More Than Results: The Clinical and Research Relationship in the Evolving Detection and Surveillance of SARS-CoV-2

INTRODUCTION

During the coronavirus disease 2019 (COVID-19) pandemic, real-time reverse transcription polymerase chain reaction (RT-PCR) became an essential tool for laboratories to provide high-sensitivity qualitative diagnostic testing for patients and real-time data to public health officials. Here we explore the predictive value of quantitative data from RT-PCR cycle threshold (Ct) values in epidemiological measures, symptom presentation, and variant transition.

METHODS

To examine the association with hospitalizations and deaths, data from 74,479 patients referred to the Avera Institute for Human Genetics (AIHG) for COVID-19 testing in 2020 were matched by calendar week to epidemiological data reported by the South Dakota Department of Health. We explored the association between symptom data, patient age, and Ct values for 101 patients. We also explored changes in Ct values during variant transition detected by genomic surveillance sequencing of the AIHG testing population during 2021.

RESULTS

Measures from AIHG diagnostic testing strongly explain variance in the South Dakota state positivity percentage (R2 = 0.758), a two-week delay in hospitalizations (R2 = 0.856), and a four-week delay in deaths (R2 = 0.854). Based on factor analysis of patient symptoms, three groups could be distinguished which had different presentations of age, Ct value, and time from collection. Additionally, conflicting Ct value results among SARSCoV- 2 variants during variant transition may reflect the community transmission dynamics.

CONCLUSIONS

Measures of Ct value in RT-PCR diagnostic assays combined with routine screening have valuable applications in monitoring the dynamics of SARS-CoV-2 within communities.

B cell-dependent subtypes and treatment-based immune correlates to survival in stage 3 and 4 lung adenocarcinomas

Lung cancer is the leading cause of cancer-related deaths worldwide. Surgery and chemoradiation are the standard of care in early stages of non-small cell lung cancer (NSCLC), while immunotherapy is the standard of care in late-stage NSCLC. The immune composition of the tumor microenvironment (TME) is recognized as an indicator for responsiveness to immunotherapy, although much remains unknown about its role in responsiveness to surgery or chemoradiation. In this pilot study, we characterized the NSCLC TME using mass cytometry (CyTOF) and bulk RNA sequencing (RNA-Seq) with deconvolution of RNA-Seq being performed by Kassandra, a recently published deconvolution tool. Stratification of patients based on the intratumoral abundance of B cells identified that the B-cell rich patient group had increased expression of CXCL13 and greater abundance of PD1+ CD8 T cells. The presence of B cells and PD1+ CD8 T cells correlated positively with the presence of intratumoral tertiary lymphoid structures (TLS). We then assessed the predictive and prognostic utility of these cell types and TLS within publicly available stage 3 and 4 lung adenocarcinoma (LUAD) RNA-Seq datasets. As previously described by others, pre-treatment expression of intratumoral 12-chemokine TLS gene signature is associated with progression free survival (PFS) in patients who receive treatment with immune checkpoint inhibitors (ICI). Notably and unexpectedly pre-treatment percentages of intratumoral B cells are associated with PFS in patients who receive surgery, chemotherapy, or radiation. Further studies to confirm these findings would allow for more effective patient selection for both ICI and non-ICI treatments.

Case report: 16-yr life history and genomic evolution of an ER+ HER2- breast cancer

Metastatic breast cancer is one of the leading causes of cancer-related death in women. Limited studies have been done on the genomic evolution between primary and metastatic breast cancer. We reconstructed the genomic evolution through the 16-yr history of an ER+ HER2- breast cancer patient to investigate molecular mechanisms of disease relapse and treatment resistance after long-term exposure to hormonal therapy. Genomic and transcriptome profiling was performed on primary breast tumor (2002), initial recurrence (2012), and liver metastasis (2015) samples. Cell-free DNA analysis was performed at 11 time points (2015-2017). Mutational analysis revealed a low mutational burden in the primary tumor that doubled at the time of progression, with driver mutations in PI3K-Akt and RAS-RAF signaling pathways. Phylogenetic analysis showed an early branching off between primary tumor and metastasis. Liquid biopsies, although initially negative, started to detect an ESR1 E380Q mutation in 2016 with increasing allele frequency until the end of 2017. Transcriptome analysis revealed 721 (193 up, 528 down) genes to be differentially expressed between primary tumor and first relapse. The most significantly down-regulated genes were TFF1 and PGR, indicating resistance to aromatase inhibitor (AI) therapy. The most up-regulated genes included PTHLH, S100P, and SOX2, promoting tumor growth and metastasis. This phylogenetic reconstruction of the life history of a single patient's cancer as well as monitoring tumor progression through liquid biopsies allowed for uncovering the molecular mechanisms leading to initial relapse, metastatic spread, and treatment resistance.

Abstract P4-05-20: Case report - 16 year life history and genomic evolution of an ER+ HER2- breast cancer

Introduction

Metastasis is the primary cause of cancer-related death, with genomic evolution between primary and metastatic breast cancer only recently being studied in smaller numbers. We reconstructed the tumor evolution of a female patient originally diagnosed with localized ER+ HER2- disease to investigate the molecular changes that triggered relapse after long term aromatase inhibitor (AI) therapy and tracked them during subsequent treatments. The patient was diagnosed in 2002, relapsed in 2012 (regional lymph node), progressed in 2015 (liver metastasis), and passed away in 2018. We performed DNA- and RNA-sequencing on FFPE tumor samples and multiple liquid biopsies. The patient underwent eight lines of therapy including genome guided targeted therapy.

Materials and Methods

Whole exome and transcriptome sequencing was performed on the patient's primary tumor site at diagnosis (T1) and a metastatic lymph node (M1). Targeted DNA sequencing was performed on a metastatic liver sample (M2, 315 genes) and on liquid biopsies (n=11, 70 genes) every 2-3 months from 2015-2018.

Results

The mutational landscape between timepoints T1, M1 and M2 revealed low mutational burden at diagnosis which ultimately doubled at progression with active mutational processes (APOBEC, POLE) showing concordance between timepoints. DNA-based analysis revealed multiple mutations in the PI3K-Akt signaling pathway. Two mutations were shared between the samples: a clonal PIK3CA Q546R and a TP53 E180K mutation detected as clonal in M1/M2 and subclonal in T1. Individual samples carried private driver mutations, ranging from n=4 in T1, n=7 in M1 to n=16 in M2. While T1 harbored a single clonal driver mutation, with additional driver mutations being subclonal, M1 and M2 harbored multiple clonal driver mutations and a smaller percentage of subclonal driver mutations. A phylogenetic tree showed branching off between T1 and M1/M2. Liquid biopsies, while initially negative, started to detect mutations found among T1, M1 and M2, with increasing allele frequency (AF) throughout time. By the end of 2016, an ESR1 E380Q mutation not previously detected was found at a low AF that had rapidly increased by the end of 2017. RNA-Seq analysis revealed 908 (209 up, 699 down) genes to be differentially expressed between T1 and M1. Most significantly downregulated genes in M1 were TFF1 and PGR indicating loss-of-sensitivity / resistance to AI therapy. Most upregulated genes in M1 included PTHLH, S100P, and SOX2 which have been implicated in promoting tumor growth and metastasis. Pathway analysis between T1 and M1 showed enrichment for the hallmark gene sets ‘Estrogen Response early and late’ and ‘Epithelial mesenchymal transition’.

Conclusions

This phylogenetic reconstruction of the life history of a single patient's cancer revealed an increased mutational rate over time between the patient's primary tumor at diagnosis and samples taken at relapse; and a high level of heterogeneity with metastatic sites sharing only one driver mutation with the primary tumor at diagnosis and having acquired multiple de-novo driver mutations. Transcriptome profiling aided in uncovering the mechanisms that lead to the patient's initial relapse, indicating expression profile changes that promote tumor progression and metastasis as well as reduced sensitivity / resistance to the patients AI based therapy. Monitoring tumor progression through frequent liquid biopsies allowed for the detection of mutations from multiple metastatic sites, in addition to the detection and growth of an AI resistant clone harboring an ESR1 E380Q mutation that was not present in any of the solid tissue samples.

Citation Format: Bing Xu, Anu Amallraja, Padmapriya Swaminathan, Rachel Elsey, Christel Davis, Stephanie Theel, Sarah Viet, Jason Petersen, Amy Krie, Gareth E Davies, Casey B Williams, Erik Ehli, Tobias Meissner. Case report - 16 year life history and genomic evolution of an ER+ HER2- breast cancer [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 P4-05-20.

Deep targeted sequencing analysis of hot spot mutations in non-small cell lung cancer patients from the Middle Eastern population

Background

The overall 5-year survival of lung cancer remains dismal despite the current treatment regimens. Testing for driver mutations has become routine practice for oncologists due to the presence of targeted therapy readily available for patients. Deep targeted sequencing through next generation sequencing (NGS) is an adequate methodology to detect mutations at multi-genetic levels. The molecular pathology of non-small cell lung cancer (NSCLC) is poorly understood in the Middle East and, to date, no other reports have been published on deep targeted sequencing of lung adenocarcinoma (LUAD) tissues.

Methods

Deep targeted sequencing using TruSeq Amplicon Cancer panel of 48 genes was performed on 85 formalin-fixed paraffin-embedded tissues from patients with LUAD who were treatment-naive at the time of the collection. Variants with an allele frequency higher than 10% were retained.

Results

Variant calling identified a total of 2,455 variants of which missense mutations were the most frequent (75.6%). All of our samples showed at least one mutation in one of the 10 most commonly mutated genes with FLT3 being the gene with the highest mutation rate (67%). TP53, KRAS and STK11 were the second, third and fourth most commonly mutated genes, respectively while EGFR mutation rate reached 22.4%.

Conclusions

To the best of our knowledge, this is the first hot spot profiling study on patients from this area. The frequencies of mutated genes presented in our study showed similarity to other reported outcomes. At least one mutation was detected in our cohort of LUAD.

RU 58,668, a new pure antiestrogen inducing a regression of human mammary carcinoma implanted in nude mice

RU 58,668, a new steroidal antiestrogen, has been synthesized. Its in vitro and in vivo pharmacological activities have been compared to those of tamoxifen and ICI 182,780. In vitro, it displayed affinities for human and murine estrogen receptors equivalent to those of 4-hydroxy-tamoxifen, along with moderate affinities for progestin and glucocorticoid receptors. RU 58,668 proved to be a potent antiproliferative agent on MCF-7 cells stimulated by estradiol, or by exogenous or endogenous growth factors (IC50, 0.01 nM). It also inhibited the growth of the insulin-stimulated T47D cell line. In vivo, RU 58,668 displayed a total anti-uterotrophic activity in mice or rats without exhibiting any agonistic effect. Moreover, RU 58,668 was the only antiestrogenic compound tested so far to be able to induce a long term regression of human mammary MCF-7 tumors implanted in nude mice, suggesting its potential use for the treatment of advanced breast cancer.

Quantitation of exposure to benzo[a]pyrene with monoclonal antibodies

It is now possible to quantitate carcinogen adducts on DNA by highly sensitive immunoassays. These techniques are particularly useful for screening human populations for exposure to potential environmental carcinogens. We have developed a panel of monoclonal antibodies that react with benzo(a)pyrene (BP) modified DNA to be used in an enzyme linked immunoassay (ELISA) to quantitate adduct levels of both human and animal samples. BALBc/Cr mice were immunized with either DNA modified by 7 beta, 8 alpha-dihydroxy-9 alpha, 10 alpha-epoxy-7,8,9, 10-tetrahydrobenzo(a)pyrene (BPDE-I-DNA) complexed electrostatically to methylated bovine serum albumin or with BPDE-I-modified guanosine conjugated with bovine serum albumin (BPDE-I-G-BSA). Four stable clones were produced from the spleen cells of animals immunized with BPDE-I-DNA and one from BPDE-I-G-BSA immunized animals. All antibodies were shown to be highly specific for BPDE-I-DNA and did not crossreact with nonmodified DNA or with N-2-acetylaminofluorene or 1-aminopyrene modified DNA. The antibodies differed in their sensitivity to BPDE-II-DNA, BPDE-I-poly G, BPDE-I-tetraols and BPDE-I-dG. In general, all the antibodies showed the greatest affinity for their original antigen. Those generated against modified DNA showed highest reactivity against modified DNA while the one antibody generated against the monoadduct showed highest reactivity with the monoadduct. These antibodies are currently being used in a highly sensitive competitive ELISA to quantitate levels of BP-DNA adducts in various animal and human tissue samples.