Efficacy of Systemic Chemotherapy in Patients With Low-grade Mucinous Appendiceal Adenocarcinoma: A Randomized Crossover Trial

Importance

Appendiceal adenocarcinoma is a rare tumor, and given the inherent difficulties in performing prospective trials in such a rare disease, there are currently minimal high-quality data to guide treatment decisions, highlighting the need for more preclinical and clinical investigation for this disease.

Objective

To prospectively evaluate the effectiveness of fluoropyrimidine-based systemic chemotherapy in patients with inoperable low-grade mucinous appendiceal adenocarcinoma.

Design, Setting, and Participants

This open-label randomized crossover trial recruited patients at a single tertiary care comprehensive cancer center from September 2013 to January 2021. The data collection cutoff was May 2022. Enrollment of up to 30 patients was planned. Eligible patients had histological evidence of a metastatic low-grade mucinous appendiceal adenocarcinoma, with radiographic imaging demonstrating the presence of mucinous peritoneal carcinomatosis and were not considered candidates for complete cytoreductive surgery. Key exclusion criteria were concurrent or recent investigational therapy, evidence of bowel obstruction, and use of total parenteral nutrition. Data were analyzed from November 2021 to May 2022.

Interventions

Patients were randomized to either 6 months observation followed by 6 months of chemotherapy, or initial chemotherapy followed by observation.

Main Outcomes and Measures

The primary end point was the percentage difference in tumor growth in treatment and observation groups. Key secondary end points included patient-reported outcomes in the chemotherapy and observation periods, objective response rate, rate of bowel complications, and differences in overall survival (OS).

Results

A total of 24 patients were enrolled, with median (range) age of 63 (38 to 82) years, and equal proportion of men and women (eg, 12 men [50%]); all patients had ECOG performance status of 0 or 1. A total of 11 patients were randomized to receive chemotherapy first, and 13 patients were randomized to receive observation first. Most patients (15 patients [63%]) were treated with either fluorouracil or capecitabine as single agent; 3 patients (13%) received doublet chemotherapy (leucovorin calcium [folinic acid], fluorouracil, and oxaliplatin or folinic acid, fluorouracil, and irinotecan hydrochloride), and bevacizumab was added to cytotoxic chemotherapy for 5 patients (21%). Fifteen patients were available to evaluate the primary end point of difference in tumor growth during treatment and observation periods. Tumor growth while receiving chemotherapy increased 8.4% (95% CI, 1.5% to 15.3%) from baseline but was not significantly different than tumor growth during observation (4.0%; 95% CI, -0.1% to 8.0%; P = .26). Of 18 patients who received any chemotherapy, none had an objective response (14 patients [77.8%] had stable disease; 4 patients [22.2%] had progressive disease). Median (range) OS was 53.2 (8.1 to 95.5) months, and there was no significant difference in OS between the observation-first group (76.0 [8.6 to 95.5] months) and the treatment-first group (53.2 [8.1 to 64.1] months; hazard ratio, 0.64; 95% CI, 0.16-2.55; P = .48). Patient-reported quality-of-life metrics identified that during treatment, patients experienced significantly worse fatigue (mean [SD] score, 18.5 [18.6] vs 28.9 [21.3]; P = .02), peripheral neuropathy (mean [SD] score, 6.67 [12.28] vs 38.89 [34.88]; P = .01), and financial difficulty (mean [SD] score, 8.9 [15.2] vs 28.9 [33.0]; P = .001) compared with during observation.

Conclusions and Relevance

In this prospective randomized crossover trial of systemic chemotherapy in patients with low-grade mucinous appendiceal adenocarcinoma, patients did not derive clinical benefit from fluorouracil-based chemotherapy, given there were no objective responses, no difference in OS when treatment was delayed 6 months, and no difference in the rate of tumor growth while receiving chemotherapy.

Trial Registration

ClinicalTrials.gov Identifier: NCT01946854.

Abstract 2454: Identification of colorectal cancer stem cells from single cell RNA sequencing

Cancer stem cells (CSCs) play a critical role in metastasis, relapse and therapy resistance in colorectal cancer (CRC). Although the normal lineage of cell development in the intestine has identified many of the genes involved in the induction and maintenance of pluripotency, recent studies of CSCs suggest significant heterogeneity and lack of common surface markers for identification. In this study, we perform single cell RNA sequencing (scRNA-seq) to extract a single cell stemness signature (SCS_sig) for colorectal CSCs identification and as a potential predictor of relapse after surgical resection. A total of 26 fresh surgery specimens (6 colon tumor, 3 colon matched normal, 9 liver metastasis, 8 liver matched normal) from neoadjuvant chemotherapy (NAC) treated patients with single-cell transcriptome generated using 10X Chromium scRNA-seq and Illumina platforms were analyzed. Following extensive quality control and batch effect correction, we identified 20k epithelial cells using canonical epithelial cell marker genes (EPCAM, KRT8 and KRT18) from a total of 111,200 cells, with mean 1113 epithelial cell per sample (excluding liver normal samples).To obtain the CSCs profiling signature, we first annotated a ‘gold-standard’ set of CSC that expressed all canonical colon CSC marker genes (LGR5, ASCL2, EPHB2, PROM1, AXIN2, LEFTY1, RNF43, CD44 and SLC12A2), identifying 346 CSCs (1.71% of epithelial cells). Published stemness signatures were significantly enriched in the gold standard stem cells (false discovery rate (FDR) < 0.05). Then we selected the 50 most significantly up-regulated genes in this gold standard set (relative to other epithelial cells) as a single-cell stemness signature (named SCS_sig hereafter). Interesting, we saw that in every tumor there was a continuum of stemness, rather than distinct stem and differentiated populations. The stemness state by SCS_sig was positively correlated with less differentiated state calculated by CytoTRACE score (r = 0.76, p< 0.001), a computational method that predicts the differentiation state of cells from scRNA-seq data. The SCS_sig was significantly higher in tumor cells compared to normal cells in our cohort as well as the previously published SMC cohort (fold change = 2.52 and p < 0.001, fold change = 1.44 and p < 0.001, respectively). There was notable heterogeneity in the fraction of stem-like tumor cells with in 15 tumor samples, with the tumor with greatest CSC percentage having the shortest time to relapse. The SCS_sig generated from stem-like cells can identify the stemness state of epithelial cells in scRNAseq data. A signature score is more simple and robust than using few or panel of CSCs marker genes to identify single CSC because of the reads dropout in scRNA-seq. Further investigation of the SCS_sig as a predictive and prognostic biomarker in CRC is ongoing in larger patient cohorts.

Citation Format: Kangyu Lin, Mohammad Zeineddine, Saikat Chowdhury, Nicholas Hornstein, Sendurai Mani, Scott Kopetz, John Paul Shen. Identification of colorectal cancer stem cells from single cell RNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2454.

Factors Associated With Hospitalization Among Breast Cancer Patients With COVID-19: A Diverse Multi-Center Los Angeles Cohort Study

BACKGROUND

The SARS-CoV-2 virus has infected and killed millions of people worldwide. Breast cancer is the most prevalent cancer in women and few studies have investigated the outcomes of patients with a history of breast cancer and COVID-19. We report the clinical outcomes of patients with invasive breast cancer who tested positive for SARS-CoV-2, including hospitalization and death, and evaluate demographic and cancer-related factors associated with these outcomes.

PATIENTS

Patients with a history of invasive breast cancer and positive SARS-CoV-2 test from January 1 to December 31, 2020 at two large, academic Los Angeles health systems were included.

METHODS

Retrospective chart review of the electronic medical record was performed. Data for demographic and cancer-related factors were manually abstracted. Relationships between outcomes and clinical variables were evaluated using Fisher's exact test and linear regression analysis.

RESULTS

Among a total of 132 patients, 40 (30.3%) were hospitalized, while 11 (8.3%) required intensive care support, and 8 patients (6.1%) died. Older age and presence of one or more additional comorbidities were associated with hospitalization and death (P = .010, P = .003, P = .034, P < .001). Hispanic/Latinx ethnicity was associated with hospitalization (P = .047). Cancer treatment was not associated with hospitalization or death.

CONCLUSION

In our diverse, multi-center, breast cancer cohort, Hispanic/Latinx ethnicity, older age and presence of other comorbidities were associated with worse outcomes from COVID-19. Breast cancer treatment, including surgery, radiation, systemic therapy, and endocrine therapy, was not associated with hospitalization in our cohort. Further studies are needed to explore the relationship between breast cancer and COVID-19 outcomes.

The Natural History of a Patient With COVID-19 Pneumonia and Silent Hypoxemia

A patient who declined all interventions, including oxygen, and recovered highlights the importance of treating the individual instead of clinical markers and provides a time course for recovery from pneumonia and severe hypoxemia.

Mimic of malignancy: delineating IgG4-related disease and lymphoma

Here, we describe the case of a 74-year-old man who was incidentally found to have a hepatic lesion during routine screening. Additional diagnostic studies demonstrated elevated IgG4 levels, IgG4 plasma cell-predominant lymphadenopathy and an inflammatory retroperitoneal mass encasing the bilateral ureters and the aorta. Given the concurrence of a lymphomatous process and IgG4-related disease (IgG4-RD), a multidisciplinary approach was required to determine whether targeting the lymphoma or IgG4-RD would be most efficacious. Discussions led to the decision to target treatment against IgG4-RD with systemic glucocorticoids, and subsequent imaging showed resolution of all lesions. To date, the patient remains symptom-free and has not experienced recurrence of his disease. This case highlights the importance of multidisciplinary care and the challenge inherent in targeting treatment between IgG4-RD and a concomitant lymphomatous process.

Abstract 6614: Association between immune gene signatures and neoepitopes with electrostatic charge opposite to their HLA-B binding pocket in melanoma (MEL) and lung adenocarcinoma (LUAD)

Purpose: Immune checkpoint blockade (ICB) has revolutionized treatment of melanoma and lung cancer. Recent evidence suggests that human leukocyte antigen (HLA) B supertype influences efficacy of ICB. HLA-B27 and B44 supertypes have electronegative and electropositive binding pockets, respectively, and preferentially bind and display oppositely charged neoepitopes. We sought to evaluate the relationship between baseline immune activation and charged neoepitopes in the context of oppositely charged HLA-B binding pockets.

Methods: Datasets from a total of 466 MEL and 513 LUAD patients included in the TCGA were used. HLA type was obtained with OptiType. Nonsynonymous mutations were annotated with SnpEff, Ensembl VEP, and VAtools. Only transcribed variants were filtered for analysis. pVAC-Seq using NetMHCpan algorithm predicted nonamer neoepitopes. Favorable B27 neoepitopes were defined as having new positively charged amino acid (AA) substitutions (H/K/R) from oppositely charged or uncharged wildtype AA, while neoepitopes with new negatively charged AAs (D/E) were considered favorable for B44. Three gene signatures were evaluated with normalized RNA expression values from 14 antigen presentation, 15 immunostimulator, and 11 immunoinhibitor genes. Linear regression tests were performed between gene expression values and fraction of nonsynonymous mutations resulting in neoepitopes with new positively and negatively charged AAs. Paired t-tests were performed between the mean of Pearson's r for fraction of new positively versus negatively charged AAs compared to gene expression values, and subsetted to B27/B44. Heterozygotes for B27/B44 were excluded from analysis to avoid competing charges.

Results: 26.4% and 48.7% of MEL patients had B27 and B44, respectively. In LUAD, 28.6% had B27 and 47.2% had B44. Of new charged AAs resulting from nonsynonymous mutations, 72.6% in MEL and 75.0% in LUAD were positively charged (p=0.0053). In MEL, difference in Pearson's r values between fraction of new positively and negatively charged AAs as compared to immunostimulator (B27 p=.016; B44 p&lt;.001), immunoinhibitor (B27 p=.020; B44 p=.009), and antigen presentation (B27 p&lt;.001; B44 p&lt;.001) gene signatures showed association with positively charged AAs in B27 and negatively charged AAs in B44. In LUAD, differences in Pearson's r values between oppositely charged AAs were only significant for B27 (stimulator p=.004; inhibitor p&lt;.001; antigen presentation p&lt;.001), showing association with positively charged AAs.

Conclusion: Immune gene signatures showed association with neoepitopes that have oppositely charged AAs than their HLA-B binding pocket in both MEL and LUAD, indicating that presentation of favorable neoepitopes stimulates an immune response. The association was limited to B27 in LUAD and strongest for B44 in MEL.

Citation Format: Charlene M. Fares, Amy L. Cummings, Matthew K. Theisen, Nicholas Hornstein, Jaklin Gukasyan, Wisdom Akingbemi, Debory Li, Paige Brodrick, Aaron Lisberg, Edward B. Garon. Association between immune gene signatures and neoepitopes with electrostatic charge opposite to their HLA-B binding pocket in melanoma (MEL) and lung adenocarcinoma (LUAD) [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 6614.

Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice

FMRP (fragile X mental retardation protein) is a polysome-associated RNA-binding protein encoded by Fmr1 that is lost in fragile X syndrome. Increasing evidence suggests that FMRP regulates both translation initiation and elongation, but the gene specificity of these effects is unclear. To elucidate the impact of Fmr1 loss on translation, we utilize ribosome profiling for genome-wide measurements of ribosomal occupancy and positioning in the cortex of 24-day-old Fmr1 knockout mice. We find a remarkably coherent reduction in ribosome footprint abundance per mRNA for previously identified, high-affinity mRNA binding partners of FMRP and an increase for terminal oligopyrimidine (TOP) motif-containing genes canonically controlled by mammalian target of rapamycin-eIF4E-binding protein-eIF4E binding protein-eukaryotic initiation factor 4E (mTOR-4E-BP-eIF4E) signaling. Amino acid motif- and gene-level analyses both show a widespread reduction of translational pausing in Fmr1 knockout mice. Our findings are consistent with a model of FMRP-mediated regulation of both translation initiation through eIF4E and elongation that is disrupted in fragile X syndrome.

Abstract 145: Isolation & Characterization of Heart-field Specific Cardiomyocytes

Cardiovascular disease (CVD) is the leading cause of death worldwide. Human embryonic stem cell (hESC)-derived cardiovascular progenitors (CVPs) or cardiomyocytes (CMs) represent a promising candidate for cell-based therapies to treat CVD. Myocardial infarction leads to extensive CM death mainly within the left ventricle, which is predominantly derived from the first heart field (FHF) during embryonic development. We postulate that the generation of chamber-specific CMs may play a key role in the development of safe and efficacious regenerative therapy. As a first step, we generated and characterized a FHF-specific TBX5-TdTomato +/W hESC reporter line. We show that TBX5 + cells represent an enriched population of FHF CVPs that can give rise to CMs, endothelial, and smooth muscle cells in vitro . Interestingly, we observed that TBX5 - cells can also generate contractile CMs. Bulk RNA-sequencing analysis at different stages of development suggested that TBX5 - cells are enriched for second heart field (SHF) CMs. To enable prospective isolation of FHF and SHF CMs, we generated a double transgenic TBX5-TdTomato +/W /NKX2-5 eGFP/W hESC reporter line. We performed detailed electrophysiological, functional, and transcriptional studies to characterize the heart-field specificity of these hESC-derived CMs. Electrophysiological studies revealed that, despite the presence of atrial and ventricular action potentials (APs) in both FHF and SHF, there are significant differences in their AP duration and cycle length. In addition, both FHF and SHF CMs responded appropriately to adrenergic stimuli. Single-cell RNA sequencing analysis confirmed the absence of nodal genes within these populations and provided evidence of unique molecular signatures for isolating FHF- and SHF-like CMs. Finally, we identified CORIN as a novel cell surface marker for FHF CMs. Our studies provide a platform for investigating in vitro cardiovascular development, drug screening, and may facilitate a safe approach for cell therapy in heart disease.

Abstract 1841: Characterization of neuronal alterations in a new mouse model of low grade glioma

Diffusely infiltrating gliomas are the most common type of primary brain tumor seen in adults. Patients with low grade glioma (LGG) can survive for many years, but often suffer from seizures and cognitive impairment, and these symptoms are associated with an unfavorable prognosis. Glioma cells diffusely infiltrate cortical tissue, where tumor cells aggregate around neuronal cell bodies, a growth pattern referred to as perineuronal satellitosis, however the effects of tumor cells on neurons has not been well defined. To address this important issue we generated a mouse model that recapitulates the genetic and histological features of diffusely infiltrating LGG. In our model tumor growth is driven by PDGFA overexpression and p53 deletion in a RiboTag-Camk2a-Cre transgenic mouse. The RiboTag system allows for the isolation and sequencing of ribosome-bound transcripts from Camk2a neurons to obtain a measure of transcription and translation. Our analysis in non-tumor bearing brains identified neuron-specific genes that are highly regulated at the level of translation. mTOR signaling regulates cell growth, proliferation, and translation in response to diverse stimuli. To characterize mTOR signaling in our model we used immunohistochemical staining of pS6 as a marker of mTOR activity and found that neurons within the glioma infiltrated cortex have lower levels of pS6 staining compared to neurons in the surrounding cortex. To further assess these results we are using the RiboTag system to identify alterations in neuronal transcription and translation that occur in our model during glioma formation and in response to mTOR targeted treatments. These studies will provide new insights into the neuronal alterations contributing to seizures and cognitive impairment in glioma and enable the identification of potential molecular targets for novel therapies to treat the devastating consequences of cortical dysfunctions associated with glioma.

Citation Format: Daniela Torres, Angeliki Mela, Sohani Das Sharma, Nicholas Hornstein, Peter Sims, Peter Canoll. Characterization of neuronal alterations in a new mouse model of low grade glioma [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 1841. doi:10.1158/1538-7445.AM2017-1841

Ligation-free ribosome profiling of cell type-specific translation in the brain

Ribosome profiling has emerged as a powerful tool for genome-wide measurements of translation, but library construction requires multiple ligation steps and remains cumbersome relative to more conventional deep-sequencing experiments. We report a new, ligation-free approach to ribosome profiling that does not require ligation. Library construction for ligation-free ribosome profiling can be completed in one day with as little as 1 ng of purified RNA footprints. We apply ligation-free ribosome profiling to mouse brain tissue to identify new patterns of cell type-specific translation and test its ability to identify translational targets of mTOR signaling in the brain.