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Human health and development depend on dynamic networks of physical, and functional, interactions between proteins. However, the details of these networks – how they are formed and how they function – are largely unknown.
Matthias Stadtfeld, PhD
Assistant Professor, Cell Biology in Medicine
Principal Investigator, Stadtfeld Lab
Weill Cornell Medical College
New York, NY
“Understanding developmental and pathological epigenome remodeling using pluripotent stem cell”
Muzlifah Haniffa, FMedSci
Professor, Dermatology and Immunology
Wellcome Trust Senior Research Fellow in Clinical Science
Wellcome Sanger Institute
Alejandro Sánchez Alvarado, PhD
Principal Investigator, Sánchez Alvarado Lab
Executive Director and Chief Scientific Officer
Stowers Institute for Medical Research
Kansas City, MO
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CReM in the News!
Dysfunction of alveolar epithelial type 2 cells (AEC2s), the facultative progenitors of lung alveoli,
is implicated in pulmonary disease pathogenesis, highlighting the importance of human in vitro
models. However, AEC2-like cells in culture have yet to be directly compared to their in vivo
counterparts at single-cell resolution. Here, we performed head-to-head comparisons among the
transcriptomes of primary (1°) adult human AEC2s, their cultured progeny, and human induced
pluripotent stem cell–derived AEC2s (iAEC2s). We found each population occupied a distinct
transcriptomic space with cultured AEC2s (1° and iAEC2s) exhibiting similarities to and differences
from freshly purified 1° cells. Across each cell type, we found an inverse relationship between
proliferative and maturation states, with preculture 1° AEC2s being most quiescent/mature and
iAEC2s being most proliferative/least mature. Cultures of either type of human AEC2s did not
generate detectable alveolar type 1 cells in these defined conditions; however, a subset of iAEC2s
cocultured with fibroblasts acquired a transitional cell state described in mice and humans to arise
during fibrosis or following injury. Hence, we provide direct comparisons of the transcriptomic
programs of 1° and engineered AEC2s, 2 in vitro models that can be harnessed to study human lung
health and disease.
Individuals homozygous for the ‘‘Z’’ mutation in alpha-1 antitrypsin deficiency are known to be at increased
risk for liver disease. It has also become clear that some degree of risk is similarly conferred by the heterozygous
state. A lack ofmodel systems that recapitulate heterozygosity in human hepatocytes has limited the
ability to study the impact of a single Z alpha-1 antitrypsin (ZAAT) allele on hepatocyte biology. Here, we
describe the derivation of syngeneic induced pluripotent stem cells (iPSCs) engineered to determine the
effects of ZAAT heterozygosity in iPSC-hepatocytes (iHeps). We find that heterozygous MZ iHeps exhibit
an intermediate disease phenotype and share with ZZ iHeps alterations in AAT protein processing and
downstream perturbations including altered endoplasmic reticulum (ER) and mitochondrial morphology,
reduced mitochondrial respiration, and branch-specific activation of the unfolded protein response in cell
subpopulations. Our model of MZ heterozygosity thus provides evidence that a single Z allele is sufficient
to disrupt hepatocyte homeostatic function.
A robust method of producing mature T cells from iPSCs is needed to realize their therapeutic potential. NOTCH1 is known to be required for the production of hematopoietic progenitor cells with T cell potential in vivo. Here we identify a critical window during mesodermal
differentiation when Notch activation robustly improves access to definitive hematopoietic progenitors with T/NK cell lineage potential. Low-density progenitors on either OP9-hDLL4 feeder cells or hDLL4-coated plates favored Tcell maturation into TCRab+CD3+CD8+ cells
that express expected T cell markers, upregulate activation markers, and proliferate in response to T cell stimulus. Single-cell RNAseq shows Notch activation yields a 6-fold increase in multi-potent hematopoietic progenitors that follow a developmental trajectory toward Tcells with clear similarity to post-natal human thymocytes.We conclude that early mesodermal Notch activation during hematopoietic differentiation is a missing stimulus with broad implications for producing hematopoietic progenitors with definitive characteristics.
Andrew A. Wilson MD as the Alpha-1 Foundation’s new Scientific Director FOR IMMEDIATE RELEASE November 10, 2022- The Alpha-1 Foundation announces the appointment of Andrew A. Wilson, MD as its new Scientific Director. Dr. Wilson assumes this role with a long-standing passion and commitment to the Alpha-1 community. “On behalf of the Alpha-1 Foundation, I am excited to work with Dr. Wilson to continue the mission-focused work of the Foundation that has been at the forefront of Alpha-1 research for nearly 30 years,” states Scott Santarella, President and CEO of the Alpha-1 Foundation. As a pulmonary and critical care clinician-scientist with a focus on regenerative medicine and stem cell biology, Dr. Wilson’s goal is to advance understanding of and treatment for genetic causes of chronic obstructive pulmonary disease (COPD) and the most common genetic cause of COPD, Alpha-1 Antitrypsin Deficiency (Alpha-1). He has been an active member of the Alpha-1 community since 2006, serving as the head of the Clinical Resource Center (CRC) at Boston University Chobanian & Avedisian School of Medicine, member of the Grant Advisory Committee (GAC) and member of the Research Registry Working Group. Dr Wilson is also site Principal Investigator of the Alpha-1 Biomarkers Consortium (A1BC) study and also of the Alpha-1 Antitrypsin Deficiency Adult Clinical and Genetic Linkage Study at Boston University. Dr. Wilson first became involved with the Alpha-1 Foundation through research during his pulmonary and critical care fellowship at Boston University Chobanian & Avedisian School of Medicine. Interested in developing gene therapies for lung disease, he applied for grant funding from the Alpha-1 Foundation in 2006 and was fortunate to be the recipient of a fellowship grant. Over time, his interest in Alpha-1 grew as he became acquainted with the late John W. Walsh and met Alpha-1 patients at Foundation meetings and events. “I am honored and humbled to have been selected as the new Scientific Director of the Alpha-1 Foundation. Many researchers who are currently working on Alpha-1 research, myself included, probably wouldn’t be doing so if it were not for the support they have received from the Alpha-1 Foundation over the years. In the same vein, having an organized patient community is key since translational research relies upon access to patients with the disease. Researchers must be able to find patients. We are fortunate that Alphas are so enthusiastic and generous in their participation in research. I hope that as Scientific Director I will be able to help the Foundation to advance its mission and work towards a cure for AATD.” In 2012, Dr. Wilson opened the Alpha-1 Center, combining the CRC and the Alpha-1 research program, which has since grown into one of the largest CRCs in the Northeast. The CRC at Boston University Chobanian & Avedisian School of Medicine is highly engaged with the Alpha-1 community through a variety of mechanisms. The Wilson Lab, located at the Center for Regenerative Medicine (CReM) of Boston University/ Boston Medical Center, maintains an active research program focused on Alpha-1. They use patient-derived stem cells, called “induced pluripotent stem cells” or “iPSCs” that can be coaxed to become liver or lung cells in a dish. These cells are used to study how Alpha-1 works in patient cells in the lab and use that system to test potential therapeutics. They also share the cells with other researchers for use in their research efforts directed at developing treatments for Alpha-1 patients. The four core areas of Dr. Wilson’s research are: I) to confirm the clinical significance of the iPSC platform to model in vivo patient biology and demonstrate its potential for testing potential therapeutic agents; II) to better understand the genetic factors and mechanistic drivers that predispose subsets of Alpha-1 patients to develop clinical disease; III) to elucidate the mechanistic contribution of putative COPD susceptibility genes to lung disease pathogenesis; and IV) to develop gene or cell-based therapies for Alpha-1. Dr. Wilson and the Wilson Lab have been actively involved in the Alpha-1 community, participating as a team in the annual Escape to the Cape bike trek on Cape Cod for the past eight years and hosting Alpha-1 support groups from Massachusetts to Maine for visits to CReM many times over the years. These visits have helped inform the CRC about what is important to the patient community and have allowed patients to hear about ongoing research. In some cases, patients have even been able to see their own cells growing in the lab. The Alpha-1 community honored Dr. Wilson in 2014 with the Shillelagh award at the annual Celtic Connection fundraising event to honor his outstanding commitment to Alpha-1
Cystic fibrosis is a monogenic lung disease caused by dysfunction of the cystic fibrosis
transmembrane conductance regulator anion channel, resulting in significant morbidity and
mortality. The progress in elucidating the role of CFTR using established animal and cellbased
models led to the recent discovery of effective modulators for most individuals with CF.
However, a subset of individuals with CF do not respond to these modulators and there is an
urgent need to develop novel therapeutic strategies. In this study, we generate a panel of
airway epithelial cells using induced pluripotent stem cells from individuals with common or
rare CFTR variants representative of three distinct classes of CFTR dysfunction. To measure
CFTR function we adapt two established in vitro assays for use in induced pluripotent stem
cell-derived airway cells. In both a 3-D spheroid assay using forskolin-induced swelling as
well as planar cultures composed of polarized mucociliary airway epithelial cells, we detect
genotype-specific differences in CFTR baseline function and response to CFTR modulators.
These results demonstrate the potential of the human induced pluripotent stem cell platform
as a research tool to study CF and in particular accelerate therapeutic development for CF
caused by rare variants.
Liver damage and an exacerbated inflammatory response are hallmarks of Ebola virus (EBOV) infection. Little is known about the
intrinsic response to infection in human hepatocytes and their contribution to inflammation. Here, we present an induced pluripotent
stem cell (iPSC)-derived hepatocyte-like cell (HLC) platform to define the hepato-intrinsic response to EBOV infection.We used this platform
to show robust EBOV infection, with characteristic ultrastructural changes and evidence for viral replication. Transcriptomics analysis
revealed a delayed response with minimal early transcriptomic changes, followed by a general downregulation of hepatic function
and upregulation of interferon signaling, providing a potential mechanism by which hepatocytes participate in disease severity and liver
damage. Using RNA-fluorescence in situ hybridization (FISH), we showed that IFNB1 and CXCL10 were mainly expressed in non-infected
bystander cells. We did not observe an inflammatory signature during infection. In conclusion, iPSC-HLCs are an immune competent
platform to study responses to EBOV infection.
Genome-wide association studies (GWAS) have identified dozens of loci associated with chronic obstructive
pulmonary disease (COPD) susceptibility; however, the function of associated genes in the cell type(s) affected in
disease remains poorly understood, partly due to a lack of cell models that recapitulate human alveolar biology.
Here, we apply CRISPR interference to interrogate the function of nine genes implicated in COPD by GWAS in
induced pluripotent stem cell–derived type 2 alveolar epithelial cells (iAT2s). We find that multiple genes
implicated by GWAS affect iAT2 function, including differentiation potential, maturation, and/or proliferation.
Detailed characterization of the GWAS gene DSP demonstrates that it regulates iAT2 cell-cell junctions, proliferation,
mitochondrial function, and response to cigarette smoke–induced injury. Our approach thus elucidates the
biological function, as well as disease-relevant consequences of dysfunction, of genes implicated in COPD by GWAS
in type 2 alveolar epithelial cells.
Hematopoietic stem cells (HSCs) reside at the top of the hematopoietic hierarchy and can give rise to all the mature blood cell types in our body, while at the same time maintaining a pool of HSCs through self-renewing divisions. This potential is reflected in their functional definition as cells that are capable of long-term multi-lineage engraftment upon transplantation. While all HSCs meet these criteria, subtle differences exist between developmentally different populations of these cells. Here we present a comprehensive overview of traditional and more recently described markers for phenotyping HSCs and their downstream progeny. To address the need to assess the growing number of surface molecules expressed in various HSC-enriched fractions at different developmental stages, we have developed an extensive multi-parameter spectral flow cytometry panel to phenotype hematopoietic stem and multipotent progenitor cells (HSC/MPPs) throughout development. In this study we then employ this panel to comprehensively profile the HSC compartment in the human fetal liver (FL), which is endowed with superior engraftment potential compared to postnatal sources. Spectral cytometry lends an improved resolution of marker expression to our comprehensive approach, allowing to extract combinatorial expression signatures of several relevant HSC/MPP markers to precisely characterize the HSC/MPP fraction in a variety of tissues.
Type 2 alveolar epithelial cells (AT2s), facultative progenitor cells of the lung alveolus, play a vital role in the biology of the distal lung. In vitro model systems that incorporate human cells, recapitulate the biology of primary AT2s, and interface with the outside environment could serve as useful tools to elucidate functional characteristics of AT2s in homeostasis and disease. We and others recently adapted human induced pluripotent stem cell–derived AT2s (iAT2s) for air-liquid interface (ALI) culture. Here, we comprehensively characterize the effects of ALI culture on iAT2s and benchmark their transcriptional profile relative to both freshly sorted and cultured primary human fetal and adult AT2s…
Human induced pluripotent stem cells (hiPSCs) were differentiated into a specific mesoderm subset characterized by KDR+CD56+APLNR+ (KNA+) expression. KNA+ cells had high clonal proliferative potential and specification into endothelial colony-forming cell (ECFCs) phenotype. KNA+ cells differentiated into perfused blood vessels when implanted subcutaneously into the flank of nonobese diabetic/severe combined immunodeficient mice and when injected into the vitreous of type 2 diabetic mice (db/db mice). Transcriptomic analysis showed that differentiation of hiPSCs derived from diabetics into KNA+ cells was sufficient to change baseline differences in gene expression caused by the diabetic status and reprogram diabetic cells to a pattern similar to KNA+ cells derived from nondiabetic hiPSCs. Proteomic array studies performed on retinas of db/db mice injected with either control or diabetic donor–derived KNA+ cells showed correction of aberrant signaling in db/db retinas toward normal healthy retina. These data provide “proof of principle” that KNA+ cells restore perfusion and correct vascular dysfunction in db/db mice.