Vincent Liu

All Publications

• Latent human herpesvirus 6 is reactivated in CAR T cells. Nature Lareau, C. A., Yin, Y., Maurer, K., Sandor, K. D., Daniel, B., Yagnik, G., Peña, J., Crawford, J. C., Spanjaart, A. M., Gutierrez, J. C., Haradhvala, N. J., Riberdy, J. M., Abay, T., Stickels, R. R., Verboon, J. M., Liu, V., Buquicchio, F. A., Wang, F., Southard, J., Song, R., Li, W., Shrestha, A., Parida, L., Getz, G., Maus, M. V., Li, S., Moore, A., Roberts, Z. J., Ludwig, L. S., Talleur, A. C., Thomas, P. G., Dehghani, H., Pertel, T., Kundaje, A., Gottschalk, S., Roth, T. L., Kersten, M. J., Wu, C. J., Majzner, R. G., Satpathy, A. T. 2023

  Abstract

  Cell therapies have yielded durable clinical benefits for patients with cancer, but the risks associated with the development of therapies from manipulated human cells are understudied. For example, we lack a comprehensive understanding of the mechanisms of toxicities observed in patients receiving T cell therapies, including recent reports of encephalitis caused by reactivation of human herpesvirus 6 (HHV-6)1. Here, through petabase-scale viral genomics mining, we examine the landscape of human latent viral reactivation and demonstrate that HHV-6B can become reactivated in cultures of human CD4+ T cells. Using single-cell sequencing, we identify a rare population of HHV-6 'super-expressors' (about 1 in 300-10,000 cells) that possess high viral transcriptional activity, among research-grade allogeneic chimeric antigen receptor (CAR) T cells. By analysing single-cell sequencing data from patients receiving cell therapy products that are approved by the US Food and Drug Administration2 or are in clinical studies3-5, we identify the presence of HHV-6-super-expressor CAR T cells in patients in vivo. Together, the findings of our study demonstrate the utility of comprehensive genomics analyses in implicating cell therapy products as a potential source contributing to the lytic HHV-6 infection that has been reported in clinical trials1,6-8 and may influence the design and production of autologous and allogeneic cell therapies.

  View details for DOI 10.1038/s41586-023-06704-2

  View details for PubMedID 37938768

  View details for PubMedCentralID 9827115

• Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Nature protocols Lareau, C. A., Liu, V., Muus, C., Praktiknjo, S. D., Nitsch, L., Kautz, P., Sandor, K., Yin, Y., Gutierrez, J. C., Pelka, K., Satpathy, A. T., Regev, A., Sankaran, V. G., Ludwig, L. S. 2023

  Abstract

  Natural sequence variation within mitochondrial DNA (mtDNA) contributes to human phenotypes and may serve as natural genetic markers in human cells for clonal and lineage tracing. We recently developed a single-cell multi-omic approach, called 'mitochondrial single-cell assay for transposase-accessible chromatin with sequencing' (mtscATAC-seq), enabling concomitant high-throughput mtDNA genotyping and accessible chromatin profiling. Specifically, our technique allows the mitochondrial genome-wide inference of mtDNA variant heteroplasmy along with information on cell state and accessible chromatin variation in individual cells. Leveraging somatic mtDNA mutations, our method further enables inference of clonal relationships among native ex vivo-derived human cells not amenable to genetic engineering-based clonal tracing approaches. Here, we provide a step-by-step protocol for the use of mtscATAC-seq, including various cell-processing and flow cytometry workflows, by using primary hematopoietic cells, subsequent single-cell genomic library preparation and sequencing that collectively take ~3-4 days to complete. We discuss experimental and computational data quality control metrics and considerations for the extension to other mammalian tissues. Overall, mtscATAC-seq provides a broadly applicable platform to map clonal relationships between cells in human tissues, investigate fundamental aspects of mitochondrial genetics and enable additional modes of multi-omic discovery.

  View details for DOI 10.1038/s41596-022-00795-3

  View details for PubMedID 36792778

  View details for PubMedCentralID 7307462

• Single-cell multi-omic profiling and clonal tracing of the human gynecological tumor microenvironment Liu, V., Sandor, K., Daniel, B., Berthoin, L., Sabri, S., Panagiotopoulou, S., Yin, Y., Hiam-Galvez, K., Sit, R., Fan, Z., Galvin, B., Khan, O., Bezman, N., Grogan, J., Howitt, B., Zheng, G., Lareau, C., Satpathy, A. AMER ASSOC CANCER RESEARCH. 2022

  View details for Web of Science ID 000892509506622

• Compatibility rules of human enhancer and promoter sequences. Nature Bergman, D. T., Jones, T. R., Liu, V., Ray, J., Jagoda, E., Siraj, L., Kang, H. Y., Nasser, J., Kane, M., Rios, A., Nguyen, T. H., Grossman, S. R., Fulco, C. P., Lander, E. S., Engreitz, J. M. 2022

  Abstract

  Gene regulation in the human genome is controlled by distal enhancers that activate specific nearby promoters1. One model for this specificity is that promoters might have sequence-encoded preferences for certain enhancers, for example mediated by interacting sets of transcription factors or cofactors2. This "biochemical compatibility" model has been supported by observations at individual human promoters and by genome-wide measurements in Drosophila3-9. However, the degree to which human enhancers and promoters are intrinsically compatible has not been systematically measured, and how their activities combine to control RNA expression remains unclear. Here we designed a high-throughput reporter assay called ExP STARR-seq (enhancer x promoter self-transcribing active regulatory region sequencing) and applied it to examine the combinatorial compatibilities of 1,000 enhancer and 1,000 promoter sequences in human K562 cells. We identify simple rules for enhancer-promoter compatibility: most enhancers activated all promoters by similar amounts, and intrinsic enhancer and promoter activities combine multiplicatively to determine RNA output (R2=0.82). In addition, two classes of enhancers and promoters showed subtle preferential effects. Promoters of housekeeping genes contained built-in activating motifs for factors such as GABPA and YY1, which decreased the responsiveness of promoters to distal enhancers. Promoters of variably expressed genes lacked these motifs and showed stronger responsiveness to enhancers. Together, this systematic assessment of enhancer-promoter compatibility suggests a multiplicative model tuned by enhancer and promoter class to control gene transcription in the human genome.

  View details for DOI 10.1038/s41586-022-04877-w

  View details for PubMedID 35594906

• Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. Nature biotechnology Miller, T. E., Lareau, C. A., Verga, J. A., DePasquale, E. A., Liu, V., Ssozi, D., Sandor, K., Yin, Y., Ludwig, L. S., El Farran, C. A., Morgan, D. M., Satpathy, A. T., Griffin, G. K., Lane, A. A., Love, J. C., Bernstein, B. E., Sankaran, V. G., van Galen, P. 2022

  Abstract

  The combination of single-cell transcriptomics with mitochondrial DNA variant detection can be used to establish lineage relationships in primary human cells, but current methods are not scalable to interrogate complex tissues. Here, we combine common 3' single-cell RNA-sequencing protocols with mitochondrial transcriptome enrichment to increase coverage by more than 50-fold, enabling high-confidence mutation detection. The method successfully identifies skewed immune-cell expansions in primary human clonal hematopoiesis.

  View details for DOI 10.1038/s41587-022-01210-8

  View details for PubMedID 35210612

• The emergent landscape of the mouse gut endoderm at single-cell resolution NATURE Nowotschin, S., Setty, M., Kuo, Y., Liu, V., Garg, V., Sharma, R., Simon, C. S., Saiz, N., Gardner, R., Boutet, S. C., Church, D. M., Hoodless, P. A., Hadjantonakis, A., Pe'er, D. 2019; 569 (7756): 361-+

  Abstract

  Here we delineate the ontogeny of the mammalian endoderm by generating 112,217 single-cell transcriptomes, which represent all endoderm populations within the mouse embryo until midgestation. We use graph-based approaches to model differentiating cells, which provides a spatio-temporal characterization of developmental trajectories and defines the transcriptional architecture that accompanies the emergence of the first (primitive or extra-embryonic) endodermal population and its sister pluripotent (embryonic) epiblast lineage. We uncover a relationship between descendants of these two lineages, in which epiblast cells differentiate into endoderm at two distinct time points-before and during gastrulation. Trajectories of endoderm cells were mapped as they acquired embryonic versus extra-embryonic fates and as they spatially converged within the nascent gut endoderm, which revealed these cells to be globally similar but retain aspects of their lineage history. We observed the regionalized identity of cells along the anterior-posterior axis of the emergent gut tube, which reflects their embryonic or extra-embryonic origin, and the coordinated patterning of these cells into organ-specific territories.

  View details for DOI 10.1038/s41586-019-1127-1

  View details for Web of Science ID 000468123700030

  View details for PubMedID 30959515

  View details for PubMedCentralID PMC6724221