OP0232 HIGH PLASMA C4d/C4 IDENTIFIES LUPUS NEPHRITIS PATIENTS WITH DISEASE MEDIATED BY ACTIVATION OF THE CLASSICAL COMPLEMENT PATHWAY

Background

Proliferative lupus nephritis (LN) involves immune complex deposition in the kidney that can severely impact normal renal clearance mechanisms. Immune complexes can activate C1q and the classical complement cascade, and along with pathogenic anti-C1q antibodies (PACAs), may amplify inflammation and disease progression. Martin et al reported that circulating C4d, a marker of complement activation downstream of the C1 complex, correlated well with C4d immunohistochemistry score in kidney tissue and could be a sensitive and specific biomarker for diagnosing active LN.1

Objectives

To confirm and extend observations by Martin et al, and to extend a link between C4d, C1q activation, and PACA levels to identify patients most likely to have the classical complement pathway as a driving component of disease. Such patients would be potential candidates for anti-C1q therapy, such as ANX009, to dampen disease activity and slow disease progression (NCT04535752).

Methods

Plasma samples were collected from a cohort of 40 LN patients (20 with disease flare and 20 without disease flare) from the California Lupus Epidemiology Study (CLUES), a multi-racial/ethnic cohort of individuals with physician-confirmed systemic lupus erythematosus, and 20 healthy controls (Table 1). A panel of complement factors, including 15 complement protein and relevant complexes, were measured using an enzyme-linked immunosorbent assay. Clinical disease activity was measured using the Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) and proteinuria was evaluated by a random spot urine protein to creatinine ratio (UPCR).

Table 1.

Patient Demographics

CharacteristicsHealthy Control(n=20)LN Flare(n=20)LN Without Flare(n=20)Median age (years)*50 (31-60.8)28.5 (26-34.5)43.5 (33.5-52)Sex, n (%)Female18 (90)17 (85)18 (90)Demographics, n (%)Caucasian8 (40)1 (5)5 (25)Hispanic3 (15)9 (45)4 (20)African American1 (5)3 (15)3 (15)Asian8 (40)7 (35)8 (40)Median UPCR (mg/mg)*N/A1.8 (1.3-6.5)0.4 (0.2-0.6)Median SLEDAI*N/A12 (9-16)2 (2-4)

*Reported as median (IQR).

LN, lupus nephritis; N/A, not applicable; SLEDAI, Systemic Lupus Erythematosus Disease Activity Index; UPCR, urine protein:creatinine ratio.

Results

We observed evidence of coordinated complement activation in LN patients relative to healthy controls. Specifically, levels of C4d and the C4d/C4 ratio were highly increased in LN patients with flare, while levels of C1q, C1s, and C4 were decreased, consistent with activation of the classical complement pathway (increased activation and component consumption). The C4d/C4 ratio also correlated with levels of PACA isotypes 1 and 3 that are known to activate the classical pathway. Improvements in C4 and C4d/C4 ratio were associated with improvements in proteinuria and SLEDAI following treatment for disease flare, indicating their potential value as biomarkers of treatment response.

Conclusion

A subset of LN patients exhibited high C4d/C4 ratio along with specific markers of classical pathway activation, indicating that the classical complement pathway may be a driving component of their disease. Reduction in this ratio appears to correlate with treatment response, but its levels are generally not normalized, suggesting an insufficient resolution of complement-mediated inflammation by currently available treatments. Our data support a clinical hypothesis that a subset of LN patients may benefit from a precision medicine approach targeting the classical complement pathway (Figure 1). This hypothesis will be evaluated in a forthcoming clinical trial testing the subcutaneously administered C1q inhibitor ANX009 in patients with active LN.

References

[1]Martin M, Trattner R, Nilsson SC, et al. Plasma C4d Correlates With C4d Deposition in Kidneys and With Treatment Response in Lupus Nephritis Patients. Front Immunol. 2020;11:582737.

Acknowledgements

Supported by: Annexon Biosciences

Disclosure of Interests

Ann Mongan Employee of: Annexon Biosciences, Poojan Suri Employee of: Annexon Biosciences, Maze Therapeutics, Dean Richard Artis Shareholder of: Annexon Biosciences, Bristol Myer Squibb, Roche, Sanofi, BMS, J&J, Employee of: Annexon Biosciences, Ellen Cahir-McFarland Shareholder of: Annexon Biosciences, Employee of: Annexon Biosciences, Biogen, Henk-André Kroon Shareholder of: Annexon Biosciences, Employee of: Annexon Biosciences, Yaisa Andrews-Zwilling Employee of: Annexon Biosciences, Shawn Rose Employee of: Annexon, Johnson & Johnson, Sanjay Keswani Shareholder of: Annexon Biosciences, Nura Bio, Employee of: Annexon Biosciences, Nura Bio, Maria Dall’Era Consultant of: GSK, AstraZeneca, Biogen, Annexon Biosciences, Pfizer, Aurinia, Grant/research support from: Annexon Biosciences, GSK, Ted Yednock Shareholder of: Annexon Biosciences, Consultant of: Cortexyme, Employee of: Annexon Biosciences

Impact of long-term ibrutinib treatment on circulating immune cells in previously untreated chronic lymphocytic leukemia

This study evaluated long-term immunophenotypic changes in circulating levels of 24 immune cell subsets through 4 years of continuous treatment with first-line ibrutinib (420 mg once daily) in 31 patients with chronic lymphocytic leukemia (CLL) from the RESONATE-2 study, and compared them with untreated age-matched healthy donors (n = 20). Ibrutinib progressively decreased total B-cell counts and preferentially targeted malignant CLL B cells over normal B cells. Elevated counts of chronically activated, exhausted, and effector memory T cells were normalized within 6-16 months, while naive T cells remained mostly within healthy donor range (HDR). Immunosuppressive regulatory T cells and myeloid-derived suppressor cells were normalized within the first 1-2 years and then plateaued. Additionally, ibrutinib restored low counts of innate cell populations associated with antitumor immunity: plasmacytoid dendritic cells were restored to HDR after 2 years, and classical monocyte counts progressively and continuously increased toward HDR. Ibrutinib also consistently preserved circulating mature natural killer cell counts. The data indicate that ibrutinib continuously exerted positive effects on immune cell populations throughout 4 years of treatment, consistent with improved clinical outcomes observed in patients. The normalization of adaptive and innate immune cell populations suggests that long-term ibrutinib treatment mediates restoration of immunity.

Ibrutinib restores immune cell numbers and function in first-line and relapsed/refractory chronic lymphocytic leukemia

Ibrutinib positively modulates many T-cell subsets in chronic lymphocytic leukemia (CLL). To understand ibrutinib's effects on the broader landscape of immune cell populations, we comprehensively characterized changes in circulating counts of 21 immune blood cell subsets throughout the first year of treatment in patients with relapsed/refractory (R/R) CLL (n = 55, RESONATE) and previously untreated CLL (n = 50, RESONATE-2) compared with untreated age-matched healthy donors (n = 20). Ibrutinib normalized abnormal immune cell counts to levels similar to those of age-matched healthy donors. Ibrutinib significantly decreased pathologically high circulating B cells, regulatory T cells, effector/memory CD4⁺ and CD8⁺ T cells (including exhausted and chronically activated T cells), natural killer (NK) T cells, and myeloid-derived suppressor cells; preserved naive T cells and NK cells; and increased circulating classical monocytes. T-cell function was assessed in response to T-cell receptor stimulation in patients with R/R CLL (n = 21) compared with age-matched healthy donors (n = 18). Ibrutinib significantly restored T-cell proliferative ability, degranulation, and cytokine secretion. Over the same period, ofatumumab or chlorambucil did not confer the same spectrum of normalization as ibrutinib in multiple immune subsets. These results establish that ibrutinib has a significant and likely positive impact on circulating malignant and nonmalignant immune cells and restores healthy T-cell function.

Relative Selectivity of Covalent Inhibitors Requires Assessment of Inactivation Kinetics and Cellular Occupancy: A Case Study of Ibrutinib and Acalabrutinib

Kinases form an attractive class of targets for small molecule inhibitors, but similarity among their adenosine triphosphate binding sites presents difficulties for developing selective drugs. Standard methods of evaluating selectivity of most reversibly bound drugs account for binding affinity but not the two-step process, affinity and inactivation, occurring during covalent inhibition. To illustrate this concept, we assessed the selectivity of Bruton's tyrosine kinase (BTK) over TEC kinases by two novel therapeutics: ibrutinib and acalabrutinib. The two-step process and time-dependent inhibition unique to covalent inhibitors were evaluated with two biochemical assays measuring enzymatic function and inhibition kinetics. The selectivity for BTK over TEC found in these biochemical analyses was 1-1.5 for ibrutinib and 3.0-4.2 for acalabrutinib. To further assess drug selectivity in a more physiologically relevant context, we developed cell-based occupancy assays that quantify the percentage of drug-inactivated kinases. Cellular selectivity of BTK over TEC was determined after MWCL-1 cells, and samples from patients with chronic lymphocytic leukemia (CLL) were treated for durations and concentrations based on human pharmacokinetics of each drug. In MWCL-1 cells, BTK/TEC selectivities measured at 0.5, 1, and 3 hours were 2.53, 1.05, and 1.51 for ibrutinib and 0.97, 1.13, and 2.56 for acalabrutinib, respectively. The equivalent selectivity measured in samples from patients with CLL were 1.31 ± 0.27 and 1.09 ± 0.11 for ibrutinib and acalabrutinib, respectively. Collectively, our data show that when properly accounting for time-dependent factors and relevant cellular context, ibrutinib and acalabrutinib demonstrate similar selectivity for BTK over TEC. SIGNIFICANCE STATEMENT: This study shows relative selectivity of covalent inhibitors toward different kinase targets should be assessed with both affinity and inactivation kinetics to accurately account for time-dependent effects of covalent binding and assessed in a cellular matrix to reproduce the physiologic context of target inhibition. This is illustrated with a case study of ibrutinib and acalabrutinib for which selectivity assessment with appropriate assays, as opposed to measuring binding affinity with KINOMEscan alone, corroborate emerging clinical data demonstrating similar safety profiles between the therapies.

Abstract 1631: Sequencing the circulating and infiltrating T-cell repertoire on the Ion S5TM

T-cell repertoire (TCR) sequencing by next-generation sequencing (NGS) is a valuable tool for building a deeper understanding of the adaptive immune system. As immunotherapies, particularly T-cell dependent therapies, show increasing potential in treating cancer, the ability to gain a detailed, unbiased view of the TCR becomes imperative for biomarker discovery, immune response to treatment, and study of tumor microenvironments. A key question the field seeks to understand is the relationship between circulating T-cells and infiltrating T-cells at the tumor site. Here, we present a novel approach for TCR sequencing using the Ion S5 ™ sequencer which leverages simplified library construction workflows and offers a more complete characterization of the entire V(D)J region of TCRB. This method can leverage mRNA as input, minimizing requirements in starting materials and focusing sequencing to productive TCRB arrangements. This approach targets the constant (C) and the FR1 regions, minimizing the potential for primer bias and greatly increasing the phylogenetic information content compared to techniques that exclusively characterize the CDR3 domain. Our results show that the observed circulating T-cell repertoire size is approximately 2 orders of magnitude higher than the infiltrating T-cell repertoire. Accordingly, while it is difficult to fully capture the complete repertoire of circulating T-cells due to its vast diversity, we show that it is possible to reliably capture the complete infiltrating T-cell repertoire with as high as 10 samples on the Ion 530 ™ chip. Replicate sequencing runs of infiltrating T-cells offers correlation of ~0.9, indicating that the results were reproducible, and the samples were sequenced to appropriate depth. In summary, we believe that this workflow will allow researchers to more routinely characterize the infiltrating T-cell repertoire and offers the field a better understanding of the impact of repertoire diversity on tumor elimination.

Citation Format: Geoffrey Lowman, Elizabeth Linch, Lauren Miller, Denise Topacio-Hall, Timothy Looney, Alex Pankov, Yongming Sun, Xinzhan Peng, Mark Andersen, Fiona Hyland, Ann Mongan. Sequencing the circulating and infiltrating T-cell repertoire on the Ion S5TM [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 1631. doi:10.1158/1538-7445.AM2017-1631

Abstract 5363: Measuring gene expression at the tumor microenvironment: A comparison between nCounter PanCancer Immune Profiling Panel and Oncomine Immune Response Research Assay

The tumor microenvironment, especially infiltrating T lymphocytes and inflammatory molecules, is believed to be highly relevant to the tumor’s sensitivity to cancer checkpoint blockade therapy. At the same time, the exact markers that are predictive of response for each therapeutic agent are still the subject of active investigations. To address the need for better understanding of the effect of different T cell subsets, antigen presentation, and tumor killing, gene expression profiling presents an attractive means to simultaneously evaluate the tumor microenvironment and cancer cells. In this study we compare the results and performance of the nCounter PanCancer Immune Profiling Panel and the Oncomine Immune Response Research Assay, both of which are designed to measure the expression of genes indicative of an immune response and potential immune-editing activities by tumor cells. The nCounter panel detects gene expression by counting unique probes that hybridize target mRNA, while the Oncomine panel employs NGS to sequence and count reads derived from the targets. While both panels are designed to work with FFPE samples, The nCounter panel expects 100 ng of unamplified RNA, while the Oncomine panel requires only 10 ng total RNA with its AmpliSeq technology. The two panels share 254 common genes, which constitute the basis for this comparison. Across 12 cancer samples (breast, H&N, melanoma, NSCLC, and RCC), results show that the Oncomine panel offers 20% higher dynamic range, thereby providing more robust readouts about the differences among samples. More importantly, with virtually no background noise, the underlying NGS technology provides an absolute zero readout for non-expressing genes which significantly improves the sensitivity for detecting low expressing genes, as their presence can be confirmed by as few as two reads. The two technologies show moderate correlation (R ~ 0.7), with the Oncomine panel more strongly correlating with qPCR (R ~ 0.9). Finally, when clustered using all genes on the panel, only the Oncomine panel provides clear stratification of cancer types, thus allowing the panel to be used for tissue type confirmation in addition to evaluating the immune response.

Citation Format: Ann Mongan, Warren Tom, Janice Au-Young, Aleksandr Pankov, Gauri Ganpule, Fiona Hyland. Measuring gene expression at the tumor microenvironment: A comparison between nCounter PanCancer Immune Profiling Panel and Oncomine Immune Response Research Assay [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 5363. doi:10.1158/1538-7445.AM2017-5363

Abstract 3567: Sequencing the human TCRβ repertoire on the Ion S5™ System

Next-generation Sequencing (NGS) is proving an important tool in increasing understanding of the human immune system, and thereby cancer immunology. αβ-T cells are the primary constituents of human cell-mediated adaptive immunity. The antigen specificity of each αβ-T cell is encoded in the 500-600 bp transcript encompassing the variable portion of the rearranged TCRα and TCRβ subunits, which can be read via NGS in a process termed repertoire sequencing. Until now, the main challenge the field faces is the lack of a technology that can provide a contiguous read of 600 bp to minimize the complexity of designing bias-prone primers and informatics challenges of stitching short reads. Here we leverage the long read capability of Ion 530™ chip to comprehensively sequence all three CDR domains of the TCRβ chain. The Ion 530™ chip offers greater than 15 M productive reads, allowing a multiplex of 2-4 samples with sufficient coverage for most repertoire profiling studies. Initial testing with Leukocyte total RNA demonstrates that this multiplex PCR assay produced repertoires that were much more similar to data derived from 5’RACE protocol than the commonly used BIOMED2 primer set. This result suggested that the use of long reads minimizes bias by allowing targeting of less variable regions. To further assess the performance of the assay, we designed a model system of 30 plasmid controls containing common human T-cell CDR3 sequences. Each plasmid was amplified individually and sequenced to confirm the detection of a single clonal population. Analytical sensitivity of the assay and accuracy of the accompanied analysis solution were further evaluated by spiking in plasmid concentrations from 10 pg to 0.0001 pg (5 million to 50 copies) in a background of 100 ng cDNA reverse transcribed from leukocyte total RNA. Results showed the assay offers linearity over 5 orders of magnitude of decreasing input concentration. In summary, we have demonstrated a NGS workflow for TCRβ sequencing that offers multiplex flexibility on Ion S5 with sample to answer in less than 48 hours. For Research Use Only. Not for use in diagnostic procedures.

Citation Format: Denise S. Topacio-Hall, Tim Looney, Yongming Sun, Lauren Miller, Elizabeth Linch, Geoffrey Lowman, Lifeng Lin, Mark Andersen, Fiona Hyland, Ann Mongan. Sequencing the human TCRβ repertoire on the Ion S5™ System [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 3567. doi:10.1158/1538-7445.AM2017-3567

Abstract 5364: A targeted NGS solution to evaluate gene expression signature of the tumor microenvironment from 40 NSCLC FFPE and matched fresh frozen samples

Cancer cells and their surrounding non-malignant cells, including immune cells, signaling molecules, stromal and extracellular matrix, create the tumor microenvironment (TME). The composition of this TME plays important roles in tumor progression, evading growth suppressors and activating metastasis. However, the regulatory mechanism and function of each constituent remains poorly understood. With several checkpoint blockade therapy studies, the presence of PD-L1 has been reported to be a promising marker to predict positive response. Current IHC methods to measure PD-L1 are subjective and highly variable. A higher-throughput and standardized solution that can systematically measure gene expression of cells present in the TME has emerged to be a more desirable alternative. Here, we applied the OncomineTM Immune Response Research Assay to measure the expression of 395 genes in non-small cell lung cancer (NSCLC) samples from 40 matched FFPE and fresh frozen sample types. This assay leverages NGS technology to sequence and count reads derived from the original transcript. With an input requirement of 10 ng of total RNA, libraries were generated, templated on the Ion ChefTM and sequenced on the Ion S5TM System. Results showed that, despite small input amount, the expression profiles of FFPE and fresh frozen samples are highly correlated with an average correlation greater than 0.9. We selected 22 genes out of the panel to validate expression with qPCR using FFPE samples. These genes were selected to cover a range of low, medium, and high expressors per our NGS data. Again, we observed a strong correlation (R ~ 0.9) between NGS and qPCR data. Approximately 80% of the 40 samples show moderate to high expression of CD8+ T cell cytokines, IFNG and TNFa. We further found that the expression of CD8A and CD8B are highly correlated with CD4, suggesting the co-presence of both cytotoxic and helper T cells. High correlation among CD4, FOXP3, TGFB1, and IL2RA (CD25) also suggests that their expression can be used as markers for the presence of Treg cells. We conducted a differential expression analysis between a group of samples (n=8) with high percentage of surrounding and infiltrating lymphocytes and another group (n=5) with low stromal content but devoid of infiltrating lymphocytes. Interestingly, we found a large number of genes which annotated as markers for infiltrating lymphocytes (CTSS, CXCR4, CD37, SRGN, FCER1G, SAMHD1, and GZMA) are significantly up-regulated in samples with high percentage of surrounding and infiltrating lymphocytes. In summary, this study highlights the robustness of using a targeted panel to understand the composition and regulatory mechanism of the TME and tumor immune response.

Citation Format: Yuan-Chieh Ku, Warren Tom, Yongming Sun, Alex Pankov, Tim Looney, Fiona Hyland, Janice Au-Young, Ann Mongan. A targeted NGS solution to evaluate gene expression signature of the tumor microenvironment from 40 NSCLC FFPE and matched fresh frozen samples [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 5364. doi:10.1158/1538-7445.AM2017-5364

Abstract 3994: Using NGS to characterize 40 NSCLC tumor with gene expression and tumor infiltrating T cell repertoire profiling from FFPE and matched Fresh Frozen samples

The tumor microenvironment (TME) is made up of stromal cells, immune cells, signaling molecules, and blood vessels surrounding the tumor cells. It has emerged as a key factor in multiple stages of cancer progression, immune-escaping, and disease progression. The composition and activity of TME co-evolve with tumor cells and may likely affect how the cancer responses to immunotherapy. A clear understanding of the functional effect and evolution of the TME necessitates a comprehensive approach to identify key immune cells as well as to characterize signaling and inflammatory (immune-editing) activities at the tumor site. Here we are describing the use of a targeted NGS panel to detect aggregated gene expression and a novel AmpliSeqTM approach to profile the relative abundance of different T cell clones at the TME. Specifically, we measured the expression of 395 relevant genes that capture interferon and chemokine signaling, T and B cell activation, checkpoint pathway, tumor proliferation, and antigen presentation. By looking at the expression of markers specific to different effector cell types, this gene panel offers a high-level view of the composition of different lymphocyte infiltrates. Complementarily, the TCR sequencing assay provides an estimate of T cell diversity and therefore offering a different dimension of the immune response. We studied 40 NSCLC tumor samples, of which we have matched FFPE and fresh frozen specimens. With a targeted panel, we could detect expression of transcripts present as few as 50 copies in 10 ng of total RNA as input. Across 40 NSCLC samples, we were able to measure expression of many low expressing cytokines such as IL2, IL21, IL23, IFNG and TNF. We observed strong co-expression pattern among genes involved in type II interferon signaling, indicating that they’re informative of T cell activation. More specifically, we found strong correlation between CD8 expression and other T cell co-stimulatory receptors (CD28, CD80, CD86, CD40), suggesting that expression of these genes can be reliable surrogates for the protein counterparts as markers for CD8+ T cells. TCRβ was sequenced for each of the matched fresh frozen sample in duplicates. Clonotype abundance of replicates was highly correlated with each other, indicating that the assay was reliable, and the samples were sequenced to appropriated depth. We identified 2000-10,000 unique clones in each tumor sample; with the diversity index moderately correlated with the percentage of tumor infiltrating lymphocytes provided by pathology review. Together, these two assays provide a convenient means to characterize T cells and their activities in combating tumor cells, thereby offering insights into how that tumor may respond to a particular immunotherapy.

Note: This abstract was not presented at the meeting.

Citation Format: Ann Mongan, Geoffrey Lowman, Yuan-Chieh Ku, Timothy Looney, Lifeng Lin, Xinzhan Peng, Fiona Hyland. Using NGS to characterize 40 NSCLC tumor with gene expression and tumor infiltrating T cell repertoire profiling from FFPE and matched Fresh Frozen samples [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 3994. doi:10.1158/1538-7445.AM2017-3994

Tracking the interplay between circulating and tumor-infiltrating T cells using AmpliSeq-based Ion Torrent TCRβ immune repertoire sequencing

e14518

Background: TCRβ immune repertoire analysis by next-generation sequencing is emerging as a valuable tool for research studies of the tumor microenvironment and potential immune responses to future cancer immunotherapy. Here we describe a multiplex PCR-based TCRβ sequencing assay that takes advantage of the exceptionally low base-call error rate and long read capability of the Ion S5 530 chip. The S530 chip provides > 15M reads, allowing for sample sequencing in multiplex. The research assay utilizes AmpliSeq technology and Framework 1 and Constant gene targeting primers to provide comprehensive coverage of TCRβ CDR 1, 2 and 3 from RNA input with a hands-on time of less than 30 minutes. CDR region sequences reveal the antigen specificity of the receptor and may be genetically modified to increase TCR affinity for tumor antigen. Methods: We evaluated assay performance by sequencing TCRβ rearrangements from normal donor peripheral blood leukocyte (PBL) cDNA that had been spiked with 30 reference rearrangements taken from the literature. We then used our assay to evaluate the extent of clonal overlap between matched tumor infiltrating lymphocyte (TIL) and peripheral blood leukocyte repertoires in an individual with squamous cell carcinoma of lung. Results: Results from sequencing of spike-in reference rearrangements indicate that the assay is accurate and sensitive over 5 logs of input template amount while showing minimal amplification bias. Sequencing of matched PBL and TIL repertoires revealed that a subset of the PBL repertoire (8%) consisted of clones also found in TIL. Technical replicates showed high concordance (r > .96) in the frequency of detected clones, indicating that the results were reproducible and samples were sequenced to an appropriate depth. Conclusions: In summary, these data suggest that AmpliSeq-based multiplex PCR and Ion Torrent sequencing provide unbiased, reproducible, scalable, complete, and accurate information for immune repertoire research sequencing applications.

Verification of targeted gene expression profiling panel for identifying biomarker signatures for immunotherapy research

e23208

Background: Immunotherapy has led to an unprecedented and long-lasting response in susceptible populations. Despite the therapeutic potential of the treatment, identifying biomarkers and stratifying populations that are likely to respond has been a challenge. While gene expression profiling has previously been successfully used to stratify individuals, there exist limitations with the prevalent technologies. In particular, full transcriptome gene expression estimates use limited biological material to measure the concentrations of thousands of uninformative genes and often lacks the depth required to accurately measure expression of lowly-expressed genes. These low-expressing genes may be critical to the identification of a signature associated with susceptible population. Methods: To efficiently measure the expression of the genes potentially informative of an immunotherapy response, we developed a high-throughput targeted gene expression solution measured with our RNA Ion Oncomine™ Immune Response Research Assay panel* containing 395 genes. This panel provides information about the expression of genes involved in tumor checkpoint inhibition, as well as markers of T cell signaling pathway, interferon signaling, tumor infiltrating lymphocytes (TIL). Results: We used publicly-available TCGA data to characterize the complexities of estimating unbiased gene expression from a targeted panel and developed a solution using a new normalization procedure that allows for accurate comparisons of samples within cancer types. Furthermore, we verified that lowering the RNA input amount or changing the assay operator does not contribute to a large variation in the gene expression estimates; each only accounts for less than 10% of variance of the average gene when the assay is compared across biological samples. Conclusions: Creating a panel that achieved high reproducibility and accurate expression estimates of key immune response genes allowed us to accurately separate high and low TIL samples within squamous and adenocarcinoma samples, emphasizing the utility of the panel to biomarker immunotherapy research. *For Research Use Only. Not for use in diagnostic procedures.

Abstract B17: Validation of targeted gene expression profiling panel for identifying biomarker signatures of immunotherapy responders

Cancer immunotherapy has led to an unprecedented, long-lasting response in populations susceptible to the therapies. Despite the therapeutic potential, identifying biomarkers and stratifying populations that are likely to respond has been a challenge. Gene expression profiling has previously been successfully used to stratify individuals based on survival and treatment characteristics, but there exist limitations with the prevalent technologies. In particular, full transcriptome gene expression estimates use limited biological material to measure the concentrations of tens of thousands uninformative genes and often lack the depth required to accurately measure expression levels of lowly-expressed genes. These genes may be critical to the identification of a signature associated with immunotherapy responders. To efficiently measure the expression of the key genes potentially informative of an immunotherapy response, we developed a high-throughput targeted gene expression solution measured by our RNA Ion Oncomine Immune Response Profiling panel* containing 395 genes. This panel provides information about the expression of genes involved in tumor checkpoint inhibition (including CTLA4, PD-1, PD-L1, OX-40, 4-1BB, TIM3, LAG3) and other targets such as CSF1R, and IDO1, as well as additional markers of T cell signaling pathway, interferon signaling, and markers of tumor infiltrating lymphocytes (TIL). We used publicly available TCGA data to demonstrate the need and develop a solution for a new normalization procedure that allows for accurate comparisons of samples within various cancer types. Furthermore, we verified a linear and unbiased estimate of fold change in our assays across mixing concentrations of a cell-line titration experiment. Finally, by achieving a high correlation (r > .99) of technical replicates, along with robust expression estimation even at low input amounts (10 ng RNA), our panel offers a valuable solution for biomarker research in cancer immunotherapy.

*For research use only. Not for use in diagnostic procedures.

Citation Format: Aleksandr Pankov, Yongming Sun, Yuan-Chieh Ku, Warren Tom, Jianping Zheng, Timothy Looney, Janice Au-Yong, Fiona Hyland, Ann Mongan. Validation of targeted gene expression profiling panel for identifying biomarker signatures of immunotherapy responders. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr B17.

Abstract 3622: Complete workflow for detection of low frequency somatic mutations from cell-free DNA using Ion Torrent™ platforms

Research detecting of somatic mutations in circulating cell-free DNA (cfDNA) using research blood samples from subjects previously diagnosed with cancer provides a potential non-invasive approach to monitor cancer status and evaluate cancer evolution in the future. However, most of the existing mutation detection methods show insufficient sensitivity to detect cfDNA mutations since only small amount of mutant gene fragments, derived from tumor cells, is present in a large amount of normal circulating DNA background.

We demonstrated a complete workflow that includes blood collection, cfDNA isolation, library preparation, sequencing, and data analysis to enable detection of rare DNA variants in blood plasma samples. Blood samples were collected using Streck™ DNA tubes followed by plasma preparation and cfDNA isolation using MagMAX™ Cell-Free DNA Isolation Kit. Library preparation was performed using Oncomine™ lung cfDNA kit. Barcoded libraries were pooled and sequenced on Ion Torrent™ Next Generation Sequencing Platforms. Sequencing data was analyzed in Torrent Suite™ using variantCaller-cfDNA plugin. ∼150 biomarkers relevant to non-small cell lung cancer were interrogated in one sequencing run.

We demonstrated detection sensitivity at 0.1% frequency using engineered mutants that were spiked into control DNA samples. The workflow was tested on a set of research samples from matched tumor FFPE and blood plasma collected from research subjects with non-small cell lung cancer (NSCLC). About 1 mL of plasma was processed using the workflow described above. RecoverAll™ Multi-Sample RNA/DNA Isolation Workflow was used to isolate DNA from FFPE samples, followed by library preparation, sequencing and data analysis using the same workflow described above. Summary of variant calls from matched cfDNA and FFPE tumor samples are presented here. Results indicate high sensitivity of the workflow and expected levels of concordance between variants detected in the two types of research samples.

In this study, we developed a highly sensitive and reliable research workflow to detect rare somatic mutations in circulating cfDNA samples. Significant overlapping of mutations discovered in FFPE tumor and cfDNA samples suggests that this workflow may be used to monitor tumor dynamics in NSCLC and potentially other tumors in the future.

Disclaimer: For research use only. Not for use in diagnostic procedures.

Citation Format: Jian Gu, Dumitru Brinza, Ann Mongan, Richard Chien, Dalia Dhingra, Fiona Hyland, Kelli Bramlett. Complete workflow for detection of low frequency somatic mutations from cell-free DNA using Ion Torrent™ platforms. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3622.

Abstract 3941: Novel biomarkers and multiplexed NGS to stratify FFPE NSCLC by tumor infiltrating lymphocytes and histopathology phenotypes

There is increasing evidence supporting the association of tumor infiltrating lymphocytes (TIL) and drug sensitivity of solid tumors. In particular, primary and meta-analyses have reported a positive correlation between TIL level and outcome in advanced non-small cell lung cancer (NSCLC) treated with checkpoint inhibitors such as PD-1 and PD-L1. Recent trials with immunotherapies have started including TIL assessment in the study protocol in recognition of this metric as a predictive and prognostic biomarker. TIL levels are typically quantified by visual assessment of H&E-stained tumor sections. While this approach is generally accepted as the standard, there is an increased recognition that visual assessment of H&E-stained slides lacks precision and is relatively subjective (Salgado R, 2015; Schalper KA, 2015). Furthermore, as investigators are often also interested in measurements of additional biomarkers such as IFNg as well as the drug targets, a gene panel approach offers a convenient solution to objectively quantify expression levels of these informative markers. Here we report the discovery and verification of a unique gene expression signature that is capable of stratifying FFPE samples of NSCLC tumors by TIL levels and histopathology phenotypes (adenocarcinoma vs. squamous cell carcinoma). Gene expression was measured by an RNA Ion AmpliSeq Gene Expression research panel* containing 200 assays. Each research sample was measured with replicates at library generation step and sequencing step. Technical replicates were found to have >0.99 correlation among each other. Assays on the panels were also found to be robust with respect to low input amount (1-10 ng RNA). *For Research Use Only. Not for use in diagnostic procedures.

Citation Format: Ann Mongan, Sophie Rozenzhak, Geoffrey Bien, David Chi, Hiroyoshi Nishikawa, Fiona Hyland, Jim Godsey. Novel biomarkers and multiplexed NGS to stratify FFPE NSCLC by tumor infiltrating lymphocytes and histopathology phenotypes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3941.

Abstract 3959: Detection of somatic mutations at 0.1% frequency from cfDNA in peripheral blood with a multiplex next-generation sequencing assay

Background:

Effective blood screening for tracking of recurrence and resistance of tumors may improve outcomes in the future. Research studies suggest that virtually all tumors carry somatic DNA mutations, and these may serve as biomarkers that also can be tracked in blood. One of the sources containing tumor DNA in blood is circulating cell-free DNA (cfDNA). Tumor DNA comes from different tumor clones, and its abundance in plasma can be very low at critical stages such as early recurrence or development of resistance. Hence, there is great interest in being able to detect mutation biomarkers at very low frequency from cfDNA for detection and characterization of tumor clones.

Method:

We present a research use only analysis workflow for peripheral monitoring that enables detection of low frequency DNA variants in blood.

We developed an analysis algorithm that models errors accumulated during amplification and sequencing, and accurately reconstructs sequence of original DNA molecules based on multiple next generation sequencing reads. The reads contain genomic sequence and an adaptor that allows identification of reads originated from the same DNA molecule. We then developed a variant calling method that uses accurately reconstructed sequences to enable sensitive and specific detection of somatic mutations to 0.1% allele ratio. We demonstrate the analysis in control and archived cfDNA research samples.

We used a next generation sequencing assay that allows interrogation of ∼150 biomarkers relevant in lung from COSMIC and Oncomine™ databases, and de-novo variant detection at ∼1,700 genomic positions in 11 genes implicated in non-small cell lung cancer (NSCLC).The assay delivers >95% on target reads and highly uniform amplification across targeted cfDNA molecules.

Results:

We tested the limits of variant detection in controlled dilution series and in cfDNA. First, we diluted engineered AcroMetrix™ Oncology Hotspot Control plasmids into background GM24385 genomic DNA down to 0.1% frequency, and then fragmented into fragments with average size of 170bp. The Acrometrix sample contains ∼45 common tumor mutations interrogated by our assay. Next, we used 0.1% Horizon's (HD780) cfDNA reference sample that contains 8 mutations at our hotspot positions including two large insertion and deletion variants of size >10bp. Finally, we performed analytical verification of variant detection performance in cfDNA using a dilution series of normal blood samples.

We achieved >95% sensitivity with >20ng input DNA and >90% sensitivity with ∼20ng input DNA and <1 false call per sample for variants in hotspot positions present at frequency 0.1%.

Conclusions:

This new lung cfDNA analysis workflow may facilitate researchers to study relevant NSCLC biomarkers at 0.1% frequency in cfDNA. Analysis is compatible with lower frequency variant detection, but will require higher input DNA amount and higher sequencing coverage.

Citation Format: Dumitru Brinza, Ann Mongan, Richard Chen, Dalia Dhingra, Jian Gu, Janice Au-Young, Fiona Hyland, Kelli Bramlett. Detection of somatic mutations at 0.1% frequency from cfDNA in peripheral blood with a multiplex next-generation sequencing assay. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3959.

Abstract 31: A new research solution for circulating cell free DNA with short amplicons allow accurate detection of 70 COSMIC mutations at 1% detection limit

Non-invasive determination of the resistance or recurrence of tumor development will allow for a safer, more cost effective method for cancer research. As circulating tumor DNA makes up only a small fraction of cell-free DNA (cfDNA) recovered from blood plasma, targeted sequencing offers an ideal tool for mutation detection. Furthermore, as cfDNA is more fragmented than genomic DNA, it presents new technical challenges. In particular, reports in the literature have shown that the majority of cfDNA fragment sizes fall between 120-200 bp, with a median length of 170 bp. Consistent with these reports, we observed an amplicon size dependent improvement in coverage with input samples containing high amounts of fragmented DNA (FFPE or cfDNA). To optimize for cfDNA selection, we have released an Ion AmpliSeq™ designer that offers amplicons of 100-140 bp in size. In this study we conducted a head-to-head comparison between short (100-140 bp) and long (135-175 bp) designs for the same set of targets. These two panels evaluate 1000 COSMIC hotspot mutations from 73 frequently mutated genes. We applied a protocol using magnetic beads to isolate cfDNA from one control (Coriel GM23485) and 3 cfDNA samples. We completed the molecular characterization of the isolated cfDNA using the multiplexing capabilities of Ion AmpliSeq™ library preparation and Ion PGM™ sequencer. Our results showed the short amplicon design led to an improvement of library yield that correlated with the amounts of fragmented DNA contained in the cfDNA samples. The shorter amplicon design also offered improved depth coverage and uniformity for fragmented DNA, while maintaining high performance with genomic DNA. Variant analysis of GM23485 with 70 known mutations at 1% allelic frequency showed >95% positive predictive value with no false negative. In short, the bead-based cfDNA isolation protocol and short amplicon designs offer a simple sample preparation workflow to facilitate rapid mutation detection for cfDNA in cancer research.

Citation Format: Ann Mongan, Richard Chien, Antonio Martinez-Alcantara, Fiona Hyland. A new research solution for circulating cell free DNA with short amplicons allow accurate detection of 70 COSMIC mutations at 1% detection limit. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 31.

High-throughput microarray-based enzyme-linked immunosorbent assay (ELISA)

A new generation biochip is described as capable of supporting high-throughput (HT), multiplexed enzyme-linked immunosorbent assays (ELISAs). These biochips consist of an optically flat, glass plate containing 96 wells formed by an enclosing hydrophobic Teflon mask. The footprint dimensions of each well and the plate precisely match those of a standard microplate. Each well contains four identical 36-element arrays (144 elements per well) comprising 8 different antigens and a marker protein. Arrays are formed by a custom, continuous flow, capillary-based print head attached to a precise, high-speed, X-Y-Z robot. The array printing capacity of a single robot exceeds 20,000 arrays per day. Arrays are quantitatively imaged using a custom, high-resolution, scanning charge-coupled device (CCD) detector with an imaging throughout of 96 arrays every 30 s. Using this new process, arrayed antigens were individually and collectively detected using standard ELISA techniques. Experiments demonstrate that specific multiplex detection of protein antigens arrayed on a glass substrate is feasible. Because of the open microarray architecture, the 96-well microarray format is compatible with automated robotic systems and supports a low-cost, highly parallel assay format. Future applications of this new high-throughput screening (HTS) format include direct cellular protein expression profiling, multiplexed assays for detection of infectious agents and cancer diagnostics.