The genomic landscape of advanced gastrointestinal (GI) neuroendocrine tumors (NET) and carcinomas (NEC)

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Background: The impact of specific genomic alterations in advanced GI neuroendocrine malignancies on prognosis and treatment decisions has not been fully characterized. In this study, we seek to evaluate next-generation sequencing (NGS) panels and corresponding clinical outcomes in patients with metastatic GI NET/NEC. Methods: Patients with GI-NET/NEC were identified from a database of NGS reports performed at the Cleveland Clinic, and clinical variables were extracted by chart review through an IRB-approved protocol. We provide an analysis of this cohort. Results: Of a total n=45 patients, 53% were male. Median age at diagnosis was 60 (range: 35-90 years) and 82% were non-Hispanic white, while 9% were black. There were n=25 GI-NETs, mostly intermediate or high grade (11 G3, 7 G2), and n=20 GI-NECs. There was a balanced distribution of primary sites, including colorectal (27%), pancreas (24%), small intestine (18%), unknown primary (24%) and a single case of biliary primary. High grade GI-NETs and GI-NECs were over-represented in the colorectal primary group vs other sites. (n=10 of 12; p=0.021). The majority of patients (73%) had at least one somatic variant, including 12 patients (27%) with one or more mutations deemed actionable, but only one patient (with MSH2 mutation) has received a mutation-matched drug (pembrolizumab). Some recurrent alterations appeared to co-segregate with aggressive histology (NEC vs NET), including 12 of 13 TP53 mutations (p<0.05 by Fisher Exact Test), 7 of 8 RB1 (p<0.05), and 5 of 6 APC (p=0.074). The most common mutations per person based on primary site is shown. Microsatellite instability high was rare (n=1) and median tumor mutational burden (TMB) was 3/mb, with TMB lower in NETs vs NECs. A number of patients (35%) underwent germline testing, with 6 of 16 having a pathogenic germline variant. Conclusions: As 42% of the 12 patients with actionable mutations were alive at time of analysis, it is possible that additional patients could be treated with mutation-matched therapies. More input will be needed from providers as to the role played by alternative effective treatments and barriers such as insurance coverage and prior authorization to implementing mutation-matched therapies. Given the overall low TMB of GI-NETs, with several tumors having zero or 1 reported mutation on targeted NGS, whole genome sequencing may prove useful. Finally, certain mutations such as RB1 and TP53 were associated with more aggressive histology (i.e. NEC). Lastly, only 9% of our cohort with NGS were black, a significant under-representation based on epidemiological data, which raises concerns about disparate accessibility and barriers to NGS testing. Further studies are needed to address any possible racial disparity.[Table: see text]

Overall survival (OS) in gastrointestinal (GI) neuroendocrine tumors (NETs) based on primary site, stage, and surgery

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Background: There are limited data on the impact of primary site and surgical intervention on long-term outcomes in GI-NETs. We hypothesized that primary site would be associated with differences in stage-specific OS. Methods: In the National Cancer DataBase, using histology codes, we identified 124,081 GI-NETs diagnosed between 2004-2019 in individuals 18 years or older. OS was estimated by the Kaplan-Meier method. Differences in survival based on primary site, stage, and surgical intervention were assessed using a Cox proportional hazards model, accounting for multiple comorbidities, e.g. Charlson-Deyo Comorbidity Index. Results: The most common primary site for GI-NETs was small intestine (33.6%), followed by colon, rectum, pancreas, and stomach comprising 19.8%, 17.5%, 15.5%, and 9.2%, respectively. Patients with stage I-III NETs undergoing surgery had significantly better median OS compared to those without surgery (mOS 197 vs 115 mo., p<0.0001 by log rank test). Patients with stage IV NETs undergoing primary resection also had improved mOS vs those with no surgery (125 vs 54 mo., p<0.0001). For stage I-III patients without surgery, 2-yr and 5-yr survival rates were highest in the rectum and lowest in small intestine ( p<0.0001). Among those with stage I-III with surgery, 2-yr and 5-yr survival rates were also highest in the rectum, and lowest in the biliary system at 89% and 82% ( p<0.0001). In contrast, for stage IV patients without primary resection, 2-yr and 5-yr survival rates were highest among small intestine and lowest in the rectum ( p<0.0001). Among those who had primary tumor resection, 2-yr and 5-yr survival rates were highest in pancreas and lowest in colon at 2 yrs and rectum at 5 yrs ( p<0.0001). Conclusions: Surgical intervention for GI-NETs is associated with improved OS in both localized and stage IV disease, with consistent trends across different primary sites. Primary tumor resection was associated with the largest increase in 5-yr survival for stage IV NETs arising from pancreas and stomach. Patient selection for surgery undoubtedly contributed to the improved OS, but resection of primary tumors in stage IV GI-NETs may have a disease modifying effect. Further study is warranted with more granular data to identify patients with stage IV GI-NETs who may benefit from primary tumor resection.[Table: see text]

Targeting TRK: A fast-tracked application of precision oncology and future directions

The NTRK genes encode the tropomyosin-related receptor tyrosine kinases TrkA, TrkB and TrkC. TRK receptors regulate the proliferation, differentiation, and survival of many neuronal and non-neuronal glial cells during embryogenesis, thus playing a critical role in synaptic plasticity and the development of nociceptive pathways. Recurrent genomic alterations in NTRK genes, typically fusions involving the 3' region encoding the kinase domain juxtaposed to 5' sequences from numerous partner genes, occur at a low frequency in a wide diversity of adult and pediatric cancers. The contributions of the resulting constitutively activated kinase to oncogenesis and cancer progression are being elucidated. Larotrectinib and entrectinib are potent first-generation TRK inhibitors with IC₅₀ values in the nanomolar range across cancer cell lines harboring NTRK fusions. Larotrectinib is highly selective for TRK receptors, whereas entrectinib also potently inhibits ROS1 and ALK. Clinical trials of both drugs demonstrated significant and durable responses in patients with tumors harboring NTRK alterations, leading to first of its kind cancer agnostic FDA approvals in the United States for drugs targeting a genomic alteration. Unfortunately, acquired resistance inevitably develops. The second-generation TRK inhibitors selitrectinib and repotrectinib are designed to overcome known mechanisms of resistance.

Distribution of cancer genes in human chromosomes

We increasingly recognize the importance of alterations in DNA in the development of cancer. Beginning with the first somatic mutation identified in a urinary bladder carcinoma cell line, recombinant-DNA technology has led to an explosion of this field, bringing a wealth of data, yet to be fully analyzed. As the number of putative cancer genes has grown several groups have compiled lists of cancer genes with the Catalogue Of Somatic Mutations In Cancer, list as one of several highly regarded. With an interest in the distribution of cancer genes in human chromosomes and discerning whether some chromosomes predominated in cancer gene content, we undertook this review of their distribution in the modern-day human genome. We conclude that cancer genes are uniformly distributed across all human chromosomes having been accreted to the evolving human genome likely in a random fashion over the millennia.

Emerging Therapeutic Implications of STK11 Mutation: Case Series

STK11 was first recognized as a tumor suppressor gene in the late 1990s based on linkage analysis of patients with Peutz-Jeghers syndrome. STK11 encodes LKB1, an intracellular serine-threonine kinase involved in cellular metabolism, cell polarization, regulation of apoptosis, and DNA damage response. Recurrent somatic loss-of-function mutations occur in multiple cancer types, most notably in 13% of lung adenocarcinomas. Recent reports indicate that KRAS-mutant non-small cell lung cancers harboring co-mutations in STK11 do not respond to PD-1 axis inhibitors. We present three patients with STK11-mutated tumors and discuss the proposed mechanisms by which germline and somatic alterations in STK11 promote carcinogenesis, potential approaches for therapeutic targeting, and the new data on resistance to immune checkpoint inhibitors. KEY POINTS: STK11 is a tumor suppressor gene, and loss-of-function mutations are oncogenic, due at least in part to loss of AMPK regulation of mTOR and HIF-1-α. Clinical trials are under way, offering hope to patients whose STK11-mutated tumors are refractory and/or have progressed on chemotherapeutic regimens. Whether gastrointestinal cancers with STK11 loss of function will show the same outcome and potential refractoriness to immune therapy that were reported for lung cancer is unknown. However, physicians managing such patients should consider the experience in lung cancer, particularly outside the context of a clinical trial. In the CheckMate-057 trial lung tumors harboring co-mutations in KRAS and STK11 had an inferior response to PD-1 axis inhibitors. Coupled with the observation that STK11-mutated tumors were found to have a cold immune microenvironment regardless of KRAS status, the conclusion could extend to KRAS wild-type tumors with STK11 mutation. Current data suggest that the use of PD-1 axis inhibitors may be ill advised in the presence of STK11 mutation.

Abstract P4-10-19: Utilization of next generation sequencing (NGS)-guided therapy in breast cancer (BC): Single-institution retrospective analysis of 315 patients

Background:In the United States, more than 3 million women are affected by BC and approximately 41,760 women are expected to die from it in 2019. Although improvements have been made in the past decades, there is still a strong need for the development of new cancer drugs to increase survival and reduce drug toxicities. Currently there is a lack of sufficient data regarding the use of NGS in treatment of BC. In this report, we discuss our results with NGS in a large cohort of BC patients.

Methods:This project was IRB approved. We subsequently identified BC patients treated at the Sylvester Comprehensive Cancer Center (SCCC) at University of Miami, whose cancer specimens had NGS analysis. Data was collected in the following categories: tumor characteristics, genomic mutation profiles, demographics, cancer treatment history, and response to targeted therapy (TT) after 3 months, 6 months, 1 year, 2 years, and 5 years, respectively.

Results:Between January 2013 to April 2019, 315 BC patients underwent NGS at SCCC. The average age at diagnosis was 50 among this cohort. Fifty-two percent had estrogen receptor (ER)+, HER2- BC, 30.2% had triple-negative BC, 12.8% had HER2+, ER+ BC, and 6% had HER2+, ER- BC. Ninety-eight percent of the patients had at least one mutation, of which 80% had at least one targetable mutation. One hundred and twenty-six patients received TT between January 2016 to April 2019. This was in stark contrast to the 2013-2015 period, when only 30 patients received TT. After the first 3 months of receiving TT among the total of 156 patients, 53% were found to have stable disease (SD); 39% were found to have progressive disease (PD), and 8% had partial response (PR). At the 6-month interval, 76 patients were still receiving TT, of which 52% continued to have SD, 36% developed PD, and 12% had PR. A total of 27 patients remained on TT for at least 1 year, of which 38% continued to have SD, 54% developed PD, and 8% had PR. One patient was lost to follow up.The most common targetable mutations were PIK3CA, FGFR1, ERBB2, and BRCA1/2, found in 85, 39, 35, and 22 patients, respectively. Of note, 66 out of 199 (33%) ER+ BC patients had PIK3CA mutation. It is also important to mention that 8 patients, whose specimens were found to be HER2-negative based on IHC/FISH, were revealed to have positive ERBB2-mutated BC and were subsequently treated with HER2-TT. Two of these patients had SD for 3 months; two patients had SD for 6 months; one patient had SD for 1 year, and 1 patient had SD for 5 years. One patient developed PD after only 3 months and 1 patient was lost to follow up.

Conclusions: The majority of BC patients in our series had actionable mutations. Significantly more number of patients were offered TT in the recent years (2016-2019) compared to those in 2013-2015 (126 vs. 30). Our cohort findings are in line with the literature as we found that 33% of ER+ BC patients had PIK3CA mutation. Given the recent approval of Alpelisib for the treatment of hormone receptor positive, HER2-negative, PIK3CA mutated advanced or metastatic BC (MBC)following disease progression on or after an endocrine-based regimen, NGS should be used early in the diagnosis of MBC. We also found that 2.5% of our cohort had ERBB2-mutated BC, whose tumor was considered to be HER2-negative based on IHC/FISH. The majority of them had their disease controlled with HER2-directed therapy, which only emphasizes the importance of using this technology even more for BC patients.

Response to Targeted Therapy Including HER2 Targeted TherapyPercentage of SD, PD, and PR at Different Time IntervalsPercentage of SDPercentage of PDPercentage of PRTotal Number of Patients Remaining on TT3 months53%39%8%1566 months52%36%12%761 year38%54%8%27

Citation Format: Bahar Laderian, Robert Hsu, Ana Sandoval, Dorraya El-Ashry, Marc Lippman. Utilization of next generation sequencing (NGS)-guided therapy in breast cancer (BC): Single-institution retrospective analysis of 315 patients [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-10-19.

Role of radiomics to differentiate benign from malignant pheochromocytomas and paragangliomas on contrast enhanced CT scans

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Background: Radiomics features, which are quantitative features generated by computational analysis of routine clinical imaging like CT scans, have been shown to be associated with clinical outcomes and tumor’s behavior in some solid tumors. We compared the radiomic features of malignant and benign pheochromocytomas/paragangliomas (P/P). Methods: Through an IRB approved study at our institution, we identified 20 consecutive patients with P/P and with available contrast-enhanced abdominopelvic CT. A radiologist with experience in oncologic imaging identified and segmented tumors on every slice using a MatLab-based imaging platform. The entire tumor image then underwent computational analysis generating 1160 radiomics features reflecting tumor size, shape, density, textural heterogeneity, and margins. These radiomics features were compared between malignant and benign P/P using Wilcoxon-Rank sum test. Results: Of the twenty patients included in this analysis, there were 6 patients with malignant P/P and 14 patients with benign tumors. Patients had been followed for at least 5 and many for at least 10 years after resection of the tumor. At diagnosis, the mean age of patients with benign and malignant tumors were 51 and 45, respectively. A 60% majority of patients with benign tumors were females while a 77% majority of patients with malignant tumors were male. Benign P/P were significantly different from malignant ones in: tumor intensity textures (spatial correlation [p-value = 0.0010], Laws [p-value = 0.0064], LoG [p-value = 0.0087], and Gabor [p-value = 0.0325]), and tumor local surface shape (Shape Index SI7 [p-value = 0.0325]). Conclusions: This initial analysis sought to discern differences in these rare tumors that might be exploited clinically. The results show that compared to benign tumors, malignant P/P tend to have more heterogenous texture, irregular edges, and less rounded shape on contrast enhanced abdominal CT scan. However, because these radiomics phenotype properties are subtle, they cannot be made reliably in an objective fashion using human visual assessment and thus these radiomics features may have a role as a quantitative imaging biomarker in P/P to predict tumor behavior. The cohort is being expanded and data will be updated at the time of the presentation. With larger numbers, the contribution to the radiomics profile of a SDHx mutation will be explored in greater depth to understand the differential impact of SDHx loss and of evolution into a cancer to the radiomics profiles.

A closer look at next generation sequencing (NGS) in breast cancer: A retrospective analysis

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Background: Targeted cancer therapy has been posited to revolutionize treatment paradigms in oncology. There are, a paucity of data regarding the use of NGS in breast cancer (BC). Herein we report our experience with NGS in a consecutive series of BC patients. Methods: Using an IRB approved protocol, we retrospectively identified patients with BC treated at the Sylvester Comprehensive Cancer Center (UMMSOM) who underwent NGS. Data were collected on demographics, tumor characteristics, genomic mutation profiles, and subsequent response to targeted therapy after 3 months. Results: Between January 2013 and April 2016, 101 BC patients underwent NGS. The mean age at diagnosis was 49. Ninety-one percent were stage IV, 6% were stage III, 2% were stage II, and 1% were stage I. Fifty percent had estrogen receptor (ER)+, HER2- tumors, 31% had triple-negative tumors, 13% had HER2+, ER+ tumors, and 6% had HER2+, ER- tumors. Ninety-six percent had at least one mutation, of which 78% had a targetable mutation. Sixteen patients received targeted therapy (TT). The average time between NGS and TT was 5 months ranging 0-22 months, during which seven patients received other systemic therapy. The most common reasons for not receiving TT were no actionable mutations (24%), not meeting criteria for an available clinical trial (14%), stable disease (SD) (13% ), lost to follow up (11%), physician decision (11%). Of the 16 patients who received TT, 7 patients had progression of disease, 3 died before response could be evaluated and presumably had no benefit, 2 discontinued TT due to side effects, 1 had SD, 1 had a partial response, and 2 were too early to be assessed. Conclusions: The majority of BC patients in our series had actionable mutations. However, TT was not offered to a significant number of patients for a multiplicity of reasons and the clinical benefit in those patients treated according to NGS findings was dismal. While NGS is surely a promising technology that should be utilized in combination with molecular tumor board, a host of reasons limit its usefulness at this time and its expense may well not justify its use outside of clinical trials.

Fish oil supplementation does not lower C-reactive protein or interleukin-6 levels in healthy adults

BACKGROUND

The n-3 polyunsaturated fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) may prevent a range of chronic conditions through anti-inflammatory actions. However, as clinical trials using these fatty acids for primary prevention are yet unavailable, their putative role in disease prevention rests, in part, on evidence of anti-inflammatory actions in healthy individuals.

OBJECTIVE

To investigate in a double-blind, placebo-controlled clinical trial whether supplementation with a moderate dose of EPA+DHA reduces common biomarkers of chronic, systemic inflammation in healthy individuals.

METHODS

A total of 261 healthy individuals aged 30-54 years who were free of inflammatory conditions and consumed ≤ 300 mg per day EPA+DHA were included in the study. Participants were randomly assigned to 18 weeks of either fish oil supplementation providing 1400 mg per day EPA+DHA or matching placebo. Outcome measures were serum levels of C-reactive protein (CRP) and interleukin (IL)-6. In a substudy, ex vivo cytokine production was measured. Missing data for CRP and IL-6 were estimated using regression imputation. Data analyses conformed to intention-to-treat principles.

RESULTS

Participant blinding was verified. Red blood cell EPA+DHA increased by 64% in the active treatment group, but serum CRP and IL-6 were not affected by supplementation (P ≥ 0.20). Findings were consistent with and without imputed values and across subgroups. Similarly, EPA+DHA supplementation did not alter ex vivo production of four pro-inflammatory cytokines (P ≥ 0.20).

CONCLUSIONS

Supplementation with 1400 mg EPA+DHA did not reduce common markers of systemic inflammation in healthy adults. Whether this or a higher dose affects other measures of inflammation, oxidative stress or immune function warrants examination.