Publications

2017
Briggs, J, Li, VC, Lee, S, Woolf, C, Klein, AM, Kirschner, M. Mouse embryonic stem cells can differentiate via multiple paths to the same state . bioRxiv [Internet]. 2017. Publisher's Version
Weinreb, C, Wolock, SL, Klein, AM. SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. bioRxiv [Internet]. 2017. Publisher's Version
Weinreb, C, Wolock, SL, Tusi, BK, Socolovsky, M, Klein, AM. Fundamental limits on dynamic inference from single cell snapshots . bioRxiv [Internet]. 2017. Publisher's Version
Mesa, KR, Kawaguchi, K, Gonzalez, D, Cockburn, K, Boucher, J, Xin, T, Klein, AM, Greco V. Epidermal stem cells self-renew upon neighboring differentiation. bioRxiv [Internet]. 2017. Publisher's Version
Klein, AM, Macosko, E. InDrops and Drop-seq technologies for single-cell sequencing. Lab Chip. 2017;17 (15).
Wagner, BK, Klein AM. Genetic screening enters the single-cell era. . Nature Methods. 2017;14 (3) :237-38.
Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, L. M. Single-cell barcoding and sequencing using droplet microfluidics. Nature Protocols. 2017;12 (1) :44-73.
2016
Baron, M, Veres, A, Wolock, SL, Faust, AL, Gaujoux, R, Vetere, A, Yu R, Wagner, BK, Shen-Orr, SS, Klein, AM, et al. single-Cell Transciptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. . Cell Systems. 2016;4712 (16).
Derr, A, Yang, C, Zilionis, R, Sergushichev, A, Blodgett, DM, Redick, S, Bortell, R, Luban, J, Harlan, DM, Kadener, S, et al. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res . 2016;26 (10) :1397-1410.
Rompolas, P, Mesa, KR, Kawaguchi, K, Park, D, Gonzalez, D, Brown, S, Boucher, J, Klein, AM, Greco V. Spatiotemporal coordination of stem cell commitment during epidermal homeostasis. Science. 2016;352 (6292) :Epub.
2015
Peshkin, L, Wühr, M, Pearl, E, Haas, W, Freeman, RM Jr, Gerhart, JC, Klein, AM, Horb, M, Gygi, SP, Kirschner MW. On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development. Developmental Cell. 2015;35 (33) :383-94.
Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 2015;161 (5) :1187-201.Abstract
It has long been the dream of biologists to map gene expression at the single-cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single-cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing. The method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. We analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after leukemia inhibitory factor (LIF) withdrawal. The reproducibility of these high-throughput single-cell data allowed us to deconstruct cell populations and infer gene expression relationships. VIDEO ABSTRACT.
2014
Kronen MR, Schoenfelder KP, Klein AM, Nystul TG. Basolateral junction proteins regulate competition for the follicle stem cell niche in the Drosophila ovary. PLoS One. 2014;9 (7) :e101085.Abstract
Epithelial stem cells are routinely lost or damaged during adult life and must therefore be replaced to maintain homeostasis. Recent studies indicate that stem cell replacement occurs through neutral competition in many types of epithelial tissues, but little is known about the factors that determine competitive outcome. The epithelial follicle stem cells (FSCs) in the Drosophila ovary are regularly lost and replaced during normal homeostasis, and we show that FSC replacement conforms to a model of neutral competition. In addition, we found that FSCs mutant for the basolateral junction genes, lethal giant larvae (lgl) or discs large (dlg), undergo a biased competition for niche occupancy characterized by increased invasion of neighboring FSCs and reduced loss. Interestingly, FSCs mutant for a third basolateral junction gene, scribble (scrib), do not exhibit biased competition, suggesting that Lgl and Dlg regulate niche competition through a Scrib-independent process. Lastly, we found that FSCs have a unique cell polarity characterized by broadly distributed adherens junctions and the lack of a mature apical domain. Collectively, these observations indicate that Lgl and Dlg promote the differentiation of FSC progeny to a state in which they are less prone to invade the neighboring niche. In addition, we demonstrate that the neutral drift model can be adapted to quantify non-neutral behavior of mutant clones.
2013
Lim X, Tan SH, Koh WLC, Chau RMW, Yan KS, Kuo CJ, van Amerongen R, Klein AM, Nusse R. Interfollicular epidermal stem cells self-renew via autocrine Wnt signaling. Science. 2013;342 (6163) :1226-30.Abstract
The skin is a classical example of a tissue maintained by stem cells. However, the identity of the stem cells that maintain the interfollicular epidermis and the source of the signals that control their activity remain unclear. Using mouse lineage tracing and quantitative clonal analyses, we showed that the Wnt target gene Axin2 marks interfollicular epidermal stem cells. These Axin2-expressing cells constitute the majority of the basal epidermal layer, compete neutrally, and require Wnt/β-catenin signaling to proliferate. The same cells contribute robustly to wound healing, with no requirement for a quiescent stem cell subpopulation. By means of double-labeling RNA in situ hybridization in mice, we showed that the Axin2-expressing cells themselves produce Wnt signals as well as long-range secreted Wnt inhibitors, suggesting an autocrine mechanism of stem cell self-renewal.
2012
Doupé DP, Alcolea MP, Roshan A, Zhang G, Klein AM, Simons BD, Jones PH. A single progenitor population switches behavior to maintain and repair esophageal epithelium. Science. 2012;337 (6098) :1091-3.Abstract
Diseases of the esophageal epithelium (EE), such as reflux esophagitis and cancer, are rising in incidence. Despite this, the cellular behaviors underlying EE homeostasis and repair remain controversial. Here, we show that in mice, EE is maintained by a single population of cells that divide stochastically to generate proliferating and differentiating daughters with equal probability. In response to challenge with all-trans retinoic acid (atRA), the balance of daughter cell fate is unaltered, but the rate of cell division increases. However, after wounding, cells reversibly switch to producing an excess of proliferating daughters until the wound has closed. Such fate-switching enables a single progenitor population to both maintain and repair tissue without the need for a "reserve" slow-cycling stem cell pool.
Hernández AR, Klein AM, Kirschner MW. Kinetic responses of β-catenin specify the sites of Wnt control. Science. 2012;338 (6112) :1337-40.Abstract
Despite more than 30 years of work on the Wnt signaling pathway, the basic mechanism of how the extracellular Wnt signal increases the intracellular concentration of β-catenin is still contentious. Circumventing much of the detailed biochemistry, we used basic principles of chemical kinetics coupled with quantitative measurements to define the reactions on β-catenin directly affected by the Wnt signal. We conclude that the core signal transduction mechanism is relatively simple, with only two regulated phosphorylation steps. Their partial inhibition gives rise to the full dynamics of the response and subsequently maintains a steady state in which the concentration of β-catenin is increased.
2011
Waks Z, Klein AM, Silver PA. Cell-to-cell variability of alternative RNA splicing. Mol Syst Biol. 2011;7 :506.Abstract
Heterogeneity in the expression levels of mammalian genes is large even in clonal populations and has phenotypic consequences. Alternative splicing is a fundamental aspect of gene expression, yet its contribution to heterogeneity is unknown. Here, we use single-molecule imaging to characterize the cell-to-cell variability in mRNA isoform ratios for two endogenous genes, CAPRIN1 and MKNK2. We show that isoform variability in non-transformed, diploid cells is remarkably close to the minimum possible given the stochastic nature of individual splicing events, while variability in HeLa cells is considerably higher. Analysis of the potential sources of isoform ratio heterogeneity indicates that a difference in the control over splicing factor activity is one origin of this increase. Our imaging approach also visualizes non-alternatively spliced mRNA and active transcription sites, and yields spatial information regarding the relationship between splicing and transcription. Together, our work demonstrates that mammalian cells minimize fluctuations in mRNA isoform ratios by tightly regulating the splicing machinery.
Klein AM, Lande-Diner L. The critical discussion group: fostering personal and scientific growth. Mol Cell. 2011;44 (2) :167-9.Abstract
As scientists, we greatly benefit from discussing our work with our peers. Informal, unstructured interactions often yield highly creative feedback. With this in mind, we created a group that fosters discussion of its members' work. The group engages us in new research fields and ways of thinking, and provides us with an opportunity for co-mentoring. Three key components were essential for making this group work: the emphasis on non-hierarchical debate; the diversity of the group members; and the mutual respect existing among the participants.
Magenheim J, Klein AM, Stanger BZ, Ashery-Padan R, Sosa-Pineda B, Gu G, Dor Y. Ngn3(+) endocrine progenitor cells control the fate and morphogenesis of pancreatic ductal epithelium. Dev Biol. 2011;359 (1) :26-36.Abstract
During pancreas development, endocrine and exocrine cells arise from a common multipotent progenitor pool. How these cell fate decisions are coordinated with tissue morphogenesis is poorly understood. Here we have examined ductal morphology, endocrine progenitor cell fate and Notch signaling in Ngn3(-/-) mice, which do not produce islet cells. Ngn3 deficiency results in reduced branching and enlarged pancreatic duct-like structures, concomitant with Ngn3 promoter activation throughout the ductal epithelium and reduced Notch signaling. Conversely, forced generation of surplus endocrine progenitor cells causes reduced duct caliber and an excessive number of tip cells. Thus, endocrine progenitor cells normally provide a feedback signal to adjacent multipotent ductal progenitor cells that activates Notch signaling, inhibits further endocrine differentiation and promotes proper morphogenesis. These results uncover a novel layer of regulation coordinating pancreas morphogenesis and endocrine/exocrine differentiation, and suggest ways to enhance the yield of beta cells from stem cells.
Klein AM, Nikolaidou-Neokosmidou V, Doupé DP, Jones PH, Simons BD. Patterning as a signature of human epidermal stem cell regulation. J R Soc Interface. 2011;8 (65) :1815-24.Abstract
Understanding how stem cells are regulated in adult tissues is a major challenge in cell biology. In the basal layer of human epidermis, clusters of almost quiescent stem cells are interspersed with proliferating and differentiating cells. Previous studies have shown that the proliferating cells follow a pattern of balanced stochastic cell fate. This behaviour enables them to maintain homeostasis, while stem cells remain confined to their quiescent clusters. Intriguingly, these clusters reappear spontaneously in culture, suggesting that they may play a functional role in stem cell auto-regulation. We propose a model of pattern formation that explains how clustering could regulate stem cell activity in homeostatic tissue through contact inhibition and stem cell aggregation.

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