Single-Cell Transcriptomic Analysis of Kaposi Sarcoma

Kaposi Sarcoma (KS) is a complex tumor caused by KS-associated herpesvirus 8 (KSHV). Histological analysis reveals a mixture of "spindle cells", vascular-like spaces, extravasated erythrocytes, and immune cells. In order to elucidate the infected and uninfected cell types in KS tumors, we examined skin and blood samples from twelve subjects by single cell RNA sequence analyses. Two populations of KSHV-infected cells were identified, one of which represented a proliferative fraction of lymphatic endothelial cells, and the second represented an angiogenic population of vascular endothelial tip cells. Both infected clusters contained cells expressing lytic and latent KSHV genes. Novel cellular biomarkers were identified in the KSHV infected cells, including the sodium channel SCN9A. The number of KSHV positive tumor cells was found to be in the 6% range in HIV-associated KS, correlated inversely with tumor-infiltrating immune cells, and was reduced in biopsies from HIV-negative individuals. T-cell receptor clones were expanded in KS tumors and blood, although in differing magnitudes. Changes in cellular composition in KS tumors were identified in subjects treated with antiretroviral therapy alone, or immunotherapy. These studies demonstrate the feasibility of single cell analyses to identify prognostic and predictive biomarkers.

Author Summary

Kaposi sarcoma (KS) is a malignancy caused by the KS-associated herpesvirus (KSHV) that causes skin lesions, and may also be found in lymph nodes, lungs, gastrointestinal tract, and other organs in immunosuppressed individuals more commonly than immunocompetent subjects. The current study examined gene expression in single cells from the tumor and blood of these subjects, and identified the characteristics of the complex mixtures of cells in the tumor. This method also identified differences in KSHV gene expression in different cell types and associated cellular genes expressed in KSHV infected cells. In addition, changes in the cellular composition could be elucidated with therapeutic interventions.

Abstract P2-02-14: Circulating tumor DNA predicts clinical outcome in early stage triple negative breast cancer

Background- Triple negative breast cancer (TNBC) is the most aggressive subtype of breast cancer as these patients have the highest risk of recurrence and death. Only 35% of TNBC patients achieve a pathologic complete response (pCR) following neoadjuvant chemotherapy. Patients who do not achieve pCR have a 27% risk of distant recurrence and ultimate death at 3 years compared to 9% for pCR. Unidentified micrometastases are responsible for ultimate overt progression and death. Developing strategies to identify patients with minimal residual disease following curative treatment is an unmet need. Circulating tumor DNA (ctDNA) can characterize and monitor advanced cancers. In this study, we sought to assess if ctDNA can predict clinical outcome in TNBC.

Methods-Biospecimens were obtained from patients with stages II and III TNBC enrolled on a neoadjuvant trial (NCT02124902). Patients have a research biopsy and plasma for ctDNA collected at baseline, cycle 1 day 3, definitive surgery for those with residual disease, and at recurrence for those who relapse. Plasma for ctDNA is also collected every 6 months for 5 years after treatment. Patients receive docetaxel and carboplatin every 3 weeks X 6 cycles. Surgery is 3-5 weeks after chemotherapy. Six patients' serial tumor samples and germline DNA were studied by whole exome sequencing. The median sequencing depth was 90.13x. Sequencing was performed on samples with high cellularity (≥50%). All 6 patients also had serial ctDNA analyzed using Swift Biosciences Accel-Amplicon™ 56G Oncology Panel v2. After identifying somatic mutations in each breast tumor series, we determined the subset of mutations that intersected with the regions targeted by the Swift 56 gene panel. We then evaluated whether corresponding mutations could be detected in ctDNA, and if ctDNA predicted clinical outcome.

Results-Four of the 6 patients were non-pCR with residual disease following chemotherapy. We identified 627 somatic variants by exome analysis that were called by at least two somatic variant callers and passed additional quality filtering steps. Of these, 10 variants overlapped with the Swift panel. TP53 variants were identified in all 6 patients' tumor tissue samples. At least one TP53 variant was identified in 4 patients' baseline pre-chemotherapy ctDNA samples. Both pCR patients had either no detectable ctDNA TP53 mutations (NTN007-ref. in baseline tumor tissue was 19.58% variant allele frequency [VAF]); or clearance of ctDNA following chemotherapy from 4.45% VAF at baseline to 0.06% following chemotherapy (NTN004-ref. in baseline tumor tissue 37.34% VAF). Three non-PCR patients had persistent TP53 mutations in ctDNA during the treatment course. One non-pCR patient did not have detectable mutations in ctDNA. The only patient with recurrent disease whose ctDNA TP53 mutation persisted during the treatment course (baseline VAF-1.65%, cycle 1 day 3-0.78%, definitive surgery-0.09%), was found to have a higher ctDNA VAF at recurrence (29.55%).

Conclusion-In this pilot study, mutation tracking by ctDNA is sensitive and distinguishes pCR from non-pCR in TNBC patients receiving neoadjuvant chemotherapy. ctDNA also identifies recurrence following curative therapy. Evaluating ctDNA as a biomarker of outcome in TNBC is warranted.

Citation Format: Ademuyiwa F, Feng Y-Y, Skidmore Z, Kunisaki J, Walker J, Fulton R, Krysiak K, Skinner T, Weilbaecher K, Ma C, Griffith O, Griffith M. Circulating tumor DNA predicts clinical outcome in early stage triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-02-14.

Abstract PD6-02: The genomics of response to neoadjuvant trastuzumab and chemotherapy in HER2-positive breast cancer – Results from the ACOSOG Z1041 (Alliance) trial

Support: Alliance U10CA180821; Alliance Statistical Center grant U10CA180882; ACOSOG grant U10CA76001

HER2 gene amplification and its corresponding overexpression are present in approximately 12% of invasive breast cancers. While HER2-targeted agents (e.g. trastuzumab, pertuzumab, and lapatinib) are effective treatments, resistance remains a major cause of death from HER2-positive breast cancer. Mechanisms of resistance are poorly understood. Without a molecular understanding of these mechanisms, therapeutic advances will be delayed. We have generated molecular profiles of primary HER2-positive breast cancers treated on a neoadjuvant clinical trial, and compared features associated with response to treatment.

The American College of Surgeons Oncology Group (ACOSOG) Z1041 trial in HER2-positive breast cancer was designed to compare the pathologic complete response (pCR) rate of a regimen of paclitaxel and trastuzumab, followed by trastuzumab administered with fluorouracil, epirubicin, and cyclophosphamide (FEC-75) to a regimen of FEC-75 alone followed by paclitaxel and trastuzumab. The trial identified no difference in pCR rates between the regimens (Buzdar et al., The Lancet Oncology 2013). In supplement to the tissues obtained from 37 of the patients enrolled in the Z1041 trial, an additional 11 cases were obtained from a single institution study (201101961) of patients treated with neoadjuvant trastuzumab that had pre-treatment core biopsies suitable for genomic studies.

We have extracted genomic DNA from both pretreatment tumor biopsies and blood samples of these 48 patients and performed whole genome (WGS) and exome sequencing. Coincident with these efforts, we have extracted high quality RNA from 42 of the 48 biopsies, and have processed RNA-seq profiles of the tumors. Among patients in this cohort, 24 (50%) achieved a pCR. Because no difference was observed between arms of the Z1041 trial, patients with or without a pCR were directly compared without adjusting for treatment regimen.

On average, each tumor and normal sample pair were sequenced to a depth of 49.4x and 32.5x by WGS respectively. In total, 15,027 candidate somatic variants were identified in known genes, including 11,606 missense, 860 nonsense, and 418 frameshift insertions or deletions. Preliminary results identified mutations in HER2 that were associated with the failure to achieve pCR in several cases. Furthermore, tumors assigned to the HER2-enriched subtype by RNA-seq analysis were more likely to achieve a pCR (19 compared to 8) than tumors with genomic features indicative of either the luminal or basal-like subtypes (3 compared to 12); a significant difference in the proportion of cases that achieve pCR (Fisher's exact test p-value = 0.0032). The identification of these features suggests that it may be possible to predict, at the time of diagnosis, those patients who will not respond to the current standard of care for HER2-positive breast cancer.

Citation Format: Lesurf R, Griffith O, Griffith M, Watson MA, Hoog J, Ellis MJ, Ota D, Suman VJ, Meric-Bernstam F, Leitch AM, Boughey JC, Unzeitig G, Buzdar AU, Hunt KK, Mardis ER. The genomics of response to neoadjuvant trastuzumab and chemotherapy in HER2-positive breast cancer – Results from the ACOSOG Z1041 (Alliance) trial. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD6-02.

Additional variables other than AJCC staging show clinical utility for predicting survival in colon cancer

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Background: The most important predictor of colon cancer patient outcome is disease stage at the time of surgery. However, staging does not accurately predict survival for all patients undergoing a resection with curative intent. The aim of this study was to analyze clinical and pathological characteristics of patients undergoing curative colon cancer, in order to identify characteristics, in addition to stage, predictive of disease outcome. Methods: Between 1997 and 2005 data for 114 patients undergoing curative resection for colon cancer at a tertiary care institution were collected. Clinical and pathological characteristics evaluated were: age, gender, tumor location, tumor size, scheduled vs emergent surgery, pathologic margin status, TNM stage, pathologic grade, number of positive lymph nodes, total number of lymph nodes resected, vascular and lymphatic invasion. Characteristics found to be significant in a Kaplan-Meier univariate survival analysis were included in a multivariate stepwise logistic regression analysis. Patient outcomes studied were overall survival, cancer specific survival, and disease free survival. Results: From the 114 patients examined in this cohort the mean age was 67 years, the male to female ratio was 0.8:1, and the mean follow up time was 2.61 years. Overall survival, cancer specific survival, and disease free survival were calculated to be 83.3%, 91.2% and 84.2%, respectively. Statistically significant variables by univariate analysis were: AJCC stage, number of positive lymph nodes, pathologic N stage, lymphatic and vascular invasion by the primary tumor. Further multivariate analysis revealed that lymphatic invasion was the only significant independent influence for predicting disease recurrence. Conclusions: Clinicopathologic characteristics, in addition to AJCC disease stage, may be of clinical utility in predicting outcome for patients who have undergone curative resection for colon cancer. Further evaluation of these clinicopathologic characteristics should be carried out in a larger colon cancer patient cohort.

No significant financial relationships to disclose.

Technetium-99m sestamibi uptake in human breast carcinoma cell lines displaying glutathione-associated drug-resistance

An in vitro study was designed to evaluate the uptake of sestamibi (MIBI) in P-glycoprotein (Pgp) and glutathione-associated (GSH) multidrug-resistant (MDR) cell lines. MIBI uptake was studied in various human breast carcinoma cell lines, i.e. in wild-type (MCF7/wt) cells, in adriamycin-resistant (MCF7/adr) cells which express Pgp and in melphalan-resistant (MCF7/mph) cells with increased levels of GSH. The effects of buthiomine sulphoximine (BSO) and verapamil on MIBI uptake were also studied in the MCF7/mph and MCF7/adr cells respectively. The cells were incubated for 1 h with a dose of 0.1 MBq thallium-201 and technetium-99m MIBI. Both MIBI and 201Tl uptakes were higher for MCF7/mph cells than for the other cells studied. The mean MIBI uptake in MCF7/adr cells was significantly lower than that in MCF7/wt cells (1.9%+/-0.5% vs 3. 1%.0.6%; P <0.01). Verapamil treatment increased the MIBI uptake in MCF7/adr cells (to 2.6%.0.3%; P <0.05). Treatment of MCF7/mph cells with BSO resulted in a significant reduction in GSH content (from 243.2+/-81.1 nmol/mg protein to 17.6+/-4.4 nmol/mg protein; P <0. 001). However, MIBI uptake in BSO-treated and untreated MCF7/mph cells was similar (4.43%+/-0.5% and 5.93%+/-1.7%, respectively; P >0. 1). This study suggests that the uptake of MIBI is not diminished by glutathione-associated drug resistance and that MIBI uptake in a tumour sample does not necessarily indicate that a cancer is sensitive to drugs.