Abstract 220: Performance assessment of the novel G4 sequencing platform for cancer research applications

Introduction: Next-generation sequencing (NGS) has become a critical tool for both biological research and in-vitro diagnostics, though there remains a need for new DNA sequencing platforms that combine high accuracy, speed, and flexible throughput to provide timely results and cost-effective operations. Here we evaluate the utility of the novel Singular Genomics G4 sequencing platform for cancer research applications by performing whole exome sequencing (WGS) of the human reference control HG001. We further demonstrate performance for methyl-seq, bulk RNA-seq, and scRNA-seq.

Methods: To assess performance, we prepared a human whole exome library (IDT xGen Exome) from HG001 gDNA, then sequenced the library via the G4 sequencing platform with F2 flowcells (150M read throughput) to yield 483M 2x150bp reads. Sequence quality and mapping metrics were obtained via GATK4 after read alignment to Grch38 via bwa mem. Germline variants were identified via DeepVariant v1.4 using the Illumina WES model, implemented via Parabricks; performance was assessed by hap.py. Methyl-seq performance was examined by methylDackel analysis of an EM-Seq library (NEB) prepared from 50ng HG001 gDNA and sequencing to 20x coverage via 2x150bp reads. Bulk RNA-seq performance was assessed by replicate sequencing of UHR total RNA on the G4 and Illumina NextSeq platforms. Single cell RNA-seq libraries were prepared from healthy donor PBMC via the 10x Chromium, sequenced on the G4 and Illumina NovaSeq, then analyzed via Cell Ranger, Scanpy and scvi-tools.

Results: Exome sequencing of HG001 yielded high quality data (single pass accuracy > 99.7% for R1 and R2) with even coverage of the genome (fold 80 =1.42). hap.py analysis of DeepVariant calls yielded a SNP and Indel F1 of 99.06 and 96.05%, respectively, over high confidence regions. Performance was high over challenging features such as low complexity DNA and GC rich regions. EM-Seq analysis revealed global distributions of cytosine methylation that closely matched public EM-Seq data derived from the Illumina NovaSeq. Bulk RNA-seq transcript counts were highly correlated across technical replicates (R2 = .990) and platforms (R2= .988). Pseudo-bulk analysis of scRNA-seq libraries showed high cross-platform correlation (R2= .982), with nearly identical CellTypist annotations (Adjusted Rand Index = .999).

Conclusions: The G4 sequencer delivers sequencing data on par with the state-of-the-art in NGS, but with a faster turnaround than traditional SBS systems. Notably, we observe a high concordance with the leading NGS platform for human DNA variant detection, methyl-seq, bulk RNA-seq and scRNA-Seq. We anticipate the rapid turnaround and flexible throughput of the G4 will have broad utility for basic and translational cancer research applications.

Citation Format: Kenneth Gouin, Liz LaMarca, Yu Xiang, Anne Decker, Sabrina Shore, Ryan Shultzaberger, Daan Witters, Timothy Looney, Martin M. Fabani, Eli Glezer. Performance assessment of the novel G4 sequencing platform for cancer research applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 220.

733 Immunological mechanisms of resistance to CDK4/CDK6 inhibitors in breast cancer

Background

Hormone receptor+ (HR+) breast cancer (BC) is the most frequent cause of BC-related deaths. CDK4/6 inhibitors (CDK4/6i) combined with endocrine therapy (ET) emerged as an effective approach for metastatic HR+ BC. However, >60% women with HR+ BC receiving CDK4/6i+ET ultimately relapse, potentially due to activation of poorly characterized immunosuppressive pathways in the tumor microenvironment (TME).1 Thus, strategies breaking resistance to CDK4/6i+ET in women with HR+ BC are urgently awaited. Radiation therapy (RT) mediates immunostimulatory effects that only partially overlap with those of CDK4/6i+ET,2 standing out as a promising therapeutic partner. Consistent with this notion, we recently demonstrated that RT followed by the CDK4/6i palbociclib + ET (RT-P+ET) enables superior tumor control in various immunocompetent mouse models of HR+ BC.3 These findings have inspired the design of a randomized phase II clinical trial testing P+ET vs. RT-P+ET in patients with oligometastatic HR+ BC (CIMER, NCT04563507). In this context, we set out to dissect the immunological mechanisms underlying sensitivity vs. resistance to treatment in HR+ BC exposed to P+ET vs. RT-P+ET.

Methods

To dissect the impact of these treatments on immune contexture in HR+ BC, we performed single-cell RNAseq on CD45+ cells infiltrating MPA/DMBA (M/D)-driven carcinomas established in immunocompetent mice (a unique model of luminal B BC), coupled to bulk RNAseq, bioinformatic analysis on public patient datasets, functional studies on ex vivo immune cells and efficacy studies.

Results

We observed that (1) RT and P+ET alone mediate partial efficacy correlating with accumulation of immunosuppressive TREG and IL17A-producing γδ T cells, respectively, (2) γδ T cell depletion improves the efficacy of P+ET, (3) RT-P+ET mediates superior (but incomplete) tumor control, which is partially offset by CD4+/CD8+ T cell co-depletion and correlates with limited infiltration by γδ T cells and TREGS, but accumulation of PD-L1 expressing myeloid cells and M2-polarized TREM2+ macrophages, which have been ascribed robust immunosuppressive effects in multiple settings4; and (4) that PD-1 blockage does not ameliorate the therapeutic effects of RT-P+ET (not shown), pointing to TREM2+ macrophages as to the main culprits for resistance in this setting.

Conclusions

Our observations suggest that γδ T cells and TREM2+ macrophages support the resistance of HR+ BC to CDK4/6i and RT-CDK4/6i, and hence constitute potential targets to delay disease progression.

References

Pandey et al. Molecular mechanisms of resistance to CDK4/6 inhibitors in breast cancer: a review. Int J Cancer 2019;145(5):1179–1188.

Rodriguez-Ruiz et al. Immunological impact of cell death signaling driven by radiation on the tumor microenvironment. Nat Immunol 2020;21(2):120–134.

Petroni et al. Radiotherapy delivered before CDK4/6 inhibitors mediates superior therapeutic effects in ER + Breast cancer. Clin Cancer Res 2021;27(7):1855–1863.

Xiong et al. A gene expression signature of TREM2 hi macrophages and γδ T cells predicts immunotherapy response. Nat Commun 2020;11(1):5084.

Ethics Approval

Animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) of Weill Cornell Medical College (n° 2019–2022).

Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans

A mysterious feature of Crohn's disease (CD) is the extra-intestinal manifestation of "creeping fat" (CrF), defined as expansion of mesenteric adipose tissue around the inflamed and fibrotic intestine. In the current study, we explore whether microbial translocation in CD serves as a central cue for CrF development. We discovered a subset of mucosal-associated gut bacteria that consistently translocated and remained viable in CrF in CD ileal surgical resections, and identified Clostridium innocuum as a signature of this consortium with strain variation between mucosal and adipose isolates, suggesting preference for lipid-rich environments. Single-cell RNA sequencing characterized CrF as both pro-fibrotic and pro-adipogenic with a rich milieu of activated immune cells responding to microbial stimuli, which we confirm in gnotobiotic mice colonized with C. innocuum. Ex vivo validation of expression patterns suggests C. innocuum stimulates tissue remodeling via M2 macrophages, leading to an adipose tissue barrier that serves to prevent systemic dissemination of bacteria.

Complimentary mechanisms of dual checkpoint blockade expand unique T-cell repertoires and activate adaptive anti-tumor immunity in triple-negative breast tumors

Triple-negative breast cancer (TNBC) is an aggressive and molecularly diverse breast cancer subtype typified by the presence of p53 mutations (∼80%), elevated immune gene signatures and neoantigen expression, as well as the presence of tumor infiltrating lymphocytes (TILs). As these factors are hypothesized to be strong immunologic prerequisites for the use of immune checkpoint blockade (ICB) antibodies, multiple clinical trials testing single ICBs have advanced to Phase III, with early indications of heterogeneous response rates of <20% to anti-PD1 and anti-PDL1 ICB. While promising, these modest response rates highlight the need for mechanistic studies to understand how different ICBs function, how their combination impacts functionality and efficacy, as well as what immunologic parameters predict efficacy to different ICBs regimens in TNBC. To address these issues, we tested anti-PD1 and anti-CTLA4 in multiple models of TNBC and found that their combination profoundly enhanced the efficacy of either treatment alone. We demonstrate that this efficacy is due to anti-CTLA4-driven expansion of an individually unique T-cell receptor (TCR) repertoire whose functionality is enhanced by both intratumoral Treg suppression and anti-PD1 blockade of tumor expressed PDL1. Notably, the individuality of the TCR repertoire was observed regardless of whether the tumor cells expressed a nonself antigen (ovalbumin) or if tumor-specific transgenic T-cells were transferred prior to sequencing. However, responsiveness was strongly correlated with systemic measures of tumor-specific T-cell and B-cell responses, which along with systemic assessment of TCR expansion, may serve as the most useful predictors for clinical responsiveness in future clinical trials of TNBC utilizing anti-PD1/anti-CTLA4 ICB.

A comprehensive method for identification of suitable reference genes in extracellular vesicles

Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is one of the most sensitive, economical and widely used methods for evaluating gene expression. However, the utility of this method continues to be undermined by a number of challenges including normalization using appropriate reference genes. The need to develop tailored and effective strategies is further underscored by the burgeoning field of extracellular vesicle (EV) biology. EVs contain unique signatures of small RNAs including microRNAs (miRs). In this study we develop and validate a comprehensive strategy for identifying highly stable reference genes in a therapeutically relevant cell type, cardiosphere-derived cells. Data were analysed using the four major approaches for reference gene evaluation: NormFinder, GeNorm, BestKeeper and the Delta Ct method. The weighted geometric mean of all of these methods was obtained for the final ranking. Analysis of RNA sequencing identified miR-101-3p, miR-23a-3p and a previously identified EV reference gene, miR-26a-5p. Analysis of a chip-based method (NanoString) identified miR-23a, miR-217 and miR-379 as stable candidates. RT-qPCR validation revealed that the mean of miR-23a-3p, miR-101-3p and miR-26a-5p was the most stable normalization strategy. Here, we demonstrate that a comprehensive approach of a diverse data set of conditions using multiple algorithms reliably identifies stable reference genes which will increase the utility of gene expression evaluation of therapeutically relevant EVs.