Samantha A Morris

Washington University in St. Louis | WUSTL , Wash U · Department of Genetics, Department of Developmental Biology

Human diseases such as heart failure, diabetes, neurodegenerative disorders, and many others result from the deficiency or dysfunction of critical cell types. Strategies for therapeutic tissue repair or regeneration require the in vitro manufacture of clinically relevant quantities of defined cell types. In addition to transplantation therapy, the...

Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering t...

Engineering clinically relevant cells in vitro holds promise for regenerative medicine, but most protocols fail to faithfully recapitulate target cell properties. To address this, we developed CellNet, a network biology platform that determines whether engineered cells are equivalent to their target tissues, diagnoses aberrant gene regulatory netwo...

Direct lineage reprogramming involves the conversion of cellular identity. Single-cell technologies are useful for deconstructing the considerable heterogeneity that emerges during lineage conversion. However, lineage relationships are typically lost during cell processing, complicating trajectory reconstruction. Here we present ‘CellTagging’, a co...

Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics. However, reliance on transcriptional profiling limits adaptation to other single-cell assays. With CellTag-mult...

White adipose tissue is crucial in various physiological processes. In response to high caloric intake, adipose tissue may expand by generating new adipocytes. Adipocyte precursor cells (progenitors and preadipocytes) are essential for generating mature adipocytes, and single- cell RNA sequencing provides new means to identify these populations. He...

Recovery of cardiac function is the holy grail of heart failure therapy yet is infrequently observed and remains poorly understood. In this study, we performed single-nucleus RNA sequencing from patients with heart failure who recovered left ventricular systolic function after left ventricular assist device implantation, patients who did not recove...

Cell identity is governed by the complex regulation of gene expression, represented as gene-regulatory networks¹. Here we use gene-regulatory networks inferred from single-cell multi-omics data to perform in silico transcription factor perturbations, simulating the consequent changes in cell identity using only unperturbed wild-type data. We apply...

Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics enabling high-resolution analysis of cell states while preserving lineage relationships. However, reliance on tr...

In direct lineage conversion, transcription factor (TF) overexpression reconfigures gene regulatory networks (GRNs) to reprogram cell identity. We previously developed CellOracle, a computational method to infer GRNs from single-cell transcriptome and epigenome data. Using inferred GRNs, CellOracle simulates gene expression changes in response to T...

Recovery of cardiac function is the ultimate goal of heart failure therapy. Unfortunately, cardiac recovery remains a rare and poorly understood phemomenon. Herein, we performed single nucleus RNA-sequencing (snRNA-seq) from non-diseased donors and heart failure patients. By comparing patients who recovered LV systolic function following LV assist...

In direct lineage reprogramming, transcription factor (TF) overexpression reconfigures Gene Regulatory Networks (GRNs) to convert cell identities between fully differentiated cell types. We previously developed CellOracle, a computational pipeline that integrates single-cell transcriptome and epigenome profiles to infer GRNs. CellOracle leverages t...

Measuring cell identity in development, disease, and reprogramming is challenging as cell types and states are in continual transition. Here, we present Capybara, a computational tool to classify discrete cell identity and intermediate “hybrid” cell states, supporting a metric to quantify cell fate transition dynamics. We validate hybrid cells usin...

Introducing iTracer, a system for long-term measurement of lineage dynamics at high resolution.

Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differ...

Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differ...

Epithelial cells are charged with protection at barrier sites, but whether this normally beneficial response might sometimes become dysfunctional still needs definition. Here we identify a pattern of imbalance marked by basal epithelial cell growth and differentiation that replaces normal airspaces in a mouse model of progressive post-viral lung di...

Development of the human striatum revealed Deep in the brain, the striatum receives and coordinates inputs from other parts of the brain. Bocchi et al. surveyed molecular features as the striatum develops in the human brain. Single-cell surveys of long intergenic noncoding RNAs revealed a progenitor for medium spiny neurons and provide insight into...

Human embryonic stem cells cultured in 2D micropatterns with BMP4 differentiate into a radial arrangement of germ layers and extraembryonic cells. Single-cell transcriptomes demonstrate generation of cell types transcriptionally similar to their in vivo counterparts in Carnegie stage 7 human gastrula. Time-course analyses indicate sequential differ...

Anti-regenerative scarring obstructs spinal cord repair in mammals and presents a major hurdle for regenerative medicine. In contrast, adult zebrafish possess specialized glial cells that spontaneously repair spinal cord injuries by forming a pro-regenerative bridge across the severed tissue. To identify the mechanisms that regulate differential re...

The first meetup for Computational Stem Cell Biologists was held at the 2020 annual meeting of the International Society for Stem Cell Research. The discussions highlighted opportunities and barriers to computational stem cell research that require coordinated action across the stem cell sector.

Computational biology is enabling an explosive growth in our understanding of stem cells and our ability to use them for disease modeling, regenerative medicine, and drug discovery. We discuss four topics that exemplify applications of computation to stem cell biology: cell typing, lineage tracing, trajectory inference, and regulatory networks. We...

The generation of the hematopoietic stem cells (HSCs) from human pluripotent stem cells (hPSCs) is a major goal for regenerative medicine. In the embryo, HSCs derive from a HOXA+ population known as hemogenic endothelium (HE) in a retinoic acid (RA)-dependent manner. Using hPSCs, we have previously identified a KDR+CD235a− mesodermal population tha...

Lineage tracing and fate mapping, overlapping yet distinct disciplines to follow cells and their progeny, have evolved rapidly over the last century. Lineage tracing aims to identify all progeny arising from an individual cell, placing them within a lineage hierarchy. The recent emergence of genomic technologies, such as single-cell and spatial tra...

During mammalian gastrulation, germ layers arise and are shaped into the body plan while extraembryonic layers sustain the embryo. Human embryonic stem cells, cultured with BMP4 on extracellular matrix micro-discs, reproducibly differentiate into gastruloids, expressing markers of germ layers and extraembryonic cells in radial arrangement. Using si...

Cell-fate conversion generally requires reprogramming effectors to both introduce fate programs of the target cell type and erase the identity of starting cell population. Here, we reveal insights into the activity of microRNAs miR-9/9∗ and miR-124 (miR-9/9∗-124) as reprogramming agents that orchestrate direct conversion of human fibroblasts into m...

Fetal and adult hematopoietic stem cells (HSCs) have distinct proliferation rates, lineage biases, gene expression profiles, and gene dependencies. Although these differences are widely recognized, it is not clear how the transition from fetal to adult identity is coordinated. Here we show that murine HSCs and committed hematopoietic progenitor cel...

The generation of the hematopoietic stem cells (HSCs) from human pluripotent stem cells (hPSCs) is a major goal for regenerative medicine. In the embryo, HSCs derive from a HOXA+ population known as hemogenic endothelium (HE) in a retinoic acid (RA)-dependent manner. Using hPSCs, we have previously identified a KDR+CD235a- mesodermal population tha...

Cellular heterogeneity confounds in situ assays of transcription factor (TF) binding. Single-cell RNA sequencing (scRNA-seq) deconvolves cell types from gene expression, but no technology links cell identity to TF binding sites (TFBS) in those cell types. We present self-reporting transposons (SRTs) and use them in single-cell calling cards (scCC),...

Transitions in cell identity are fundamental to development, reprogramming, and disease. Single-cell technologies enable the dissection of tissue composition on a cell-by-cell basis in complex biological systems. However, highly-sparse single-cell RNA-seq data poses challenges for cell-type identification algorithms based on bulk RNA-seq. Single-ce...

Cell identity is governed by Gene Regulatory Networks (GRNs), a complex system of molecular interactions resulting in the precise spatial and temporal regulation of gene expression. Here, we present CellOracle, a computational tool that integrates single-cell transcriptome and epigenome profiles, integrating prior biological knowledge via regulator...

Single-cell technologies are offering unparalleled insight into complex biology, revealing the behavior of rare cell populations that are masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are typically lost as a result of cell processing. We recently established a method, CellTagging,...

During mammalian gastrulation, germ layers arise and are shaped into the body plan while extraembryonic layers sustain the embryo. Human embryonic stem cells, cultured with BMP4 on extracellular matrix micro-discs, reproducibly differentiate into gastruloids, expressing markers of germ layers and extraembryonic cells with radial organization. Singl...

The discovery that cell differentiation can be reversed challenged theories of how cell identity is determined, laying the foundations for modern methods of reprogramming cell identity and promising new regenerative therapies. Looking back at the original cell-reprogramming experiments.

To celebrate this year’s Peer Review Week theme, “Quality in Peer Review,” we asked editors across Cell Press to nominate some of their best reviewers to give their philosophies on peer reviewing.

The generation of the hematopoietic stem cells (HSCs) from human pluripotent stem cells (hPSCs) is a major goal for regenerative medicine. In the embryo, HSCs derive from a HOXA+ population known as hemogenic endothelium (HE) in a retinoic acid (RA)-dependent manner. Using hPSCs, we have previously identified a KDR+CD235a- mesodermal population tha...

Fueled by recent advances in single cell biology, we are moving away from qualitative and undersampled assessments of cell identity, toward building quantitative, high-resolution cell atlases. However, it remains challenging to precisely define cell identity, leading to renewed debate surrounding this concept. Here, I present three pillars that I p...

Background & aims: The small intestine (SI) displays regionality in nutrient and immunological function. Following SI tissue loss (as occurs in short gut syndrome, or SGS), remaining SI must compensate, or "adapt"; the capacity of SI epithelium to reprogram its regional identity has not been described. Here, we apply single-cell resolution analyse...

High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are heritable, enabling cell populations to be tag...

Knowing the gene-expression pattern of individual cells can unlock their identity. A refined method for generating cellular RNA profiles offers a way to obtain such data at a high level of spatial resolution in intact tissues. Method for RNA profiling of tissues retains spatial information.

Background & Aims: The small intestine (SI) displays regionality in nutrient and immunological function. Following SI tissue loss (as occurs in short gut syndrome, or SGS), remaining SI must compensate, or 'adapt'; the capacity of SI epithelium to reprogram its regional identity has not been described. Here, we apply single-cell resolution analyses...

Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data colle...

Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data colle...

Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data colle...

In situ measurements of transcription factor (TF) binding are confounded by cellular heterogeneity and represent averaged profiles in complex tissues. Single cell RNA-seq (scRNA-seq) is capable of resolving different cell types based on gene expression profiles, but no technology exists to directly link specific cell types to the binding pattern of...

Open Peer Review Article

The mechanisms underlying limb regeneration in axolotl have remained elusive due to limitations in isolating and tracking the cells that replenish lost tissues. In recent work, Elly Tanaka and Barbara Treutlein unite their expertise in axolotl limb regeneration and single-cell analysis to reveal cellular mechanisms underpinning regeneration.

Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data colle...

Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data colle...

Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data colle...

Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data colle...

Kidney organoids derived from human pluripotent stem cells have great utility for investigating organogenesis and disease mechanisms and, potentially, as a replacement tissue source, but how closely organoids derived from current protocols replicate adult human kidney is undefined. We compared two directed differentiation protocols by single-cell t...

Single-cell technologies have seen rapid advancements in recent years, along with new analytical challenges and opportunities. These high-throughput assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing a...

Here, we outline p-Creode, a new algorithm to construct multi-branching cell lineage trajectories from single-cell data. Application of this platform to diverse sources of single-cell data demonstrates its robustness and scalability, while the discovery of a new origin for rare gut tuft cells showcases the utility of p-Creode.

Kidney organoids differentiated from human pluripotent stem cells hold great promise for understanding organogenesis, modeling disease and ultimately as a source of replacement tissue. Realizing the full potential of this technology will require better differentiation strategies based upon knowledge of the cellular diversity and differentiation sta...

Cellular reprogramming can be achieved by ectopically expressing transcription factors that directly convert one differentiated cell type into another, bypassing embryonic states. A number of different cell types have been generated by such ‘direct lineage reprogramming’ methods, but their practical utility has been limited because, in most protoco...

Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. The application of these methodologies to cell fate reprogramming holds particular promise as the manipulation of cell identity is typically inefficient, generating...

We know a great deal about the development of the mammalian embryo until the time that the blastocyst implants into the uterus. With model organisms such as the mouse, we have also developed a considerable understanding of development immediately around gastrulation as embryos can be recovered at this stage for short-term in vitro culture. However,...

Although many approaches have been employed to generate defined fate in vitro, the resultant cells often appear developmentally immature or incompletely specified, limiting their utility. Growing evidence suggests that current methods of direct lineage conversion may rely on the transition through a developmental intermediate. Here, I hypothesize t...

Single-cell RNA sequencing (RNA-seq) technology is hitting its stride and is beginning to be widely adopted. One of the major challenges faced by this rapidly growing field lies in data analysis. Li et al. now present Sinova, a single-cell analytical platform offering temporal, spatial, and regulatory reconstruction of developmental processes.

Blood flow promotes emergence of definitive hematopoietic stem cells (HSCs) in the developing embryo, yet the signals generated by hemodynamic forces that influence hematopoietic potential remain poorly defined. Here we show that fluid shear stress endows long-term multilineage engraftment potential upon early hematopoietic tissues at embryonic day...

Lineage specification in the preimplantation mouse embryo is a regulative process. Thus, it has been difficult to ascertain whether segregation of the inner-cell-mass (ICM) into precursors of the pluripotent epiblast (EPI) and the differentiating primitive endoderm (PE) is random or influenced by developmental history. Here, our results lead to a u...

Significant miRNA 3′ end modification in the livers of 8-day-old mice. Levels at which (A) adenosine and (B) uridine nucleotides were found at the 3′ terminal end of miRNAs from the livers of 8 day old control mice. The 40 most highly modified sequences are shown. Error bars indicate standard error from three separate libraries. (EPS)

Engineering and postnatal development of Zcchc11−/− mice. (A) PCR confirmation of β-gal insertion into the Zcchc11 gene. (B) RT-PCR confirmation of β- gal incorportation into the Zcchc11 ORF. (C) Overall body weight of male and female wild type and Zcchc11 deficient mice through the first 20 weeks of life. *p<0.05 by two-way ANOVA. (D) H & E staini...

Overview of library adaptor trimming and alignment. (PDF)

Oligonucleotide sequences used in molecular analyses. (PDF)

The Zcchc11 enzyme is implicated in microRNA (miRNA) regulation. It can uridylate let-7 precursors to decrease quantities of the mature miRNA in embryonic stem cell lines, suggested to mediate stem cell maintenance. It can uridylate mature miR-26 to relieve silencing activity without impacting miRNA content in cancer cell lines, suggested to mediat...

Movie of GFP:GPI transgenic half and whole embryos imaged in the same culture drop from the four(eight)-cell stage until the late-blastocyst stage.

High-resolution time-lapse confocal imaging of a whole embryo injected with GAP43-RFP to visualize cell membranes. Imaging begins at the transition from the 8- to 16-cell stage. The blastomere marked with a red dashed line divides asymmetrically to generate inside and outside daughters. Frames from this movie are shown in Figure 1D. Time: hours:min...

Movie of GAP43-RFP-injected half and whole embryos to visualize cell membranes, imaged in the same culture drop. Blastomeres compact with very similar timing.

High-resolution time-lapse confocal imaging of a half embryo injected with GAP43-RFP to visualize cell membranes. Frames from this movie are shown in Figure 1D. Imaging begins at the transition from the 4(8)- to 8(16)-cell stage. The blastomeres marked with red dashed lines divide to generate daughters with outside domains. Daughters marked in yell...

Plasticity is a well-known feature of mammalian development, and yet very little is known about its underlying mechanism. Here, we establish a model system to examine the extent and limitations of developmental plasticity in living mouse embryos. We show that halved embryos follow the same strict clock of developmental transitions as intact embryos...

Early development of the mouse comprises a sequence of cell fate decisions in which cells are guided along a pathway of restricted potential and increasing specialisation. The first choice faced by cells of the embryo is whether to become trophectoderm (TE) or inner cell mass (ICM); TE is an extra-embryonic tissue which will form the embryonic port...