Bio

Bio


Postdoctoral research fellow interested in computational biology, single-cell genomics, immunology, and machine learning.

Honors & Awards


  • Stanford Science Fellow, Stanford University (2020)
  • NIH Ruth L. Kirschstein National Research Service Award (F31), National Cancer Institute (2018)
  • NSF GRFP, National Science Foundation (2015)
  • DAAD Rise Fellow, Deutscher Akademischer Austauschdienst (2013, 2014)
  • Barry M. Goldwater Scholar, Goldwater Foundation (2013)

Professional Education


  • Doctor of Philosophy, Harvard University (2020)
  • Master of Arts, Harvard University (2017)
  • PhD, Harvard University (2020)
  • AM, Harvard University (2017)
  • BS, University of Tulsa (2015)

Stanford Advisors


Publications

All Publications


  • Inference and effects of barcode multiplets in droplet-based single-cell assays NATURE COMMUNICATIONS Lareau, C. A., Ma, S., Duarte, F. M., Buenrostro, J. D. 2020; 11 (1): 866

    Abstract

    A widespread assumption for single-cell analyses specifies that one cell's nucleic acids are predominantly captured by one oligonucleotide barcode. Here, we show that ~13-21% of cell barcodes from the 10x Chromium scATAC-seq assay may have been derived from a droplet with more than one oligonucleotide sequence, which we call "barcode multiplets". We demonstrate that barcode multiplets can be derived from at least two different sources. First, we confirm that approximately 4% of droplets from the 10x platform may contain multiple beads. Additionally, we find that approximately 5% of beads may contain detectable levels of multiple oligonucleotide barcodes. We show that this artifact can confound single-cell analyses, including the interpretation of clonal diversity and proliferation of intra-tumor lymphocytes. Overall, our work provides a conceptual and computational framework to identify and assess the impacts of barcode multiplets in single-cell data.

    View details for DOI 10.1038/s41467-020-14667-5

    View details for Web of Science ID 000514928000007

    View details for PubMedID 32054859

    View details for PubMedCentralID PMC7018801

  • Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility NATURE BIOTECHNOLOGY Lareau, C. A., Duarte, F. M., Chew, J. G., Kartha, V. K., Burkett, Z. D., Kohlway, A. S., Pokholok, D., Aryee, M. J., Steemers, F. J., Lebofsky, R., Buenrostro, J. D. 2019; 37 (8): 916-+

    Abstract

    Recent technical advancements have facilitated the mapping of epigenomes at single-cell resolution; however, the throughput and quality of these methods have limited their widespread adoption. Here we describe a high-quality (105 nuclear fragments per cell) droplet-microfluidics-based method for single-cell profiling of chromatin accessibility. We use this approach, named 'droplet single-cell assay for transposase-accessible chromatin using sequencing' (dscATAC-seq), to assay 46,653 cells for the unbiased discovery of cell types and regulatory elements in adult mouse brain. We further increase the throughput of this platform by combining it with combinatorial indexing (dsciATAC-seq), enabling single-cell studies at a massive scale. We demonstrate the utility of this approach by measuring chromatin accessibility across 136,463 resting and stimulated human bone marrow-derived cells to reveal changes in the cis- and trans-regulatory landscape across cell types and under stimulatory conditions at single-cell resolution. Altogether, we describe a total of 510,123 single-cell profiles, demonstrating the scalability and flexibility of this droplet-based platform.

    View details for DOI 10.1038/s41587-019-0147-6

    View details for Web of Science ID 000482876100023

    View details for PubMedID 31235917

  • Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis CELL REPORTS Ludwig, L. S., Lareau, C. A., Bao, E. L., Nandakumar, S. K., Muus, C., Ulirsch, J. C., Chowdhary, K., Buenrostro, J. D., Mohandas, N., An, X., Aryee, M. J., Regev, A., Sankaran, V. G. 2019; 27 (11): 3228-+

    Abstract

    Human erythropoiesis serves as a paradigm of physiologic cellular differentiation. This process is also of considerable interest for better understanding anemias and identifying new therapies. Here, we apply deep transcriptomic and accessible chromatin profiling to characterize a faithful ex vivo human erythroid differentiation system from hematopoietic stem and progenitor cells. We reveal stage-specific transcriptional states and chromatin accessibility during various stages of erythropoiesis, including 14,260 differentially expressed genes and 63,659 variably accessible chromatin peaks. Our analysis suggests differentiation stage-predominant roles for specific master regulators, including GATA1 and KLF1. We integrate chromatin profiles with common and rare genetic variants associated with erythroid cell traits and diseases, finding that variants regulating different erythroid phenotypes likely act at variable points during differentiation. In addition, we identify a regulator of terminal erythropoiesis, TMCC2, more broadly illustrating the value of this comprehensive analysis to improve our understanding of erythropoiesis in health and disease.

    View details for DOI 10.1016/j.celrep.2019.05.046

    View details for Web of Science ID 000470993200011

    View details for PubMedID 31189107

    View details for PubMedCentralID PMC6579117

  • Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors NATURE Grunewald, J., Zhou, R., Garcia, S. P., Iyer, S., Lareau, C. A., Aryee, M. J., Joung, J. 2019; 569 (7756): 433-+

    Abstract

    CRISPR-Cas base-editor technology enables targeted nucleotide alterations, and is being increasingly used for research and potential therapeutic applications1,2. The most widely used cytosine base editors (CBEs) induce deamination of DNA cytosines using the rat APOBEC1 enzyme, which is targeted by a linked Cas protein-guide RNA complex3,4. Previous studies of the specificity of CBEs have identified off-target DNA edits in mammalian cells5,6. Here we show that a CBE with rat APOBEC1 can cause extensive transcriptome-wide deamination of RNA cytosines in human cells, inducing tens of thousands of C-to-U edits with frequencies ranging from 0.07% to 100% in 38-58% of expressed genes. CBE-induced RNA edits occur in both protein-coding and non-protein-coding sequences and generate missense, nonsense, splice site, and 5' and 3' untranslated region mutations. We engineered two CBE variants bearing mutations in rat APOBEC1 that substantially decreased the number of RNA edits (by more than 390-fold and more than 3,800-fold) in human cells. These variants also showed more precise on-target DNA editing than the wild-type CBE and, for most guide RNAs tested, no substantial reduction in editing efficiency. Finally, we show that an adenine base editor7 can also induce transcriptome-wide RNA edits. These results have implications for the use of base editors in both research and clinical settings, illustrate the feasibility of engineering improved variants with reduced RNA editing activities, and suggest the need to more fully define and characterize the RNA off-target effects of deaminase enzymes in base editor platforms.

    View details for DOI 10.1038/s41586-019-1161-z

    View details for Web of Science ID 000468123700044

    View details for PubMedID 30995674

    View details for PubMedCentralID PMC6657343

  • Interrogation of human hematopoiesis at single-cell and single-variant resolution NATURE GENETICS Ulirsch, J. C., Lareau, C. A., Bao, E. L., Ludwig, L. S., Guo, M. H., Benner, C., Satpathy, A. T., Kartha, V. K., Salem, R. M., Hirschhorn, J. N., Finucane, H. K., Aryee, M. J., Buenrostro, J. D., Sankaran, V. G. 2019; 51 (4): 683-+
  • Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics CELL Ludwig, L. S., Lareau, C. A., Ulirsch, J. C., Christian, E., Muus, C., Li, L. H., Pelka, K., Ge, W., Oren, Y., Brack, A., Law, T., Rodman, C., Chen, J. H., Boland, G. M., Hacohen, N., Rozenblatt-Rosen, O., Aryee, M. J., Buenrostro, J. D., Regev, A., Sankaran, V. G. 2019; 176 (6): 1325-+

    Abstract

    Lineage tracing provides key insights into the fate of individual cells in complex organisms. Although effective genetic labeling approaches are available in model systems, in humans, most approaches require detection of nuclear somatic mutations, which have high error rates, limited scale, and do not capture cell state information. Here, we show that somatic mutations in mtDNA can be tracked by single-cell RNA or assay for transposase accessible chromatin (ATAC) sequencing. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their utility as highly accurate clonal markers to infer cellular relationships. We track native human cells both in vitro and in vivo and relate clonal dynamics to gene expression and chromatin accessibility. Our approach should allow clonal tracking at a 1,000-fold greater scale than with nuclear genome sequencing, with simultaneous information on cell state, opening the way to chart cellular dynamics in human health and disease.

    View details for DOI 10.1016/j.cell.2019.01.022

    View details for Web of Science ID 000460509600009

    View details for PubMedID 30827679

    View details for PubMedCentralID PMC6408267

  • The cis-Regulatory Atlas of the Mouse Immune System CELL Yoshida, H., Lareau, C. A., Ramirez, R. N., Rose, S. A., Maier, B., Wroblewska, A., Desland, F., Chudnovskiy, A., Mortha, A., Dominguez, C., Tellier, J., Kim, E., Dwyer, D., Shinton, S., Nabekura, T., Qi, Y., Yu, B., Robinette, M., Kim, K., Wagers, A., Rhoads, A., Nutt, S. L., Brown, B. D., Mostafavi, S., Buenrostro, J. D., Benoist, C., Immunological Genome Project 2019; 176 (4): 897-+

    Abstract

    A complete chart of cis-regulatory elements and their dynamic activity is necessary to understand the transcriptional basis of differentiation and function of an organ system. We generated matched epigenome and transcriptome measurements in 86 primary cell types that span the mouse immune system and its differentiation cascades. This breadth of data enable variance components analysis that suggests that genes fall into two distinct classes, controlled by either enhancer- or promoter-driven logic, and multiple regression that connects genes to the enhancers that regulate them. Relating transcription factor (TF) expression to the genome-wide accessibility of their binding motifs classifies them as predominantly openers or closers of local chromatin accessibility, pinpointing specific cis-regulatory elements where binding of given TFs is likely functionally relevant, validated by chromatin immunoprecipitation sequencing (ChIP-seq). Overall, this cis-regulatory atlas provides a trove of information on transcriptional regulation through immune differentiation and a foundational scaffold to define key regulatory events throughout the immunological genome.

    View details for DOI 10.1016/j.cell.2018.12.036

    View details for Web of Science ID 000457969200019

    View details for PubMedID 30686579

    View details for PubMedCentralID PMC6785993

  • Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation CELL Buenrostro, J. D., Corces, M., Lareau, C. A., Wu, B., Schep, A. N., Aryee, M. J., Majeti, R., Chang, H. Y., Greenleaf, W. J. 2018; 173 (6): 1535-+

    Abstract

    Human hematopoiesis involves cellular differentiation of multipotent cells into progressively more lineage-restricted states. While the chromatin accessibility landscape of this process has been explored in defined populations, single-cell regulatory variation has been hidden by ensemble averaging. We collected single-cell chromatin accessibility profiles across 10 populations of immunophenotypically defined human hematopoietic cell types and constructed a chromatin accessibility landscape of human hematopoiesis to characterize differentiation trajectories. We find variation consistent with lineage bias toward different developmental branches in multipotent cell types. We observe heterogeneity within common myeloid progenitors (CMPs) and granulocyte-macrophage progenitors (GMPs) and develop a strategy to partition GMPs along their differentiation trajectory. Furthermore, we integrated single-cell RNA sequencing (scRNA-seq) data to associate transcription factors to chromatin accessibility changes and regulatory elements to target genes through correlations of expression and regulatory element accessibility. Overall, this work provides a framework for integrative exploration of complex regulatory dynamics in a primary human tissue at single-cell resolution.

    View details for PubMedID 29706549

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