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Up to 20% of idiopathic interstitial lung disease is familial, referred to as Familial Pulmonary Fibrosis (FPF). We performed an integrated analysis of FPF genetic risk by comprehensively evaluating for genetic rare variants (RVs) in a large cohort of FPF kindreds.We performed whole-exome sequencing and/or candidate gene sequencing from affected individuals in 569 FPF kindreds, followed by co-segregation analysis in large kindreds, gene burden analysis, gene-based risk scoring, cell type enrichment analysis, and co-expression network construction.We found that 14.9% - 23.4% of genetic risk in kindreds could be explained by RVs in genes previously linked to FPF, predominantly telomere related genes. We identified new candidate genes in a small number of families, including SYDE1, SERPINB8, GPR87, and NETO1, and developed tools for evaluation and prioritization of RV-containing genes across kindreds. Several pathways were enriched for RV-containing genes in FPF, including focal adhesion and mitochondrial complex I assembly. By combining single cell transcriptomics with prioritized candidate genes, we discovered that expression of RV-containing genes was enriched in smooth muscle cells, type II alveolar epithelial cells, and endothelial cells.In the most comprehensive FPF genetic study to date, we defined the prevalence of RVs in known FPF-related genes and identified new candidate genes and pathways relevant to FPF. However, we did not identify new RV-containing genes shared across multiple kindreds, thereby suggesting that heterogeneous genetic variants involving a variety of genes and pathways mediate genetic risk in most FPF kindreds.

Loss of secretory IgA (SIgA) is common in chronic obstructive pulmonary disease (COPD) small airways and likely contributes to disease progression. We hypothesized that loss of SIgA results from reduced expression of pIgR (polymeric immunoglobulin receptor), a chaperone protein needed for SIgA transcytosis, in the COPD small airway epithelium. pIgR-expressing cells were defined and quantified at single-cell resolution in human airways using RNA

Immune cells have been implicated in idiopathic pulmonary fibrosis (IPF), but the phenotypes and effector mechanisms of these cells remain incompletely characterized. We performed mass cytometry to quantify immune cell subsets in lungs of 12 patients with IPF and 15 organ donors without chronic lung disease and used existing single-cell RNA-sequencing data to investigate transcriptional profiles of immune cells overrepresented in IPF. Among myeloid cells, we found increased numbers of alveolar macrophages (AMØs) and dendritic cells (DCs) in IPF, as well as a subset of monocyte-derived DCs. In contrast, monocyte-like cells and interstitial macrophages were reduced in IPF. Transcriptomic profiling identified an enrichment for IFN-γ response pathways in AMØs and DCs from IPF, as well as antigen processing in DCs and phagocytosis in AMØs. Among T cells, we identified three subsets of memory T cells that were increased in IPF, including CD4(+) and CD8(+) resident memory T cells (T(RM)) and CD8(+) effector memory cells. The response to the IFN-γ pathway was enriched in CD4 T(RM) and CD8 T(RM) cells in IPF, together with T cell activation and immune response–regulating signaling pathways. Increased AMØs, DCs, and memory T cells were present in IPF lungs compared with control subjects. In IPF, these cells possess an activation profile indicating increased IFN-γ signaling and upregulation of adaptive immunity in the lungs. Together, these studies highlight critical features of the immunopathogenesis of IPF.

Stem cells undergo dynamic changes in response to injury to regenerate lost cells. However, the identity of transitional states and the mechanisms that drive their trajectories remain understudied. Using lung organoids, multiple in vivo repair models, single-cell transcriptomics and lineage tracing, we find that alveolar type-2 epithelial cells undergoing differentiation into type-1 cells acquire pre-alveolar type-1 transitional cell state (PATS) en route to terminal maturation. Transitional cells undergo extensive stretching during differentiation, making them vulnerable to DNA damage. Cells in the PATS show an enrichment of TP53, TGFβ, DNA-damage-response signalling and cellular senescence. Gain and loss of function as well as genomic binding assays revealed a direct transcriptional control of PATS by TP53 signalling. Notably, accumulation of PATS-like cells in human fibrotic lungs was observed, suggesting persistence of the transitional state in fibrosis. Our study thus implicates a transient state associated with senescence in normal epithelial tissue repair and its abnormal persistence in disease conditions.

Summary Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity in the region. In a comparison with European datasets, we identify eQTLs shared between Indonesia and Europe as well as population-specific eQTLs that exhibit differences in allele frequencies and/or overall expression levels between populations. By combining local ancestry and archaic introgression inference with eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits, and further comparison with European datasets reflects the poor overall transferability of GWAS statistics across diverse populations. Our findings illustrate how population-specific genetic architecture, local ancestry, and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations and highlight the need for performing association studies on non-European populations., Graphical abstract

BackgroundLoss of secretory immunoglobulin A (SIgA) is common in COPD small airways and likely contributes to disease progression. We hypothesized loss of SIgA results from reduced expression of pIgR, a chaperone protein needed for SIgA transcytosis, in the COPD small airway epithelium.MethodspIgR-expressing cells were defined and quantified at single-cell resolution in human airways using RNA in-situ hybridization, immunostaining, and single-cell RNA sequencing. Complementary studies in mice utilized immunostaining, primary murine tracheal epithelial cell (MTEC) culture, and transgenic mice with secretory or ciliated cell-specific knockout of pIgR. SIgA degradation by human neutrophil elastase or secreted bacterial proteases from non-typeable Haemophilus influenzae (NTHi) was evaluated in vitro.ResultsWe found that secretory cells are the predominant cell type responsible for pIgR expression in human and murine airways. Loss of SIgA in small airways was not associated with a reduction in secretory cells but rather a reduction in pIgR protein expression despite intact PIGR mRNA expression. Neutrophil elastase and NTHi-secreted proteases are both capable of degrading SIgA in vitro and may also contribute to a deficient SIgA immunobarrier in COPD.InterpretationLoss of the SIgA immunobarrier in small airways of patients severe COPD is complex and likely results from both pIgR-dependent defects in IgA transcytosis and SIgA degradation.Key MessagesWhat is the key question? Localized SIgA deficiency in small airways is an established driver of COPD pathogenesis, but the mechanism of loss remains unclear. We hypothesized loss of SIgA is due to reduced numbers of pIgR-expressing cells in SIgA-deficient small airways.What is the bottom line? pIgR is primarily expressed by secretory cells in human and murine airways. Although numbers of secretory cells are similar between SIgA-deficient and SIgA-replete airways in COPD, there is reduced expression of pIgR protein, but not mRNA, in SIgA-deficient airways. Additionally, host and bacterial proteases degrade SIgA in vitro, suggesting loss of SIgA may relate to both impaired transcytosis and increased degradation.Why read on? This study highlights the complexity of SIgA immunobarrier maintenance and suggests that strategies aimed at restoring the SIgA immunobarrier will need to account for both impaired transcytosis and degradation by host and/or bacterial proteases.

Precision-cut lung slices (PCLS) are increasingly utilized for ex vivo disease modeling, but a high-resolution characterization of cellular phenotype stability in PCLS has not been reported. Comparing the single-cell transcriptomic profile of human PCLS after five days of culture to freshly isolated human lung tissue, we found striking changes in endothelial cell and alveolar epithelial cell programs, reflecting both injury and pathways activated in static culture, while immune cell frequencies and programs remained largely intact and similar to the native lung. These cellular dynamics should be considered when utilizing PCLS as a model of the human lung.

Multiple myeloma (MM) is a malignancy of plasma cells in the bone marrow and the second most common hematological malignancy. MM is characterized by a high degree of heterogeneity and has a hereditary genetic component with relatives of MM patients having a higher risk of disease development. Additionally, MM displays a disparity in occurrence and mortality among sexes with males having a higher risk than females. Although new therapies have significantly improved survival rates, MM remains incurable as most patients experience relapses. Therefore, understanding the genetic control underlying complex outcomes is important for the development of better treatments for MM patients. While the majority of research has been focusing on protein-coding regions of the genome, recent studies have started to illuminate the role of non-coding variations on MM. For example, many of the 176 GWAS risk loci associated with MM susceptibility are located within or adjacent to regulatory regions, indicating a role in transcriptional regulation. However, how the non-coding genetic variations affect gene expression, tumor etiology and outcome is poorly understood. To better understand the genetic and biological underpinnings of MM, we utilize genomic approaches to examine non-coding germline and somatic effects on gene expression and cancer outcome. First, we analyzed whole-genome sequencing (WGS) from peripheral blood and WGS and RNA-seq from baseline tumor specimens of 607 participants from the CoMMpass longitudinal study of the Multiple Myeloma Research Foundation. Using both joint and sex-stratified analyses, we detected 6,504 unique germline variants associated with changes in gene expression, i.e. expression quantitative trait loci (eQTLs), corresponding to 4,598 unique eGenes. Among the identified eQTLs, 33.76% exhibit sex-specific effects and 654 variants are associated with genes that influence survival in the CoMMpass cohort. In addition to the germline eQTLs, we identified 266 somatic eQTLs, corresponding to 208 eGenes. Among the identified eQTLs, 566 germline and 88 somatic eQTLs overlap with an ATACseq peak in MM cell lines. Second, we selected a set of eQTLs to validate their functions in transcriptional activity in MM cell lines (2 females, 2 males) using CRISPR interference screens (CRISPRi) with a scRNA-seq readout. By analyzing global transcriptional changes, we identify potential downstream targets that may play essential roles in MM genesis and progression. In conclusion, using computational and functional genomics approaches, we have identified germline and somatic eQTLs that are associated with gene expression and survival in MM, thus providing insights into how these non-coding variations contribute to tumor etiology and outcome. Citation Format: Linh T. Bui, Heini M. Natri, Lance M. Peter, Bianca Argente, Austin J. Gutierrez, Arnold Federico, Mei-I Chung, Jonathan Keats, Nicholas E. Banovich. Functions of genetic variation on gene expression and survival in multiple myeloma [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 5780.

SummaryLung organogenesis requires precisely timed shifts in the spatial organization and function of parenchymal cells, especially during the later stages of lung development. To investigate the mechanisms governing lung parenchymal dynamics during development, we performed a single cell RNA sequencing (scRNA-seq) time-series yielding 92,238 epithelial, endothelial, and mesenchymal cells across 8 time points from embryonic day 12 (E12) to postnatal day 14 (P14) in mice. We combined new computational analyses with RNAin situhybridization to explore transcriptional velocity, fate likelihood prediction, and spatiotemporal localization of cell populations during the transition between the saccular and alveolar stages. We interrogated this atlas to illustrate the complexity of type 1 pneumocyte function during the saccular and alveolar stages, and we demonstrate an integrated view of the cellular dynamics during lung development.

While transient fibroblast activation is a normal and adaptive aspect of injury-repair in many contexts, persistent fibroblast activation is a hallmark of idiopathic pulmonary fibrosis (IPF) and other chronic fibrotic lung diseases. The mechanisms regulating persistent fibroblast activation in IPF have not been fully elucidated. In the lungs of IPF patients and in mice with experimental lung fibrosis, we observed that expression of the thromboxane-prostanoid receptor (TBXA2R) was increased in fibroblasts. Genetic deletion of TBXA2R, but not inhibition of thromboxane synthase, protected mice from bleomycin-induced lung fibrosis, suggesting an alternative ligand activates profibrotic TBXA2R signaling. We found that F2-isoprostanes (F2-IsoPs), nonezymatic products of arachidonic acid metabolism generated in the setting of reactive oxygen species (ROS), are persistently elevated in experimental lung fibrosis and act as an alternative TBXA2R ligand. Further studies demonstrated that F2-isoprostanes signal through TBXA2R to activate Smad signaling, revealing TBXA2R as a previously unrecognized regulator of the transforming growth factor beta (TGF-β) pathway. Further, treatment with the small-molecule TBXA2R antagonist ifetroban protected mice from lung fibrosis in three pre-clinical models: bleomycin treatment, Hermansky-Pudlak Syndrome, and radiation-induced fibrosis. Importantly, treatment with ifetroban during the fibrotic phase of bleomycin injury markedly enhanced fibrotic resolution. Together, these studies implicate TBXA2R signaling as a crucial mediator linking oxidative stress to fibroblast activation and indicate that TBXA2R antagonists could be efficacious for treatment of IPF and other chronic fibrotic disorders.

Previously published comparative functional genomic data sets from primates using frozen tissue samples, including many data sets from our own group, were often collected and analyzed using nonoptimal study designs and analysis approaches. In addition, when samples from multiple tissues were studied in a comparative framework, individuals and tissues were confounded. We designed a multitissue comparative study of gene expression and DNA methylation in primates that minimizes confounding effects by using a balanced design with respect to species, tissues, and individuals. We also developed a comparative analysis pipeline that minimizes biases attributable to sequence divergence. Thus, we present the most comprehensive catalog of similarities and differences in gene expression and DNA methylation levels between livers, kidneys, hearts, and lungs, in humans, chimpanzees, and rhesus macaques. We estimate that overall, interspecies and inter-tissue differences in gene expression levels can only modestly be accounted for by corresponding differences in promoter DNA methylation. However, the expression pattern of genes with conserved inter-tissue expression differences can be explained by corresponding interspecies methylation changes more often. Finally, we show that genes whose tissue-specific regulatory patterns are consistent with the action of natural selection are highly connected in both gene regulatory and protein-protein interaction networks., L.E.B. was supported by the National Science Foundation Graduate Research Fellowship (DGE-1144082). Additionally, L.E.B. and I.E. were funded by the National Institutes of Health (NIH) Genetics and Gene Regulation Training Grant (T32 GM07197). J.R. was funded by a Swiss National Science Foundation postdoc mobility fellowship (PBLAP3- 134342) and the FP7 Marie Curie International Outgoing Fellowship PRIMATE_REG_ EVOL. This project was funded in part by the Office of Research Infrastructure/Office of the Director (ORIP/OD) P51OD011132 grant. T.M.-B. is supported by BFU2017-86471-P (Ministry of Economy and Competitiveness/ European Regional Development Fund, European Union), NIH U01 MH106874 grant, Howard Hughes Medical Institute: International Early Career, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and Centres de Recerca de Catalunya Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya

BackgroundDespite its importance in health and disease, the cellular diversity of the lung endothelium has not been systematically characterized in humans. Here we provide a reference atlas of human lung endothelial cells (ECs), to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium, both in health and disease.MethodsWe reprocessed control single cell RNA sequencing (scRNAseq) data from five datasets of whole lungs that were used for the analysis of pan-endothelial markers, we later included a sixth dataset of sorted control EC for the vascular subpopulation analysis. EC populations were characterized through iterative clustering with subsequent differential expression analysis. Marker genes were validated by immunohistochemistry andin situhybridization. Signaling network between different lung cell types was studied using connectomic analysis. For cross species analysis we applied the same methods to scRNAseq data obtained from mouse lungs.ResultsThe six lung scRNAseq datasets were reanalyzed and annotated to identify over 15,000 vascular EC cells from 73 individuals. Differential expression analysis of EC revealed signatures corresponding to endothelial lineage, including pan-endothelial, pan-vascular and subpopulation-specific marker gene sets. Beyond the broad cellular categories of lymphatic, capillary, arterial and venous ECs we found previously indistinguishable subpopulations; among venous EC we identified two previously indistinguishable populations, pulmonary-venous ECs (COL15A1neg) localized to the lung parenchyma and systemic-venous ECs (COL15A1pos) localized to the airways and the visceral pleura; among capillary EC we confirmed their subclassification into recently discovered aerocytes characterized by EDNRB, SOSTDC1 and TBX2 and general capillary EC. We confirmed that all six endothelial cell types, including the systemic-venous EC and aerocytes are present in mice and identified endothelial marker genes conserved in humans and mice. Ligand-Receptor connectome analysis revealed important homeostatic crosstalk of EC with other lung resident cell types. Our manuscript is accompanied by an online data mining tool (www.LungEndothelialCellAtlas.com).ConclusionOur integrated analysis provides the comprehensive and well-crafted reference atlas of lung endothelial cells in the normal lung and confirms and describes in detail previously unrecognized endothelial populations across a large number of humans and mice.

Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity on the region. In a comparison with a European dataset, we identify 166 uniquely Indonesia-specific eQTLs, highlighting the benefits of performing association studies on non-European populations. By combining local ancestry and archaic introgression inference eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits. Our findings illustrate how local ancestry and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations.

The SARS-CoV-2 novel coronavirus global pandemic (COVID-19) has led to millions of cases and hundreds of thousands of deaths around the globe. While the elderly appear at high risk for severe disease, hospitalizations and deaths due to SARS-CoV-2 among children have been relatively rare. Integrating single-cell RNA sequencing (scRNA-seq) of the developing mouse lung with temporally-resolved RNA-in-situ hybridization (ISH) in mouse and human lung tissue, we found that expression of SARS-CoV-2 Spike protein primerTMPRSS2was highest in ciliated cells and type I alveolar epithelial cells (AT1), andTMPRSS2expression was increased with aging in mice and humans. Analysis of autopsy tissue from fatal COVID-19 cases revealed SARS-CoV-2 RNA was detected most frequently in ciliated and secretory cells in the airway epithelium and AT1 cells in the peripheral lung. SARS-CoV-2 RNA was highly colocalized in cells expressingTMPRSS2.Together, these data demonstrate the cellular spectrum infected by SARS-CoV-2 in the lung epithelium, and suggest that developmental regulation ofTMPRSS2may underlie the relative protection of infants and children from severe respiratory illness.

BackgroundSingle-cell RNA-sequencing (scRNA-seq) is a rapidly evolving technology that enables measurement of gene expression levels at an unprecedented resolution. Despite the explosive growth in the number of cells that can be assayed by a single experiment, scRNA-seq still has several limitations, including high rates of dropouts, which result in a large number of genes having zero read count in the scRNA-seq data, and complicate downstream analyses.MethodsTo overcome this problem, we treat zeros as missing values and develop nonparametric deep learning methods for imputation. Specifically, our LATE (Learning with AuToEncoder) method trains an autoencoder with random initial values of the parameters, whereas our TRANSLATE (TRANSfer learning with LATE) method further allows for the use of a reference gene expression data set to provide LATE with an initial set of parameter estimates.ResultsOn both simulated and real data, LATE and TRANSLATE outperform existing scRNA-seq imputation methods, achieving lower mean squared error in most cases, recovering nonlinear gene-gene relationships, and better separating cell types. They are also highly scalable and can efficiently process over 1 million cells in just a few hours on a GPU.ConclusionsWe demonstrate that our nonparametric approach to imputation based on autoencoders is powerful and highly efficient.

CAR T cell therapy is emerging as a promising strategy to treat cancer and may offer new therapeutic options for individuals diagnosed with glioblastoma (GBM) and other solid tumors. While early clinical studies evaluating CAR T cell therapy in GBM have established evidence of safety and bioactivity, objective clinical responses have been limited. It remains unclear whether productive CAR T cell therapy for solid tumors requires solely CAR T cell engagement with tumor antigen, or if it also necessitates the stimulation of a patient's endogenous immune response. Focusing on our preclinical and clinical program evaluating IL13Rα2-targeted CAR-T cells for the treatment of IL13Rα2-positive glioblastoma (GBM), we set out to mechanistically interrogate the interplay between CAR T cell therapy and the host tumor microenvironment. We designed a murine CAR T cell syngeneic platform in C57BL/6 immunocompetent mice and demonstrate that single intratumoral infusion of IL13Rα2-CAR T cells mediate potent antitumor activity against established KR158 tumors, a highly invasive and poorly immunogenic murine glioma model. We demonstrate that CAR T cell treatment of mouse syngeneic GBM alters the tumor immune landscape, activates intratumoral myeloid cells and induces endogenous T cell memory responses coupled with feed forward propagation of CAR T responses. IFNγ production by CAR T cells and IFNγ-responsiveness of host immune cells is critical for tumor immune landscape remodeling to promote a more activated and less suppressive tumor microenvironment. The clinical relevance of these findings was explored in patient samples from our on-going IL13Rα2-CAR T cell phase I clinical trial [NCT02208362]. Consistent with our preclinical findings, we show that locoregional CAR T cell infusions result in spikes in inflammatory cytokines and an influx of endogenous immune cells into the cerebrospinal fluid (CSF) and resected tumor cavity. Single cell RNA-sequencing revealed unique genes upregulated in immune cells from blood and CSF samples after treatment. One patient of particular interest, who presented with recurrent multifocal GBM, remarkably achieved a complete response (CR) following locoregional delivery of IL13Rα2-CAR T cells, despite heterogeneous IL13Rα2 tumor expression (PMID: 28029927). In this responding patient, we now show the induction of endogenous tumor-specific T cell reactivity and T cell clones whose dynamics contracted with tumor volume following IL13Rα2-targeted CAR T therapy. These studies establish that CAR T cell therapy has the potential to re-shape the tumor microenvironment, creating a context permissible for eliciting endogenous antitumor immunity and emphasize the importance of the host innate and adaptive immunity in productive CAR T cell therapy of solid tumors. Citation Format: Christine E. Brown, Darya Alizadeh, Vanessa Jonsson, Jonathan Hibbard, Stephanie Yahn, Robyn A. Wong, Xin Yang, Rachel Ng, Natalie Dullerud, Madeleine Maker, Sharahreh Gholamin, Renate Starr, Nicholas Banovich, Stephen J. Forman, Behnam Badie. CAR T cell therapy reshapes the tumor microenvironment to promote host antitumor immune repsonses in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 59.

The phylogenetic and adaptive factors that cause variation in primate facial form—including differences among the major primate clades and variation related to feeding and/or social behavior—are relatively well understood. However, comparatively little is known about the genetic mechanisms that underlie diversity in facial form in primates. Because it is essential for osteoblastic differentiation and skeletal development, the runt-related transcription factor 2 (Runx2) is one gene that may play a role in these genetic mechanisms. Specifically, polymorphisms in the QA ratio (determined by the ratio of the number of polyglutamines to polyalanines in one functional domain of Runx2) have been shown to be correlated with variation in facial length and orientation in other mammal groups. However, to date, the relationship between variation in this gene and variation in facial form in primates has not been explicitly tested. To test the hypothesis that the QA ratio is correlated with facial form in primates, the current study quantified the QA ratio, facial length, and facial angle in a sample of 33 primate species and tested for correlation using phylogenetic generalized least squares. The results indicate that the QA ratio of the Runx2 gene is positively correlated with variation in relative facial length in anthropoid primates. However, no correlation was found in strepsirrhines, and there was no correlation between facial angle and the QA ratio in any groups. These results suggest that, in primates, the QA ratio of the Runx2 gene may play a role in modulating facial size, but not facial orientation. This study therefore provides important clues about the genetic and developmental mechanisms that may underlie variation in facial form in primates.

Previously, the IAP antagonist LCL161 was shown to have robust anti-myeloma activity in a transgenic mouse model where an acute inflammatory response accompanied a reduction in tumor burden. In order to fully examine alterations to the immune microenvironment, murine splenocytes from twenty mice transplanted with Vk12598 myeloma and administered single-agent treatment regimens of LCL161, cyclophosphamide, or bortezomib were harvested after 24 hours and subjected to single cell RNA-seq sequencing. After initial removal of erythrocytic and mitochondrial expressing cells, count matrices of over 50,000 total cells span twenty murine whole spleen samples. In an examination of the myeloid component, we identified 13 clusters of immune cells with unique compositions across samples due to differing treatment regimens and initial tumor burden. While minimally present in all seven non-transplanted mice, macrophages with elevated expression of complement activation system genes (C1q) were the most abundant myeloid cell population in each of our untreated, Vk12598 transplanted mice. Alternatively, populations of cDC2, pDC, moDC, and monocytes lacking expression of MHC class II markers were fixtures for healthy controls while markedly less abundant in tumor-bearing mice. Tumor burdens in three samples subjected to LCL161 therapy were significantly reduced 24-hours post treatment and accompanied by an expansion of late-stage neutrophils and migratory DCs with expression features mirroring those of DCs from mesenteric lymph nodes. This composition of immune cells was distinct from all other sample including those treated with cyclophosphamide or bortezomib. In addition, relative proportions of B, T, and NK cells were nearly fully reconstituted, matching levels observed in healthy controls, in two of these samples. In a direct functional assessment, expression levels of Fscn1 and Ccr7 (key over-expressed genes in these migratory DCs) markedly increased following treatment of bone marrow derived DCs with LCL161. Overall, the transcriptional profile of these migratory DCs indicates their pivotal role in maturation of DCs (Fscn1, Tmem123) as well as the recruitment of T and NKT cells (Cxcl16, Ccr7) and increase in antigen presentation (Cd63)–all of which may serve to ‘warm' tumors, increasing T cell infiltration necessary for immunotherapy approaches. With the increased resolution of scRNA-seq, we observe unique alterations in the composition of the immune microenvironment of MM induced by treatment with LCL161 that further detail its unique mechanism of anti-MM activity. Citation Format: Caleb K. Stein, Erin Meermeier, Seth Welsh, Victoria Garbitt, Meaghen Sharik, P. Leif Bergsagel, Nicholas Banovich, Jonathan Keats, Marta Chesi. scRNA-seq reveals restructuring of the immune microenvironment of multiple myeloma following treatment with an IAP antagonist [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5622.

Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility, and DNA methylation. Our analysis focused on a comparison of inter-individual regulatory variation across cell types. While most cell-type–specific regulatory quantitative trait loci (QTLs) lie in chromatin that is open only in the affected cell types, we found that 20% of cell-type–specific regulatory QTLs are in shared open chromatin. This observation motivated us to develop a deep neural network to predict open chromatin regions from DNA sequence alone. Using this approach, we were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on cell-type–specific chromatin accessibility.

Multiple myeloma (MM) is the second most common hematological cancer, accounting for 2% of all cancer deaths. MM is associated with a poor prognosis, with a 5-year overall survival of 50.7%. While the introduction of new therapies in the last decade has nearly doubled the survival rate, most patients still experience a relapse. To this end, The Multiple Myeloma Research Foundation developed the CoMMpass study. CoMMpass is a longitudinal clinical trial aimed at accelerating the discovery of more targeted treatments for MM. Clinical parameters and tumor specimens are collected from each of the 1,147 patients at baseline and through the eight-year observation period. To identify genetic determinants of clinical outcomes, each tumor specimen is characterized by Whole Genome, Exome and Transcriptome sequencing. This work has uncovered a number of somatic mutations and copy number alterations associated with tumor progression and response to therapy as well as a novel classification of MM into 12 distinct subtypes based on gene expression. However, the contribution of germline genetic variation to gene expression changes and MM outcome remains poorly understood. Genome-wide association studies have identified germline variants associated with MM risk, indicating inherited genetic susceptibility. Furthermore, MM exhibits a disparity in occurrence and mortality between the sexes and ethnicities, men and African Americans being in at a higher risk than women or those of European ancestry. To better understand the genetic and biological basis of MM predisposition, we utilize a systems genomics approach to examine non-coding inherited and somatic genetic effects on gene expression and MM outcome. Data from 607 CoMMpass participants with available WGS and RNAseq from normal blood and baseline tumor specimens were used to map cis-acting eQTLs. We identified 3929 genes with at least one cis-acting eQTL. Furthermore, we discovered a number of regulatory variants with differential effects on tumor gene expression between the sexes and ethnicities, as well as eQTLs overlapping MM GWAS risk loci, providing regulatory mechanisms connecting these loci to MM. Finally, we discovered eQTLs that modulate overall survival in patients with MM. To validate these putatively regulatory loci in vitro, we utilized MM cell lines and CRISPR activation/interference, successfully altering the expression of the target genes. These and analyses integrating germline and somatic variants, gene expression, and clinical outcomes support the development of personalized medicine approaches for the better treatment of MM. Citation Format: Heini M. Natri, Austin Gutierrez, Bianca Argente, Melissa Wilson Sayres, Kenneth Buetow, Nicholas Banovich. Genetic effects on gene expression and survival in patients with multiple myeloma [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 4352.

Multiple myeloma (MM) is the second most common hematologic cancer, accounting for roughly 2% of all cancer deaths. Unfortunately, MM remains incurable and nearly all patients experience relapse. Recently, we have identified a novel cIAP1 antagonist, LCL161, with remarkable anti-MM effects. Interestingly, unlike in other tumor types, our previous work found that LCL161 does not directly induce apoptosis of MM cells, but rather drives activation and infiltration of macrophages to the tumor bed and phagocytosis of tumor cells. Furthermore, in vitro experiments demonstrate that the anti-MM activity of the agent relies on the presence of the tumor, with no observed increase in MM phagocytosis when macrophages are treated in isolation. However, LCL161 is a strong and indiscriminate transcriptional activator and thus, the molecular mechanisms underlying this immune response in MM remain poorly understood. In an effort to characterize molecular signatures associated with this response, we collected whole spleens from seven WT mice and eleven mice with VK12598 transplanted myeloma for single cell RNA-seq. Of the eleven tumor-bearing mice, three remained untreated, three were treated with LCL161, three with bortezomib, and three with cyclophosphamide. Additionally, one of the WT mice was treated with LCL161. Using the 10X genomics chromium platform, we measured mRNA levels in over 90,000 individual cells. We identified groups of cells with shared expression profiles, corresponding to known cell types, using graph-based clustering. Consistent with our previous work, we observed a marked reduction in tumor cells and activation of the noncanonical NFkB pathway in mice treated with LCL161. Turning our attention to cells identified as monocytes, with a particular focus on putative macrophages, we sought to identify molecular signatures associated with LCL161 treatment. Indeed, using a binomial model we identified over 500 upregulated genes in LCL161-treated macrophages. However, our previous data suggested that the efficacy of LCL161 was dependent on the presence of tumor cells. Thus, we refined these results by comparing the expression profile of macrophages treated with LCL161 in WT and tumor-bearing mice. These contrasts identified dozens of genes that were significantly upregulated in macrophages from LCL161 treated, tumor-bearing mice. Of note, we identified a small number of genes (including Spp1, Irg1, and Lipg) that were active only in macrophages from mice treated with LCL161 and bearing a transplanted tumor and unexpressed in all other cells. We believe these genes—and the pathways in which they are active—hold promise for the development of novel targeted therapies to better treat MM. Citation Format: Nicholas Banovich, Martin Boateng, Marta Chesi, Leif Bergsagel, Jonathan Keats. Single-cell RNA sequencing identifies macrophage-specific expression signatures associated with phagocytosis of multiple myeloma after treatment with cIAP antagonist [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3135.

The advent of induced pluripotent stem cells (iPSCs) revolutionized Human Genetics by allowing us to generate pluripotent cells from easily accessible somatic tissues. This technology can have immense implications for regenerative medicine, but iPSCs also represent a paradigm shift in the study of complex human phenotypes, including gene regulation and disease. Yet, an unresolved caveat of the iPSC model system is the extent to which reprogrammed iPSCs retain residual phenotypes from their precursor somatic cells. To directly address this issue, we used an effective study design to compare regulatory phenotypes between iPSCs derived from two types of commonly used somatic precursor cells. We show that the cell type of origin only minimally affects gene expression levels and DNA methylation in iPSCs. Instead, genetic variation is the main driver of regulatory differences between iPSCs of different donors.

DNA Differences The extent to which genetic variation affects an individual's phenotype has been difficult to predict because the majority of variation lies outside the coding regions of genes. Now, three studies examine the extent to which genetic variation affects the chromatin of individuals with diverse ancestry and genetic variation (see the Perspective by Furey and Sethupathy ). Kasowski et al. (p. 750 , published online 17 October) examined how genetic variation affects differences in chromatin states and their correlation to histone modifications, as well as more general DNA binding factors. Kilpinen et al. (p. 744 , published online 17 October) document how genetic variation is linked to allelic specificity in transcription factor binding, histone modifications, and transcription. McVicker et al. (p. 747 , published online 17 October) identified how quantitative trait loci affect histone modifications in Yoruban individuals and established which specific transcription factors affect such modifications.

Author(s): Gallego Romero, Irene; Pavlovic, Bryan; Hernando-Herraez, Irene; Banovich, Nicholas; Kagan, Courtney; Burnett, Jonathan; Huang, Constance; Mitrano, Amy; Chavarria, Claudia; Ben-Nun, Inbar; Li, Yingchun; Sabatini, Karen; Leonardo, Trevor; Parast, Mana; Marques-Bonet, Tomas; Laurent, Louise; Loring, Jeanne; Gilad, Yoav | Abstract: Comparative genomics studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced pluripotent stem cell (iPSC) lines derived from fibroblasts of healthy donors. All lines appear to be free of integration from exogenous reprogramming vectors, can be maintained using standard iPSC culture techniques, and have proliferative and differentiation potential similar to human and mouse lines. To begin demonstrating the utility of comparative iPSC panels, we collected RNA sequencing data and methylation profiles from the chimpanzee iPSCs and their corresponding fibroblast precursors, as well as from 7 human iPSCs and their precursors, which were of multiple cell type and population origins. Overall, we observed much less regulatory variation within species in the iPSCs than in the somatic precursors, indicating that the reprogramming process has erased many of the differences observed between somatic cells of different origins. We identified 4,918 differentially expressed genes and 3,598 differentially methylated regions between iPSCs of the two species, many of which are novel inter-species differences that were not observed between the somatic cells of the two species. Our panel will help realise the potential of iPSCs in primate studies, and in combination with genomic technologies, transform studies of comparative evolution.