerabilities. For example, POU2F3-driven lines were more sensitive to PARP inhibitors (PARPi), despite lacking biomarkers of PARPi sensitivity in SCLC (e.g. high SLFN11, low ATM). ASCL1-driven lines were more resistant to aurora kinase inhibitors (AURKi), as predicted given their lower expression of cMYC, a predictor of AURKi sensitivity in SCLC. Our data suggest that SCLC is subdivided on the basis of three unique transcriptional programs and that each subtype is characterized by diverse protein expression and drug responses. Single-cell analyses suggest, however, that multiple transcriptional programs may coexist within a single tumor or, even, a single cell, thus providing a potential novel mechanism for lineage switching and therapeutic resistance.

Citation Format: Carl M. Gay, Lixia Diao, C. Allison Stewart, Yuanxin Xi, Robert J. Cardnell, Stephen G. Swisher, Jack A. Roth, Bonnie S. Glisson, Jing Wang, John V. Heymach, Lauren A. Byers. Inter- and intra-tumoral variations in ASCL1, NEUROD1, and POU2F3 transcriptional programs underlie three distinct molecular subtypes of small cell lung cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3772.

Abstract 2899: Single-cell analyses reveal increasing intratumoral heterogeneity as an essential component of treatment resistance in small cell lung cancer

Small cell lung cancer (SCLC) is an aggressive malignancy characterized by rapid onset of platinum-resistance. However, mechanisms underlying platinum-resistance remain obscure due to scarcity of tissue samples from relapsed patients. We generated circulating tumor cell (CTC)-derived xenograft (CDX) models from SCLC patients that recapitulate patient tumor genomics and response to platinum chemotherapy. Little is known about whether intratumoral heterogeneity (ITH) exists in SCLC and how it may contribute to clinical outcomes and development of treatment resistance. To investigate this, we performed baseline single-cell RNAseq analyses of platinum-sensitive and -resistant CDX models, as well as longitudinal single-cell RNAseq analyses of CDX models and patient CTCs over the course of therapy. Within each CDX model, we observe not only increased ITH with resistance (variance-based metric, P=0.018), but distinct cellular populations with unique gene signatures associated with resistance (e.g. EMT, DNA damage repair, MYC activation, etc.). To confirm this relationship between ITH and resistance, platinum-sensitive CDX models were subjected to extended treatment with DNA damage response targeted therapies until relapse occurred. Single-cell RNAseq confirmed that, as predicted, untreated tumors were molecularly homogeneous, while relapse was associated with increased ITH and multiple, concurrent mechanisms of resistance, including TGF beta signaling and G2/M checkpoints. Unexpectedly, we found variations in the mechanisms of resistance within replicate treatment-relapsed mice, suggesting that resistance even to molecularly targeted therapies does not follow a predictable, reproducible pathway. For example, onset of resistance to a PARP inhibitor resulted in upregulation of NOTCH signaling in one tumor, but not others. Similarly, longitudinal single-cell profiling of CTCs directly from patient blood before, during, and after platinum-relapse confirmed increased ITH post-relapse accompanying unique mechanisms of resistance within specific cell populations (e.g., MYC activation, EMT, and TNFα signaling). We independently found ITH of protein expression (e.g., SLFN11, EZH2, EMT) in CTCs isolated from patient blood, signifying a method for measuring ITH clinically. These data suggest that treatment resistance in SCLC entails a fluid process of shifting expression profiles to generate an increasingly heterogeneous tumor with multiple, disparate mechanisms of resistance. Clinically, these findings imply that drug development efforts in this disease should focus on combination or maintenance therapies for treatment-naïve SCLC tumors to maximize depth of initial responses and delay the onset of resistance defined by ITH.

Citation Format: C. Allison Stewart, Carl M. Gay, Yuanxin Xi, Junya Fujimoto, Neda Kalhor, Patrice M. Hartsfield, Hai Tran, Luisa Fernandez, David Lu, Yipeng Wang, Ryan Dittamore, Jianjun Zhang, Stephen G. Swisher, Jack A. Roth, Trudy G. Oliver, John V. Heymach, Ignacio I. Wistuba, Bonnie S. Glisson, Paul Robson, Jing Wang, Lauren A. Byers. Single-cell analyses reveal increasing intratumoral heterogeneity as an essential component of treatment resistance in small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2899.

Comprehensive Genomic Characterization of Parathyroid Cancer Identifies Novel Candidate Driver Mutations and Core Pathways

CONTEXT

Elucidating the genomic landscape of sporadic parathyroid carcinoma (PC) has been limited by low tumor incidence.

OBJECTIVE

Identify driver mutations of sporadic PC and potential actionable pathways.

METHODS

Patients undergoing surgical resection for sporadic PC between 1980 and 2016 at MD Anderson Cancer Center were identified. Patients with sporadic PC according to World Health Organization diagnostic criteria and with available formalin-fixed, paraffin-embedded (FFPE) PC tumor tissue were included and their clinical data analyzed to assess extent of disease. Patients with parathyroid tumors of uncertain malignancy or atypical parathyroid neoplasms were excluded. Thirty-one patients meeting diagnostic criteria had available tissue for analysis. FFPE PC tumors were subjected to DNA extraction and next-generation whole-exome sequencing. All variant calls are single-algorithm only. Twenty-nine samples passed quality assurance after DNA extraction.

MAIN OUTCOME MEASURES

Somatic or private germline mutations present in sporadic PC and identification of pathways involved in tumorigenesis.

RESULTS

We identified 35 genes with considerable mutational load; only eight genes were previously identified in other PC cohorts. These genes mediate critical processes, including chromosome organization, DNA repair, and cell cycle regulations. Gene mutations involved in MAPK signaling and immune response are also heavily implicated. These findings are limited by inherent molecular artifacts in FFPE tissue analysis and the absence of matched germline DNA. Additionally, variant calls are only single algorithm and may include false-positive/negative calls.

CONCLUSION

We identified 33 candidate driver genes of sporadic PC, in addition to previously known driver genes CDC73 and MEN1.

Abstract P2-01-24: Sulindac and triple negative breast cancer progression

In 2018, a total of 266,120 new cases and 40,920 deaths from breast cancer in the United States were estimated by the American Cancer Society. Breast cancer is the most common malignancy and the second leading cause of death among American women. In this study, we will focus on triple negative breast cancer (TNBC), which is viewed by oncologists as a problematic and unpredictable sub-category of breast cancer because of higher rates of recurrence and poorer prognosis. TNBC accounts for up to 20% of all breast cancers and is highly prevalent in minority and young women. On average, 70% of women with metastatic TNBC die within 5 years, regardless of chemotherapy or other treatments. As such, there is an urgent medical need to develop more effective drugs to manage this deadly disease that already raised a health disparity concern, especially in the State of Louisiana. Nonsteroidal anti-inflammatory drugs (NSAIDs) are commonly used drugs for the treatment of pain, fever, and inflammation. Epidemiological studies have reported that the long term use of NSAIDs can prevent the occurrence multiple types of cancers, including breast cancer. However, their long term use for chemoprevention is not recommended because of toxicities associated with cyclooxygenase (COX) inhibition and the suppression of physiologically important prostaglandins. Our results show that the NSAID, sulindac sulfide (SS) and its non-COX inhibitory derivatives, can significantly inhibit the growth of the major subtypes of TNBC cells (basal-like, mesenchymal, and luminal). In addition, the compounds significantly inhibit tumor cell invasion. The animal experiments using Patient Derived Xenograft models supported the in vivo efficacy of these drugs. While studying the mechanism, we found that four oncogenic miRNAs, miR-10b, miR-17, miR-21, and miR-9 can be downregulated by SS and derivatives, and they were reported to promote tumor metastasis exclusively. Therefore, we conclude that those oncogenic miRNAs are involved in anti-metastatic activities of SS and its new non-COX inhibitory derivatives in TNBC.

Citation Format: Xi Y, Yi B, Riker A. Sulindac and triple negative breast cancer progression [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-01-24.

Abstract P6-22-01: Repurposing sulindac sulfide as a notch inhibitor to target cancer stem-like cells in triple negative breast cancer

Triple negative breast cancer (TNBC) is a heterogeneous group of clinically aggressive breast cancers. TNBC patients have a high risk of recurrence and metastasis, and current treatment options remain limited. There is strong evidence supporting the involvement of Notch signaling in TNBC progression. Expression of Notch1 and its ligand Jagged1 correlate with poor prognosis. Emerging evidence suggests that cancer stem-like cells (CSCs) that escape chemo or radiation therapy in TNBC are often Notch-dependent. At the same time, there is evidence that active tumor immunity predicts good response to neo-adjuvant chemotherapy in TNBC. Notch inhibitors, including Gamma Secretase Inhibitors (GSIs) are quite effective in preclinical models of TNBC, where they eliminate CSCs resistant to chemotherapy. However, the success of GSIs in clinical trials is limited by their intestinal toxicity and adverse immunological effects. CD4 and CD8 T-cells, necessary to adaptive tumor immunity, require Notch1 for activation. Our overarching goal is to replace GSIs with agents that lack their systemic toxicity and adverse immunological effects. We identified Sulindac Sulfide (SS), the active metabolite of FDA-approved NSAID Sulindac, as a potential candidate to replace GSI. SS has Gamma Secretase Modifier (GSM) activity. We confirmed that SS inhibits Notch1 cleavage in TNBC cells. SS significantly inhibited mammosphere growth in all human and murine TNBC models we tested: 1) human MDA-MB-231 cells; 2) murine TNBC model C0321, from targeted conditional knockout of Lunatic Fringe (LFng-/-); and 3) Two TNBC patient-derived xenograft models, 2K1 and 4IC. In contrast, SS did not inhibit Notch expression or cleavage in murine T cells. In C0321 tumors, which recapitulate human mesenchymal TNBC, we found that SS had remarkable single-agent anti-tumor activity and virtually eliminated Notch1 expression in tumors. SS caused an increase in intra-tumoral CD11c+ dendritic cells, but decreased CD4 cells, which in this model are largely PD-1 positive (exhausted). CD8 cells were modestly increased. SS did not affect the number of tumor infiltrating macrophages or myeloid-derived suppressor cells (MDSC). However, SS blocked the immunosuppressive function of bone marrow-derived MDSC. We are currently investigating the mechanisms of this anti-tumor activity. Our data support further investigation of SS for the treatment of TNBC, with standard of care or with immunotherapy agents. Repurposing an FDA-approved, safe agent for the treatment of TNBC would be significantly easier and more cost-effective than developing unproven investigational agents.

Citation Format: Hossain F, Ucar D, Majumder S, Xu K, Ran Y, Minter L, Xi Y, Burow M, Golde T, Osborne B, Miele L. Repurposing sulindac sulfide as a notch inhibitor to target cancer stem-like cells in triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-22-01.

Variations in HPV function are associated with survival in squamous cell carcinoma

Incidence of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) has been increasing dramatically. Although long-term survival rates for these patients are high, they often suffer from permanent radiotherapy-related morbidity. This has prompted the development of de-escalation clinical protocols to reduce morbidity. However, a subset of patients do not respond even to standard therapy and have poor outcomes. It is unclear how to properly identify and treat the high- and low-risk HPV+ OPSCC patients. Since HPV positivity drives radiotherapy sensitivity, we hypothesized that variations in HPV biology may cause differences in treatment response and outcome. By analyzing gene expression data, we identified variations in HPV-related molecules among HPV+ OPSCC. A subset of tumors presented a molecular profile distinct from that of typical HPV+ tumors and exhibited poor treatment response, indicating molecular and clinical similarities with HPV- tumors. These molecular changes were also observed in vitro and correlated with radiation sensitivity. Finally, we developed a prognostic biomarker signature for identification of this subgroup of HPV+ OPSCC and validated it in independent cohorts of oropharyngeal and cervical carcinomas. These findings could translate to improved patient stratification for treatment deintensification and new therapeutic approaches for treatment-resistant HPV-related cancer.

SAR and QSAR models of cyclooxygenase-1 (COX-1) inhibitors

Cyclooxygenase-1 (COX-1) is one isoform of COX, and it is a main target of nonsteroidal anti-inflammatory drugs (NSAIDs). It is important to develop efficient and selective COX-1 inhibitors. In this work, 12 classification models for 1530 cyclooxygenase-1 (COX-1) inhibitors were built by support vector machine (SVM), decision tree (DT) and random forest (RF) methods. The best classification model (model 1A) was built by SVM with MACCS fingerprints. The classification accuracies for the training and test sets were 99.67% and 97.39%, respectively. The Matthews correlation coefficient (MCC) of the test set was 0.94. We also divided the 1530 COX-1 inhibitors into nine subsets according to their different scaffolds using Kohonen's self-organizing map (SOM). In addition, six quantitative structure-activity relationship (QSAR) models for 181 COX-1 inhibitors whose IC₅₀ were measured by enzyme immunoassay were built by multiple linear regression (MLR) and SVM. The best QSAR model (model 5A) was built by SVM with CORINA Symphony descriptors. The correlation coefficients of the training and test sets are 0.93 and 0.84, respectively. The models built in this study can be obtained from the authors.

[The influence of Thymidine Phosphorylase genetic variation on clinical outcomes and safety of colorectal cancer patients received adjuvant chemotherapy after R0 resection]

Objective: To study the association between Thymidine Phosphorylase (TYMP) genetic variation and clinical outcomes and safety of postoperative colorectal cancer (CRC) patients. Methods: A total of 235 patients with colorectal cancer underwent surgical treatment were included in this retrospective analysis. Peripheral blood and the postoperative tissue specimen of the CRC patients were collected for the genotyping of polymorphism and TYMP mRNA expression, respectively. The correlation between polymorphism and clinical outcomes and safety of postoperative CRC patients were analysed. Results: Located in the upstream, 5633C>T was of clinical significance. The prevalence of 5633C>T in TYMP among the CRC patients were as follows: CC genotype 149 cases (63.40%), CT genotype 73 cases (31.06%), TT genotype 13 cases (5.54%), minor allele frequency of 5633C>T is 0.21. The distribution of three genotypes was in accordance with Hardy-Weinberg Equilibrium (P=0.313). CT genotype and TT genotype patients were merged in the comparison of prognosis. The survival analysis of patients with different genotypes found that the median Overall Survival (OS) of CT/TT genotype and CC genotype were 5.8 and 4.5 year, which was statistically significant (P=0.009). Adjusted in multivariate Cox regression analysis, CT/TT genotype was an independent favorable factor for OS (HR=0.67, P=0.015). Additionally, of the 87 postoperative tissue specimens, the results showed that the expression of TYMP in cancer tissues of the patients with CT or TT genotypes were significantly higher than those of the wild type CC genotype patients (P=0.019). And the safety analysis showed that the incidence of grade 3 hand-foot syndrome among CT/TT genotype patients were higher than that of CC genotype patients (33.72% vs 20.13%, OR=1.68, P=0.021). Conclusion: The polymorphism 5633C>T of TYMP may impact the prognosis of CRC patients received adjuvant chemotherapy by influencing the mRNA expression of TYMP.

S, Fujimoto J, Tong P, Diao L, Li L, Bolisetty M, Kalhor N, Lawson P, Vasquez M, Tran H, Wistuba II, Glisson B, Zhang J, Swisher SG, Roth JA, Heymach JV, Robson P, Wang J, Byers LA. Abstract 990: Single-cell profiling of small cell lung cancer circulating tumor cell-derived xenograft models reveals intratumoral heterogeneity among mediators of chemoresistance

Small cell lung cancer (SCLC) accounts for 14% of lung cancer diagnoses in the United States and is characterized by rapid onset of chemoresistance and poor clinical outcomes. Once considered a homogeneous disease, recent analyses of SCLC have identified intratumoral heterogeneity (ITH) with respect to NOTCH signaling, ASCL1/NEUROD1 balance and MYC amplification - all of which are potential mechanisms underlying SCLC's aggressive and refractory biology. Unfortunately, patient-derived models of SCLC with which to better characterize the molecular profiles of refractory SCLC are scarce. To address this, we generated circulating tumor cell-derived xenograft (CDX) models from liquid biopsies of patients with treatment-naïve or relapsed SCLC. Each CDX model underwent pathological review to confirm tumors were consistent with SCLC based on histology and standard immunohistochemical markers (e.g., TTF1, chromogranin A, synaptophysin, NCAM). Sequencing of these models revealed mutations typical of SCLC (e.g. TP53, RB1), which were maintained in vivo over multiple passages. Importantly, each model's in vivo response to cisplatin matched the patient's platinum response at the time of CDX generation. At the proteomic level, platinum-resistant models exhibited mTOR activation, increased SOX2 and ATM, and reduced E-cadherin, suggesting a shift toward EMT and cancer stem cell expansion may contribute to resistance. To investigate ITH, we analyzed single-cell gene expression profiles by RNAseq using a droplet-based Chromium Single Cell system that analyzed a filtered subsample of 2000 cells per tumor. Consistent with SCLC, all CDX models contained large numbers of cells expressing neuroendocrine-specific genes (SYP, CHGA). However, Principle Component Analysis revealed that cells from chemosensitive CDX models had distinct expression profiles from resistant models. Using our published EMT gene signature, we found that resistant models had higher proportions of mesenchymal (vs. epithelial) cells. Several other distinctions between sensitive and resistant models were detected at the single-cell level but not in bulk RNA and protein analyses, suggesting that single-cell resolution can identify occult platinum-resistant subpopulations. For example, higher proportions of ASCL1- and DLL3-expressing cells were associated with platinum sensitivity, whereas a shift toward predominant NEUROD1-expression was observed with resistance. Cells expressing each of these three genes were identified across all tumors, suggesting platinum-sensitive and resistant subpopulations are ubiquitous but that even subtle shifts in the fractional distribution of these subsets can exert significant impact on response. These data support further use of single-cell analysis to explore the role of ITH as a driver of drug resistance in SCLC.

Citation Format: C. Allison Stewart, Carl M. Gay, Yuanxin Xi, Siva V., Junya Fujimoto, Pan Tong, Lixia Diao, Lerong Li, Mohan Bolisetty, Neda Kalhor, Patrice Lawson, Mayra Vasquez, Hai Tran, Ignacio I. Wistuba, Bonnie Glisson, Jianjun Zhang, Stephen G. Swisher, Jack A. Roth, John V. Heymach, Paul Robson, Jing Wang, Lauren A. Byers. Single-cell profiling of small cell lung cancer circulating tumor cell-derived xenograft models reveals intratumoral heterogeneity among mediators of chemoresistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 990.