A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development

Publication date: Available online 27 October 2016
Source:Cell Stem Cell
Author(s): Zizhen Yao, John K. Mich, Sherman Ku, Vilas Menon, Anne-Rachel Krostag, Refugio A. Martinez, Leon Furchtgott, Heather Mulholland, Susan Bort, Margaret A. Fuqua, Ben W. Gregor, Rebecca D. Hodge, Anu Jayabalu, Ryan C. May, Samuel Melton, Angelique M. Nelson, N. Kiet Ngo, Nadiya V. Shapovalova, Soraya I. Shehata, Michael W. Smith, Leah J. Tait, Carol L. Thompson, Elliot R. Thomsen, Chaoyang Ye, Ian A. Glass, Ajamete Kaykas, Shuyuan Yao, John W. Phillips, Joshua S. Grimley, Boaz P. Levi, Yanling Wang, Sharad Ramanathan
During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development. Bayesian analyses inferred a unified cell-type lineage tree that bifurcates between cortical and mid/hindbrain cell types. Two methods of clonal analyses confirmed these findings and further revealed the importance of Wnt/β-catenin signaling in controlling this lineage decision. Together, these findings provide a rich transcriptome-based lineage map for studying human brain development and modeling developmental disorders.

Graphical abstract

Teaser

Yao et al. perform single-cell RNA-seq during neural differentiation of hESCs. They identify many classes of neural progenitors and neurons that map to early human brain cells, computationally infer and experimentally confirm lineage relationships between them, and show that Wnt signaling influences the bifurcation between forebrain and mid/hindbrain lineages in vitro.


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Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages

Publication date: Available online 27 October 2016
Source:Cell Stem Cell
Author(s): Nigel Kee, Nikolaos Volakakis, Agnete Kirkeby, Lina Dahl, Helena Storvall, Sara Nolbrant, Laura Lahti, Åsa K. Björklund, Linda Gillberg, Eliza Joodmardi, Rickard Sandberg, Malin Parmar, Thomas Perlmann
Stem cell engineering and grafting of mesencephalic dopamine (mesDA) neurons is a promising strategy for brain repair in Parkinson's disease (PD). Refinement of differentiation protocols to optimize this approach will require deeper understanding of mesDA neuron development. Here, we studied this process using transcriptome-wide single-cell RNA sequencing of mouse neural progenitors expressing the mesDA neuron determinant Lmx1a. This approach resolved the differentiation of mesDA and neighboring neuronal lineages and revealed a remarkably close relationship between developing mesDA and subthalamic nucleus (STN) neurons, while also highlighting a distinct transcription factor set that can distinguish between them. While previous hESC mesDA differentiation protocols have relied on markers that are shared between the two lineages, we found that application of these highlighted markers can help to refine current stem cell engineering protocols, increasing the proportion of appropriately patterned mesDA progenitors. Our results, therefore, have important implications for cell replacement therapy in PD.

Graphical abstract

Teaser

Kee et al. use single-cell RNA-seq to reconstruct Lmx1a+ differentiation in silico, revealing an unexpectedly close relationship between mesDA and STN neuronal lineages during differentiation. Application of markers that distinguish the two can help optimize mesDA differentiation of hESCs with a view to improving therapeutic translation.


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Predictive Markers Guide Differentiation to Improve Graft Outcome in Clinical Translation of hESC-Based Therapy for Parkinson’s Disease

Publication date: Available online 27 October 2016
Source:Cell Stem Cell
Author(s): Agnete Kirkeby, Sara Nolbrant, Katarina Tiklova, Andreas Heuer, Nigel Kee, Tiago Cardoso, Daniella Rylander Ottosson, Mariah J. Lelos, Pedro Rifes, Stephen B. Dunnett, Shane Grealish, Thomas Perlmann, Malin Parmar
Stem cell treatments for neurodegenerative diseases are expected to reach clinical trials soon. Most of the approaches currently under development involve transplantation of immature progenitors that subsequently undergo phenotypic and functional maturation in vivo, and predicting the long-term graft outcome already at the progenitor stage remains a challenge. Here, we took an unbiased approach to identify predictive markers expressed in dopamine neuron progenitors that correlate with graft outcome in an animal model of Parkinson's disease through gene expression analysis of >30 batches of grafted human embryonic stem cell (hESC)-derived progenitors. We found that many of the commonly used markers did not accurately predict in vivo subtype-specific maturation. Instead, we identified a specific set of markers associated with the caudal midbrain that correlate with high dopaminergic yield after transplantation in vivo. Using these markers, we developed a good manufacturing practice (GMP) differentiation protocol for highly efficient and reproducible production of transplantable dopamine progenitors from hESCs.

Graphical abstract

Teaser

Kirkeby et al. show that identification and application of a set of predictive markers can help refine differentiation protocols and improve transplant outcome in a preclinical model for hESC-based treatment of Parkinson's disease.


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CD98-Mediated Adhesive Signaling Enables the Establishment and Propagation of Acute Myelogenous Leukemia

Publication date: Available online 27 October 2016
Source:Cancer Cell
Author(s): Jeevisha Bajaj, Takaaki Konuma, Nikki K. Lytle, Hyog Young Kwon, Jailal N. Ablack, Joseph M. Cantor, David Rizzieri, Charles Chuah, Vivian G. Oehler, Elizabeth H. Broome, Edward D. Ball, Edward H. van der Horst, Mark H. Ginsberg, Tannishtha Reya
Acute myelogenous leukemia (AML) is an aggressive disease associated with drug resistance and relapse. To improve therapeutic strategies, it is critical to better understand the mechanisms that underlie AML progression. Here we show that the integrin binding glycoprotein CD98 plays a central role in AML. CD98 promotes AML propagation and lethality by driving engagement of leukemia cells with their microenvironment and maintaining leukemic stem cells. Further, delivery of a humanized anti-CD98 antibody blocks growth of patient-derived AML, highlighting the importance of this pathway in human disease. These findings indicate that microenvironmental interactions are key regulators of AML and that disrupting these signals with targeted inhibitors such as CD98 antibodies may be a valuable therapeutic approach for adults and children with this disease.

Graphical abstract

Teaser

Bajaj et al. demonstrate the importance of CD98-mediated adhesion for survival of acute myelogenous leukemia (AML) and show that genetic deletion of CD98 in mice or use of a therapeutic CD98 antibody in patient-derived xenografts blocks AML growth.


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UNR/CSDE1 Drives a Post-transcriptional Program to Promote Melanoma Invasion and Metastasis

Publication date: Available online 27 October 2016
Source:Cancer Cell
Author(s): Laurence Wurth, Panagiotis Papasaikas, David Olmeda, Nadine Bley, Guadalupe T. Calvo, Santiago Guerrero, Daniela Cerezo-Wallis, Javier Martinez-Useros, María García-Fernández, Stefan Hüttelmaier, Maria S. Soengas, Fátima Gebauer
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination. Key pro-oncogenic targets of UNR included VIM and RAC1, as validated by loss- and gain-of-function studies. Our results identify UNR as an oncogenic modulator of melanoma progression, unravel the underlying molecular mechanisms, and identify potential targets for this therapeutically challenging malignancy.

Graphical abstract

Teaser

Wurth et al. find that the RNA binding protein UNR is often overexpressed in melanoma and promotes invasion and metastasis. Using iCLIP-seq, RNA-seq, and ribosome profiling, the authors identify potentially oncogenic RNA regulons, one of which includes RAC1 and VIM, whose translation is regulated by UNR.


from Cancer via ola Kala on Inoreader http://ift.tt/2eRZ7qC
via IFTTT

CD98-Mediated Adhesive Signaling Enables the Establishment and Propagation of Acute Myelogenous Leukemia

Publication date: Available online 27 October 2016
Source:Cancer Cell
Author(s): Jeevisha Bajaj, Takaaki Konuma, Nikki K. Lytle, Hyog Young Kwon, Jailal N. Ablack, Joseph M. Cantor, David Rizzieri, Charles Chuah, Vivian G. Oehler, Elizabeth H. Broome, Edward D. Ball, Edward H. van der Horst, Mark H. Ginsberg, Tannishtha Reya
Acute myelogenous leukemia (AML) is an aggressive disease associated with drug resistance and relapse. To improve therapeutic strategies, it is critical to better understand the mechanisms that underlie AML progression. Here we show that the integrin binding glycoprotein CD98 plays a central role in AML. CD98 promotes AML propagation and lethality by driving engagement of leukemia cells with their microenvironment and maintaining leukemic stem cells. Further, delivery of a humanized anti-CD98 antibody blocks growth of patient-derived AML, highlighting the importance of this pathway in human disease. These findings indicate that microenvironmental interactions are key regulators of AML and that disrupting these signals with targeted inhibitors such as CD98 antibodies may be a valuable therapeutic approach for adults and children with this disease.

Graphical abstract

Teaser

Bajaj et al. demonstrate the importance of CD98-mediated adhesion for survival of acute myelogenous leukemia (AML) and show that genetic deletion of CD98 in mice or use of a therapeutic CD98 antibody in patient-derived xenografts blocks AML growth.


http://ift.tt/2eS64Iz

UNR/CSDE1 Drives a Post-transcriptional Program to Promote Melanoma Invasion and Metastasis

Publication date: Available online 27 October 2016
Source:Cancer Cell
Author(s): Laurence Wurth, Panagiotis Papasaikas, David Olmeda, Nadine Bley, Guadalupe T. Calvo, Santiago Guerrero, Daniela Cerezo-Wallis, Javier Martinez-Useros, María García-Fernández, Stefan Hüttelmaier, Maria S. Soengas, Fátima Gebauer
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination. Key pro-oncogenic targets of UNR included VIM and RAC1, as validated by loss- and gain-of-function studies. Our results identify UNR as an oncogenic modulator of melanoma progression, unravel the underlying molecular mechanisms, and identify potential targets for this therapeutically challenging malignancy.

Graphical abstract

Teaser

Wurth et al. find that the RNA binding protein UNR is often overexpressed in melanoma and promotes invasion and metastasis. Using iCLIP-seq, RNA-seq, and ribosome profiling, the authors identify potentially oncogenic RNA regulons, one of which includes RAC1 and VIM, whose translation is regulated by UNR.


http://ift.tt/2eRZ7qC