Project 8p Research Newsletter - June 2023
💬 Research Question of the Month
How are chromosomal syndromes like trisomy 21 similar to, or different from, chromosome 8p disorder? What can we learn about one from the other? What tools can be applied to the study of both?
Let us know what you think in the Comments section below!
🔬Research Highlight
Large chromosomal copy number variants, such as trisomy 21 and 8p duplication/deletion, affect the expression of a large number of genes. A fundamental question is how do these changes in gene expression give rise to the cellular and developmental phenotypes that are characteristic of these syndromes?
At this month’s Research Roundtable, Dr. Stefan Pinter (University of Connecticut) shared how his lab has used XIST as a tool to answer some of these questions in trisomy 21. XIST is a long non-coding RNA that silences the expression of the second X chromosome present in female cells. By transplanting the XIST gene onto chromosome 21 in cells with trisomy 21, the extra copy of Chr21 is similarly silenced (Jiang et al. 2014). Dr. Pinter’s lab further developed the capabilities of this tool by creating an inducible version of XIST that can be turned on at different points of cellular development, including in terminal neural lineages, enabling them to probe questions such as which cell types, phenotypes, and developmental windows are most amenable to therapy? (Bansal et al. 2022)
8p disorder differs from trisomy 21 in that the whole of chromosome 8 is not duplicated, rather large portions of the p arm are deleted and/or duplicated and inverted. The complexity of these variants means that a tool like XIST, which is only able to silence large swaths of chromosomes, has more limited utility for the study of 8p. To address this, Dr. Pinter is working on combining CRISPR constructs that are capable of either repressing (CRISPRi) or activating (CRISPRa) gene expression with an inducible construct that drives iPSC differentiation into neurons. These molecular tools can then be used to interrogate gene function in 8p in two ways:
In a top-down approach, these constructs can be integrated into 8p cells and used to increase the expression of monogenic genes, or to decrease the expression of trisomic genes, until the effects of 8p on the cells are ameliorated.
In a bottom-up approach, these constructs can be integrated into control cells and then genes on 8p can be turned on or off until 8p cellular phenotypes are recapitulated.
Using these approaches, we can start to identify the genes on 8p that are responsible for various cellular phenotypes and to generate and test hypotheses about therapeutic interventions.
Featured image above: Euploid cells (left) and trisomy 21 cells with a dox-inducible XIST construct (middle and right) at day 28 of neural differentiation. Staining: Blue - Hoechst; Green - astroglial s100b; Red - neuronal MAP2; White - H2AK119ub. In T21 cells without doxycycline treatment (middle) the extra copy of chromosome 21 is expressed and the cells preferentially differentiate into astroglial cells (green), whereas the euploid cells show more differentiation into neurons (left, red). When the T21 cells are treated with dox (right), XIST is turned on and silences the extra copy of chromosome 21, correcting the balance of differentiation towards neurons. Image courtesy of Dr. Pinter, Bansal et al. bioRxiv 2022.05.11.491519.
You can watch the meeting on Project 8p’s YouTube channel:
💰 Open Grant Opportunities
Chan Zuberberg Initiative, Collaborative Pairs Pilot Project - LOI due June 22nd
📄 Articles and Publications
Let us know if you’ve read or published a paper or article recently that you think the 8p community should know about!
From neurodevelopment to neurodegeneration: utilizing human stem cell models to gain insight into Down syndrome. Watson, LA and Meharena, HM. Front. Genet., 30 May 2023. https://www.frontiersin.org/articles/10.3389/fgene.2023.1198129/full (Open Access)
8p Researchers Dr. Hiruy Meharena and Dr. Ashley Watson review the neurological symptoms of Down Syndrome and the cellular and animal models that have been developed to study the underlying molecular mechanisms. Some of these approaches are already being implemented in 8p research, but many still require development.
Organoid intelligence (OI): the new frontier in biocomputing and intelligence-in-a-dish. Smirnova, L. et al. Front. Sci., 28 Feb 2023 https://www.frontiersin.org/journals/science/articles/10.3389/fsci.2023.1017235 (Open Access)
This article is part of an Article Hub on Organoid Intelligence, which lays forth a roadmap for the development of organoid intelligence as a scientific discipline. 8p Researcher Dr. Alysson Muotri is a contributing author.
CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions. Li, E. et al. bioRxiv 2023.04.26.538498. https://www.biorxiv.org/content/10.1101/2023.04.26.538498v1.abstract (Open Access, This is a pre-print and has not been peer reviewed.)
In this publication, the Kampmann lab describes a new 3D co-culture system, termed iAssembloids (induced multi-lineage assembloids), that enables the rapid generation of homogenous neuron-glia spheroids. Like cortical organoids, iAssemboids can be used to study the interactions between different cell types, however they can be generated much faster. Using these iAssembloids, Li et al. performed a neuronal survival screen using CRISPRi and identified that GSK3β inhibits neuroprotective NRF2, which was not identified in previous screens using 2D monocultures.
💜 Family Corner
Data Freeze - Monday, June 19th, 2023
Participate in the Chromosome 8p Registry
Our team will be publishing Care Guidelines in 2023. Include your 8p hero by enrolling, completing surveys, and uploading your genetic report.
Community Benefits:
Care Guidelines will summarize the present clinical and patient-reported knowledge of Chromosome 8p Disorders for all areas of symptoms including the brain, vision, heart, muscular, gut, and more. It will include recommendations for clinical tests needed and how doctors and caregivers can communicate as a team.
We need to know the nuances and unique experiences for every 8p hero so we don’t miss anything. As we learn more about Chromosome 8p, we anticipate these recommendations will evolve, and future editions will be published.
📆 Upcoming Events
8p Research Roundtable, Dr. Jason Sheltzer, June 26th, 1:30 PM EST. Email whitney@perlara.com if you would like to attend.
Great information! Confirms the way I have tried to describe it for the most part, but will be sharing this with Shelby's medical team. So glad there is research to refer people/professionals to!