Class IIa HDAC4 and HDAC7 cooperatively regulate gene transcription in Th17 cell differentiation

Class II histone deacetylases (HDACs) are important in regulation of gene transcription during T cell development. However, our understanding of their cell-specific functions is limited. In this study, we reveal that class IIa Hdac4 and Hdac7 (Hdac4/7) are selectively induced in transcription, guiding the lineage-specific differentiation of mouse T-helper 17 (Th17) cells from naive CD4+ T cells. Importantly, Hdac4/7 are functionally dispensable in other Th subtypes. Mechanistically, Hdac4 interacts with the transcription factor (TF) JunB, facilitating the transcriptional activation of Th17 signature genes such as Il17a/f. Conversely, Hdac7 collaborates with the TF Aiolos and Smrt/Ncor1-Hdac3 corepressors to repress transcription of Th17 negative regulators, including Il2, in Th17 cell differentiation. Inhibiting Hdac4/7 through pharmacological or genetic methods effectively mitigates Th17 cell-mediated intestinal inflammation in a colitis mouse model. Our study uncovers molecular mechanisms where HDAC4 and HDAC7 function distinctively yet cooperatively in regulating ordered gene transcription during Th17 cell differentiation. These findings suggest a potential therapeutic strategy of targeting HDAC4/7 for treating Th17-related inflammatory diseases, such as ulcerative colitis.

Abstract 3481: A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma

Tumors exhibit widespread enhancer landscape reprogramming compared to normal tissue. The etiology is believed to be largely cell-intrinsic in non-hormonal cancers, attributed to such genomic alterations as focal amplification of non-coding regions, aberrant activation of transcription factors, and non-coding mutations creating de novo transcription factor binding sites. Here, using freshly resected primary CRC tumors and patient-matched adjacent normal colon epithelia, we find divergent epigenetic landscapes between primary CRC tumors and CRC cell lines. We identify a unique super-enhancer signature largely absent in cell culture. Intriguingly, this phenomenon extends to highly recurrent aberrant super-enhancers gained in CRC over patient-matched normal epithelium suggesting novel insight into the etiology of enhancer reprogramming in CRC and its downstream relevance to tumor biology. We find one such super-enhancer activated in epithelial cancer cells due to surrounding inflammation in the tumor microenvironment. CRISPR-dcas9-KRAB interference of this super-enhancer identifies PDZK1IP1 as its target gene. PDZK1IP1 is previously observed to be highly up-regulated in CRC. However, the mechanism behind its transcriptional activation is not fully understood. We restore both the super-enhancer and PDZK1IP1 levels following treatment with cytokines or xenotransplantation into nude mice, thus demonstrating its etiology via local tumor microenvironment acquisition. Deletion of inflammatory transcription factors RELA and STAT3 in human CRC cells inhibits PDZK1IP1 induction in xenografts. PDZK1IP1 appears to be critical for CRC growth in the setting of its super-enhancer induction as xenografts, but not in cell culture where the super-enhancer is absent and expression is largely silent. Building on its known role in glucose uptake via SGLT receptors, we demonstrate mechanistically that PDZK1IP1 enhances the reductive capacity CRC cancer cells via the pentose phosphate pathway using polar metabolomic profiling. We show this activation enables efficient growth under oxidative conditions both in vitro and in vivo, challenging the previous notion that PDZK1IP1 acts as a tumor suppressor in CRC. Collectively, these observations highlight the biologic significance of epigenomic profiling on patient-matched primary specimens and identify this microenvironment-acquired super-enhancer as an oncogenic driver in the setting of the inflamed tumor.

Citation Format: Royce Zhou, Jia Xu, Tiphaine Martin, Alexis Zachem, John He, Sait Ozturk, Deniz Demircioglu, Ankita Bansal, Andrew Trotta, Bruno Giotti, Berkley Gryder, Yao Shen, Saul Carcamo, Xuewei Wu, Kaitlyn Bosch, Benjamin Hopkins, Alexander Tsankov, Randolph Steinhagen, Drew Jones, John Asara, Jerry Chipuk, Rachel Brody, Steven Itzkowitz, Iok In Christine Chio, Dan Hasson, Emily Bernstein, Ramon Parsons. A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma [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 3481.

Abstract 4583: An essential role for Cmtr2 in endothelial cell function and vascular development

Cancer genome sequencing studies have identified multiple novel tumor suppressor genes, including the FTSJD1 or CMTR2 gene that is subject to statistically significant levels of both nonsense and frameshift mutations in lung adenocarcinoma. However, these analyses are insufficient to determine the importance and modes of action of the gene in the disease. Follow-up functional studies are essential to elucidate these gene functions. The protein product of CMTR2 has been described as an mRNA cap methyltransferase, which O-methylates the ribose of the second guanine residue of the 5’ cap, likely serving to modify efficiency of transcript processing, translation and stability, but the details of how and why specific transcripts undergo methylation by the enzyme, as well as its role in oncogenesis, remain to be elucidated. In this study we report the first comprehensive analysis of the physiologic consequences of Cmtr2 deficiency in knockout (KO) mice and primary human cells. Constitutive deletion of Cmtr2 results in embryos that die in midgestation with defects in embryo size, placental malformation and yolk sac vascularization. Endothelial-specific deletion of Cmtr2 in mice also results in vascular defects and perinatal lethality, suggesting that vascular development is a key function of Cmtr2 in animals. In summary, our study reveals that Cmtr2 plays a critical role in vascular development, maturation and remodeling. Further studies of CMTR2 function may provide insight not only into lung cancer biology but also to its broader roles in ontogeny.

Citation Format: Alena Yermalovich, Zarin Mohsenin, Bruno Giotti, Douglas Wheeler, Kelly Xu, Alexander Tsankov, Matthew Meyerson. An essential role for Cmtr2 in endothelial cell function and vascular development. [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 4583.

Abstract A47: Characterization of immune cell composition across cancer types in pan-cancer genomic cohorts

Introduction: Identifying immune cell signatures in individual tumors can help guide treatment selection for patients. Numerous deconvolution methods have been developed to estimate immune cell fractions from bulk gene expression data, but they have yet to be systematically applied and cross-validated in pan-cancer genomic cohorts. We undertook this study to cross-validate immune cell quantification methods across 25 cancer types spanning 11,011 samples and provide a public immuno-oncology resource. Methods: Using gene expression data from both The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), we employed and compared six methods to estimate immune cell fractions in each cancer type (CIBERSORT, quanTIseq, EPIC, TIMER, MCP-counter, xCell; immunedeconv R package). We mapped these results to a common vocabulary of five broad cell categories for comparison: T cells, B cells, natural killer cells (NK cells), macrophages/monocytes, and myeloid dendritic cells (mDCs). In parallel, we computed immune cell proportions for seven cancer types using single-cell RNA-seq (scRNA-seq) data from a single-cell tumor immune atlas of 217 patients. We correlated the median immune cell fractions estimated from bulk deconvolution with scRNA-seq proportions for each cancer type. To demonstrate the application of this resource, we compared the immune cell fractions (1) in adjacent normal versus tumor tissues, and (2) in head and neck squamous cell carcinoma (HNSC) and colorectal adenocarcinoma (COAD) tumor subtypes using multivariable linear regression adjusted for age and sex. Results: Overall, 9,689 TCGA samples and 1,322 ICGC samples were analyzed, and correlations across six deconvolution tools were performed. Two well-performing cell estimation methods, EPIC and quanTIseq, demonstrated good correlation between median deconvoluted T cell enrichment score and single-cell cytotoxic CD8+ T cell populations (spearman coefficient; EPIC = 0.71, quanTIseq = 0.43). However, cross-cancer type correlations between scRNA-seq and bulk estimated fractions were not statistically significant for most cancer types. In multivariable regression comparing immune cell estimates across cancer subtypes, we found increased T cell (EPIC: OR=1.65, 95% CI = 1.23-2.21, quanTIseq: OR = 1.30, 95% CI = 1.20-1.40) and B cell (EPIC: OR = 2.92, 95% CI = 2.05-4.15, quanTIseq: OR = 1.48, 95% CI = 1.37-1.60) enrichment in HPV-positive compared to HPV-negative HNSC. In COAD, we found increased T cell enrichment in the microsatellite instability (MSI) subtype compared to the genome stable subtype (OR = 1.16, 95% CI = 1.01-1.33). Conclusion: Overall, our study provides a public resource of immune cell annotations for two widely used, pan-cancer genomics cohorts and can facilitate future studies that aim to characterize the tumor immune microenvironment. Furthermore, we validated the use of this resource by demonstrating enrichment of specific immune cell subsets in HNSC and COAD subtypes, consistent with prior reports of these well-characterized cancers.

Citation Format: Makda Getachew Zewde, Daniel Fulop, Alexander Tsankov, Kuan-lin Huang. Characterization of immune cell composition across cancer types in pan-cancer genomic cohorts [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr A47.

EPCO-25. MULTI-OMIC ANALYSIS OF THE GLIOBLASTOMA EPIGENOME AND TRANSCRIPTOME INFORMS OF MIGRATORY INTERNEURON-LIKE DEVELOPMENTAL REGULATORS

Recent studies have demonstrated that, despite their nomenclature, gliomas recapitulate an interneuron progenitor-like state that drives tumor progression. During human neurodevelopment, interneurons arise from the subcortical ganglionic eminences and migrate tangentially into the neocortex, settling in the cortical plate where they integrate local neurocircuitry. Analogously, malignant glioblastoma (GBM) cells migrate from the tumor core into the surrounding healthy tissue. This innate infiltrative property renders these malignant cells elusive to surgical resection, leading to tumor recurrence. To understand the regulatory networks that drive tumor infiltration from a neurodevelopmental perspective, we generated a single-nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) dataset of 41,000 nuclei from the core and infiltrative edge of surgically resected GBM specimens (n = 4). Concurrently, we sequenced 46,000 nuclei from non-pathological, postmortem samples of second- and third-trimester neocortices (n = 17). We integrated these datasets with paired single-nucleus RNA sequencing (snRNA-seq) data and identified candidate regulatory TFs that exhibit high correlation between motif enrichment and TF expression. Using single-trajectory inference and pseudo-time analyses, we identified TCF12 as a potential driver of interneuron lineage fate in developing cortical progenitors. Given its implication in projection neuron migration, we were intrigued to find that TCF12 activity is highest in GBM cells with a migratory interneuron signature, hinting at its putative role in tumor infiltration. To understand the significance of these findings, we will interrogate other genes in the TCF12 regulatory network with the ultimate goal of identifying therapeutic targets that inhibit GBM infiltration.

IMMU-23. ELIMINATING MONOCYTE CHEMOATTRACTION INVOKES COMPENSATORY NEUTROPHIL INFLUX AND PRONEURAL TO MESENCHYMAL TRANSITION IN GLIOBLASTOMA

Myeloid cells comprise the majority of immune cells in tumors, where their content and composition is determined by tumor type and driver mutation. While these cells are essential for shaping the tumor microenvironment, promoting tumor growth, and contributing to therapeutic resistance, targeting tumor-associated myeloid cells, including bone-marrow-derived monocytes and neutrophils, has not been successful in the clinics. Monocyte chemoattractant protein (MCP) family, comprising of Ccl2, Ccl7, Ccl8, Ccl12, are essential for monocytes trafficking to the tumor sites. To eliminate monocyte recruitment, we leveraged CRISPR/Cas-9 based gene editing tool to generate a mouse strain that is devoid of all MCP genes, which we termed quadruple MCP knockout (qMCP-/-). Using these mice in combination with genetically engineered mouse models (GEMM) of glioblastoma (GBM), we abolished tumor monocyte infiltration. Due to the functional redundancy of MCP family members, we show that targeting individual MCP genes leads to compensation by other MCPs. In contrast, when all MCPs are genetically deleted and monocyte recruitment is abolished, neutrophil infiltration ensues. Single-cell RNA sequencing revealed that intratumoral neutrophils promoted proneural-to-mesenchymal transition in GBM, and supported tumor aggression by facilitating hypoxia response via TNF production. Remarkably, pharmacologic or genetic interventions that suppress both monocytes and neutrophil infiltration improve the survival of GBM-bearing mice. Taken together, our findings establish that specific subsets of myeloid cells can influence the dynamism of tumor microenvironment, and they emphasize the importance of targeting both monocytes and neutrophils simultaneously for effective GBM immunotherapy.

A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma

Tumors exhibit enhancer reprogramming compared to normal tissue. The etiology is largely attributed to cell-intrinsic genomic alterations. Here, using freshly resected primary CRC tumors and patient-matched adjacent normal colon, we find divergent epigenetic landscapes between CRC tumors and cell lines. Intriguingly, this phenomenon extends to highly recurrent aberrant super-enhancers gained in CRC over normal. We find one such super-enhancer activated in epithelial cancer cells due to surrounding inflammation in the tumor microenvironment. We restore this super-enhancer and its expressed gene, PDZK1IP1, following treatment with cytokines or xenotransplantation into nude mice, thus demonstrating cell-extrinsic etiology. We demonstrate mechanistically that PDZK1IP1 enhances the reductive capacity CRC cancer cells via the pentose phosphate pathway. We show this activation enables efficient growth under oxidative conditions, challenging the previous notion that PDZK1IP1 acts as a tumor suppressor in CRC. Collectively, these observations highlight the significance of epigenomic profiling on primary specimens.

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here, we construct a high-resolution molecular landscape of the cellular subtypes and spatial communities that compose PDAC using single-nucleus RNA sequencing and whole-transcriptome digital spatial profiling (DSP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment naive. We uncovered recurrent expression programs across malignant cells and fibroblasts, including a newly identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities with distinct contributions from malignant, fibroblast and immune subtypes: classical, squamoid-basaloid and treatment enriched. Our refined molecular and cellular taxonomy can provide a framework for stratification in clinical trials and serve as a roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.

Abstract CT205: A phase I/Ib trial of intratumoral Poly-ICLC in resectable malignant pleural mesothelioma

Background: Malignant pleural mesothelioma (MPM) is usually fatal, though multimodality therapy— now including immunotherapy— has improved survival. Recurrence after surgery is close to 100%, even with adjuvant chemotherapy and radiation. Our collaborators have performed deep immunophenotyping of treatment-naïve MPM lesions using mass cytometry (CyTOF) and single-cell RNA sequencing (scRNAseq) to define the tumor microenvironment. A population of rare CD141+ dendritic cells (DC1) is disproportionately represented in some MPM lesions analyzed. These DC1 cells— which express high levels of Toll-like receptor 3 (TLR3)— are among the most potent cross-presenters of antigen and are key to priming anti-tumor CD4+ and CD8+ T cell responses. Polyinosinic-polycytidylic acid stabilized with polylysine and carboxymethylcellulose (poly-ICLC), is a double-stranded RNA host-targeted therapeutic viral-mimic. Poly-ICLC activates multiple innate immune receptors including TLR3 and melanoma differentiation-associated gene 5 (MDA5), leading to cross-presentation of antigen to T cells and induction of strong Th1 response. We hypothesize that injection of poly-ICLC prior to surgical resection may activate intratumoral (IT) DC1s, increase tumor antigen presentation to cytotoxic T cells, and induce tumor-specific immune surveillance.

Methods: This is a phase I/Ib study to evaluate the safety of IT poly-ICLC prior to surgical resection for patients with MPM (NCT04525859). The primary endpoint is safety as assessed by frequency and severity of toxicities by CTCAE 5.0. Secondary endpoints are objective response as measured by RECIST 1.1 and recurrence free survival measured from the time of first poly-ICLC injection. Exploratory endpoints include evaluation of circulating immune cells (including regulatory T cells and NK cells), evaluation of immune cell infiltration in pre-injection tumor biopsy and surgically resected tissue, as well as characterization of immune parameters such as local B cell specificity. The protocol features a Simon’s two-stage design, with six patients enrolled in a phase I safety cohort, proceeding to a phase Ib expansion cohort (additional 13 patients) if no more than 1 dose limiting toxicity occurs. Eligible patients must have MPM deemed operable by the treating thoracic surgeon. Eligible subjects may not have uncontrolled immunocompromised states or autoimmune disorders. After enrollment, patients undergo biopsies at which time 2mg poly-ICLC is injected across two sites in the tumor. Patients then undergo resection of the tumor (pleurectomy/decortication or extra pleural pneumonectomy per standard of care) at day 21+/- 7 after poly-ICLC injection. Blood is drawn at three points (prior to poly-ICLC injection, at time of surgery, and at a post-operative visit) for immune profiling. At the time of submission six patients have been treated and phase Ib accrual is continuing as planned. Interim analysis of phase I safety and exploratory endpoints will be reported in late 2022.

Citation Format: Bailey G. Fitzgerald, Thomas U. Marron, Robert Sweeney, Jorge Gomez, Nicole Hall, Daniel O'Grady, Christian Rolfo, Raj Veluswamy, Deborah Doroshow, John Mandeli, David Yankelevitz, Nina Bhardwaj, Sacha Gnjatic, Fred R. Hirsch, Miriam Merad, Alexander Tsankov, Raja Flores, Andrea Wolf. A phase I/Ib trial of intratumoral Poly-ICLC in resectable malignant pleural mesothelioma [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 CT205.

EPCO-11. SINGLE-NUCLEI TRANSCRIPTOMICS RELATES GLIOBLASTOMA INFILTRATION TO DISTINCT GLIAL PROGENITOR STATES

Our understanding of glioblastoma (GBM) intratumoral heterogeneity, particularly in the context of neurodevelopment, has thus far been primarily focused on the more surgically accessible tumor core niche. In contrast, the biology of GBM cells at the infiltrative edge, which evade surgical resection and drive tumor recurrence, remains poorly characterized. To this end, we microdissected and performed single-nuclei RNA sequencing (snRNA-seq) on approximately 62,000 nuclei taken from the tumor core and from the infiltrative edge of six GBM tumors with diverse genomic drivers, including IDH1, EGFR, PDGFRA, FGFR3, and NF1. Unbiased clustering reveals distinct neoplastic and non-neoplastic populations, further distinguished using copy number variation analysis. After projecting previously defined signatures taken from snRNA-seq analysis of human adult neocortex/subventricular zone and prenatal germinal matrix, we find that approximately 90% of tumor cells recapitulate a neurodevelopment-like molecular phenotype, reprising gene expression signatures of prenatal astrocytes and of a distinct glial intermediate progenitor cell population (g-IPC) that precedes both astrocyte and oligodendrocyte lineage differentiation. Examining the infiltrative edge of samples with the most confident microdissection (n=4), we see that while distinct populations of tumor cells in this niche express proneural and classical signatures, these cells are overall enriched for a g-IPC-like phenotype, relative to the tumor core, irrespective of the tumors’ genomic alterations. A subset of cells at the infiltrative edge, in particular, recapitulates the signature of an uncommitted g-IPC subtype, expressing both astroglial and oligodendroglial markers. Trajectory analyses also reveal distinct branches of core and edge tumor cells, which are predominantly astrocyte- and g-IPC-like, respectively. Differential gene expression analysis of GBM cells at the infiltrative edge vs. tumor core reveals a migration signature, dominated by EGFR, ERBB4, PCDH9, and PCDH15. Ultimately, this high resolution analysis of heterogeneity at the infiltrative edge allows us to uncover potentially targetable drivers of invasion in GBM.

EPCO-20. RELATING GLIOBLASTOMA HETEROGENEITY TO HUMAN FETAL GLIAL DEVELOPMENT THROUGH HIGH RESOLUTION SINGLE NUCLEI TRANSCRIPTOMICS

Glioblastoma (GBM) is thought to be driven by a therapy-resistant cancer stem cell population that recapitulates developmental phenotypes. Direct comparisons of GBM to glial states during human fetal development are limited due to paucity of data from late prenatal gestation, when gliogenesis is thought to occur. Here, we generated a comprehensive single nuclei RNA sequencing (snRNAseq) dataset of approximately 200,000 nuclei taken from the germinal matrix and the cortical plate of 16 fetal postmortem samples, ranging from 17 to 41 gestational weeks, enabling high spatiotemporal resolution of late neurogenesis and early-to-peak gliogenesis. We performed unbiased clustering to identify broad cell types within each sample and integrated all fetal samples to analyze evolving glial states and relationships across two regions and four developmental stages. Subclustering analysis of developing glia from the germinal matrix and cortical plate resolved developmental cell type signatures that are absent in the adult brain. Trajectory inference and pseudo-time analyses reconstructed relationships within these glial lineages and states, identifying a robust common glial progenitor population (GPC) with distinct signature, preceding both oligodendrocyte progenitor cell (OPC) and astrocyte lineage commitment during late prenatal development. We then performed snRNAseq on approximately 30,000 nuclei taken from the core and infiltrating edge of two surgically resected GBM samples with IDH-mutant and IDH-wildtype status and EGFR amplification. Uniform manifold approximation and projection (UMAP) dimensionality reduction revealed distinct neoplastic and non-neoplastic population clusters within each GBM sample. Projecting our previously defined neural stem cell / progenitor signatures onto each GBM UMAP identified notable predominance of the GPC-like developmental signature throughout both GBM tumors with focal minor contributions from the OPC-, transit amplifying-, and astrocyte-like signatures. The high spatial and temporal resolution of the generated roadmap dissolves GBM intratumoral heterogeneity into distinct developmental molecular states driven by potentially targetable regulatory networks.

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution

Tumor evolution from a single cell into a malignant, heterogeneous tissue remains poorly understood. Here, we profile single-cell transcriptomes of genetically engineered mouse lung tumors at seven stages, from pre-neoplastic hyperplasia to adenocarcinoma. The diversity of transcriptional states increases over time and is reproducible across tumors and mice. Cancer cells progressively adopt alternate lineage identities, computationally predicted to be mediated through a common transitional, high-plasticity cell state (HPCS). Accordingly, HPCS cells prospectively isolated from mouse tumors and human patient-derived xenografts display high capacity for differentiation and proliferation. The HPCS program is associated with poor survival across human cancers and demonstrates chemoresistance in mice. Our study reveals a central principle underpinning intra-tumoral heterogeneity and motivates therapeutic targeting of the HPCS.

Abstract A22: Molecular subtypes and resistance programs in pancreatic ductal adenocarcinoma elucidated with single-nucleus RNA-seq

Objective: Pancreatic ductal adenocarcinoma (PDAC) remains a treatment-refractory disease as existing molecular subtypes are insufficient and do not currently inform clinical decisions. Rare cell types, including those responsible for resistance, are difficult to detect with bulk transcriptomic profiling. Indeed, several previously identified transcriptomic subtypes of PDAC are unintentionally driven by “contaminating” stromal components. Single-cell transcriptomics provides an unprecedented degree of resolution into the properties of individual cells. However, RNA extraction from RNase- and stroma-rich pancreatic tissue is difficult and prior single-cell efforts have been limited by suboptimal dissociation/RNA quality. We developed a robust single-nucleus RNA-seq (sNuc-seq) technique compatible with frozen archival PDAC specimens and computational techniques to identify the transcriptomic programs driving tumor subtypes and therapeutic resistance.

Methods: Patients with localized PDAC undergoing surgical resection with or without neoadjuvant chemoradiotherapy were consented for this IRB-approved study. Specimens were screened for RNA Integrity Number >6. Single nuclei suspensions were extracted from flash-frozen primary PDAC specimens and organoids. Approximately 8,000 nuclei were loaded on the 10x Genomics Chromium platform per sample to generate and sequence 3’ gene expression libraries (Illumina HiSeq 2500, 125 bp paired-end reads). sNuc-seq derived reads were processed using the 10X CellRanger v3.0.2 pipeline. Unsupervised clustering was utilized to identify different cell populations and known marker genes from literature were used to label cell types.

Results: Both treatment-naïve (n=12) and treatment-resistant (n=11) specimens yielded high-quality sNuc-seq data (>1,000 nuclei per sample, >1,000 median genes per nucleus). In each tumor, distinct clusters with gene expression profiles consistent with ductal, fibroblast, endothelial, endocrine, lymphocyte, and myeloid cell populations were identified. Malignant cells were confirmed by inferred copy number variation analysis (InferCNV v3.9) and segregated into several distinct clusters for each individual patient highlighting intratumoral heterogeneity. While some malignant clusters corresponded to previously identified basal-squamous and classical-progenitor bulk subtypes, others featured expression profiles distinct from known subtypes, including cells with upregulation of hypoxia-associated or cytoskeletal genes.

Conclusions: Applying sNuc-seq to treatment-naïve and pretreated PDAC specimens, we uncovered significant intratumoral heterogeneity in the malignant and stromal compartments and identified malignant cells featuring transcriptomic programs that do not fit previously identified bulk subtypes. Characterization of therapeutic resistance programs, spatial relationships among cell types, and association with clinical outcomes is ongoing.

Citation Format: William L. Hwang, Karthik A. Jagadeesh, Orr Ashenberg, Eugene Drokhlyansky, George Eng, Nicholas Van Wittenberghe, William Freed-Pastor, Clifton Rodriguez, Danielle Dionne, Julia Waldman, Michael Cuoco, Alexander Tsankov, Connor Lambden, Caroline Porter, Jason Schenkel, Laurens Lambert, Debora Ciprani, Andrew J. Aguirre, Mari Mino-Kenudson, Theodore S. Hong, Orit Rozenblatt-Rosen, Carlos Fernandez-del Castillo, Andrew S. Liss, Aviv Regev, Tyler E. Jacks. Molecular subtypes and resistance programs in pancreatic ductal adenocarcinoma elucidated with single-nucleus RNA-seq [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr A22.

Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells

Induced pluripotent stem cells (iPSCs) are an essential tool for modeling how causal genetic variants impact cellular function in disease, as well as an emerging source of tissue for regenerative medicine. The preparation of somatic cells, their reprogramming and the subsequent verification of iPSC pluripotency are laborious, manual processes limiting the scale and reproducibility of this technology. Here we describe a modular, robotic platform for iPSC reprogramming enabling automated, high-throughput conversion of skin biopsies into iPSCs and differentiated cells with minimal manual intervention. We demonstrate that automated reprogramming and the pooled selection of polyclonal pluripotent cells results in high-quality, stable iPSCs. These lines display less line-to-line variation than either manually produced lines or lines produced through automation followed by single-colony subcloning. The robotic platform we describe will enable the application of iPSCs to population-scale biomedical problems including the study of complex genetic diseases and the development of personalized medicines.

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the regulatory mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole-genome bisulfite sequencing, chromatin immunoprecipitation sequencing, and RNA sequencing reveals unique events associated with specification toward each lineage. Lineage-specific dynamic alterations in DNA methylation and H3K4me1 are evident at putative distal regulatory elements that are frequently bound by pluripotency factors in the undifferentiated hESCs. In addition, we identified germ-layer-specific H3K27me3 enrichment at sites exhibiting high DNA methylation in the undifferentiated state. A better understanding of these initial specification events will facilitate identification of deficiencies in current approaches, leading to more faithful differentiation strategies as well as providing insights into the rewiring of human regulatory programs during cellular transitions.