Improving outcomes in patients with oesophageal cancer

The care of patients with oesophageal cancer or of individuals who have an elevated risk of oesophageal cancer has changed dramatically. The epidemiology of squamous cell and adenocarcinoma of the oesophagus has diverged over the past several decades, with a marked increase in incidence only for oesophageal adenocarcinoma. Only in the past decade, however, have molecular features that distinguish these two forms of the disease been identified. This advance has the potential to improve screening for oesophageal cancers through the development of novel minimally invasive diagnostic technologies predicated on cancer-specific genomic or epigenetic alterations. Surgical techniques have also evolved towards less invasive approaches associated with less morbidity, without compromising oncological outcomes. With improvements in multidisciplinary care, advances in radiotherapy and new tools to detect minimal residual disease, certain patients may no longer even require surgical tumour resection. However, perhaps the most anticipated advance in the treatment of patients with oesophageal cancer is the advent of immune-checkpoint inhibitors, which harness and enhance the host immune response against cancer. In this Review, we discuss all these advances in the management of oesophageal cancer, representing only the beginning of a transformation in our quest to improve patient outcomes.

Programmatic Precision Oncology Decision Support for Patients With Gastrointestinal Cancer

PURPOSE

With the growing number of available targeted therapeutics and molecular biomarkers, the optimal care of patients with cancer now depends on a comprehensive understanding of the rapidly evolving landscape of precision oncology, which can be challenging for oncologists to navigate alone.

METHODS

We developed and implemented a precision oncology decision support system, GI TARGET, (Gastrointestinal Treatment Assistance Regarding Genomic Evaluation of Tumors) within the Gastrointestinal Cancer Center at the Dana-Farber Cancer Institute. With a multidisciplinary team, we systematically reviewed tumor molecular profiling for GI tumors and provided molecularly informed clinical recommendations, which included identifying appropriate clinical trials aided by the computational matching platform MatchMiner, suggesting targeted therapy options on or off the US Food and Drug Administration-approved label, and consideration of additional or orthogonal molecular testing.

RESULTS

We reviewed genomic data and provided clinical recommendations for 506 patients with GI cancer who underwent tumor molecular profiling between January and June 2019 and determined follow-up using the electronic health record. Summary reports were provided to 19 medical oncologists for patients with colorectal (n = 198, 39%), pancreatic (n = 124, 24%), esophagogastric (n = 67, 13%), biliary (n = 40, 8%), and other GI cancers. We recommended ≥ 1 precision medicine clinical trial for 80% (406 of 506) of patients, leading to 24 enrollments. We recommended on-label and off-label targeted therapies for 6% (28 of 506) and 25% (125 of 506) of patients, respectively. Recommendations for additional or orthogonal testing were made for 42% (211 of 506) of patients.

CONCLUSION

The integration of precision medicine in routine cancer care through a dedicated multidisciplinary molecular tumor board is scalable and sustainable, and implementation of precision oncology recommendations has clinical utility for patients with cancer.

Clinical and Genomic Characterization of Interval Colorectal Cancer in 3 Prospective Cohorts

BACKGROUND & AIMS

Interval colorectal cancers (CRCs), cancers diagnosed after a screening/surveillance examination in which no cancer is detected, and before the date of next recommended examination, reflect an unprecedented challenge in CRC detection and prevention. To better understand this poorly characterized CRC variant, we examined the clinical and mutational characteristics of interval CRCs in comparison with screen detected CRCs.

METHODS

We included 1175 CRCs documented in the Prostate, Lung, Colorectal, and Ovarian (PLCO) cancer screening trial and 3661 CRCs in the Nurses' Health Study (NHS) and Health Professionals Follow-up Study (HPFS). Multivariable Cox models were performed to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) of death risk. Whole exome sequencing was conducted in 147 PLCO cases and 796 NHS/HPFS cases.

RESULTS

A total of 619 deaths (312 CRC-specific) and 2404 deaths (1904 CRC-specific) were confirmed during follow-up of PLCO and NHS/HPFS, respectively. Compared with screen detected CRCs, interval CRCs had a multivariate-adjusted HR (95% CI) of 1.47 (1.21-1.78) for CRC-specific mortality and 1.27 (1.09-1.47) for overall mortality (meta-analysis combining all 3 cohorts). However, we did not observe significant differences in mutational features between interval and screen detected CRCs (false discovery rate adjusted P > .05).

CONCLUSION

Interval CRCs had a significantly increased risk of death compared with screen detected CRCs that were not explained by established clinical prognostic factors, including stage at diagnosis. The survival disadvantage of interval CRCs did not appear to be explained by differences in the genomic landscape of tumors characterized by whole exome sequencing.

AB1465 BLACK PATIENTS ARE LESS SATISFIED WITH THE PROCESS OF CARE FOLLOWING PRIMARY HIP AND KNEE ARTHROPLASTY: A RETROSPECTIVE STUDY

Background

Patients’ post-operative satisfaction with their hospital experience is important to patient care, hospital reimbursement, and comparison between hospitals. The Press Ganey (PG) inpatient survey is commonly administered to assess patient satisfaction with the process of care. However, whether patient PG survey scores following primary unilateral hip and knee arthroplasty are associated with a patient’s race and socioeconomic status (SES) is unknown.

Objectives

We aimed to determine whether patient PG survey overall assessment scores differ by race and SES.

Methods

We linked data for patients in large institutional hip and knee arthroplasty registries consisting of surgeries from July 2010–February 2012 to their PG survey responses. Patients undergoing primary unilateral surgery of Black or White race who resided in New York, New Jersey, or Connecticut at the time of surgery were included in the analysis. The primary outcome variable was the PG overall assessment score, calculated as the mean of a patient’s ratings for the three questions in the “Overall Assessment” section of the PG survey and dichotomized as either completely satisfied (score of 100) or not completely satisfied (score <100). Primary payor was used as a proxy for patient SES. Multivariable logistic regression was performed for the hip and knee cohorts separately to determine if patient race and primary payor were associated with not being completely satisfied, adjusting for age, sex, and American Society of Anesthesiology (ASA) score.

Results

There were 2,516 hip patients and 2,113 knee patients with PG overall assessment scores included in the analyses (Table 1). Black patients were more likely to be not completely satisfied compared to White patients in both cohorts [hip (odds ratio (OR)=1.64; 95% confidence interval (CI): 1.03, 2.61; p=0.04)]; [knee (OR=1.83; 95% CI: 1.16, 2.88; p=0.01). In the hip cohort, patients between 70-79 years old (OR=1.71; 95% CI: 1.09, 2.67; p=0.02) and older than 80 years (OR=2.00; 95% CI: 1.20, 3.32; p<0.01) were more likely to be not completely satisfied. In the knee cohort, patients 50-59 years old (OR=0.56; 95% CI: 0.33, 0.97; p=0.04) and 60-69 years old (OR=0.57; 95% CI: 0.33, 0.96; p=0.03) were less likely to be not completely satisfied compared to patients <50 years old.

Table 1.

Likelihood of not being completely satisfied with the process of care (PG score <100)

VariableReferenceCategoryHip Cohort (n = 2,516)Knee Cohort (n = 2,113)Odds Ratio95% CIp-valueOdds Ratio95% CIp-valueAge Group<5050-591.02(0.69, 1.50)0.9390.56(0.32, 0.97)0.039<5060-691.04(0.70, 1.54)0.8580.57(0.33, 0.96)0.034<5070-791.71(1.09, 2.67)0.0190.63(0.36, 1.11)0.113<5080+2.00(1.20, 3.32)0.0080.97(0.53, 1.77)0.912SexFemaleMale0.84(0.69, 1.02)0.0821.03(0.83, 1.26)0.816RaceWhiteBlack1.64(1.03, 2.61)0.0381.83(1.16, 2.88)0.010ASA status121.04(0.70, 1.55)0.8321.23(0.60, 2.51)0.580131.45(0.91, 2.29)0.1161.36(0.64, 2.87)0.41914<0.01(0.00, ***)0.968<0.01(0.00, ***)0.977Primary PayorMedicareMedicaid1.35(0.26, 7.01)0.718<0.01(0.00, ***)0.983MedicareOther/Unknown1.24(0.94, 1.64)0.1260.87(0.65, 1.17)0.362MedicarePrivate1.13(0.61, 2.10)0.6881.01(0.57, 1.78)0.983

ASA = American Society of Anesthesiologist (ASA) physical status classification. PG = Press Ganey. CI = Confidence Interval. *** indicates >999.99. Bold indicates p < 0.05

Conclusion

Black patients were less likely to be completely satisfied compared to White patients following total hip and knee arthroplasty. More research is needed to investigate other factors such as perceived staff courtesy and baseline pain and function to understand why these disparities exist.

Acknowledgements

This work was supported by the Stavros Niarchos Complex Joint Reconstruction Center at Hospital for Special Surgery. The content is solely the responsibility of the authors and does not necessarily represent the official views of the center.

Disclosure of Interests

J. Alex Gibbons: None declared, Orett Burke Jr: None declared, Huong Do: None declared, Emily Ying Lai: None declared, Bella Mehta Paid instructor for: Novartis, Letitia Bradford: None declared, Michael Parks Consultant of: ZimmerBiomet, Linda Russell: None declared, Anne Bass: None declared, Mark Figgie Shareholder of: HS2, Mekanika, and Wishbone, Consultant of: Lima and Wishbone, Susan Goodman Consultant of: UCB, Grant/research support from: Novartis

POS0417 LESS ACPA EPITOPE EXPANSION IS FOUND IN ACPA-POSITIVE IMMUNE CHECKPOINT INHIBITOR ARTHRITIS PATIENTS COMPARED TO ACPA-POSITIVE RHEUMATOID ARTHRITIS PATIENTS

Background

Immune checkpoint inhibitors (ICI) have markedly improved the treatment of many advanced cancers; however, they can result in immune-related adverse events (irAE) including ICI arthritis (ICI-A). ICI-A often resembles rheumatoid arthritis (RA) and ~9% of ICI-A patients are anti-citrullinated peptide antibody (ACPA) positive. In RA, ACPA epitope expansion occurs over the years prior to onset of clinical disease. In this study we examined the degree of ACPA epitope expansion in seropositive ICI-A patients in order to determine whether it is similar to early RA, or more suggestive of the pre-clinical phase of disease1.

Objectives

To compare the number of ACPA epitopes targeted in seropositive ICI-A versus RA.

Methods

We used clinical data and serum from 12 ACPA+ ICI-A patients enrolled in a prospective registry and 39 ACPA+ RA patients enrolled in the CATCH-US early RA cohort. ACPA screening was done using a commercial ELISA (positive >20 units/mL). A custom, bead-based antigen array was used to identify antibody reactivities to 16 putative RA associated citrullinated proteins. Synovial fluid (SF) samples from 3 of the ICI-A patients were also tested using the bead-based microarray. Hierarchical clustering software was used to create heatmaps to identify ACPA levels. Z-scores for fluorescence intensity were also calculated separately for each peptide, and a fluorescence level above the mean (Z-score>0) was defined as a positive ACPA. The number of positive epitopes for each patient was determined and compared categorically between the ICI-A and RA patients using Fischer’s exact test.

Results

Characteristics of ICI-A and early RA patients are listed in Table 1. Compared to RA patients, ICI-A patients were older (mean 71 years vs. 48 years), more likely to have ever smoked (67% vs. 36%) and less likely to have positive rheumatoid factor (RF) (8% vs. 69%). Median symptom duration for ICI-A patients was 3.7 months compared to 6.7 months in RA patients. The median ACPA titer was lower in ICI-A patients than RA patients (42 units/mL vs. 250 units/mL). As demonstrated in Figure 1, lower signal intensities (level of ACPA) and a lower number of distinct ACPA epitopes were seen in the serum of ICI-A patients compared to RA patients. Of ICI-A patients, 67% were positive for 0-4 ACPA epitopes, 8% for 5-10 epitopes and 25% for >10 epitopes, as opposed to 23% of RA patients positive for 0-4 epitopes, 36% for 5-10 epitopes, and 41% for >10 epitopes (p=0.02). The one ICI-A patient who was also RF positive had 12 positive ACPA epitopes. There was no significant difference in the number of ACPA epitopes in ICI-A patients who were smokers vs. nonsmokers, RA-like vs. PMR-like, or who received ICI combination vs. ICI monotherapy. In the 3 ICI-A patients with synovial fluid samples, SF ACPA was not demonstrated.

Table 1.

Baseline Characteristics of ACPA+ ICI-A and RA Patients

ICI-A (N=12)Early RA (N=39)Age in years, mean (SD)71.0 (8.3)48.2 (14.6)Female Sex7 (58%)33 (85%)White/Caucasian9 (75%)27 (69%)Symptom Duration in months, median [IQR]3.7 [1.0,11.3]6.7 [4.0,9.7]RF Positive1 (8%)27 (69%)ACPA level (units/mL), median [IQR]42.2 [29.4,70.5]250 [107.5,251.0]Obese (BMI≥30)3 (25%)9 (23%)Current/Past Smoker8 (67%)14 (36%)Cancer Typeǂ Melanoma4 (33%) Renal Cell Carcinoma3 (25%)ICI Regimen PD-1/PD-L17 (58%) CTLA-4+PD-15 (42%)ICI-A Phenotype RA-like9 (75%) PMR-like3 (25%)

ǂOther cancer types in ICI-A patients included urothelial carcinoma (n=2), non-small cell lung cancer (n=2), and head and neck cancer (n=1).

Figure 1.

Heat Map of ACPA repertoire in RA Patients and ICI-A Patients.

Conclusion

ICI-A patients had lower ACPA titers and targeted fewer ACPA epitopes than early RA patients. It remains to be determined if ICI-A represents an accelerated model of RA pathogenesis with ICI triggering an early transition from pre-clinical to clinical disease. This would require sequential sampling and analysis.

References

[1]Sokolove J. et al. PLoS One. 2012;7(5)e35296

Disclosure of Interests

Diviya Rajesh: None declared, Nilasha Ghosh: None declared, Jessica Kirschmann: None declared, Karmela Kim Chan: None declared, Deanna Jannat-Khah Shareholder of: AstraZeneca, Walgreens, and Cytodyn, Susan Goodman Consultant of: UCB Data Monitoring and Safety Board, Grant/research support from: Novartis, Vivian Bykerk Consultant of: Amgen, Bristol Myers Squibb, Genzyme, Gilead, Janssen, Pfizer, Sanofi-Aventis, and UCB, Grant/research support from: Bristol Myers Squibb, Amgen, and The Cedar Hill Foundation, William Robinson: None declared, Anne Bass: None declared.

AB1388 CHARACTERISTICS ASSOCIATED WITH MYCHART ACTIVATION AND REASONS FOR NON-USE AMONG RHEUMATOLOGY CLINIC PATIENTS

Background

Electronic patient portals, such as MyChart by Epic, allow patients to view their medical records, request medication refills, and communicate with their health care providers. Factors associated with portal use include being younger, female, White, having private insurance, and having chronic illness.1

The Hospital for Special Surgery (HSS) rheumatology clinic serves primarily patients with public insurance (Medicaid, which insures low-income adults, and Medicare, which insures adults >65 years old and those with eligible chronic illness/disability). These patients may be at increased risk for poor health outcomes due to clinical and socioeconomic factors and they are less likely to use MyChart than patients seen in HSS private practices. Increased MyChart use may benefit this high-risk group and improve health equity.

Objectives

This study aims to identify characteristics associated with MyChart activation and reasons for its underutilization among patients seen in the HSS rheumatology clinic.

Methods

We identified all patients aged ≥ 18 years seen in the HSS rheumatology clinic at least twice between January 15, 2019 and January 14, 2021, with at least one visit occurring between July 15, 2020 and January 14, 2021. MyChart status (active vs. inactive) and sociodemographic and clinical variables were extracted from the electronic health record (EHR). We used chi-square tests and t-tests to compare characteristics between patients with and without active MyChart; p-value <0.05 was considered significant (Table 1). In addition, 10 rheumatology fellows were prompted on 3 occasions over 6 weeks to informally survey their own clinic patients with inactive MyChart accounts by asking: “What is your primary reason for not using MyChart?”.

Table 1.

Baseline Characteristics of Hospital for Special Surgery Rheumatology Clinic Patients Stratified by MyChart Activation Status

MyChart Active (N=726)MyChart Inactive (N=501)p-valueAge, yrs - Mean (SD)50.3 (15.6)60.0 (15.3)<0.01Female - N (%)601 (82.8)412 (82.2)0.80Race - N (%)0.37•White/Caucasian275 (37.9)184 (36.7)•Black/African American185 (25.5)135 (27.0)•Asian58 (8.0)25 (5.0)•Other189 (26.0)145 (28.9)•Unknown18 (2.5)11 (2.2)Ethnicity - N (%)0.27•Hispanic/Latino294 (40.5)226 (45.1)•Not Hispanic/Latino422 (58.1)268 (53.5)•Unknown10 (1.4)7 (1.4)Preferred language - N (%)<0.01•English611 (84.2)332 (66.3)•Spanish72 (9.9)134 (26.8)•Other43 (5.9)35 (7.0)Needs interpreter - N (%)106 (14.6)156 (31.1)<0.01

Results

There were 1,227 patients included (93.2% with Medicaid and/or Medicare insurance). Compared to patients with inactive MyChart (42.9%), those with active MyChart (57.1%) were younger (50.3 ± 15.6 vs. 60.0 ± 15.3 years, p<0.01). The majority of patients in both groups was female. There was no significant difference in race or ethnicity between groups. Patients without active MyChart were less likely to identify English as their preferred language and more likely to require an interpreter for clinic visits (Table 1).

The rheumatology fellows collectively asked 16 clinic patients with inactive MyChart their primary reason for non-use. The most commonly cited reason was difficulty using the technology (n=8; 50.0%); others included visual impairment (n=2; 12.5%), preference for using the telephone (n=2; 12.5%), concerns about security/spam (n=2; 12.5%), not having a smart phone/computer (n=1; 6.3%), and having a language barrier (n=1; 6.3%).

Conclusion

In the HSS rheumatology clinic, patients who did not have active MyChart were older and less likely to be English-speaking than those who did. The most common barrier to MyChart use reported by patients was difficulty with the technology. This pilot data suggests a need for interventions to facilitate patient-provider communication, specifically targeting older and non-English-speaking rheumatology clinic patients, with the goal of advancing patient engagement and health equity.

References

[1]Ancker JS, et al. J Gen Intern Med. 2011 June 7. doi: 10.1007/s11606-011-1749-y.

Disclosure of Interests

Caroline Siegel: None declared, Anne Bass: None declared, Deanna Jannat-Khah Shareholder of: AstraZeneca, Walgreens, Cytodyn, Omar Bruce: None declared, Justin Olmscheid: None declared, Nilasha Ghosh: None declared, Sebastian E. Sattui Grant/research support from: AstraZeneca, Monica Schwartzman: None declared, Diane Zisa: None declared, Amit Lakhanpal: None declared, Kevin Yip: None declared, Linda Yue: None declared, Juliet Aizer Grant/research support from: Pfizer and Lilly, Jessica Berman: None declared

POS0402 CLONALLY EXPANDED CD38hi CYTOTOXIC CD8 T CELLS DEFINE THE T CELL INFILTRATE IN CHECKPOINT INHIBITOR-ASSOCIATED ARTHRITIS

Background

Immune checkpoint inhibitor (ICI) therapies that promote T cell activation have improved outcomes for advanced malignancies yet can also elicit harmful autoimmune reactions. The T cell mechanisms mediating these iatrogenic autoimmune events remain unclear.

Objectives

To investigate the immunophenotype, transcriptomic feature and clonotypes of T cells from joints of patients affected by ICI-induced inflammatory arthritis (ICI-arthritis).

Methods

Detailed immunophenotyping was performed on mononuclear cells from synovial fluid (SF) using mass cytometry and flow cytometry to identify significantly altered populations in ICI-A compared to seropositive rhrumatoid arthritis (RA) and psoriatic arthritis (PsA) (p<0.05). Bulk RNA-seq was performed on altered SF CD8 T cell subsets from ICI-A, RA and PsA to investigate their transcriptomic features. Cytokine profile and pathways enriched in ICI-A CD8 T cells were examined using differentially expressed genes, intracellular staining, and in vitro culture. TCR clonotypes were examined using single cell RNA-seq of T cells from synovial fluid, tissue and blood of ICI-A.

Results

Compared to the autoimmune arthritides RA and PsA, ICI-arthritis joints contained an expanded CD38hi CD127- CD8+ T cell subset that displays cytotoxic, effector, and interferon (IFN) response signatures. Exposure of synovial T cells to Type I IFN, more so than IFN-γ, induced the CD38hi cytotoxic phenotype. Single cell transcriptomic and T cell repertoire (TCR) analyses indicated that the abundance of CD38hi CD8 T cells in ICI-arthritis resulted from proliferation of a limited number of clones. The CD38hi population appeared distinct from dysfunctional T cells and clonally most related to TCF7+ memory populations. Comparison of synovial tissue from bilateral knees of the same patient demonstrated considerable sharing of TCR clonotypes among CD38hi CD8 T cells between the two joints. Further, TCR clonotypes expanded in synovial fluid of ICI-arthritis patients were detected in circulating T cells, and circulating CD38hi CD8 T cells are also expanded in ICI-arthritis patients.

Conclusion

These results define a distinct CD8 T cell subset in the synovial fluid and in the circulation of patients with ICI-A that may be directly activated by ICI therapy to mediate a tissue-specific autoimmune response.

Disclosure of Interests

None declared.

Pan-ERBB kinase inhibition augments CDK4/6 inhibitor efficacy in oesophageal squamous cell carcinoma

OBJECTIVE

Oesophageal squamous cell carcinoma (OSCC), like other squamous carcinomas, harbour highly recurrent cell cycle pathway alterations, especially hyperactivation of the CCND1/CDK4/6 axis, raising the potential for use of existing CDK4/6 inhibitors in these cancers. Although CDK4/6 inhibition has shown striking success when combined with endocrine therapy in oestrogen receptor positive breast cancer, CDK4/6 inhibitor palbociclib monotherapy has not revealed evidence of efficacy to date in OSCC clinical studies. Herein, we sought to elucidate the identification of key dependencies in OSCC as a foundation for the selection of targets whose blockade could be combined with CDK4/6 inhibition.

DESIGN

We combined large-scale genomic dependency and pharmaceutical screening datasets with preclinical cell line models, to identified potential combination therapies in squamous cell cancer.

RESULTS

We identified sensitivity to inhibitors to the ERBB family of receptor kinases, results clearly extending beyond the previously described minority of tumours with EGFR amplification/dependence, specifically finding a subset of OSCCs with dual dependence on ERBB3 and ERBB2. Subsequently. we demonstrated marked efficacy of combined pan-ERBB and CDK4/6 inhibition in vitro and in vivo. Furthermore, we demonstrated that squamous lineage transcription factor KLF5 facilitated activation of ERBBs in OSCC.

CONCLUSION

These results provide clear rationale for development of combined ERBB and CDK4/6 inhibition in these cancers and raises the potential for KLF5 expression as a candidate biomarker to guide the use of these agents. These data suggested that by combining existing Food and Drug Administration (FDA)-approved agents, we have the capacity to improve therapy for OSCC and other squamous cancer.

POS0285 ARE RACIAL DISPARITIES IN REVISION TKA OUTCOMES ASSOCIATED WITH HOSPITAL OR SURGEON VOLUME?

Background:

Total knee arthroplasty (TKA) outcomes are linked to surgical volume,1 despite the increase in TKA utilization, racial disparities in TKA outcomes persist. Blacks in the US are at a higher risk of aseptic revision of TKA (R-TKA) when compared to Whites, yet the reasons for this are not understood.

Objectives:

The objective of this study is to examine the relationship between hospital and surgeon annual TKA volume and R-TKA outcomes by race.

Methods:

This is an observational cohort study. New York Statewide Planning and Research Cooperative System data for 2004 – 2013 was used to identify patients who underwent primary TKA. Data through 2015 was used to identify R-TKA within 2 years of the index TKA. Hospital characteristics were obtained from the AHA Annual Survey. Surgeon data was collected from New York State Education Department and New York State Physician Profile. Surgeon annual TKA volume was categorized based on cutoffs established by Wilson et al1 as </=12, 13-59, 60-145 or >/= 146, and hospital TKA volume as </=89, 90-235, 236-644 and >/=645. We calculated the odds of R-TKA in Whites and Blacks separately and generated crude odds ratios (OR) comparing Blacks to Whites to examine trends across volume categories. A multivariable logistic regression model adjusted for known R-TKA risk factors was also performed.

Results:

A total of 163,576 patients were included. Mean (SD) age was 66.4 (10.4) years, 107,233 (65.6%) were female, 124,277 (76.6%) were White and 15,990 (9.8%) were Black. 2925 patients underwent aseptic R-TKA. In logistic regression analysis, Blacks had a higher risk of R-TKA (OR 1.42, 95%CI 1.26-1.6) (Table 1). Risk of R-TKA was also higher when surgeon annual volume was </=12 (OR 1.5, 95%CI 1.25-1.8) or 13-59 (OR 1.16, 95%CI 1.04-1.29) TKA compared to the highest volume surgeons (>/=146). Patients who had surgery at a hospital with annual volume of 236-634 TKA were less likely to undergo R-TKA compared to the highest volume hospitals (>/=645) (OR 0.88, 95%CI 0.79-0.98). Other risk factors for R-TKA were younger age and worker’s compensation, while patients with inflammatory arthritis had a lower risk. Figures 1A and 1B show the odds of R-TKA in Whites and Blacks, respectively, by hospital and surgeon volume. Figure 1C shows the crude OR for Blacks to Whites for each category pair. The OR ranged from 0.9 to 2.5, with the largest disparity found in patients who have TKA performed by surgeons with 60-145 annual TKA volume at the highest volume hospitals (>/=645).

Conclusion:

Patients having TKA by a surgeon performing <60 TKA per year have higher risk of R-TKA. Racial disparities in R-TKA risk are highest for TKA by surgeons performing 60-145 TKA per year at hospitals performing >/=645 TKA per year. Future studies should examine factors, such as whether trainees are involved the surgery, that may vary based on social determines of health, such as patient race and payor.

References:

[1]Wilson S. et al Meaningful thresholds for the volume-outcome relationship in total knee arthroplasty. Journal of bone and joint surgery. 2016;98:1683

Table 1.

Logistic regression of risk for R-TKA

Variable (reference)LevelOdds ratio95% CIp-valueAge--0.950.94-0.95<.001Sex (female)Male1.070.99-1.150.108Race (whiteAsian0.650.42-0.960.031Black1.421.26-1.6<.001Unknown0.810.64-1.020.07Other1.050.92-1.210.446Insurance (Medicare)Medicaid0.890.75-1.060.193Other0.890.7-1.130.331Private0.820.74-0.91<.001Work compensation1.561.35-1.8<.001Surgeon volume (>/=146)</=121.51.25-1.8<.00113-591.161.04-1.290.00660-1451.00.91-1.110.957Hospital volume (>/=645)</= 890.980.84-1.150.84890-2350.990.88-1.120.869236-6440.880.79-0.980.018Hospital bed size (>400 beds)6-1991.131.02-1.250.024200-3991.060.96-1.170.262

Other variables in model: diabetes, obesity, renal disease, COPD, osteoarthritis, osteonecrosis, dislocation, inflammatory arthritis, surgical complication, infection, no college, poverty >20%, years since residency, US/Canada medical school, orthopedic board certified, AHA control, teaching, rural hospital

Disclosure of Interests:

Serene Mirza: None declared, Susan Goodman: None declared, Yi Zhang: None declared, Huong Do: None declared, Bella Mehta: None declared, Stephen Lyman: None declared, Lisa A. Mandl: None declared, Mark Figgie: None declared, Michael Parks Consultant of: Zimmer biomet, Grant/research support from: Zimmer biomet, Linda Russell: None declared, Anne Bass: None declared

Physician engagement in regularly scheduled rounds

BACKGROUND

Physician participation in regularly scheduled series (RSS), also known as grand rounds, was explored with a particular focus on physician perceptions about the elements that affected their engagement in RSS and the unanticipated benefits to RSS.

METHODS

A qualitative study using semi-structured interviews and thematic analysis examined physicians' perception of their knowledge and educational needs and the factors that contributed to engagement in their local hospital RSS.

RESULTS

Physician engagement in RSS was affected by four major themes: Features that Affect the RSS' Quality; Collegial Interactions; Perceived Outcomes of RSS; and Barriers to participation in RSS. Features that Affect RSS' Quality were specific modifiable features that impacted the perceived quality of the RSS. Collegial Interactions were interactions that occurred between colleagues directly or indirectly as a result of attending RSS. Outcomes of RSS were specific outcome measures used in RSS sessions. Barriers were seen as reasons why physicians were unwilling or unable to participate in RSS. All of the elements identified within the four themes contributed to the development of physician engagement. Physicians also identified changes directly and indirectly due to RSS.

DISCUSSION

Specific features of RSS result in enhanced physician engagement. There are benefits that may not be accounted for in continuing medical education (CME) outcome study designs.

Mist1+ gastric isthmus stem cells are regulated by Wnt5a and expand in response to injury and inflammation in mice

BACKGROUND AND AIMS

The gastric epithelium undergoes continuous turnover. Corpus epithelial stem cells located in the gastric isthmus serve as a source of tissue self-renewal. We recently identified the transcription factor Mist1 as a marker for this corpus stem cell population that can give rise to cancer. The aim here was to investigate the regulation of the Mist1+ stem cells in the response to gastric injury and inflammation.

METHODS

We used Mist1CreERT;R26-Tdtomato mice in two models of injury and inflammation: the acetic acid-induced ulcer and infection with Helicobacter felis. We analysed lineage tracing at both early (7 to 30 days) and late (30 to 90 days) time points. Mist1CreERT;R26-Tdtomato;Lgr5DTR-eGFP mice were used to ablate the corpus basal Lgr5+ cell population. Constitutional and conditional Wnt5a knockout mice were used to investigate the role of Wnt5a in wound repair and lineage tracing from the Mist1+ stem cells.

RESULTS

In both models of gastric injury, Mist1+ isthmus stem cells more rapidly proliferate and trace entire gastric glands compared with the normal state. In regenerating tissue, the number of traced gastric chief cells was significantly reduced, and ablation of Lgr5+ chief cells did not affect Mist1-derived lineage tracing and tissue regeneration. Genetic deletion of Wnt5a impaired proliferation in the gastric isthmus and lineage tracing from Mist1+ stem cells. Similarly, depletion of innate lymphoid cells, the main source of Wnt5a, also resulted in reduced proliferation and Mist1+ isthmus cell tracing.

CONCLUSION

Gastric Mist1+ isthmus cells are the main supplier of regenerated glands and are activated in part through Wnt5a pathway.

Abstract PO-093: Evaluating dependencies by rapid image-based ex vivo cancer biosensors

Successful mapping of cancer dependencies requires conducting genetic and drug screens on a diversity of models. However, the difficulty in generating long-term models of many cancers limits the share of patient samples that can be studied. Such long-term models have likely also lost the cellular heterogeneity present in the original tumor due to in vitro propagation. To overcome these limitations, we are developing image-based ex vivo cancer biosensors from early patient material. Using freshly received gastroesophageal cancer ascites, we are optimizing perturbation methods and utilizing single-cell transcriptomics and label-free microscopy to infer a subpopulation-specific vulnerability profile. We show that label-free microscopy can infer cell identity and viability in heterogeneous early patient samples. Additionally, early drug perturbation recapitulates observations made in established gastroesophageal cancer organoids. Successful implementation of ex vivo biosensors will expand the cancer dependency space by making perturbational studies accessible to more diverse samples, and by identifying and validating hits in a more immediate setting to the original tumor.

Citation Format: Mushriq Al-Jazrawe, Csaba Molnar, Niklas Rindtorff, Pinar Eser, Sean Misek, Maria Alimova, Oana Ursu, William Colgan, Adel Attari, Natalie Tsang, Paula Keskula, Carmen Rios, Moony Tseng, Anne Carpenter, James McFarland, Adam Bass, Samuel Klempner, Jesse Boehm. Evaluating dependencies by rapid image-based ex vivo cancer biosensors [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-093.

Rab11-FIP1 mediates epithelial-mesenchymal transition and invasion in esophageal cancer

Esophageal squamous cell carcinoma (ESCC) is the most common subtype of esophageal cancer worldwide. The most commonly mutated gene in ESCC is TP53. Using a combinatorial genetic and carcinogenic approach, we generate a novel mouse model of ESCC expressing either mutant or null p53 and show that mutant p53 exhibits enhanced tumorigenic properties and displays a distinct genomic profile. Through RNA-seq analysis, we identify several endocytic recycling genes, including Rab Coupling Protein (Rab11-FIP1), which are significantly downregulated in mutant p53 tumor cells. In 3-dimensional (3D) organoid models, genetic knockdown of Rab11-FIP1 results in increased organoid size. Loss of Rab11-FIP1 increases tumor cell invasion in part through mutant p53 but also in an independent manner. Furthermore, loss of Rab11-FIP1 in human ESCC cell lines decreases E-cadherin expression and increases mesenchymal lineage-specific markers, suggesting induction of epithelial-mesenchymal transition (EMT). Rab11-FIP1 regulates EMT through direct inhibition of Zeb1, a key EMT transcriptional factor. Our novel findings reveal that Rab11-FIP1 regulates organoid formation, tumor cell invasion, and EMT.

Abstract 3453: Cancer Cell Line Factory: A systematic approach to create next-generation cancer model at scale

Precision cancer medicine is based on the ability to predict the dependencies of a given tumor from its molecular makeup. Despite successes in multiple common cancers, such prediction remains challenging for the majority of rare and understudied tumors given the absence of laboratory model systems in which to discover and/or validate therapeutic hypotheses. Here, we describe our efforts to address this challenge systematically with the ultimate goal of making it possible to learn how to predict ex vivo growth requirements for cancer samples based on technical, clinical and genomic properties of the starting tumor material. Over the last 5 years, we have processed nearly 2,000 tumor biospecimens and created over 375 genomically-confirmed patient-derived cell lines, organoids and neurosphere cultures, with &gt;10% of these representing rare cancers. To make this possible, we have implemented three key workflows including (1) direct-to-patient sample sourcing, (2) a tissue cryopreservation and genomic credentialing system to ensure quality prior to model creation, and (3) a systematic empirical approach to screening rich medias and variations on organoid technologies ex vivo (HYBRID). We have begun performing genome-wide CRISPR viability screens in these cultures as part of our larger activities to generate a systematic laboratory-based functional map of cancer dependencies (a ‘Cancer Dependency Map'). The novel organoid, spheroid and cell line models created as part of this effort are being made publically available to the scientific community. Looking ahead, as the barriers to culturing rare tumors are overcome, we expect that preclinical functional genomics data will be useful for difficult-to-treat tumors without existing molecularly guided standard-of-care regimens.

Citation Format: Yuen-Yi Tseng, Mushriq AI-Jazrawe, Rebecca Deasy, Paula Keskula, Grace Johnson, Andrew Hong, Priya Chatterji, Francisca Vasquez, Adam Bass, Barbara Van Hare, David Sandak, Keith Ligon, Jesse Boehm. Cancer Cell Line Factory: A systematic approach to create next-generation cancer model at scale [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 3453.

Abstract PR09: A systematic approach to create patient-derived models of rare tumors

Precision cancer medicine is based on the ability to predict the dependencies of a given tumor from its molecular makeup. Despite successes in multiple common cancers, such prediction remains challenging for the majority of rare and understudied tumors, given the absence of laboratory model systems in which to discover and/or validate therapeutic hypotheses. Here, we describe our efforts to address this challenge systematically with the ultimate goal of making it possible to learn how to predict ex vivo growth requirements for cancer samples based on technical, clinical, and genomic properties of the starting tumor material. Over the last 5 years, we have processed nearly 2,000 tumor biospecimens and created over 375 genomically confirmed patient-derived cell lines, organoids, and neurosphere cultures, with &gt;10% of these representing rare cancers. To make this possible, we have implemented three key workflows including (1) direct-to-patient sample sourcing, (2) a tissue cryopreservation and genomic credentialing system to ensure quality prior to model creation, and (3) a systematic empirical approach to screening rich media and variations on organoid technologies ex vivo (HYBRID). We have begun performing genome-wide CRISPR viability screens in these cultures as part of our larger activities to generate a systematic laboratory-based functional map of cancer dependencies (a “Cancer Dependency Map”). The novel organoid, spheroid, and cell line models created as part of this effort are being made publicly available to the scientific community. Looking ahead, as the barriers to culturing rare tumors are overcome, we expect that preclinical functional genomics data will be useful for difficult-to-treat tumors without existing molecularly guided standard-of-care regimens.

This abstract is also being presented as Poster A06.

Citation Format: Yuen-Yi Tseng, Paula Keskula, Rebecca Deasy, Andrew Hong, Priya Chatterji, Francisca Vazquez, Adam Bass, Barbara Van Hare, David Sandak, Keith Ligon, Jesse Boehm. A systematic approach to create patient-derived models of rare tumors [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR09.

OP0328 A UNIQUE PD1+CD38+ CD8+ T CELL POPULATION CHARACTERIZES CHECKPOINT INHIBITOR-ASSOCIATED INFLAMMATORY ARTHRITIS

Background:

Immune checkpoint inhibitors (CI) are monoclonal antibodies that block CTLA-4, PD-1 or PD-L1, resulting in cytotoxic T cell activation in the tumor microenvironment. They have revolutionized the management of metastatic cancer but unleash “immune related adverse events” in > 80% of treated patients, including inflammatory arthritis in ~4%1. CI-associated arthritis (CI-A) often presents as a symmetrical polyarthritis, phenotypically indistinguishable from rheumatoid arthritis (RA), but whether it shares cellular and molecular features of RA has not been determined.

Objectives:

To compare synovial fluid (SF) T cell populations from CI-A patients to those in patients with RA, phenotypically and functionally.

Methods:

We immunophenotyped SF mononuclear cells from patients with CI-A caused by anti-PD-(L)1 therapy (n=9), seropositive RA (n=5), and psoriatic arthritis (PsA) (n=5) using a 39-marker mass cytometry (CyTOF) panel. FlowSOM was used to cluster CD4 and CD8 T cells into 15 ‘metaclusters’ based on multidimensional phenotypes. We used Kruskal-Wallis or Mann-Whitney tests to identify significantly altered populations (p<0.05), which we confirmed by biaxial gating. Flow cytometry was used to confirm SF findings in an independent cohort, and to identify cells of interest in peripheral blood. Cytokine staining was performed on sorted T cells populations after CDCD3/CD28 stimulation for 72 hours, followed by 4 hour PMA/ION+BRA/MON restimulation.

Results:

In CI-A patients, T cells represented 50% of SF mononuclear cells (53% CD4, 40% CD8), followed by monocytes (24%) and NK cells (8%), comparable to RA and PsA. However, FlowSOM analysis revealed expansion of a distinct population of PD-1+CD38hiCD127-CD8 T cells (CD8 metacluster2) (Fig. 1). These cells comprised 30% of CD8+ SF T cells in CI-A, a 3.4-fold increase over RA/PsA, p=0.0002 (Fig. 2). Over 40% of these cells expressed Ki67 in CI-A, suggesting active proliferation. Flow cytometry on SF cells from an independent cohort of CI-A patients (n= 5) and RA/PsA comparators (n= 9) confirmed our findings. PD-1+CD38hiCD127-CD8 T cells were also expanded in the blood of CI-A patients, where they represented 4.6% of CD8 Tcells, a 2.8-fold increase over RA, p = 0.0057. In addition to expressing high levels of PD-1, CD38hiCD127-, these CD8 T cells express other immune checkpoint receptors including ICOS and TIGIT. After in vitro stimulation, CD38hiCD127-CD8 T cells produced granzyme B along with TNF and IFN-γ at comparable levels to other CD8 populations, suggesting that they are not functionally exhausted.

Figure 1.

Mass cytometry CD8+T cells (tSNE plots) with FlowSOM metaclusters.

Figure 2.

Synovial fluid PD-1+CD38hiCD127-CD8+T cells

FlowSOM analysis of SF CD4 T cells in CI-A patients revealed the expansion of a subpopulation of CD4 cells with a similar surface phenotype of PD-1+CD38hiCD127-(metacluster2, 10% of CD4s in CI-A, a 2.4-fold increase over RA/PsA, p=0.0047). In contrast, RA patients had a significantly expanded population of PD-1hiICOS+ CD4 T peripheral helper (Tph) cells (metacluster5, 30% of CD4s in RA, p=0.006), but these cells were not expanded in CI-A (Fig 3).

Figure 3.

Synovial fluid CD4+T peripheral helper cells

Conclusion:

CyTOF analysis of SF revealed a uniquely expanded PD-1+CD38hiCD127-CD8 T cell population in CI-A not present in RA or PsA, and a similar PD-1+CD38hiCD127-CD4 T cell population. These cells may contribute to the amplified immune response seen in CI-A patients. Further functional and transcriptional analysis of these cells will help to elucidate their function may reveal key mechanisms driving CI-associated immune related adverse events.

References:

[1]Kostine M. Ann Rheum Dis 2018;77(3):393-398

Disclosure of Interests:

Runci Wang: None declared, Karmela Kim Chan: None declared, Amy Cunningham-Bussel: None declared, Laura Donlin Consultant of: Consultant – Genentech/Roche, Gregory Vitone: None declared, Aidan Tirpack: None declared, Caroline Benson: None declared, Gregory Keras: None declared, A. Helena Jonsson: None declared, Michael Brenner: None declared, Anne Bass: None declared, Deepak Rao Grant/research support from: Has received research grant support from Celgene and Merck., Consultant of: Has received consulting fees or honoraria from Merck, Pfizer, GlaxoSmithKine, Bristol-Myers Squibb, Janssen, and Scipher Medicine

Incidental bilateral calcaneal fractures following overground walking with a wearable robotic exoskeleton in a wheelchair user with a chronic spinal cord injury: is zero risk possible?

Many individuals with spinal cord injury (SCI) rely on wheelchairs as their primary mode of locomotion leading to reduced weight-bearing on the lower extremities, which contributes to severe bone loss and increased risk of fragility fractures. Engaging in a walking program may reverse this vicious cycle, as this promotes lower extremity weight-bearing and mobility, which may reduce bone loss and fragility fracture risk. However, fragility fracture risk associated with the use of wearable robotic exoskeletons (WREs) in individuals with SCI needs consideration. A 35-year-old man with chronic complete sensorimotor SCI (neurological level = T₆) and low initial bone mineral density enrolled in a 6- to 8-week WRE-assisted walking program after successfully completing an initial clinical screening process and two familiarization sessions with the WRE. However, after the first training session with the WRE, he developed bilateral localized ankle edema. Training was suspended, and a CT-scan revealed bilateral calcaneal fractures, which healed with conservative treatment over a 12-week period. Opportunities for improving clinical screening and WRE design are explored. The relevance of developing clinical practice guidelines for safe initiation and progression of intensity during WRE-assisted walking programs is highlighted. This case of bilateral calcaneal fractures illustrates that aiming for "zero risk" during WRE-assisted walking programs may not be realistic. Although WREs are a relatively new technology, current evidence confirms their potential to greatly improve health and quality of life in individuals with chronic SCI. Hence, ensuring their safe use remains a key priority.

Abstract C130: Precision oncology decision support within the Gastrointestinal Cancer Center at Dana-Farber Cancer Institute (GI TARGET)

Precision oncology is fast becoming the new paradigm for cancer treatment. This approach involves molecular profiling of patient tumors and tailoring of a treatment regimen based on the unique combination of targetable alterations identified therein. At Dana-Farber Cancer Institute (DFCI), over 24,000 patient tumors have been sequenced using the NGS platform OncoPanel since 2013. OncoPanel is a comprehensive genomic characterization of a tumor and it can be time-consuming to discern those alterations that are interesting from an academic or research perspective from those that can be leveraged to direct patient care. To address this issue, the GI TARGET (Treatment Assistance Regarding Genomic Evaluation of Tumors) project was initiated to provide decision support for oncologists within the DFCI Gastrointestinal Cancer Center (GCC). GI TARGET is a collaboration between the DFCI GCC, the Brigham & Women’s Hospital (BWH) Center for Advanced Molecular Diagnostics (CAMD), and the DFCI Knowledge Systems Group, developers of the precision medicine clinical trial matching platform MatchMiner. Report generation involves review of OncoPanel data in the context of patient clinical history via one of two workflows; complex genomic cases are reviewed in a weekly Molecular Tumor Board comprised of oncologists, molecular pathologists, a PhD-level Clinical Genomics Scientist, and representatives from the MatchMiner team, while ‘simple’ genomic cases are reviewed by both an oncologist and a PhD-level Clinical Genomics Scientist. Since the launch of the project in January 2018, we have signed out over 1000 GI TARGET reports. We are assessing the utility of these reports using a number of metrics including clinical trial enrollment tracking via MatchMiner, follow-up on recommendations via chart abstraction, and oncologist feedback. The aims of GI TARGET are 1) to reduce the burden of genomic analysis on the treating oncologist by providing expert-led deep review of OncoPanel and exploration of associated therapy/additional patient care considerations, 2) to support clinical trial enrollment by matching the results of somatic testing with ongoing clinical studies, and 3) to provide an example framework for how precision oncology can be incorporated into standard clinical cancer care, which may be helpful to guide efforts in other care settings, particularly in community hospitals where the vast majority (an estimated 80%-85%) of cancer patients in the United States receive their care.

Citation Format: Rachel B Keller, Tali Mazor, Marios Giannakis, Jonathan Nowak, Lynette Sholl, Andrew Aguirre, Adam Bass, Nilay Sethi, Ankur Nagaraja, Lauren Brais, Emma Reilly, Ethan Cerami, Brian Wolpin. Precision oncology decision support within the Gastrointestinal Cancer Center at Dana-Farber Cancer Institute (GI TARGET) [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C130. doi:10.1158/1535-7163.TARG-19-C130

Colorectal adenocarcinoma-derived EGFR mutants are oncogenic and sensitive to EGFR-targeted monoclonal antibodies, cetuximab and panitumumab

Somatic mutations of epidermal growth factor receptor (EGFR) occur in ~3% of colorectal cancer (CRC) patients. Here, through systematic functional screening of 21 recurrent EGFR mutations selected from public data sets, we show that 11 colon cancer-derived EGFR mutants (G63R, E114K, R165Q, R222C, S492R, P596L, K708R, E709K, G719S, G724S and L858R) are oncogenic and able to transform cells in a ligand-independent manner. We demonstrate that cellular transformation by these mutants requires receptor dimerization. Importantly, the EGF-induced and constitutive oncogenic potential of these EGFR mutants are inhibited by cetuximab or panitumumab in vivo and in vitro. Taken together, we propose that a subset of EGFR mutations can serve as genomic predictors for response to anti-EGFR antibodies and that metastatic CRC patients with such mutations may benefit from these drugs as part of the first-line therapy.

Subtypes of Barrett's oesophagus and oesophageal adenocarcinoma based on genome-wide methylation analysis

OBJECTIVE

To identify and characterise DNA methylation subtypes in oesophageal adenocarcinoma (EAC) and its precursor Barrett's oesophagus (BE).

DESIGN

We performed genome-wide DNA methylation profiling on samples of non-dysplastic BE from cancer-free patients (n=59), EAC (n=23), normal squamous oesophagus (n=33) and normal fundus (n=9), and identified methylation subtypes using a recursively partitioned mixture model. We assessed genomic alterations for 9 BE and 22 EAC samples with massively parallel sequencing of 243 EAC-associated genes, and we conducted integrative analyses with transcriptome data to identify epigenetically repressed genes. We also carried out in vitro experiments treating EAC cell lines with 5-Aza-2'-Deoxycytidine (5-Aza-dC), short hairpin RNA knockdown and anticancer therapies.

RESULTS

We identified and validated four methylation subtypes of EAC and BE. The high methylator subtype (HM) of EAC had the greatest number of activating events in ERBB2 (p<0.05, Student's t-test) and the highest global mutation load (p<0.05, Fisher's exact test). PTPN13 was silenced by aberrant methylation in the HM subtype preferentially and in 57% of EACs overall. In EAC cell lines, 5-Aza-dC treatment restored PTPN13 expression and significantly decreased its promoter methylation in HM cell lines (p<0.05, Welch's t-test). Inhibition of PTPN13 expression in the SK-GT-4 EAC cell line promoted proliferation, colony formation and migration, and increased phosphorylation in ERBB2/EGFR/Src kinase pathways. Finally, EAC cell lines showed subtype-specific responses to topotecan, SN-38 and palbociclib treatment.

CONCLUSIONS

We identified and characterised methylator subtypes in BE and EAC. We further demonstrated the biological and clinical relevance of EAC methylator subtypes, which may ultimately help guide clinical management of patients with EAC.

Abstract 1228: Comparative genomic analysis of young-onset and late-onset colorectal cancer

Background: Young-onset colorectal cancer, the majority of which are sporadic, may have distinct molecular characteristics and etiologies. However, thus far, the genomic landscape of young-onset CRCs has remained largely uncharacterized. This study aimed to compare somatic mutation differences between young-onset and late-onset CRCs using the AACR GENIE data, a consortium of patients treated at 8 global cancer centers. Methods: Clinical and DNA mutation data on 2,081 CRC samples were downloaded from Sage Bionetworks (Synapse ID: syn7222066). A total of 162 samples from CRC patients who had more than one samples or were likely to have Lynch syndrome were excluded. Young-onset CRCs were defined as cancers arising at age &lt;50 years old while late-onset CRCs were defined as cancers arising at age ≥50 years old. Mutation rate per megabase (Mb) was calculated for each CRC and compared between groups by Wilcoxon rank sum test. The mutation frequency of each gene in young-onset and late-onset CRC was calculated separately for primary CRCs and metastatic CRCs. Mutation frequency differences between young- vs late-onset CRCs were tested by the Fisher's exact test with significance defined at the 5% alpha level. Results: Mutation data on 613 genes were analyzed on 955 primary and 676 metastatic CRCs. Overall, the most frequently mutated genes with a &gt;10% mutation frequency include: TP53 (66.86%), APC (59.46%), KRAS (47.42%), PIK3CA (18.40%), SMAD4 (12.71%) and BRAF (10.06%). The metastatic CRCs were on average slightly older than primary CRCs (mean age=56.96 vs. 55.90, two sample t test P=0.09). Comparing gene mutation between 300 young-onset versus 655 late-onset primary CRCs, mutation rate per Mb was slightly but not significantly higher in the latter (median=3.74 vs. 4.14, P=0.2199). DOT1L (9.82% vs. 1.95%, P=0.0014), IGF1R (6.12% vs. 1.72%, P=0.0057), BRCA1 (5.61% vs. 1.47%, P=0.0069), JUN (6.25% vs. 1.17%, P=0.0104), PTCH1 (7.14% vs. 2.7%, P=0.0151), TSHR (5.36% vs. 1.17%, P=0.0253), EIF1AX (3.06% vs. 0%, P=0.02811), JAK2 (2.0% vs. 0.46%, P=0.0311), EP300 (8.67% vs. 4.41%, P=0.0414), PHOX2B (2.20% vs. 0.27%, P=0.0419), SMC1A (3.57% vs. 0%, P=0.0446) and CSF1R (3.02% vs. 1.03%, P=0.0439) had a significantly higher mutation rate in the young-onset primary CRCs. Meanwhile, KRAS was mutated more frequently in late-onset primary CRCs (44.0% vs. 51.3%, P=0.03679). For metastatic CRCs, NTRK1 was found mutated in 12 (3.80%) out of 316 later-onset metastatic CRCs but none out of 129 young-onset metastatic CRCs (P=0.0223). Meanwhile, CIC was mutated in only 1 out of 103 young-onset metastatic CRCs but 17 (6.44%) out of 264 late-onset metastatic CRCs (P=0.0302) and TP53 had a nearly 8% higher mutation rate in young-onset metastatic CRCs (79.01% vs. 71.19%, P=0.0488). Conclusions: Mutation rates were found significantly higher in many genes among young-onset primary CRCs compared to late-onset primary CRCs.

Citation Format: Jingqin Luo, Marios Giannakis, Graham Colditz, Jean Wang, William Chapman, Adetunji T. Toriola, Yoshiko Mito, Reiko Nishihara, Jonathan Nowak, Charles Fuchs, Edward Giovannucci, Andrew T. Chan, Adam Bass, Shuji Ogino, Ryan Fields, Yin Cao. Comparative genomic analysis of young-onset and late-onset colorectal cancer [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 1228.

Abstract B38: In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis

In vivo interrogation of the function of genes implicated in tumorigenesis is limited by the need to generate and cross germline mutant mice. Here we describe approaches to model colorectal cancer (CRC) and metastasis that rely on in situ gene editing and orthotopic organoid transplantation in mice without cancer-predisposing mutations. Autochthonous tumor formation is induced by CRISPR/Cas9-based editing of the Apc and Trp53 tumor suppressor genes in colon epithelial cells and by orthotopic transplantation of Apc-edited colon organoids. ApcΔ/Δ;KrasG12D/+;Trp53Δ/Δ (AKP) mouse colon organoids and human CRC organoids engraft in the distal colon and metastasize to the liver. Finally, we apply the orthotopic transplantation model to characterize the clonal dynamics of Lgr5+ stem cells and demonstrate sequential activation of an oncogene in established colon adenomas. These experimental systems enable rapid in vivo characterization of cancer-associated genes and reproduce the entire spectrum of tumor progression and metastasis.

Citation Format: Jatin Roper, Tuomas Tammela, Naniye Malli Cetinbas, Adam Akkad, Ali Roghanian, Steffen Rickelt, Mohammad Almeqdadi, Katherine Wu, Matthias Oberli, Francisco Sánchez-Rivera, Yoona Park, Xu Liang, George Eng, Martin S. Taylor, Roxana Azimi, Dmitriy Kedrin, Rachit Neupane, Semir Beyaz, Ewa T. Sicinska, Yvelisse Suarez, James Yoo, Lillian Chen, Lawrence Zukerberg, Pekka Katajisto, Vikram Deshpande, Adam Bass, Philip N. Tsichlis, Jacqueline Lees, Robert Langer, Richard O. Hynes, Jianzhu Chen, Arjun J. Bhutkar, Tyler Jacks, Ömer H. Yilmaz. In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr B38.

Rituximab Treatment Prevents Lymphoma Onset in Gastric Cancer Patient-Derived Xenografts

Patient-Derived Xenografts (PDXs), entailing implantation of cancer specimens in immunocompromised mice, are emerging as a valuable translational model that could help validate biologically relevant targets and assist the clinical development of novel therapeutic strategies for gastric cancer.

More than 30% of PDXs generated from gastric carcinoma samples developed human B-cell lymphomas instead of gastric cancer. These lymphomas were monoclonal, Epstein Barr Virus (EBV) positive, originated tumorigenic cell cultures and displayed a mutational burden and an expression profile distinct from gastric adenocarcinomas. The ability of grafted samples to develop lymphomas did not correlate with patient outcome, nor with the histotype, the lymphocyte infiltration level, or the EBV status of the original gastric tumor, impeding from foreseeing lymphoma onset. Interestingly, lymphoma development was significantly more frequent when primary rather than metastatic samples were grafted.

Notably, the development of such lympho-proliferative disease could be prevented by a short rituximab treatment upon mice implant, without negatively affecting gastric carcinoma engraftment.

Due to the high frequency of human lymphoma onset, our data show that a careful histologic analysis is mandatory when generating gastric cancer PDXs. Such care would avoid misleading results that could occur if testing of putative gastric cancer therapies is performed in lymphoma PDXs. We propose rituximab treatment of mice to prevent lymphoma development in PDX models, averting the loss of human-derived samples.

Abstract A02: Expanding tumor chemical-genetic interaction map using next-generation cancer models

The development of new cancer therapeutics requires sufficient genetic and phenotypic diversity of cancer models. Current collections of human cancer cell lines are limited and for many rare cancer types, zero models exist that are broadly available. Here, we report results from the pilot phase of the Cancer Cell Line Factory (CCLF) project that aims to overcome this obstacle by systematically creating next-generation in vitro cancer models from adult and pediatric cancer patients' specimens and making these models broadly available.

We first developed a workflow of laboratory, genomics and informatics tools that make it possible to systematically compare published ex vivo culture conditions for each individual tumor to enable the scientific community to iterate towards disease-specific culture recipes. Based on sample volume and rarity, 4-100 conditions were applied to each sample and all data was captured in a custom Laboratory Information Management System to enhance subsequent predictions. We developed a $150, 5-day turnaround genomics panel to validate cultures based on genomics. Importantly, we show that tumor genomics can be retained in such patient-derived models and tumor genomics are generally stable across 20 passages. Since the inception of this project, we have processed over 600 patient cancer specimens from 450 patients across 16 tumor types and report the successful generation of over 100 genomically characterized adult and pediatric cancer and normal models.

We next hypothesized that novel patient-derived cell models could be used to enhance dependency predictions. To do so, we tested 72 cell lines against the informer set of 440 compounds developed by the Broad Cancer Target Discovery and Development (CTD2) Center. We show that generating cell lines and testing their sensitivities within 3 months is feasible and the high-throughput drug responses are reproducible. Moreover, to strengthen relationships between drug sensitivities and cellular features, we compared results with recently published data on the identical compounds tested against 860 existing cell lines. With this approach, we show that many chemical-genetic interaction vulnerabilities can be rapidly assessed. Importantly, adding more cancer models with the dimensions of quantity and diversity increases the predictive power of chemical-genetic interaction map. We are currently evaluating these drug sensitivity predictors for novel co-dependencies. Overall, our proof-of-concept framework demonstrates initial feasibility of rapidly generating cancer models at scale and expanding the chemical-genetic interaction map to identify new cancer vulnerability.

Citation Format: Yuen-Yi (Moony) Tseng, Andrew Hong, Shubhroz Gill, Paula Keskula, Srivatsan Raghavan, Jaime Cheah, Aviad Tsherniak, Francisca Vazquez, Sahar Alkhairy, Anson Peng, Abeer Sayeed, Rebecca Deasy, Peter Ronning, Philip Kantoff, Levi Garraway, Mark Rubin, Calvin Kuo, Sidharth Puram, Adi Gazdar, Nikhil Wagle, Adam Bass, Keith Ligon, Katherine Janeway, David Root, Stuart Schreiber, Paul Clemons, Todd Golub, William Hahn, Jesse Boehm. Expanding tumor chemical-genetic interaction map using next-generation cancer models [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr A02.

Abstract LB-280: The landscape of somatic microsatellite indels across cancer: detection and identification of driver events

Microsatellites (MSs) are tracts of variable-length repeats of short DNA motifs that are abundant in the human genome and exhibit high rates of mutations in the form of insertions or deletions of the repeated motif (MS indels). Despite their prevalence, the contribution of somatic MS indels to cancer is largely unexplored due to difficulties in detecting them and assessing their significance. Here, we present a comprehensive analysis of MS indels across 20 tumor types. We characterize the overall MS indel landscape and detect genes with candidate driver MS indel events. We present two novel tools: MSMuTect for accurate detection of somatic MS indels and MSMutSig for identifying candidate cancer genes containing events at higher frequency than expected by chance. We observe high variability of the frequency of MS indels across tumors and demonstrate that the number and pattern of MS indels can accurately distinguish microsatellite stable (MSS) tumors from tumors with microsatellite instability (MSI). Applying MSMutSig across 6,788 tumors from 20 different tumor types identified 7 genes with significant MS indel hotspots: ACVR2A, RNF43, DOCK3, MSH3, ESRP1, PRDM2 and JAK1. In the four genes that have been previously implicated in cancer (ACVR2A, RNF43, JAK1 and MSH3), we identified previously unreported MS indels events. Three of the genes with significant loci - DOCK3, PRDM2 and ESRP1- had not been previously listed as cancer genes. MS indels in DOCK3, a negative regulator of the WNT pathway, were mutually exclusive with mutations in CTNNB1. MS indels in ESRP1, an RNA processing gene, correlated with alternative splicing of FGFR2, an event associated with the epithelial-to-mesenchymal transition. Overall, our comprehensive analysis of somatic MS indels across cancer highlights their importance, particularly in

MSI tumors, significantly contributes to the ongoing global efforts to detect cancer genes, and may improve classification of patients into clinically-relevant subgroups.

Citation Format: Yosef E. Maruvka, Kent W. Mouw, Rosa Karlic, Rasanna Parasuraman, Atanas Kamburov, Paz Polak, Nicholas J. Haradhvala, Julian M. Hess, Esther Rheinbay, Yehuda Brody, Lior Z. Braunstein, Alan D’Andrea, Michael S. Lawrence, Adam Bass, Andre Bernards, Franziska Michor, Gad Getz. The landscape of somatic microsatellite indels across cancer: detection and identification of driver events [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-280. doi:10.1158/1538-7445.AM2017-LB-280

Abstract 1953: Accelerating prediction of pediatric and rare cancer vulnerabilities using next-generation cancer models

Ongoing pre-clinical efforts aim to deploy genome-scale CRISPR/Cas9 technology and large collections of small molecules to catalog maps of cancer vulnerabilities at scale. However, such efforts in pediatric and rare cancers have lagged behind comparable efforts in more common cancer types due to the dearth of cell models. Here, we present an update from our “Cancer Cell Line Factory” project on efforts to overcome key laboratory and biologistics challenges precluding progress in pediatric and rare cancers. This effort, now in it’s 3rd year, represents an industry scale pipeline aiming to generate, characterize and share novel cancer models of many tumor types with the scientific community. Overall, we have processed 1153 samples from 818 patients across over 16 cancer types through this pipeline with a 28% success rate overall, including over 350 patient samples from rare and pediatric cancers. To optimize conditions for each tumor type, we have systematically compared published methods including (1) next-generation 2-dimension, (2) organoid and (3) standard approaches and have captured all information with a data management system that should enhance the ability to predict optimal ex vivo propagation conditions for future samples. Among the successful cell models verified already as part of this effort, we have generated a series of over 30 unique pediatric and rare cancer models, many of which represent the first of their kind. We screened these and other models against a library of highly annotated 440 small molecules that were previously tested against 860 existing cancer cell lines. Our results suggest that dependency data generated with novel next-generation cell cultures is potentially backwards-compatible with existing small molecule dependency datasets. Furthermore, we tested the novel Broad Institute Drug Repurposing library consisting of 4100 approved therapeutics, or those under investigation for any disease, against the first cell line models of several of these rare next generation models including angioimmunoblastic T-cell lymphoma and renal medullary carcinoma, leading to several novel drug repurposing hypotheses for rare cancers. Given these proof-of-concept studies, in partnership with the Rare Cancer Research Foundation, we launched an online matchmaking platform to connect patients with rare cancers to available research studies, facilitate online consent and provide biologistics support to enable fresh tissue donation to support cancer model generation from any clinical site in the United States. We will present results from this novel direct-to-patient approach to facilitate the generation of even larger numbers of next generation models from rare and pediatric cancers, propelling the generation of pre-clinical dependency maps of these tumors for the scientific community.

Citation Format: Yuen-Yi Tseng, Andrew Hong, Paula Keskula, Shubhroz Gill, Jaime Cheah, Grigoriy Kryukov, Aviad Tsherniak, Francisca Vazquez, Glenn Cowley, Sahar Alkhairy, Coyin Oh, Anson Peng, Rebecca Deasy, Abeer Sayeed, Peter Ronning, Samuel Ng, Steven Corsello, Corrie Painter, David Sandak, Levi Garraway, Mark Rubin, Calvin Kuo, Sidharth Puram, David Weinstock, Adam Bass, Nikhil Wagle, Keith Ligon, Katherine Janeway, David Root, Stuart Schreiber, Paul Clemons, Aly Shamji, Aly Shamji, William Hahn, Todd Golub, Jesse Boehm. Accelerating prediction of pediatric and rare cancer vulnerabilities using next-generation cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1953. doi:10.1158/1538-7445.AM2017-1953

Abstract 3851: Targeting HER2 in gastric cancer: Hints from a gastric PDX platform

Introduction: Gastric cancer is the 3rd leading cause of cancer mortality worldwide. Surgery is the only curative treatment strategy and conventional chemotherapy has shown limited efficacy. Trastuzumab (a HER2 mAb), is the only therapy targeting molecular alterations approved so far in gastric cancer, for HER2+ patients with advanced disease. However only a fraction (&lt;20%) of HER2 amplified patients benefits from treatment.

Methods: We have recently generated a molecularly annotated colony of gastro-esophageal PDXs (at the moment, &gt; 70 PDXs). The platform also comprises primary cell lines and 3D-cultured organoids derived from gastric cancer PDXs.

Results and Discussion: At present, we have identified several HER2+ PDXs and generated the corresponding in vitro derivatives. Four HER2+ PDXs, showing 3+ HercepTest score and HER2 amplification &gt; 8 copies (thus theoretically sensitive to Trastuzumab), were selected to undergo ‘xenotrials’ with the following anti-HER2 drugs/combos: Trastuzumab (T); Pertuzumab (P, anti-HER2 mAb); Lapatinib (L, a dual HER2-EGFR tyrosine kinase inhibitor). According to RECIST-like criteria, T induced tumor regression in only 1 out of 4 HER2+ PDXs. Interestingly, in all the tumors but one the combos T+P and T+L were able to bypass resistance to T monotherapy and to induce tumor regression. One tumor was resistant to all the tested therapeutic approaches.

Conclusion: We identified PDXs displaying HER2 gene amplification. Only a minor fraction of them benefited from the anti-HER2 mono-therapy, despite the presence of a strong HER2 gene amplification, while the association of two HER2 inhibiting drugs resulted in intense and prolonged response. This suggests that monotherapy with T might not be the most effective therapeutic approach in gastric cancer patients. We are currently investigating the cause of resistance to anti-HER2 drugs to identify mutations/CNV in tumors showing resistance to Trastuzumab.

Note: This abstract was not presented at the meeting.

Citation Format: Simona Corso, Cristina Migliore, Maria Apicella, Silvia Menegon, Eirini Pectasides, Tania Capeloa, Stefania Durando, Marilisa Cargnelutti, Paola Cassoni, Anna Sapino, Maurizio de Giuli, Adam Bass, Silvia Giordano. Targeting HER2 in gastric cancer: Hints from a gastric PDX platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3851. doi:10.1158/1538-7445.AM2017-3851

The effect of white coats and gender on medical students' perceptions of physicians

BACKGROUND

Despite the fact that medical schools spend a considerable effort to rate clinical instructors, there is limited evidence regarding the effect of physical characteristics on instructor ratings. White coats have been shown to alter patients' perceptions of physicians although it has not been determined if preceptors who wear white coats are rated differently than their colleagues.

METHODS

Second year medical students were administered a questionnaire with four clinical scenarios depicting medical errors accompanied by a picture of a physician of different sexes and ethnicities. The packages were randomized so that the physicians depicted either had or did not have a white coat.

RESULTS

White coats did not alter the perception of physicians' ratings by medical students although sex and ethnicity/case were associated with the perception of trustworthiness, physician management, competence, professionalism and the perception of medical error.

CONCLUSIONS

Physical characteristics may alter students' ratings of physicians.

Abstract B26: Accelerating prediction of tumor vulnerabilities using next-generation cancer models

The development of new cancer therapeutics requires sufficient genetic and phenotypic diversity of cancer models. Current collections of human cancer cell lines are limited and for many rare cancer types, zero models exist that are broadly available. Here, we report results from the pilot phase of the Cancer Cell Line Factory (CCLF) project that aims to overcome this obstacle by systematically creating next-generation in vitro cancer models from adult and pediatric cancer patients' specimens and making these models broadly available.

We first developed a workflow of laboratory, genomics and informatics tools that make it possible to systematically compare published ex vivo culture conditions for each individual tumor to enable the scientific community to iterate towards disease-specific culture recipes. Based on sample volume and rarity, 4-100 conditions were applied to each sample and all data was captured in a custom Laboratory Information Management System to enhance subsequent predictions. We developed a $150, 5-day turnaround genomics panel to validate cultures based on genomics. Importantly, we show that tumor genomics can be retained in such patient-derived models and tumor genomics are generally stable across 20 passages. Since the inception of this project, we have processed over 650 patient cancer specimens from 450 patients across 16 tumor types and report the successful generation of over 100 genomically characterized adult and pediatric cancer and normal models.

We next hypothesized that novel patient-derived cultures could be used to enhance dependency predictions. To do so, we tested 65 cell lines against the “informer” set of 440 compounds developed by the Broad Cancer Target Discovery and Development (CTD2) Center. We show that generating cell lines and testing their sensitivities within 3 months is feasible and the drug responses are reproducible. Moreover, to strengthen relationships between drug sensitivities and cellular features, we compared results with recently published data on the identical compounds tested against 860 existing cell lines. With this approach, we are able to identify many known drug dependencies in these novel models and exhibit the consistency sensitivities compared to existing cell lines. We are also evaluating drug sensitivity predictors for novel dependencies. Overall, our proof-of-concept framework demonstrates initial feasibility of rapidly generating cancer models and assessing drug sensitivities at scale.

Citation Format: Yuen-Yi Tseng, Paula Keskula, Andrew L. Hong, Shubhroz Gill, Jaime H. Cheah, Gregory V. Kryukov, Aviad Tsherniak, Francisca Vazquez, Glenn Cowley, Coyin Oh, Anson Peng, Abeer Sayeed, Rebecca Deasy, Peter Ronning, Philip Kantoff, Levi Garraway, Mark A. Rubin, Calvin Kuo, Sidharth Puram, Adi Gazdar, Filemon S. Dela Cruz, Jr., Adam Bass, Jr., Nikhil Wagle, Keith L. Ligon, Katherine Janeway, David Root, Stuart L. Schreiber, Paul A. Clemons, Aly Shamji, William C. Hahn, Todd R. Golub, Jesse S. Boehm. Accelerating prediction of tumor vulnerabilities using next-generation cancer models. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B26.

Abstract 2780: Genome-wide methylation analysis reveals methylator subtypes of Barrett's esophagus and esophageal adenocarcinoma

Esophageal adenocarcinoma (EAC) arises from Barrett's Esophagus (BE) through a progression sequence driven by the accumulation of epi/genetic alterations. Genetic alterations and aberrantly methylated genes/loci, the best-characterized epigenetic alteration, vary among individual BE and EAC cases. To better understand the molecular heterogeneity in BE/ EAC, we analyzed genome-wide DNA methylation patterns in BE (N = 98), EAC (N = 23), and normal esophagus and stomach (N = 78) collected via Esophagus Translational Research Network (BETRNet) using Human Methylation 450K (HM450K) arrays. We identified methylation-based subtypes using a model-based recursively partitioned mixture model and unsupervised resampling-based hierarchical cluster analysis with the most variable probes based on standard deviation. All analyses were performed in R. Four methylator subtypes were identified in the BE/EAC dataset using our clustering approach: high (HM); intermediate (IM); low (LM); and minimal (MM). The clusters showed widespread methylation differences in CpGs primarily located in CpG islands (72% of 414 total probes). Each methylation subtype showed distinct genetic and clinical features suggesting underlying biological differences (Table 1). HM exhibited methylation patterns reminiscent of a CpG Island Methylator Phenotype (CIMP). Among BE/EAC cases with known TP53 mutation status, the majority of mutants were among HM and IM clusters (15/19, 78.9%), Finally, identification of methylation subtypes in an independent HM450K dataset of EAC samples (N = 89) from the Cancer Genome Atlas validated the existence of the BE/EAC methylation subtypes. In summary, our data suggest genome wide alterations in DNA methylation occur in the BE stage of the BE-to-EAC progression. We also identified four distinct methylation subtypes of BE/EAC, including a CIMP-like HM subtype, and found more TP53 mutants in the HM and IM subtypes, revealing molecular heterogeneity in different methylation subtypes. Table 1.Characteristics of primary BE/EAC dataset and subtypes from cluster analyses.Cluster CharacteristicSubtypesHigh N (%)Intermediate N (%)Low N (%)Minimal N (%)Total N (%)Case CountsTotal31 (26%)44 (36%)28 (23%)18 (23%)121 (100%)BE23 (23%)34 (35%)24 (24%)17 (17%)98 (100%)EAC8 (35%)10 (43%)4 (17%)1 (4%)23 (100%)Demographic VariablesGenderM28 (28%)35 (35%)23 (23%)14 (14%)100 (100%)GenderF3 (14%)9 (43%)5 (24%)4 (19%)21 (100%)Age (mean ± sd)68 ± 1163 ± 1361 ± 1461 ± 1064 ± 13TP53 Mutations***Mutation*6 (32%)9 (47%)4 (21%)0 (0%)19 (100%)WT6 (30%)8 (40%)5 (25%)1 (5%)20 (100%)Unknown1927191782*** Mutation categories included: Frame Shift Deletion; In Frame Insertion; In Frame Deletion; Missense Mutation; Nonsense Mutation; and Splice Site

Citation Format: Ming Yu, Sean Maden, Andrew Kaz, Tai Heinzerling, Rachele O’Leary, Matthew Stachler, Adam Bass, Amitabh Chak, Joseph Willis, Sanford Markowitz, William Grady. Genome-wide methylation analysis reveals methylator subtypes of Barrett's esophagus and esophageal adenocarcinoma. [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 2780.

Abstract 4367: Accelerating prediction of tumor vulnerabilities using next-generation cancer models

The mapping of cancer genomes is rapidly approaching completion. The genomic information encoded by individual patients’ tumors should, in principle, provide a guide for predicting dependencies, but our ability to do so is suboptimal. The challenge stems from the absence of clinical data relating genotypes with dependencies since most cancer mutations are rare and our arsenal of cancer drugs is incomplete. If it was possible to build a preclinical ‘cancer dependency map’ at a scale that captured the genomic diversity of cancer (for instance, models of all genotypes tested for genetic and small-molecule dependencies), it should be feasible to improve dependency predictions. New technologies (e.g. CRISPR/Cas9 libraries) make such an effort now feasible. However, we lack a sufficient diversity of cancer models derived directly from patient samples to reflect the genetic diversity of cancer and the ability to systematically create functional data for each cancer patient to expand the map.

In an attempt to overcome these obstacles, we have established an industry-scale pipeline to generate new cancer models directly from patient samples, a “Cancer Cell Line Factory”. We have processed over 620 samples from 400 patients across 16 cancer types through this pipeline with a 25% success rate overall. To optimize conditions for each tumor type, we have systematically compared published cell line generation methods with standard approaches and captured all information with a data management system that will enhance the ability to predict optimal ex vivo propagation conditions for future samples. In all, we report the successful derivation of over 100 new genomically confirmed cancer and normal cell lines, including a series of unique pediatric cancer models derived from rare tumors.

We hypothesized that novel patient-derived cultures could be used to enhance dependency predictions. To test this hypothesis, we tested dependencies of 65 of these novel cultures against an identical set of 440 small molecules that were previously tested against 860 existing cancer cell lines. Our results suggest that dependency data generated with novel cell cultures is potentially backwards-compatible with existing small molecule dependency datasets. Finally, we demonstrate proof-of-concept that such new models can successfully used in CRISPR-Cas9 screens and integrate results with small molecule sensitivities to uncover CDK4 and XPO1 dependencies in a rare pediatric undifferentiated sarcoma. In aggregate, these proof-of-concept studies demarcate a path by which pre-clinical dependency maps may enhance clinical dependency predictions from genomic data alone.

Citation Format: Yuen-Yi Tseng, Andrew Hong, Paula Keskula, Shubhroz Gill, Jaime Cheah, Grigoriy Kryukov, Aviad Tsherniak, Francisca Vazquez, Glenn Cowley, Coyin Oh, Anson Peng, Abeer Sayeed, Rebecca Deasy, Peter Ronning, Philip Kantoff, Levi Garraway, Mark Rubin, Calvin Kuo, Sidharth Puram, Adi Gazdar, Filemon Dela Cruz, Adam Bass, Nikhil Wagle, Keith Ligon, Katherine Janeway, David Root, Stuart Schreiber, Paul Clemons, Aly Shamji, William Hahn, Todd Golub, Jesse S. Boehm. Accelerating prediction of tumor vulnerabilities using next-generation cancer models. [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 4367.

Abstract 2678: Notch1 regulates epithelial-mesenchymal transition and tumor-initiating capability in esophageal squamous-cell carcinoma

Introduction: Notch signaling may act as a tumor suppressor during the development of squamous cell carcinomas (SCCs); yet, Notch activation promotes tumor growth in a subset of SCC cells. The roles of Notch in the pathogenesis of esophageal squamous cell carcinoma (ESCC) remain elusive.

Methods: Notch1 activation and epithelial-mesenchymal transition (EMT) were determined in an esophageal epithelium-targeted cell-lineage traceable (K5CreERT2-Rosa26tdTomatolsl) mouse model of ESCC induced by 4-nitroquinoline 1-oxide (4NQO), which was coupled with flow cytometry and single cell-derived ESCC organoid formation assays. Tumor-initiating capability was assessed in xenograft transplantation experiments with TE11 human ESCC cells carrying either Crispr-Cas9-deleted Notch1 loci or tetracycline-inducible expression of the activated form of Notch1 (ICN1). Surgically resected primary tumors and adjacent normal mucosa from ESCC patients (n = 152) were analyzed by immunohistochemistry for Notch1 activation and the EMT marker ZEB1.

Results: 4NQO-treated mice developed tdTomato-positive primary and metastatic ESCC tumors with EpCAM-negative ESCC cells displaying traits compatible with EMT. Notch1 activation and ZEB1 expression were co-localized in ESCC cells at the stromal interface, a finding that was further recapitulated in ESCC tumor organoids. Interestingly, Cre-mediated ex vivo Notch1 deletion in a single cell suspension from Notch1loxP/loxP mouse-derived ESCC tumors decreased organoid formation rate. TE11 xenograft tumors appeared to contain a unique ESCC cell fraction containing EpCAM-negative cells, where ICN1 conferred tumorigenicity upon serial transplantation. This population displayed upregulation of Notch1 target genes and the ESCC-lineage survival factor/oncogene SOX2. Moreover, Notch1 deletion in TE11 not only limited tumor formation, but also decreased EMT in culture. A subset of ESCC patients (49/140, 33%) showed ICN1-positive ESCC cells with concurrent ZEB1 expression at the tumor invasive front. The presence of such ESCC cells was associated with poor 5-year survival (P = 0.001), tumor depth (P = 0.01), lymphatic and venous invasion (P = 0.003) and distant metastasis (P = 0.002). Moreover, such ICN1-expressing cells were increased in ESCC patients (7/12, 58%) who received pre-surgical neoadjuvant therapy.

Conclusions: Cell-lineage tracing experiments validate for the first time Notch1 activation and EMT in the 4NQO-induced mouse model of ESCC. Analyses of single cell-derived ESCC tumor organoids, xenograft and primary ESCC tumors reveal that Notch1 activation may be associated with tumor initiating capability, EMT and chemotherapy resistance, implicating Notch1 activation in the pathogenesis of ESCC and potentially other SCCs.

Citation Format: Koji Tanaka, Kelly A. Whelan, Naryan L. Rustgi, Prasanna M. Chandramouleeswaran, Seiji Naganuma, Shingo Kagawa, Mitsuteru Natsuizaka, Yoshiaki Kita, Shoji Natsugoe, Que Jianwen, Devraj Basu, Andres J. Klein-Szanto, Adam Bass, J. Alan Diehl, Hiroshi Nakagawa. Notch1 regulates epithelial-mesenchymal transition and tumor-initiating capability in esophageal squamous-cell carcinoma. [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 2678.

Abstract 4621: Validation and calibration of next-generation sequencing to identify Epstein-Barr Virus-positive gastric cancer

Background: Gastric adenocarcinoma was recently classified by a large genomic study into four molecular subtypes, including one defined by Epstein-Barr virus (EBV)-positivity. EBV infection in tumors is conventionally assessed by in situ hybridization (ISH), but detection of viral nucleic acids by next-generation sequencing represents a potential alternative.

Methods: Normalized EBV read counts were determined by whole genome, whole exome, mRNA and miRNA sequencing for 295 fresh-frozen gastric tumor samples. Formalin-fixed, paraffin-embedded tissue sections were retrieved for ISH confirmation of 13 high-EBV and 11 low-EBV cases selected at random.

Results: By each sequencing method, numbers of EBV reads were bimodally distributed across tumors, with a minority having much higher counts. In pairwise comparisons, individual samples were either consistently high or consistently low by all genomic methods for which data were available. Empiric cut-offs based on molecular data of 1000 normalized reads for whole genome, 100 for exome, 4 for mRNA and 5000 for miRNA had perfect concordance identifying 26 (9%) tumors as EBV-positive. One sample tested by ISH lacked tumor cells. For the 23 tumors with EBV status determined by both approaches, EBV-positivity or -negativity by molecular testing was confirmed by EBER-ISH in all but one case (kappa = 0.91). The exception was a microsatellite instability-type cancer EBV-negative by both mRNA and miRNA sequencing, with equivocally positive ISH interpretation.

Conclusions: EBV-positive gastric tumors may be accurately identified by quantifying viral sequences in genomic data. Simultaneous analyses of human and viral DNA, mRNA and miRNA could streamline tumor profiling for clinical care and research.

Citation Format: M. Constanza Camargo, Reanne Bowlby, Andy Chu, Chandra S. Pedamallu, Vesteinn Thorsson, Sandra Elmore, Andrew Mungall, Adam Bass, Margaret L. Gulley, Charles S. Rabkin. Validation and calibration of next-generation sequencing to identify Epstein-Barr Virus-positive gastric cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4621. doi:10.1158/1538-7445.AM2015-4621

The treatment of an unstable slipped capital femoral epiphysis by either intracapsular cuneiform osteotomy or pinning in situ

We undertook a retrospective comparative study of all patients with an unstable slipped capital femoral epiphysis presenting to a single centre between 1998 and 2011. There were 45 patients (46 hips; mean age 12.6 years; 9 to 14); 16 hips underwent intracapsular cuneiform osteotomy and 30 underwent pinning in situ, with varying degrees of serendipitous reduction. No patient in the osteotomy group was lost to follow-up, which was undertaken at a mean of 28 months (11 to 48); four patients in the pinning in situ group were lost to follow-up, which occurred at a mean of 30 months (10 to 50). Avascular necrosis (AVN) occurred in four hips (25%) following osteotomy and in 11 (42%) following pinning in situ. AVN was not seen in five hips for which osteotomy was undertaken > 13 days after presentation. AVN occurred in four of ten (40%) hips undergoing emergency pinning in situ, compared with four of 15 (47%) undergoing non-emergency pinning. The rate of AVN was 67% (four of six) in those undergoing pinning on the second or third day after presentation.

Pinning in situ following complete reduction led to AVN in four out of five cases (80%). In comparison, pinning in situ following incomplete reduction led to AVN in 7 of 21 cases (33%). The rate of development of AVN was significantly higher following pinning in situ with complete reduction than following intracapsular osteotomy (p = 0.048). Complete reduction was more frequent in those treated by emergency pinning and was strongly associated with AVN (p = 0.005).

Non-emergency intracapsular osteotomy may have a protective effect on the epiphyseal vasculature and should be undertaken with a delay of at least two weeks. The place of emergency pinning in situ in these patients needs to be re-evaluated, possibly in favour of an emergency open procedure or delayed intracapsular osteotomy. Non-emergency pinning in situ should be undertaken after a delay of at least five days, with the greatest risk at two and three days after presentation. Intracapsular osteotomy should be undertaken after a delay of at least 14 days. In our experience, closed epiphyseal reduction is harmful.

Cite this article: Bone Joint J 2015;97-B:412–19.

Masking epistasis between MYC and TGF-β pathways in antiangiogenesis-mediated colon cancer suppression

BACKGROUND

The c-Myc oncoprotein is activated in the majority of colorectal cancers (CRCs), whereas the TGF-β pathway is frequently affected by loss-of-function mutations, for example in SMAD2/3/4 genes. The canonical model places Myc downstream of inhibitory TGF-β signaling. However, we previously demonstrated that Myc also inhibits TGF-β signaling through the miR-17~92 microRNA cluster, raising the question about functional relationships between these two pathways.

METHODS

We engineered a series of genetically complex murine and human CRC cell lines in which Myc and TGF-β activities could be manipulated simultaneously. This was achieved through retroviral expression of the Myc-estrogen receptor fusion protein and through Smad4 short hairpin RNA knockdown. Cell lines thus modified were injected subcutaneously in immunocompromised mice, and the resultant tumors (n = 5-10 per treatment group) were analyzed for overall growth and neovascularization. Additionally, the distribution of MYC and TGF-β pathway mutations was analyzed in previously profiled human CRC samples.

RESULTS

In kras-mutated/trp53-deleted murine colonocytes, either Myc activation or TGF-β inactivation increased tumor sizes and microvascular densities approximately 1.5- to 2.5-fold, chiefly through downregulation of thrombospondin-1 and related type I repeat-containing proteins. Combining Myc activation with TGF-β inactivation did not further accelerate tumorigenesis. This redundancy and the negative effect of TGF-β signaling on angiogenesis were also demonstrated using xenografts of human CRC cell lines. Furthermore, the analysis of the Cancer Genome Atlas data revealed that in CRC without microsatellite instability, overexpression of Myc and inactivation of Smads (including acquired mutations in SMAD2) are mutually exclusive, with odds ratio less than 0.1.

CONCLUSIONS

In human CRC, gain-of-function alterations in Myc and loss-of-function alterations in TGF-β exhibit a masking epistatic interaction and are functionally redundant.

In-group bias in residency selection

BACKGROUND

More than half of all Canadian medical graduates match to residency programs within the same university as their medical school. Here we describe two studies designed to explore whether there is partiality for internal applicants in the resident selection process.

METHODS

We first performed an observational study in which we compared the ratings of 14 'internal' and 89 'external' applicants to the University of Calgary Internal Medicine Training Program by resident and faculty raters. Following this we then asked residents to rate anonymous application packages in which we manipulated applicants' affiliation to our training program.

RESULTS

In our first study, we found that residents rated internal applicants significantly higher for both application packages (mean (SD)) rating for internal versus external applicants (4.86 (0.36) vs. 4.36 (0.57), d = 1.05, p = 0.002) and interviews (4.93 (0.27) vs. 4.36 (0.7), d = 1.07, p = 0.003). There was no difference in the faculty ratings of internal and external applicants. In our second study, we found that residents rated applicants with an affiliation to our program - either attending the local medical school or having completed an elective - higher than applicants with no affiliation to our program.

CONCLUSIONS

Our finding support in-group bias during resident selection, possibly due to the interdependent relationship between residents and students. Considering the career implications of residency matching, we feel that further studies are needed to identify and mitigate sources of bias in the residency application process.

Experienced physicians benefit from analyzing initial diagnostic hypotheses

BACKGROUND

Most incorrect diagnoses involve at least one cognitive error, of which premature closure is the most prevalent. While metacognitive strategies can mitigate premature closure in inexperienced learners, these are rarely studied in experienced physicians. Our objective here was to evaluate the effect of analytic information processing on diagnostic performance of nephrologists and nephrology residents.

METHODS

We asked nine nephrologists and six nephrology residents at the University of Calgary and Glasgow University to diagnose ten nephrology cases. We provided presenting features along with contextual information, after which we asked for an initial diagnosis. We then primed participants to use either hypothetico-deductive reasoning or scheme-inductive reasoning to analyze the remaining case data and generate a final diagnosis.

RESULTS

After analyzing initial hypotheses, both nephrologists and residents improved the accuracy of final diagnoses (31.1% vs. 65.6%, p < 0.001, and 40.0% vs. 70.0%, p < 0.001, respectively). We found a significant interaction between experience and analytic processing strategy (p = 0.02): nephrology residents had significantly increased odds of diagnostic success when using scheme-inductive reasoning (odds ratio [95% confidence interval] 5.69 [1.59, 20.33], p = 0.07), whereas the performance of experienced nephrologists did not differ between strategies (odds ratio 0.57 [0.23, 1.39], p = 0.20).

DISCUSSION

Experienced nephrologists and nephrology residents can improve their performance by analyzing initial diagnostic hypotheses. The explanation of the interaction between experience and the effect of different reasoning strategies is unclear, but may relate to preferences in reasoning strategy, or the changes in knowledge structure with experience.

The impact of nocturnal hemodialysis on sexual function

Background

Sexual dysfunction is common in patients with end stage renal disease (ESRD) and treatment options are limited. Observational studies suggest that nocturnal hemodialysis may improve sexual function. We compared sexual activity and responses to sexual related questions in the Kidney Disease Quality of Life Short Form questionnaire among patients randomized to frequent nocturnal or thrice weekly conventional hemodialysis.

Methods

We performed a secondary analysis of data from an RCT which enrolled 51 patients comparing frequent nocturnal and conventional thrice weekly hemodialysis. Sexual activity and responses to sexual related questions were assessed at baseline and six months using relevant questions from the Kidney Disease Quality of Life Short Form questionnaire.

Results

Overall, there was no difference in sexual activity, or the extent to which people were bothered by the impact of kidney disease on their sex life between the two groups between randomization and 6 months. However, women and patients age < 60 who were randomized to frequent nocturnal hemodialysis were less bothered by the impact of kidney disease on their sex life at 6 months, compared with patients allocated to conventional hemodialysis (p = 0.005 and p = 0.024 respectively).

Conclusions

Our results suggest that frequent nocturnal hemodialysis is not associated with an improvement in sexual activity in all patients but might have an effect on the burden of kidney disease on sex life in women and patients less than 60 years of age. The validity of these subgroup findings require confirmation in future RCTs.

Abstract LB-410: Targeted resequencing of genes frequently mutated in esophageal adenocarcinoma using highly multiplexed Ion Torrent AmpliSeqTM technology and semiconductor sequencing

Introduction: Whole genome and whole exome sequencing by large collaborative research groups is providing us with an unprecedented view of the mutations that occur in cancer. Identifying clinically-relevant and actionable mutations however remains a challenge that will most likely be met by individual groups focused on specific clinical questions and scenarios. Such studies will rely on targeted resequencing of selected genes in large numbers of well-annotated clinical specimens. These specimens are most often formalin-fixed and paraffin-embedded (FFPE) and some of the most valuable samples are small biopsies or fine needle aspirates (FNA's). Translational and clinical researchers require rapid and flexible resequencing approaches that are compatible with the small amounts of highly degraded nucleic acids derived from these challenging samples. Materials & Methods: Using Illumina whole exome sequence data from &gt;60 esophageal adenocarcinoma (EAC) specimens, we identified a set of 20 genes that are frequently mutated in this tumor. PCR amplicons no larger than 140bp were designed to cover all exons from these genes, using the Ion Torrent AmpliSeqTM Designer pipeline. Primers were pooled for a 1285-plex multiplex PCR preamplification step starting with 1-20ng of input DNA from both FFPE and frozen tissue and the resulting amplicon products were used to generate sequencing libraries. Semiconductor sequencing was performed on the Ion Personal Genome MachineTM (PGMTM) sequencer. Metrics evaluated included reads on target, base accuracy, uniform coverage of bases and sequencing base read depth. Mutations detected in EAC samples were compared between the two sequencing platforms. Data from dysplastic and metaplastic esophageal biopsies are now being generated to identify mutations that occur in the development of EAC. Results: 1285 PCR primer pairs were designed that covered 66103bp of the coding region of the 20 target genes. Sequencing data covered &gt;99% with at least 100 reads indicating minimal drop-out during preamplification. Average base read depth was &gt;1900X and no significant differences were observed between FFPE and frozen tissue derived DNA. Initial studies demonstrate 100% concordance of mutations (n=42) detected in the 20 target genes and mutant allele frequencies are highly correlated between the two sequencing approaches (slope =0.96; R2 =0.85; range 4-78%). Conclusion: We have used the Ion Torrent AmpliSeqTM technology to detect mutations in EAC specimens and precursor lesions with high sensitivity and accuracy. The flexible primer design pipeline combined with AmpliSeqTM technology provides a fast and easy approach to targeted resequencing in particularly challenging clinical specimens including FFPE biopsies.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-410. doi:1538-7445.AM2012-LB-410

Alemtuzumab more effective than interferon β-1a at 5-year follow-up of CAMMS223 clinical trial

OBJECTIVE

To report the long-term safety and efficacy results from CAMMS223 comparing alemtuzumab with interferon β-1a in early, active relapsing-remitting multiple sclerosis (RRMS). What are the long-term effects of alemtuzumab treatment, received 36 to 48 months previously, on relapse and disability in early, active RRMS? This study provides evidence of the effectiveness of alemtuzumab in reducing the relapse rate and accumulation of disability compared with interferon β-1a (IFNβ-1a) through extended follow-up (up to 60 months from baseline).

METHODS

Of 334 patients originally randomized, 198 participated in the extension phase (151 [68%] alemtuzumab and 47 [42%] IFNβ-1a). Disability, relapses, and safety were assessed as in the original study period. Efficacy outcomes were analyzed from baseline of the original trial period to 60 months. Safety data extended beyond 60 months.

RESULTS

Over 5 years, alemtuzumab lowered the risk of sustained accumulation of disability by 72% and the rate of relapse by 69% compared with IFNβ-1a (both p < 0.0001). The annualized relapse rate from baseline to month 60 was 0.11 for alemtuzumab and 0.35 for IFNβ-1a. Complete safety follow-up reflected 988 and 376 person-years for alemtuzumab and IFNβ-1a patients, respectively. Serious infections were seen in 7% of alemtuzumab patients and 3% of IFNβ-1a patients, and thyroid disorders were seen in 30% of alemtuzumab patients vs 4% of IFNβ-1a patients. Immune thrombocytopenia occurred in 3% of alemtuzumab patients and 0.9% of IFNβ-1a patients during the initial study period; no additional events were reported during the extension phase. One alemtuzumab patient developed Goodpasture disease 39 months after the second annual cycle of alemtuzumab.

CONCLUSIONS

Through extended follow-up, alemtuzumab remained significantly more efficacious than IFNβ-1a, with a safety profile consistent with previous reports.

CLASSIFICATION OF EVIDENCE

This study provides Class III evidence that alemtuzumab is more effective than interferon β-1a in reducing relapses and disability in patients with RRMS in a long-term follow-up of a rater-blinded, randomized clinical trial with 59.5% of patients participating in the extended follow-up period.