Harmonization of tumor mutation burden testing with comprehensive genomic profiling assays: an IQN Path initiative

BACKGROUND

Although conflicting results emerged from different studies, the tumor mutational burden (TMB) appears as one of most reliable biomarkers of sensitivity to immune checkpoint inhibitors. Several laboratories are reporting TMB values when performing comprehensive genomic profiling (CGP) without providing a clinical interpretation, due to the lack of validated cut-off values. The International Quality Network for Pathology launched an initiative to harmonize TMB testing with CGP assay and favor the clinical implementation of this biomarker.

METHODS

TMB evaluation was performed with three commercially available CGP panels, TruSight Oncology 500 (TSO500), Oncomine Comprehensive Plus Assay (OCA) and QIAseq Multimodal Panel (QIA), versus the reference assay FoundationOne CDx (F1CDx). Archived clinical samples derived from 60 patients with non-small cell lung cancer were used for TMB assessment. Adjusted cut-off values for each panel were calculated.

RESULTS

Testing was successful for 91.7%, 100%, 96.7% and 100% of cases using F1CDx, TSO500, OCA and QIA, respectively. The matrix comparison analysis, between the F1CDx and CGP assays, showed a linear correlation for all three panels, with a higher correlation between F1CDx and TSO500 (rho=0.88) than in the other two comparisons (rho=0.77 for QIA; 0.72 for OCA). The TSO500 showed the best area under the curve (AUC, value 0.96), with a statistically significant difference when compared with the AUC of OCA (0.83, p value=0.01) and QIA (0.88, p value=0.028). The Youden Index calculation allowed us to extrapolate TMB cut-offs of the different panels corresponding to the 10 mutations/megabase (muts/Mb) cut-off of F1CDx: 10.19, 10.4 and 12.37 muts/Mb for TSO500, OCA and QIA, respectively. Using these values, we calculated the relative accuracy measures for the three panels. TSO500 showed 86% specificity and 96% sensitivity, while OCA and QIA had lower yet similar values of specificity and sensitivity (73% and 88%, respectively).

CONCLUSION

This study estimated TMB cut-off values for commercially available CGP panels. The results showed a good performance of all panels on clinical samples and the calculated cut-offs support better accuracy measures for TSO500. The validated cut-off values can drive clinical interpretation of TMB testing in clinical research and clinical practice.

Low Impact of Clonal Hematopoiesis on the Determination of RAS Mutations by Cell-Free DNA Testing in Routine Clinical Diagnostics

Targeted sequencing of circulating cell-free DNA (cfDNA) is used in routine clinical diagnostics for the identification of predictive biomarkers in cancer patients in an advanced stage. The presence of KRAS mutations associated with clonal hematopoiesis of indeterminate potential (CHIP) might represent a confounding factor. We used an amplicon-based targeted sequencing panel, covering selected regions of 52 genes, for circulating cell-free total nucleic acid (cfTNA) analysis of 495 plasma samples from cancer patients. The cfDNA test failed in 4 cases, while circulating cell-free RNA (cfRNA) sequencing was invalid in 48 cases. In the 491 samples successfully tested on cfDNA, at least one genomic alteration was found in 222 cases (45.21%). We identified 316 single nucleotide variants (SNVs) in 21 genes. The most frequently mutated gene was TP53 (74 variants), followed by KRAS (71), EGFR (56), PIK3CA (33) and BRAF (19). Copy number variations (CNVs) were detected in 36 cases, while sequencing of cfRNA revealed 6 alterations. Analysis with droplet digital PCR (ddPCR) of peripheral blood leukocyte (PBL)-derived genomic DNA did not identify any KRAS mutations in 39 cases that showed KRAS mutations at cfDNA analysis. These findings suggest that the incidence of CHIP-associated KRAS mutations is relatively rare in routine clinical diagnostics.

Next Generation Sequencing-Based Profiling of Cell Free DNA in Patients with Advanced Non-Small Cell Lung Cancer: Advantages and Pitfalls

Lung cancer (LC) is the main cause of death for cancer worldwide and non-small cell lung cancer (NSCLC) represents the most common histology. The discovery of genomic alterations in driver genes that offer the possibility of therapeutic intervention has completely changed the approach to the diagnosis and therapy of advanced NSCLC patients, and tumor molecular profiling has become mandatory for the choice of the most appropriate therapeutic strategy. However, in approximately 30% of NSCLC patients tumor tissue is inadequate for biomarker analysis. The development of highly sensitive next generation sequencing (NGS) technologies for the analysis of circulating cell-free DNA (cfDNA) is emerging as a valuable alternative to assess tumor molecular landscape in case of tissue unavailability. Additionally, cfDNA NGS testing can better recapitulate NSCLC heterogeneity as compared with tissue testing. In this review we describe the main advantages and limits of using NGS-based cfDNA analysis to guide the therapeutic decision-making process in advanced NSCLC patients, to monitor the response to therapy and to identify mechanisms of resistance early. Therefore, we provide evidence that the implementation of cfDNA NGS testing in clinical research and in the clinical practice can significantly improve precision medicine approaches in patients with advanced NSCLC.

The potential of monitoring treatment response in non-small cell lung cancer using circulating tumour cells

Introduction: Circulating tumor cell (CTC) counts represent an attractive strategy for monitoring response to therapy in patients with advanced non-small cell lung cancer (NSCLC). Changes in the CTCs number during the treatment have been proposed as a predictive biomarker of response to both chemotherapy and targeted therapies. Profiling of CTCs might also allow the assessment of the dynamics of predictive biomarkers such as EGFR, ALK, ROS1, and PD-L1, and provide relevant information in patients progressing on treatment with targeted agents including immunotherapeutics. Areas covered: A search of peer-reviewed literature in bibliographic databases was undertaken to discuss studies on CTCs and their predictive role in NSCLC. Expert opinion: To date, some challenges limit the clinical utility of CTCs in monitoring the response to treatment in NSCLC. The standardization of techniques for CTCs isolation and characterization and their validation on larger cohorts of patients might help to translate CTCs analysis in the clinic. However, studies on CTCs can provide information on molecular mechanisms involved in NSCLC progression and in the acquired resistance to treatments.

Genomic Profiling of KRAS/NRAS/BRAF/PIK3CA Wild-Type Metastatic Colorectal Cancer Patients Reveals Novel Mutations in Genes Potentially Associated with Resistance to Anti-EGFR Agents

Previous findings suggest that metastatic colorectal carcinoma (mCRC) patients with KRAS/NRAS/BRAF/PIK3CA wild-type (quadruple-wt) tumors are highly sensitive to anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (MoAbs). However, additional molecular alterations might be involved in the de novo resistance to these drugs. We performed a comprehensive molecular profiling of 21 quadruple-wt tumors from mCRC patients enrolled in the "Cetuximab After Progression in KRAS wild-type colorectal cancer patients" (CAPRI-GOIM) trial of first line FOLFIRI plus cetuximab. Tumor samples were analyzed with a targeted sequencing panel covering single nucleotide variants (SNVs), insertions/deletions (Indels), copy number variations (CNVs), and gene fusions in 143 cancer-related genes. The analysis revealed in all 21 patients the presence of at least one SNV/Indel and in 10/21 cases (48%) the presence of at least one CNV. Furthermore, 17/21 (81%) patients had co-existing SNVs/Indels in different genes. Quadruple-wt mCRC from patients with the shorter progression free survival (PFS) were enriched with peculiar genetic alterations in KRAS, FBXW7, MAP2K1, and NF1 genes as compared with patients with longer PFS. These data suggest that a wide genetic profiling of quadruple-wt mCRC patients might help to identify novel markers of de novo resistance to anti-EGFR MoAbs.

Pharmacokinetic drug evaluation of palbociclib for the treatment of breast cancer

INTRODUCTION

Cyclin-dependent kinases (CDKs) 4 and 6 regulate the transition from G0/G1-phase to S-phase of the cell cycle and have been identified as key drivers of proliferation in hormone receptor (HR)-positive breast cancer. The CDK4/6 inhibitor palbociclib in combination with endocrine therapy has been approved for treatment of HR-positive/HER2-negative breast cancer patients. Areas covered: In this article, we provide an update of the data on pharmacodynamics, pharmacokinetics, preclinical, and clinical studies of palbociclib in breast cancer. We performed a search of data on palbociclib in the PubMed and the clinicaltrials.gov databases, in the FDA website and in the ASCO and AACR proceedings. Expert opinion: In order to optimize the clinical outcome of HR-positive breast cancer patients treated with palbociclib, predictive biomarkers allowing patient selection are urgently needed. A recent study suggested that early dynamics of PIK3CA mutations in circulating tumor DNA might be a potential predictive biomarker for CDK4/6 inhibitors. Several clinical trials are ongoing with the aim to explore the activity of combinations of palbociclib with targeted agents and/or immunotherapy in the different subtypes of breast cancer in both metastatic and early phases of the disease. These combinations might allow improving the sensitivity and overcoming mechanisms of resistance.

RANTES and IL-6 cooperate in inducing a more aggressive phenotype in breast cancer cells

Both the CC chemokine ligand 5 (CCL5/RANTES) and interleukin-6 (IL-6), released by mesenchymal stem cells (MSCs) as well as by neoplastic cells, promote breast cancer cell progression through autocrine and paracrine mechanisms. In order to assess the effects of the simultaneous overexpression of RANTES and IL-6 on the tumor cell phenotype, we overexpressed both proteins in MCF-7 and MDA-MB-231 human breast cancer cell lines. MCF-7 cells co-expressing RANTES and IL-6 had a greater ability to form colonies in soft agar, compared to cells overexpressing RANTES or IL-6. In addition, both MCF-7 and MDA-MB-231 clones co-expressing RANTES and IL-6 showed a significantly higher ability to migrate and to invade. The analysis of phosphorylated ERK1/2, AKT and STAT3 signal transduction proteins revealed that several signaling pathways are simultaneously activated in cells overexpressing both factors. Finally, the overexpression of RANTES and IL-6 in MCF-7 cells significantly increased the in vivo tumor growth. Collectively, our data suggest that the simultaneous expression of IL-6 and RANTES produces a more aggressive phenotype in breast cancer cells and provide evidence that IL-6 and RANTES might represent potential targets for novel therapeutic strategies aimed to block the tumor-stroma interaction.

VEGF as a potential target in lung cancer

Introduction The vascular endothelial growth factor A (VEGF) is the main mediator of angiogenesis. In addition, VEGF contributes to cancer growth and metastasis directly targeting tumor cells. VEGF overexpression and/or high VEGF serum levels have been reported in lung cancer. Areas covered We searched Pubmed for relevant preclinical studies with the terms 'lung cancer' 'VEGF' and 'in vivo'. We also searched the Clinicaltrials.gov database, the FDA and the EMA websites for the most recent updates on clinical development of anti-VEGF agents. Expert opinion VEGF plays an important role in sustaining the development and progression of lung cancer and it might represent an attractive target for therapeutic strategies. Nevertheless, clinical trials failed to attend the promising expectations deriving from preclinical studies with anti-VEGF agents. To improve the efficacy of anti-VEGF therapies in lung cancer, potential strategies might be the employment of combinatory therapies with immune checkpoint inhibitors or agents that inhibit signaling pathways and proangiogenic factors activated in response to VEGF blockade, and the identification of novel targets in the VEGF cascade. Finally, the identification of predictive markers might help to select patients who are more likely to respond to anti-angiogenic drugs.

Abstract 4343: Effects of the co-expression of RANTES and IL-6 on the transformed phenotype of breast cancer cells

Introduction: Cells of the tumor microenvironment play an important role in the progression of breast cancer through their interaction with cancer cells. In this regard, mesenchymal stem cells greatly increased the metastatic potential of breast cancer cells through the secretion of the chemokine CCL5/RANTES. In addition, we demonstrated that breast cancer cells migrate in response to either recombinant RANTES or interleukin-6 (IL-6). Starting from this observation, we analyzed whether the co-expression of RANTES and IL-6 induced a more aggressive phenotype in breast cancer cells.

Methods: MCF-7 and MDA-MB-231 breast cancer cells were transfected with expression vectors coding for human RANTES and IL-6. XMAP Bio-Plex Cytokine arrays were employed to measure the levels of secreted RANTES and IL-6. To evaluate the proliferation of stable clones, anchorage-independent growth assays were used. Migration and invasion were analyzed using commercially available kits. Tumor growth in vivo was determined after injection of transfected cells in the mammary fat pad of nude mice.

Results: MCF-7 and MDA-MB-231 clones that stably overexpressed RANTES and/or IL-6 were isolated after selection with appropriate antibiotics. Stable transfectants produced higher levels of secreted RANTES and IL-6 than control cells trasfected with mock vectors. To evaluate whether RANTES and IL-6 induced a more aggressive phenotype in breast cancer cells, we analyzed the proliferation, migration and invasive ability of stable clones. MCF-7 cells co-expressing RANTES and IL-6 had a greater ability to form colonies in soft agar, compared to cells overexpressing RANTES or IL-6. In addition, both MCF-7 and MDA-MB-231 clones co-expressing RANTES+IL6 showed a significantly higher ability to migrate through a fibronectin-coated and to invade through a matrigel-coated matrix. The analysis of phosphorylated ERK1/2, AKT and STAT3 signal transduction proteins revealed that in cells overexpressing both RANTES and IL-6 more signaling pathways are simultaneously activated as compared with cells overexpressing a single factor. Finally, MCF-7 cells overexpressing RANTES+IL6 showed a significant increase in in vivo tumor growth when clones were injected in the mammary fat pad of nude mice.

Conclusions: Taken together, our data suggest that the simultaneous expression of IL-6 and RANTES produce a more aggressive phenotype in breast cancer cells. This observation might be useful for the identification of potential targets for novel therapeutic strategies aimed to prevent breast cancer progression through the blockade of the tumor-stroma interaction.

Note: This abstract was not presented at the meeting.

Citation Format: Marianna Gallo, Daniela Frezzetti, Nicola Normanno, Antonella De Luca. Effects of the co-expression of RANTES and IL-6 on the transformed phenotype of breast cancer cells [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 4343. doi:10.1158/1538-7445.AM2017-4343

RNA-seq analysis reveals significant effects of EGFR signalling on the secretome of mesenchymal stem cells

Bone marrow-derived mesenchymal stem cells (MSCs) contribute to breast cancer progression by releasing soluble factors that sustain tumor progression. MSCs express functional epidermal growth factor receptor (EGFR) and breast cancer cells secrete EGFR-ligands including transforming growth factor-α (TGFα). Using RNA-sequencing, we analysed the whole transcriptome of MSCs stimulated with TGFα. We identified 1,640 highly differentially regulated genes: 967 genes up-regulated with Fold Induction (FI)≥1.50 and 673 genes down-regulated with FI≤0.50. When highly regulated genes were categorized according to GO molecular function classification and KEGG pathways analysis, a large number of genes coding for potentially secreted proteins or surface receptors resulted enriched following TGFα treatment, including VEGFA, IL6, EREG, HB-EGF, LIF, NGF, NRG1, CCL19, CCL2, CCL25 and CXCL3. Secretion of corresponding proteins was confirmed for selected factors. Finally, we identified 4,377 and 4,262 alternatively spliced genes in untreated and TGFα-treated MSCs, respectively. Among these, an unannotated splice variant of VEGFA coding for a secreted VEGF protein of 172 aminoacids (VEGFA₁₇₂), was found only in MSCs stimulated with TGFα. These findings suggest that EGFR activation in MSCs leads to a significant change in the expression of a wide array of genes coding for secreted proteins that can significantly enhance tumor progression.

Abstract 1509: Transcriptome analysis reveals significant effects of EGFR signaling on the secretome of mesenchymal stem cells

Mesenchymal stem cell (MSCs) are recruited by developing tumors, where MSCs release factors that enhance tumor cell proliferation and migration. Since different carcinomas synthesize epidermal growth factor (EGF)-like peptides and MSCs express the EGF receptor (EGFR), we hypothesize that EGFR signaling might mediate the interaction between MSCs and tumor cells. In order to comprehensively assess the mechanisms and factors that are regulated by EGFR signaling in MSCs and are involved in the interaction between MSCs and tumor cells, we analysed the transcriptome of MSCs cultured in absence or in presence of transforming growth factor α (TGFα), one of the main ligands of the EGFR, by using massively parallel sequencing. Libraries were prepared from poly-A RNA from not-stimulated (MSC-CTRL) or TGFα-stimulated (MSC-TGFα) MSCs. Sequencing was performed on the SOLiD 5500xl platform using the paired-end protocol (75bp + 35bp). The experiments were repeated in quadruplicate, and the average number of reads obtained in the 4 replicates resulted of about 37 million for MSC-CTRL, and 47 million for MSC-TGFα. The quality analysis of raw data showed that 75% of reads at the 75th position had quality values above 14. The mapping of the sequence reads to human hg19 reference genome evidenced a coverage ranging between 79.5% and 81.7% for MSC-CTRL, and between 76.3% and 79.0% for MSC-TGFα. The number of observed counts was normalized for the length of the element and the number of mapped reads, namely RPKM (Reads Per Kilobase per Million of mapped reads). The RPKM values obtained in the 4 replicates were compared by ANOVA test and the very high p-value (of about 1) demonstrated that the replicates were not statistically different. The differential gene expression in MSC-CTRL and MSC-TGFα was represented as fold induction (FI). When selecting genes for which the average count value of the 4 replicates was equal or higher than 1, 8946 genes resulted to have FI>1 and 10305 genes FI<1 according to RPKM values. Next, we focused the attention on 274 genes coding for secreted proteins, including interleukins, chemokines, angiogenesis factors, growth factors of the EGF, IGF and FGF families and their receptors. Using as cutoff a count value equal or higher than 1, 47 genes were considered not expressed, 126 genes resulted to have FI>1.0, 91 genes FI<1.0 and 10 genes FI=1.0. Among the secreted proteins investigated, a number of angiogenic factors were significantly modulated in MSCs by TGFα treatment. Analysis of secreted proteins, performed with XMAP based assays, confirmed that activation of EGFR signaling induces in MSCs the secretion of several pro-angiogenic factors, including VEGF, IL6, IL8, HGF and G-CSF. These findings strongly suggest that the EGFR-mediated interaction between MSCs and tumor cells induces in MSCs the secretion of factors that play an important role in tumor progression.

Citation Format: Antonella De Luca, Cristin Roma, Francesca Fenizia, Francesca Bergantino, Marianna Gallo, Daniela Frezzetti, Susan Costantini, Nicola Normanno. Transcriptome analysis reveals significant effects of EGFR signaling on the secretome of mesenchymal stem cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1509. doi:10.1158/1538-7445.AM2013-1509

The microRNA-processing enzyme Dicer is essential for thyroid function

Dicer is a type III ribonuclease required for the biogenesis of microRNAs (miRNAs), a class of small non-coding RNAs regulating gene expression at the post-transcriptional level. To explore the functional role of miRNAs in thyroid gland function, we generated a thyrocyte-specific Dicer conditional knockout mouse. Here we show that development and early differentiation of the thyroid gland are not affected by the absence of Dicer, while severe hypothyroidism gradually develops after birth, leading to reduced body weight and shortened life span. Histological and molecular characterization of knockout mice reveals a dramatic loss of the thyroid gland follicular architecture associated with functional aberrations and down-regulation of several differentiation markers. The data presented in this study show for the first time that an intact miRNAs processing machinery is essential for thyroid physiology, suggesting that deregulation of specific miRNAs could be also involved in human thyroid dysfunctions.

Upregulation of miR-21 by Ras in vivo and its role in tumor growth

miR-21 is a microRNA (miRNA) frequently overexpressed in human cancers. Here we show that miR-21 is upregulated both in vitro and in vivo by oncogenic Ras, thus linking this miRNA to one of the most frequently activated oncogenes in human cancers. Ras regulation of miR-21 occurs with a delayed kinetic and requires at least two Ras downstream pathways. A screen of human thyroid cancers and non-small-cell lung cancers for the expression of miR-21 reveals that it is overexpressed mainly in anaplastic thyroid carcinomas, the most aggressive form of thyroid cancer, whereas in lung its overexpression appears to be inversely correlated with tumor progression. We also show that a LNA directed against miR-21 slows down tumor growth in mice. Consistently, a search for mRNAs downregulated by miR-21 shows an enrichment for mRNAs encoding cell cycle checkpoints regulators, suggesting an important role for miR-21 in oncogenic Ras-induced cell proliferation.

A mammalian microRNA expression atlas based on small RNA library sequencing

MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.