Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens

Single-nucleotide variants (SNVs) in key T cell genes can drive clinical pathologies and could be repurposed to improve cellular cancer immunotherapies. Here, we perform massively parallel base-editing screens to generate thousands of variants at gene loci annotated with known or potential clinical relevance. We discover a broad landscape of putative gain-of-function (GOF) and loss-of-function (LOF) mutations, including in PIK3CD and the gene encoding its regulatory subunit, PIK3R1, LCK, SOS1, AKT1 and RHOA. Base editing of PIK3CD and PIK3R1 variants in T cells with an engineered T cell receptor specific to a melanoma epitope or in different generations of CD19 chimeric antigen receptor (CAR) T cells demonstrates that discovered GOF variants, but not LOF or silent mutation controls, enhanced signaling, cytokine production and lysis of cognate melanoma and leukemia cell models, respectively. Additionally, we show that generations of CD19 CAR T cells engineered with PIK3CD GOF mutations demonstrate enhanced antigen-specific signaling, cytokine production and leukemia cell killing, including when benchmarked against other recent strategies.

Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial

We previously reported the results of a randomized phase II trial (NCT02904954) in patients with early-stage non-small cell lung cancer (NSCLC) who were treated with either two preoperative cycles of the anti-PD-L1 antibody durvalumab alone or combined with immunomodulatory doses of stereotactic radiation (DRT). The trial met its primary endpoint of major pathological response, which was significantly higher following DRT with no new safety signals. Here, we report on the prespecified secondary endpoint of disease-free survival (DFS) regardless of treatment assignment and the prespecified exploratory analysis of DFS in each arm of the trial. DFS at 2 and 3 years across patients in both arms of the trial were 73% (95% CI: 62.1-84.5) and 65% (95% CI: 52.5-76.9) respectively. For the exploratory endpoint of DFS in each arm of the trial, three-year DFS was 63% (95% CI: 46.0-80.4) in the durvalumab monotherapy arm compared to 67% (95% CI: 49.6-83.4) in the dual therapy arm. In addition, we report post hoc exploratory analysis of progression-free survival as well as molecular correlates of response and recurrence through high-plex immunophenotyping of sequentially collected peripheral blood and gene expression profiles from resected tumors in both treatment arms. Together, our results contribute to the evolving landscape of neoadjuvant treatment regimens for NSCLC and identify easily measurable potential biomarkers of response and recurrence.

Massively parallel base editing screens to map variant effects on anti-tumor hallmarks of primary human T cells

Base editing enables generation of single nucleotide variants, but large-scale screening in primary human T cells is limited due to low editing efficiency, among other challenges 1 . Here, we developed a high-throughput approach for high-efficiency and massively parallel adenine and cytosine base-editor screening in primary human T cells. We performed multiple large-scale screens editing 102 genes with central functions in T cells and full-length tiling mutagenesis of selected genes, and read out variant effects on hallmarks of T cell anti-tumor immunity, including activation, proliferation, and cytokine production. We discovered a broad landscape of gain- and loss-of-function mutations, including in PIK3CD and its regulatory subunit encoded by PIK3R1, LCK , AKT1, CTLA-4 and JAK1 . We identified variants that affected several (e.g., PIK3CD C416R) or only selected (e.g. LCK Y505C) hallmarks of T cell activity, and functionally validated several hits by probing downstream signaling nodes and testing their impact on T cell polyfunctionality and proliferation. Using primary human T cells in which we engineered a T cell receptor (TCR) specific to a commonly presented tumor testis antigen as a model for cellular immunotherapy, we demonstrate that base edits identified in our screens can tune specific or broad T cell functions and ultimately improve tumor elimination while exerting minimal off-target activity. In summary, we present the first large-scale base editing screen in primary human T cells and provide a framework for scalable and targeted base editing at high efficiency. Coupled with multi-modal phenotypic mapping, we accurately nominate variants that produce a desirable T cell state and leverage these synthetic proteins to improve models of cellular cancer immunotherapies.

Dissecting the treatment-naive ecosystem of human melanoma brain metastasis

Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma; yet, our understanding of the underlying salient biology is rudimentary. Here, we performed single-cell/nucleus RNA-seq in 22 treatment-naive MBMs and 10 extracranial melanoma metastases (ECMs) and matched spatial single-cell transcriptomics and T cell receptor (TCR)-seq. Cancer cells from MBM were more chromosomally unstable, adopted a neuronal-like cell state, and enriched for spatially variably expressed metabolic pathways. Key observations were validated in independent patient cohorts, patient-derived MBM/ECM xenograft models, RNA/ATAC-seq, proteomics, and multiplexed imaging. Integrated spatial analyses revealed distinct geography of putative cancer immune evasion and evidence for more abundant intra-tumoral B to plasma cell differentiation in lymphoid aggregates in MBM. MBM harbored larger fractions of monocyte-derived macrophages and dysfunctional TOX+CD8+ T cells with distinct expression of immune checkpoints. This work provides comprehensive insights into MBM biology and serves as a foundational resource for further discovery and therapeutic exploration.

Abstract 984: Dissecting the ecosystem of treatment-naïve melanoma brain metastasis using multi-modal single-cell analysis

Brain metastases are the most frequent malignancies in the brain and are associated with significant morbidity and mortality. Melanoma brain metastases (MBM) occur in most patients with advanced melanoma and are challenging to treat. Our understanding of the treatment-naïve landscape of MBM is still rudimentary, and there are no site-specific molecular therapies available. To gain comprehensive insights into the niche-specific biology of MBM, we performed multi-modal profiling of fresh and frozen samples using single-cell RNA-seq, single-cell TCR-seq, single-nuclei RNA-seq, and spatial transcriptional profiling. We evolved single-nucleus RNA-seq processing methods to enable profiling of minute amounts of archival, frozen specimens and compared data quality and structure between matched fresh and frozen MBM. We curated a treatment-naïve single-transcriptome atlas of MBM, collected either fresh samples over 1 year or profiled frozen samples dating back more than 15 years, and compared these samples to extracranial melanoma metastases (ECMM). In total, we profiled 25 samples with more than 114,000 transcriptomes. We identified more than 20 different cell types, including diverse tumor-infiltrating T-cell subsets and rare dendritic cell types, and tissue-specific cell types, such as activated microglia. Tumor cells in MBM showed an increase in copy number alterations (CNAs) compared to ECMM, which we validated using an external dataset of whole exome sequencing (WES) data including both MBM and ECMM. MBM-derived tumor cells show enrichment of genes involved in neuronal development and function, and site-specific metabolic programs (e.g., oxidative phosphorylation). Comparison with an external bulk RNA-seq dataset validated enriched key genes in MBM and ECMM as putative dependencies. We recovered cell-cell interactions between tumor and brain-resident cells involved in brain development, homeostasis, and disease. Similar to ECMM, the tumor microenvironment of MBM contained CD8+ T cells across a spectrum of differentiation, exhaustion and expansion, which was associated with loss of TCF7 expression and adoption of a TOX+ cell state. CD4+ T cells included T regulatory, T helper and T follicular-helper-like expression profiles. Plasma cells showed spatially localized expansion and limited heterogeneity. Myeloid cells largely adopted pro-tumorigenic cell states, including microglia, the brain-resident myeloid cells, which showed an activation trajectory characterized by expression of SPP1 (osteopontin). Spatial transcriptional analysis revealed restricted expression of antigen presentation genes with only a subset of these locations showing a type I interferon response. In summary, this work presents a multi-modal single-cell approach to dissect and compare the landscape of treatment-naïve MBM and ECMM.

Citation Format: Johannes C. Melms, Jana Biermann, Amit Dipak Amin, Yiping Wang, Somnath Tagore, Massimo Andreatta, Ajay Nair, Meri Rogava, Patricia Ho, Lindsay A. Caprio, Zachary H. Walsh, Shivem Shah, Daniel H. Vacarro, Blake Caldwell, Adrienne M. Luoma, Joseph Driver, Matthew Ingham, Suthee Rapisuwon, Jennifer Wargo, Craig L. Slinguff, Evan Z. Macosco, Fei Chen, Richard Carvajal, Michael B. Atkins, Michael A. Davies, Elham Azizi, Santiago J. Carmona, Hanina Hibshoosh, Peter D. Canoll, Jeffrey N. Bruce, Wenya L. Bi, Gary K. Schwartz, Benjamin Izar. Dissecting the ecosystem of treatment-naïve melanoma brain metastasis using multi-modal single-cell analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 984.

Abstract 1833: KLF4 regulates metabolic homeostasis in response to energy stress

Krüppel-like factor 4 (KLF4) is a zinc finger-containing transcription factor with diverse regulatory functions in cellular growth, proliferation, differentiation, autophagy and genomic stability. Furthermore, KLF4 exerts a cell-cycle checkpoint effect in part by acting as a transcriptional activator of the cyclin-dependent kinase inhibitor, p21. Our lab has found that KLF4 regulates autophagy, mitophagy, and mitochondrial dynamics. Given the close relationship these processes have with cellular metabolism, we aimed to determine how KLF4 regulates glycolytic and oxidative metabolism. Using various assays, we find that cells lacking KLF4 have both oxidative and glycolytic impairments. Using western blotting, we find that when KLF4 is overexpressed in RKO human colorectal cancer cells, Hexokinase 2 (HK2), a rate determining enzyme in glycolysis, PKM2, a facilitator of lactate production, and MCT4, a lactic acid export protein and marker of glycolysis, are all significantly upregulated. In MEFs, we find that GLUT1, a glucose transport protein, has greater expression in WT than Klf4-null cells. Furthermore, we determined that KLF4 regulates aspects of the basal cell metabolism in a p21-dependent manner. Given that KLF4 has been found to act as an immediate early gene in response to certain stresses, and given the importance of fast metabolic shifts, we also look at how KLF4 influences short term metabolic stress responses. Since metabolic stress tests showed that WT MEFs have an increased glycolytic capacity, we investigate whether the cells have an increased ability to quickly intake glucose in response to particular stresses. Accordingly, we looked at GLUT1 expression and membrane localization with respect to KLF4. Immunostaining in RKO and MEFs suggests that KLF4 plays a role in localizing GLUT1 to the outer membrane, allowing for increased glucose intake. Taken together, our findings provide a rationale for the impaired metabolism of KLF4-null MEFs, where KLF4 plays a role responding to energy stress by modifying the localization of GLUT1, and regulating various metabolic enzymes both directly, and in a p21-dependent manner.

Citation Format: William M. Rosencrans, Zachary H. Walsh, Andrew C. Blum, Engda G. Hagos. KLF4 regulates metabolic homeostasis in response to energy stress [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1833.