‘In preprints’ from Development 2022-2023

Cell-autonomous generation of the wave pattern within the vertebrate segmentation clock

Laurel A. Rohde, Arianne Bercowsky-Rama, Jose Negrete Jr., Guillaume Valentin, Sundar Ram Naganathan, Ravi A. Desai, Petr Strnad, Daniele Soroldoni, Frank Jülicher, Andrew C. Oates

https://www.biorxiv.org/content/10.1101/2021.05.29.446196v1

Much of the beauty and mystery of development comes down to the question of how embryos set up patterns of gene expression. Four recent preprints tackle this fascinating question by combining quantitative imaging, modelling, experimental embryology and careful conceptual thinking.

One particularly beautiful example of patterning occurs during somitogenesis. During …

Mechanical bistability of the mesoderm epithelium facilitates mesoderm invagination during Drosophila gastrulation

Hanqing Guo, Michael Swan, Bing He

https://doi.org/10.1101/2021.03.18.435928

In preprints: buckling under pressure during gastrulation by Margot Kossman Williams and Swathi Arur

Early in embryonic development, gastrulation produces the three primordial germ layers – endoderm, mesoderm and ectoderm – and shapes them into a rudimentary body plan. This generally involves internalization of the mesoderm and endoderm layers. In the fruit fly Drosophila melanogaster, mesoderm invagination occurs via formation of the ventral furrow (VF). During this event, future mesoderm cells along the ventral midline undergo apical constriction-driven wedging, causing the epithelial sheet to bend inward and invaginate (Sweeton et al., 1991; Leptin and Grunewald, 1990; Martin et al., 2009)…

Embryo-scale epithelial buckling forms a propagating furrow that initiates gastrulation

Julien Fierling, Alphy John, Barthélémy Delorme, Alexandre Torzynski, Guy Blanchard, Claire Lye, Grégoire Malandain, Bénédicte Sanson, Jocelyn Étienne, Philippe Marmottant, Catherine Quilliet, Matteo Rauzi

https://doi.org/10.1101/2021.12.14.472566

In preprints: buckling under pressure during gastrulation by Margot Kossman Williams and Swathi Arur

Early in embryonic development, gastrulation produces the three primordial germ layers – endoderm, mesoderm and ectoderm – and shapes them into a rudimentary body plan. This generally involves internalization of the mesoderm and endoderm layers. In the fruit fly Drosophila melanogaster, mesoderm invagination occurs via formation of the ventral furrow (VF). During this event, future mesoderm cells along the ventral midline undergo apical constriction-driven wedging, causing the epithelial sheet to bend inward and invaginate (Sweeton et al., 1991; Leptin and Grunewald, 1990; Martin et al., 2009)…

Morphogenetic forces planar polarize LGN/Pins in the embryonic head during Drosophila gastrulation

Jaclyn Camuglia, Soline Chanet, Adam C Martin

https://doi.org/10.1101/2022.01.07.475359

In preprints: buckling under pressure during gastrulation by Margot Kossman Williams and Swathi Arur

Early in embryonic development, gastrulation produces the three primordial germ layers – endoderm, mesoderm and ectoderm – and shapes them into a rudimentary body plan. This generally involves internalization of the mesoderm and endoderm layers. In the fruit fly Drosophila melanogaster, mesoderm invagination occurs via formation of the ventral furrow (VF). During this event, future mesoderm cells along the ventral midline undergo apical constriction-driven wedging, causing the epithelial sheet to bend inward and invaginate (Sweeton et al., 1991; Leptin and Grunewald, 1990; Martin et al., 2009)…

A temporally resolved, multiplex molecular recorder based on sequential genome editing

Junhong Choi, Wei Chen, Anna Minkina, Florence M. Chardon, Chase C. Suiter, Samuel G. Regalado, Silvia Domcke, Nobuhiko Hamazaki, Choli Lee, Beth Martin, Riza M. Daza, Jay Shendure

https://doi.org/10.1101/2021.11.05.467388

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

Molecular recording of sequential cellular events into DNA

Theresa B. Loveless, Courtney K. Carlson, Vincent J. Hu, Catalina A. Dentzel Helmy, Guohao Liang, Michelle Ficht, Arushi Singhai, Chang C. Liu

https://doi.org/10.1101/2021.11.05.467507

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

FRaeppli, a multispectral imaging toolbox for cell tracing and dense tissue analysis in zebrafish

Sara Caviglia, Iris A. Unterweger, Akvilė Gasiūnaitė, Alexandre E. Vanoosthuyse, Francesco Cutrale, Le A. Trinh, Scott E. Fraser, Stephan C. F. Neuhauss, Elke A. Ober

https://doi.org/10.1101/2022.01.14.476353

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

Single-cell transcriptomics of dynamic cell behaviors

Sheldon J.J. Kwok, Daniel T. Montoro, Adam L. Haber, Seok-Hyun Yun, Vladimir Vinarsky

https://doi.org/10.1101/2022.01.31.478519

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

A cell fate decision map reveals abundant direct neurogenesis in the human developing neocortex

Laure Coquand, Anne-Sophie Macé, Sarah Farcy, Clarisse Brunet Avalos, Amandine Di Cicco, Marusa Lampic, Betina Bessières, Tania Attie-Bitach, Vincent Fraisier, Fabien Guimiot, Alexandre Baffet

https://doi.org/10.1101/2022.02.01.478661

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart

Panagiota Siatra, Giannis Vatsellas, Athanasia Chatzianastasiou, Evangelos Balafas, Theodora Manolakou, Andreas Papapetropoulos, Anna Agapaki, Eleni-Taxiarchia Mouchtouri, Artemis G. Korovesi, Manolis Mavroidis, Dimitrios Thanos, Dimitris Beis, Ioannis Kokkinopoulos

https://doi.org/10.1101/2022.01.28.473428

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

Single cell RNA sequencing and lineage tracing confirm mesenchyme to epithelial transformation (MET) contributes to repair of the endometrium at menstruation

Phoebe M Kirkwood, Douglas A Gibson, Isaac Shaw, Ross Dobie, Olympia Kelepouri, Neil C Henderson, Philippa TK Saunders

https://doi.org/10.1101/2021.12.20.473495

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

Clonally heritable gene expression imparts a layer of diversity within cell types

Jeff E. Mold, Martin H. Weissman, Michael Ratz, Michael Hagemann-Jensen, Joanna Hård, Carl-Johan Eriksson, Hosein Toosi, Joseph Berghenstråhle, Leonie von Berlin, Marcel Martin, Kim Blom, Jens Lagergren, Joakim Lundeberg, Rickard Sandberg, Jakob Michaëlsson, Jonas Frisén

https://doi.org/10.1101/2022.02.14.480352

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

TiDeTree: A Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data

Sophie Seidel, Tanja Stadler

https://doi.org/10.1101/2022.02.14.480422

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

Theoretical Guarantees for Phylogeny Inference from Single-Cell Lineage Tracing

Robert Wang, Richard Zhang, Alex Khodaverdian, Nir Yosef

https://doi.org/10.1101/2021.11.21.469464

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

ClonoCluster: a method for using clonal origin to inform transcriptome clustering

LP Richman, Y Goyal, CL Jiang, A Raj

https://doi.org/10.1101/2022.02.11.480077

In preprints: the fast-paced field of single-cell lineage tracing by Alejo Rodriguez-Fraticelli and Samantha A. Morris

Tracking lineage relationships between cells is a powerful way to obtain mechanistic insights into development and cell differentiation (Kretzschmar and Watt, 2012). Over a century ago, cells and their progeny were tracked using simple dye labelling experiments. Following the same principle, powerful contemporary approaches label cells with unique heritable molecular barcodes, using single-cell RNA-sequencing to read out cell lineage and gene expression in parallel, in many individual cells. Here, we highlight several preprints in this fast-moving area of single-cell genomics-based lineage tracing…

Stem cell regulators control a G1 duration gradient in the plant root meristem

Clara Echevarria, Bénédicte Desvoyes, Marco Marconi, José Manuel Franco-Zorrila, Laura Lee, Masaaki Umeda, Robert Sablowski, Kenneth D. Birnbaum, Krzysztof Wabnik, Crisanto Gutierrez

https://doi.org/10.1101/2022.03.09.483577

In preprints: new insights into root stem cells and their diversity by Renske Vroomans and Yka Helariutt

Where stem cells are situated and how they function as part of a proliferative cell population, or ‘meristem’, to promote the growth and development of plants has been under intensive investigation for decades. The root meristem has become an important model for understanding the nature of stem cell populations in plants, primarily because it is more accessible than other meristems (Dolan et al., 1993; Scheres, 2007). Here, we highlight two recent preprints that update our current understanding of the function and diversity of root meristems…

Cellular and gene expression patterns associated with root bifurcation in Selaginella

Tao Fang, Hans Motte, Boris Parizot, Wouter Smet, Xilan Yang, Liam Walker, Maria Njo, George W. Bassel, Tom Beeckman

https://doi.org/10.1101/2022.01.03.474808

In preprints: new insights into root stem cells and their diversity by Renske Vroomans and Yka Helariutt

Where stem cells are situated and how they function as part of a proliferative cell population, or ‘meristem’, to promote the growth and development of plants has been under intensive investigation for decades. The root meristem has become an important model for understanding the nature of stem cell populations in plants, primarily because it is more accessible than other meristems (Dolan et al., 1993; Scheres, 2007). Here, we highlight two recent preprints that update our current understanding of the function and diversity of root meristems…

https://doi.org/10.1101/2022.04.26.488902

In preprints: morphogens in motion by Kristina Stapornwongkul and James Briscoe

Morphogen gradients represent one of the most influential ideas in developmental biology. Although the original notion of a morphogen can be traced back more than 80 years, to at least Dalcq and Pasteels’ suggestion that gradients of ‘morphogenetic substances’ guide the differentiation path of cells during embryogenesis (Dalcq and Pasteels, 1937), the concept has evolved over the years (Stapornwongkul and Vincent, 2021). In its current formulation, a morphogen is considered to be a chemical signal that spreads from a localised source to form a concentration gradient in a tissue. Cells within the gradient read the local morphogen concentration to acquire a specific fate…

Single-cell atlas of mouse limb development reveals a complex spatiotemporal dynamics of skeleton formation

Svetlana Markman, Mor Zada, Eyal David, Amir Giladi, Ido Amit, Elazar Zelzer

https://doi.org/10.1101/2022.05.07.490557

In preprints: new insights into proximodistal limb patterning and differentiation by Catherine McCusker and Alberto Rosello-Diez

In recent years, multiple theories have been proposed to explain how the proximodistal (PD) axis of the tetrapod limb (i.e. from shoulder to digit tips) is patterned. They can be grouped in two broad categories based on the order of specification: progressive and early patterned. The common ground in both categories is that the ∼250 µm region under the distal epithelium of the limb bud is considered undifferentiated, such that the very early bud is fully undifferentiated and, as the limb grows out, the cells that remain in the proximal side of that limit start…

Efficient Human Germ Cell Specification from Stem Cells via Combinatorial Expression of Transcription Factors

Christian Kramme, Merrick Pierson Smela, Bennett Wolf, Patrick R. Fortuna, Garyk Brixi, Kalyan Palepu, Edward Dong, Jessica Adams, Suhaas Bhat, Sabrina Koseki, Emma Tysinger, Teodora Stan, Richie E. Kohman, Songlei Liu, Mutsumi Kobayashi, Toshi Shioda, George M. Church, Pranam Chatterjee

https://doi.org/10.1101/2022.07.11.499564

In preprints: towards reconstituting an ovary by Navin B. Ramakrishna and Ramiro Alberio

Efforts towards the in vitro derivation of germ cells from stem cells have seen considerable progress in the past decade. The successful generation of oocytes in vitro, although challenging, will bring a major advance to reproductive biology – from understanding the complex developmental mechanisms of human oogenesis, to applications in disease modelling of infertility. Current attempts to achieve germ cell and somatic gonadal differentiation in vitro involve two key approaches: application of exogenous signals for induced differentiation paired with gonadal soma co-culture and, more recently, overexpression of candidate regulators. Here, we highlight two preprints…

Directed Differentiation of Human iPSCs to Functional Ovarian Granulosa-Like Cells via Transcription Factor Overexpression

Merrick Pierson Smela, Christian Kramme, Patrick Fortuna, Jessica Adams, Edward Dong, Mutsumi Kobayashi, Garyk Brixi, Emma Tysinger, Richie. E. Kohman, Toshi Shioda, Pranam Chatterjee, George M. Church

https://doi.org/10.1101/2022.07.04.498717

In preprints: towards reconstituting an ovary by Navin B. Ramakrishna and Ramiro Alberio

Efforts towards the in vitro derivation of germ cells from stem cells have seen considerable progress in the past decade. The successful generation of oocytes in vitro, although challenging, will bring a major advance to reproductive biology – from understanding the complex developmental mechanisms of human oogenesis, to applications in disease modelling of infertility. Current attempts to achieve germ cell and somatic gonadal differentiation in vitro involve two key approaches: application of exogenous signals for induced differentiation paired with gonadal soma co-culture and, more recently, overexpression of candidate regulators. Here, we highlight two preprints…

Truncated radial glia as a common precursor in the late corticogenesis of gyrencephalic mammals

Merve Bilgic, Quan Wu, Taeko Suetsugu, Atsunori Shitamukai, Yuji Tsunekawa, Tomomi Shimogori, Mitsutaka Kadota, Osamu Nishimura, Shigehiro Kuraku, Hiroshi Kiyonari, Fumio Matsuzaki

https://doi.org/10.1101/2022.05.05.490846

In preprints: new insights into truncated radial glia by Marilyn Steyert and Tomasz J. Nowakowski

Throughout developmental biology, and indeed biology as a whole, structure and function are intimately linked. This relationship is elegantly exemplified by neural stem cells of the developing cerebral cortex. These cells, which are known as radial glia, are multipotent: in addition to generating neurons, they generate astrocytes, oligodendrocyte precursor cells and, later, ependymal cells. In mice, radial glia fibers extend from the ventricular surface of the cortex all the way out to the pial surface, creating a physical scaffold along which newborn neurons can migrate radially, from the ventricular zone (VZ) to the cortical plate. By contrast…

Expansion of Ventral Foregut Primes the Enhancer Landscape for Organ Specific Differentiation

Yan Fung Wong, Yatendra Kumar, Martin Proks, Jose Alejandro Romero Herrera, Michaela Mrugala Rothová, Rita S. Monteiro, Sara Pozzi, Rachel E. Jennings, Neil A. Hanley, Wendy A. Bickmore, Joshua M. Brickman

https://doi.org/10.1101/2022.04.11.487673

In preprints: humans, the new model organism by James M. Wells and  Ziyuan Guo

Until recently, mechanistic studies of development and disease have relied on animal model systems. With the discovery of human embryonic stem cells (hESCs), then induced pluripotent stem cells (iPSCs), and finally organoids, mechanistic discovery-based research on human tissues is now routine. Cells and tissues derived from hESCs and iPSCs, collectively called human pluripotent stem cells (hPSCs), have many advantages for research. They are scalable and can be genetically manipulated, derived…

Lipid Accumulation Induced by APOE4 Impairs Microglial Surveillance of Neuronal-Network Activity

Matheus B. Victor, Noelle Leary, Xochitl Luna, Hiruy S. Meharena, P. Lorenzo Bozzelli, George Samaan, Mitchell H. Murdock, Djuna von Maydell, Audrey H. Effenberger, Oyku Cerit, Hsin-Lan Wen, Liwang Liu, Gwyneth Welch, Maeve Bonner, Li-Huei Tsai

https://doi.org/10.1101/2022.03.21.484146

In preprints: humans, the new model organism by James M. Wells and  Ziyuan Guo

Until recently, mechanistic studies of development and disease have relied on animal model systems. With the discovery of human embryonic stem cells (hESCs), then induced pluripotent stem cells (iPSCs), and finally organoids, mechanistic discovery-based research on human tissues is now routine. Cells and tissues derived from hESCs and iPSCs, collectively called human pluripotent stem cells (hPSCs), have many advantages for research. They are scalable and can be genetically manipulated, derived…

APOE deficiency impacts neural differentiation and cholesterol biosynthesis in human iPSC-derived cerebral organoids

Jing Zhao, Tadafumi C. Ikezu, Wenyan Lu, Jesse R. Macyczko, Yonghe Li, Laura J. Lewis-Tuffin, Yuka A. Martens, Yingxue Ren, Yiyang Zhu, Yan W. Asmann, Nilüfer Ertekin-Taner, Takahisa Kanekiyo, Guojun Bu

https://doi.org/10.1101/2022.06.30.498241

In preprints: humans, the new model organism by James M. Wells and  Ziyuan Guo

Until recently, mechanistic studies of development and disease have relied on animal model systems. With the discovery of human embryonic stem cells (hESCs), then induced pluripotent stem cells (iPSCs), and finally organoids, mechanistic discovery-based research on human tissues is now routine. Cells and tissues derived from hESCs and iPSCs, collectively called human pluripotent stem cells (hPSCs), have many advantages for research. They are scalable and can be genetically manipulated, derived…

Machine learning directed organoid morphogenesis uncovers an excitable system driving human axial elongation

Giridhar M. Anand, Heitor C. Megale, Sean H. Murphy, Theresa Weis, Zuwan Lin, Yichun He, Xiao Wang, Jia Liu, Sharad Ramanathan

https://doi.org/10.1101/2022.05.10.491358

In preprints: improving and interrogating embryo models by Antonio Scialdone and Nicolas Rivron

How the complexity of an embryo arises is a question at the core of developmental biology. Key discoveries have been made by observing how embryos develop. In a complementary way, a recent bottom-up approach has harnessed the ability of stem cells to self-organize into structures resembling embryos at various stages. These embryo models go under different names according to the stages or tissues they mimic (e.g. blastoids, gastruloids, axioloids, trunk-like structures, etc.) and, when efficient, predictable and predictive of development…

Chimeric 3D-gastruloids – a versatile tool for studies of mammalian peri-gastrulation development

Alexandra E. Wehmeyer, Katrin M. Schüle, Alexandra Conrad, Chiara M. Schröder, Simone Probst, Sebastian J. Arnold

https://doi.org/10.1101/2022.05.25.493377

In preprints: improving and interrogating embryo models by Antonio Scialdone and Nicolas Rivron

How the complexity of an embryo arises is a question at the core of developmental biology. Key discoveries have been made by observing how embryos develop. In a complementary way, a recent bottom-up approach has harnessed the ability of stem cells to self-organize into structures resembling embryos at various stages. These embryo models go under different names according to the stages or tissues they mimic (e.g. blastoids, gastruloids, axioloids, trunk-like structures, etc.) and, when efficient, predictable and predictive of development…

An epigenetic barrier sets the timing of human neuronal maturation

Gabriele Ciceri, Hyunwoo Cho, Meghana Kshirsagar, Arianna Baggiolini, Kelly A Aromolaran, Ryan M Walsh, Peter A Goldstein, Richard P. Koche, Christina S Leslie, Lorenz Studer

https://doi.org/10.1101/2022.06.02.490114

In preprints: releasing the brakes on neuronal maturation by Teresa Rayon and Jelle van den Ameele

In mammals, the length of gestation and the timing of developmental milestones are fixed, with only minor variation between individuals of the same species. However, across species, developmental timing is fundamentally different and little is known about the mechanisms that determine species-specific tempo. Three recent preprints, two from Lorenz Studer’s lab (Ciceri et al., 2022 preprint; Hergenreder et al., 2022 preprint) and one from Pierre Vanderhaegen’s lab (Iwata et al., 2021 preprint), describe different mechanisms that determine the timing…

Combined small molecule treatment accelerates timing of maturation in human pluripotent stem cell-derived neurons

Emiliano Hergenreder, Yana Zorina, Zeping Zhao, Hermany Munguba, Elizabeth L. Calder, Arianna Baggiolini, Andrew P. Minotti, Ryan M. Walsh, Conor Liston, Joshua Levitz, Ralph Garippa, Shuibing Chen, Gabriele Ciceri, Lorenz Studer

https://doi.org/10.1101/2022.06.02.494616

In preprints: releasing the brakes on neuronal maturation by Teresa Rayon and Jelle van den Ameele

In mammals, the length of gestation and the timing of developmental milestones are fixed, with only minor variation between individuals of the same species. However, across species, developmental timing is fundamentally different and little is known about the mechanisms that determine species-specific tempo. Three recent preprints, two from Lorenz Studer’s lab (Ciceri et al., 2022 preprint; Hergenreder et al., 2022 preprint) and one from Pierre Vanderhaegen’s lab (Iwata et al., 2021 preprint), describe different mechanisms that determine the timing…

Species-specific mitochondria dynamics and metabolism regulate the timing of neuronal development

Ryohei Iwata, Pierre Casimir, Emir Erkol, Leïla Boubakar, Mélanie Planque, Martyna Ditkowska, Katlijn Vints, Suresh Poovathingal, Vaiva Gaspariunaite, Matthew Bird, Nikky Corthout, Pieter Vermeersch, Kristofer Davie, Natalia V. Gounko, Stein Aerts, Bart Ghesquière, Sarah-Maria Fendt, Pierre Vanderhaeghen

https://doi.org/10.1101/2021.12.27.474246

In preprints: releasing the brakes on neuronal maturation by Teresa Rayon and Jelle van den Ameele

In mammals, the length of gestation and the timing of developmental milestones are fixed, with only minor variation between individuals of the same species. However, across species, developmental timing is fundamentally different and little is known about the mechanisms that determine species-specific tempo. Three recent preprints, two from Lorenz Studer’s lab (Ciceri et al., 2022 preprint; Hergenreder et al., 2022 preprint) and one from Pierre Vanderhaegen’s lab (Iwata et al., 2021 preprint), describe different mechanisms that determine the timing…

A cell surface code mediates tissue-intrinsic defense against aberrant cells in epithelia

Friedericke Fischer, Laurin Ernst, Anna Frey, Katrin Holstein, Deepti Prasad, Vanessa Weichselberger, Ramya Balaji, Anne-Kathrin Classen

https://doi.org/10.1101/2023.02.16.528665

In preprints: get to know your neighbours – cell interface surveillance through a molecular zip code by Luis Daniel Ríos-Barrera and Vincent Mirouse

One of the central questions of developmental biology has been how tissues define patterns with fixed boundaries, as exemplified by the classical French flag model from Lewis Wolpert (Wolpert, 1969). A second, related question is how do tissues maintain boundaries and prevent cells from deviating from the pattern? These mechanisms have important implications, not only for the development of organisms, but also for the emergence of cancer…

Distinct mechanisms for sebaceous gland self-renewal and regeneration provide durability in response to injury

Natalia A. Veniaminova, Yunlong Jia, Adrien M. Hartigan, Thomas J. Huyge, Shih-Ying Tsai, Marina Grachtchouk, Seitaro Nakagawa, Andrzej A. Dlugosz, Scott X. Atwood, Sunny Y. Wong

https://doi.org/10.1101/2023.05.05.539454

In preprints: progress in sebaceous gland homeostasis, regeneration and immunomodulatory functions by Marc Güell and Marlon R. Schneider

Sebaceous glands (SGs) supply the skin and hairs with sebum, a mixture of protective lipids and other rather uncharacterized compounds with antimicrobial and antioxidative functions (Dahlhoff et al., 2016; Zouboulis et al., 2022). Although its involvement in acne, the most common skin disease of adolescence, shaped SG research for decades, recent studies have addressed numerous topics beyond skin diseases, including stem cell adhesion and metabolism, lipid droplet dynamics, innate immunity…

The microbiota and immune system non-genetically affect offspring phenotypes transgenerationally

Jordan C. Harris, Natalie A. Trigg, Bruktawit Goshu, Yuichi Yokoyama, Lenka Dohnalová, Ellen K. White, Adele Harman, Christoph A. Thaiss, Elizabeth A. Grice, Colin C. Conine, Taku Kambayashi

https://doi.org/10.1101/2023.04.06.535940

In preprints: progress in sebaceous gland homeostasis, regeneration and immunomodulatory functions by Marc Güell and Marlon R. Schneider

Sebaceous glands (SGs) supply the skin and hairs with sebum, a mixture of protective lipids and other rather uncharacterized compounds with antimicrobial and antioxidative functions (Dahlhoff et al., 2016; Zouboulis et al., 2022). Although its involvement in acne, the most common skin disease of adolescence, shaped SG research for decades, recent studies have addressed numerous topics beyond skin diseases, including stem cell adhesion and metabolism, lipid droplet dynamics, innate immunity…

Tgfbr1 controls developmental plasticity between the hindlimb and external genitalia by remodeling their regulatory landscape

Anastasiia Lozovska, Artemis G. Korovesi, André Dias, Alexandre Lopes, Donald A. Fowler, Gabriel G. Martins, Ana Nóvoa, Moisés Mallo

https://doi.org/10.1101/2023.07.07.548120

In preprints: of genitalia and six-legged mice by John J. Young

It may seem unlikely that limbs would share common developmental mechanisms with external genitalia. Yet closer examination suggests that they may share homology. The genitalia and hindlimbs develop in proximity in most amniotes (Tschopp et al., 2014), and both organs begin as buds that require common signaling pathways for growth and patterning (Cohn, 2011). It is therefore not surprising that evolutionary biologists might suggest a common origin for these two organs…

Transgene directed induction of a stem cell-derived human embryo model

Bailey AT Weatherbee, Carlos W Gantner, Riza M Daza, Nobuhiko Hamazaki, Lisa K. Iwamoto-Stohl, Jay Shendure, Magdalena Zernicka-Goetz

https://doi.org/10.1101/2023.06.15.545082

In preprints: opportunities to unravel the earliest stages of human development using stem cell-based embryo models by Naomi Moris and Roger Sturmey

Several exciting advances have enabled the derivation of stem cell-based embryo-like models (SCBEMs). Such models allow us to interrogate previously intractable questions in developmental biology and ask hypothesis-driven fundamental questions such as how the body plan forms, how tissue types interact and how transcriptomic, proteomic and metabolic states influence early human development. SCBEMs provide researchers with scalable, accessible and experimentally tractable systems when access to human embryos is limited or insufficient…

Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering

Joshua Hislop, Amir Alavi, Qi Song, Rayna Schoenberger, Kamyar Keshavarz F., Ryan LeGraw, Jeremy Velazquez, Tahere Mokhtari, Mohammad Nasser Taheri, Matthew Rytel, Susana M Chuva de Sousa Lopes, Simon Watkins, Donna Stolz, Samira Kiani, Berna Sozen, Ziv Bar-Joseph, Mo R. Ebrahimkhani

https://doi.org/10.1101/2023.06.15.545118

In preprints: opportunities to unravel the earliest stages of human development using stem cell-based embryo models by Naomi Moris and Roger Sturmey

Several exciting advances have enabled the derivation of stem cell-based embryo-like models (SCBEMs). Such models allow us to interrogate previously intractable questions in developmental biology and ask hypothesis-driven fundamental questions such as how the body plan forms, how tissue types interact and how transcriptomic, proteomic and metabolic states influence early human development. SCBEMs provide researchers with scalable, accessible and experimentally tractable systems when access to human embryos is limited or insufficient…

Establishment of a novel non-integrated human pluripotent stem cell-based gastruloid model

Gege Yuan, Jiachen Wang, Zhaode Liu, Mengqi Chen, Pinmou Zhu, Hao Zhang, Zhibin Hu, Yiqiang Cui, Yan Yuan, Jiahao Sha

https://doi.org/10.1101/2023.06.28.546720

In preprints: opportunities to unravel the earliest stages of human development using stem cell-based embryo models by Naomi Moris and Roger Sturmey

Several exciting advances have enabled the derivation of stem cell-based embryo-like models (SCBEMs). Such models allow us to interrogate previously intractable questions in developmental biology and ask hypothesis-driven fundamental questions such as how the body plan forms, how tissue types interact and how transcriptomic, proteomic and metabolic states influence early human development. SCBEMs provide researchers with scalable, accessible and experimentally tractable systems when access to human embryos is limited or insufficient…

Dissecting peri-implantation development using cultured human embryos and embryo-like assembloids

Zongyong Ai, Baohua Niu, Yu Yin, Lifeng Xiang, Gaohui Shi, Kui Duan, Sile Wang, Yingjie Hu, Chi Zhang, Chengting Zhang, Lujuan Rong, Ruize Kong, Tingwei Chen, Yixin Guo, Wanlu Liu, Nan Li, Shumei Zhao, Xiaoqing Zhu, Xuancheng Mai, Yonggang Li, Ze Wu, Yi Zheng, Jianping Fu, Weizhi Ji, Tianqing Li

https://doi.org/10.1101/2023.06.15.545180

In preprints: opportunities to unravel the earliest stages of human development using stem cell-based embryo models by Naomi Moris and Roger Sturmey

Several exciting advances have enabled the derivation of stem cell-based embryo-like models (SCBEMs). Such models allow us to interrogate previously intractable questions in developmental biology and ask hypothesis-driven fundamental questions such as how the body plan forms, how tissue types interact and how transcriptomic, proteomic and metabolic states influence early human development. SCBEMs provide researchers with scalable, accessible and experimentally tractable systems when access to human embryos is limited or insufficient…

Transgene-Free Ex Utero Derivation of A Human Post-Implantation Embryo Model Solely from Genetically Unmodified Naïve PSCs

Bernardo Oldak, Emilie Wildschutz, Vladyslav Bondarenko, Alejandro Aguilera-Castrejon, Cheng Zhao, Shadi Tarazi, Mehmet-Yunus Comar, Shahd Ashouokhi, Dmitry Lokshtanov, Francesco Roncato, Sergey Viukov, Eitan Ariel, Max Rose, Nir Livnat, Tom Shani, Carine Joubran, Roni Cohen, Yoseph Addadi, Merav Kedmi, Hadas Keren-Shaul, Sophie Petropoulos, Fredrik Lanner, Noa Novershtern, Jacob H. Hanna

https://doi.org/10.1101/2023.06.14.544922

In preprints: opportunities to unravel the earliest stages of human development using stem cell-based embryo models by Naomi Moris and Roger Sturmey

Several exciting advances have enabled the derivation of stem cell-based embryo-like models (SCBEMs). Such models allow us to interrogate previously intractable questions in developmental biology and ask hypothesis-driven fundamental questions such as how the body plan forms, how tissue types interact and how transcriptomic, proteomic and metabolic states influence early human development. SCBEMs provide researchers with scalable, accessible and experimentally tractable systems when access to human embryos is limited or insufficient…

Water fluxes contribute to growth patterning in shoot meristems

Juan Alonso-Serra, Ibrahim Cheddadi, Annamaria Kiss, Guillaume Cerutti, Claire Lionnet, Christophe Godin, Olivier Hamant

https://doi.org/10.1101/2023.08.27.554993

In preprints: shrinking boundary cells reveal fluid flux in organogenesis by Karthikbabu Kannivadi Ramakanth and Yuchen Long

Water is the most abundant molecule in living organisms and makes up the largest fraction of fresh weight and volume in almost all cell types. It provides the aqueous environment, and sometimes acts as a substrate, for many biochemical reactions in and outside the cells. Water uptake also contributes to volume changes during cell expansion and lumenogenesis, often compared to filling up a balloon, and can subsequently generate forces in the forms of fluid pressure gradient, propellant, and tissue tension…

The apparent loss of PRC2 chromatin occupancy as an artefact of RNA depletion

Evan Healy, Qi Zhang, Emma H. Gail, Samuel C. Agius, Guizhi Sun, Michael Bullen, Varun Pandey, Partha Pratim Das, Jose M. Polo, Chen Davidovich

https://doi.org/10.1101/2023.08.16.553488

In preprints: revisiting RNA in PRC2 by Yuka W. Iwasaki, Haruhiko Koseki and Shinsuke Ito

The role of RNA in recruitment of various chromatin factors is widely acknowledged to contribute to nuclear transcriptional regulation. For instance, in PIWI–piRNA-mediated nuclear co-transcriptional silencing, piRNAs act as guides for the PIWI–piRNA complex, facilitating its localization at target nascent RNAs through sequence complementarity (Iwasaki et al., 2015). This complex recruits silencing effectors, including chromatin modifiers, thereby initiating co-transcriptional silencing. Similarly, long non-coding RNAs (lncRNAs) have diverse roles in nuclear…

Apparent RNA bridging between PRC2 and chromatin is an artefact of non-specific chromatin precipitation upon RNA degradation

Alex Hall Hickman, Richard G. Jenner

https://doi.org/10.1101/2023.08.16.553503

In preprints: revisiting RNA in PRC2 by Yuka W. Iwasaki, Haruhiko Koseki and Shinsuke Ito

The role of RNA in recruitment of various chromatin factors is widely acknowledged to contribute to nuclear transcriptional regulation. For instance, in PIWI–piRNA-mediated nuclear co-transcriptional silencing, piRNAs act as guides for the PIWI–piRNA complex, facilitating its localization at target nascent RNAs through sequence complementarity (Iwasaki et al., 2015). This complex recruits silencing effectors, including chromatin modifiers, thereby initiating co-transcriptional silencing. Similarly, long non-coding RNAs (lncRNAs) have diverse roles in nuclear…

Apparent RNA bridging between PRC2 and chromatin is an artefact of non-specific chromatin precipitation upon RNA degradation

Alex Hall Hickman, Richard G. Jenner

https://doi.org/10.1101/2023.08.16.553503

In preprints: revisiting RNA in PRC2 by Yuka W. Iwasaki, Haruhiko Koseki and Shinsuke Ito

The role of RNA in recruitment of various chromatin factors is widely acknowledged to contribute to nuclear transcriptional regulation. For instance, in PIWI–piRNA-mediated nuclear co-transcriptional silencing, piRNAs act as guides for the PIWI–piRNA complex, facilitating its localization at target nascent RNAs through sequence complementarity (Iwasaki et al., 2015). This complex recruits silencing effectors, including chromatin modifiers, thereby initiating co-transcriptional silencing. Similarly, long non-coding RNAs (lncRNAs) have diverse roles in nuclear…

Evaluation of the RNA-dependence of PRC2 binding to chromatin in human pluripotent stem cells

Yicheng Long, Taeyoung Hwang, Anne R. Gooding, Karen J. Goodrich, Tenaya K. Vallery, John L. Rinn, Thomas R. Cech

https://doi.org/10.1101/2023.08.17.553776

In preprints: revisiting RNA in PRC2 by Yuka W. Iwasaki, Haruhiko Koseki and Shinsuke Ito

The role of RNA in recruitment of various chromatin factors is widely acknowledged to contribute to nuclear transcriptional regulation. For instance, in PIWI–piRNA-mediated nuclear co-transcriptional silencing, piRNAs act as guides for the PIWI–piRNA complex, facilitating its localization at target nascent RNAs through sequence complementarity (Iwasaki et al., 2015). This complex recruits silencing effectors, including chromatin modifiers, thereby initiating co-transcriptional silencing. Similarly, long non-coding RNAs (lncRNAs) have diverse roles in nuclear…

Morphodynamics of human early brain organoid development

Akanksha Jain, Gilles Gut, Fátima Sanchis-Calleja, Ryoko Okamoto, Simon Streib, Zhisong He, Fides Zenk, Malgorzata Santel, Makiko Seimiya, René Holtackers, Sophie Martina Johanna Jansen, J. Gray Camp, Barbara Treutlein

https://doi.org/10.1101/2023.08.21.553827

In preprints: shaping the developing human brain by Marco Massimo and Katherine R. Long

Tissues undergo complex shape changes during development that are crucial for their later architecture and function. Understanding how these changes in shape, the morphodynamics, occur is important not only to understand developmental processes, but also to reveal how dysregulation of these processes leads to developmental defects. The precise spatiotemporal events and morphological dynamics of human brain development have remained relatively poorly understood…