Biology subjects

Craft, A. M.

Publications and source records attributed to Craft, A. M..

4 recordsLinked to original sources

bioRxiv2024

Leveraging single cell multiomic analyses to identify factors that drive human chondrocyte cell fate

Cartilage plays a crucial role in skeletal development and function, and abnormal development contributes to genetic and age-related skeletal disease. To better understand how human cartilage develops in vivo, we jointly profiled the transcriptome and open chromatin regions in individual nuclei recovered from distal femurs at 2 fetal timepoints. We used these multiomic data to identify transcription factors expressed in distinct chondrocyte subtypes, link accessible regulatory elements with gene expression, and predict transcription factor-based regulatory networks that are important for growth plate or epiphyseal chondrocyte differentiation. We developed a human pluripotent stem cell platform for interrogating the function of predicted transcription factors during chondrocyte differentiation and used it to test NFATC2. We expect new regulatory networks we uncovered using multiomic data to be important for promoting cartilage health and treating disease, and our platform to be a useful tool for studying cartilage development in vitro. Statement of SignificanceThe identity and integrity of the articular cartilage lining our joints are crucial to pain-free activities of daily living. Here we identified a gene regulatory landscape of human chondrogenesis at single cell resolution, which is expected to open new avenues of research aimed at mitigating cartilage diseases that affect hundreds of millions of individuals world-wide.

developmental biology↗

bioRxiv2023

Directed differentiation of human pluripotent stem cells into articular cartilage reveals effects caused by absence of WISP3, the gene responsible for Progressive Pseudorheumatoid Arthropathy of Childhood

ObjectivesProgressive Pseudorheumatoid Arthropathy of Childhood (PPAC), caused by deficiency of WNT1 inducible signaling pathway protein 3 (WISP3), has been challenging to study because no animal model of the disease exists and cartilage recovered from affected patients is indistinguishable from common end-stage osteoarthritis. Therefore, to gain insights into why precocious articular cartilage failure occurs in this disease, we made in vitro derived articular cartilage using isogenic WISP3-deficient and WISP3-sufficient human pluripotent stem cells (hPSCs). MethodsWe generated articular cartilage-like tissues from induced-(i)PSCs from 2 patients with PPAC and 1 wild-type human embryonic stem cell line in which we knocked out WISP3. We compared these tissues to in vitro-derived articular cartilage tissues from 2 isogenic WISP3-sufficient control lines using histology, bulk RNA sequencing, single cell RNA sequencing, and in situ hybridization. ResultsWISP3-deficient and WISP3-sufficient hPSCs both differentiated into articular cartilage-like tissues that appeared histologically similar. However, the transcriptomes of WISP3-deficient tissues differed significantly from WISP3-sufficient tissues and pointed to increased TGF{beta}, TNF/NFkB, and IL-2/STAT5 signaling and decreased oxidative phosphorylation. Single cell sequencing and in situ hybridization revealed that WISP3-deficient cartilage contained a significantly higher fraction ([~] 4-fold increase, p < 0.001) of superficial zone chondrocytes compared to deeper zone chondrocytes than did WISP3-sufficient cartilage. Conclusions WISP3-deficient and WISP3-sufficient hPSCs can be differentiated into articular cartilage-like tissues, but these tissues differ in their transcriptomes and in the relative abundances of chondrocyte sub-types they contain. These findings provide important starting points for in vivo studies when an animal model of PPAC or presymptomtic patient-derived articular cartilage becomes available. KEY MESSAGES What is already known on this topicO_LILoss-of-function mutations in WISP3 cause Progressive Pseudorheumatoid Arthropathy of Childhood (PPAC), yet the precise function of WISP3 in cartilage is unknown due to the absence of cartilage disease Wisp3 knockout mice and the lack of available PPAC patient cartilage that is not end-stage. Thus, most functional studies of WISP3 have been performed in vitro using WISP3 over-expressing cell lines (i.e., not wild-type) and WISP3-deficient chondrocytes. C_LI What this study addsO_LIWe describe 3 new WISP3-deficient human pluripotent stem cell (hPSC) lines and show they can be differentiated into articular cartilage-like tissue. C_LIO_LIWe compare in vitro-derived articular cartilage made from WISP3-deficient and isogenic WISP3- sufficient hPSCs using bulk RNA sequencing, single cell RNA sequencing, and in situ hybridization. C_LIO_LIWe observe significant differences in the expression of genes previously associated with cartilage formation and homeostasis in the TGF{beta}, TNF/NFkB, and IL-2/STAT5 signaling pathways. We also observe that WISP3-deficient cartilage-like tissues contain significantly higher fractions of chondrocytes that express superficial zone transcripts. These data suggest precocious cartilage failure in PPAC is the result of abnormal articular cartilage formation, dysregulated homeostatic signaling, or both. C_LI How this study might affect research, practice or policyO_LIThis study uses in vitro-derived articular cartilage to generate hypotheses for why cartilage fails in children with PPAC. This work prioritizes downstream studies to be performed when pre-symptomatic patient-derived cartilage samples or animal model of PPAC becomes available. It is essential to know how WISP3 functions in cartilage to develop therapies that benefit patients with PPAC and other degenerative joint diseases. C_LI

genetics↗

bioRxiv2022

Lineage-Specific Differences and Regulatory Networks Governing Human Chondrocyte Development

To address large gaps in our understanding of the molecular regulation of articular and growth plate cartilage development in humans, we used our directed differentiation approach to generate these distinct cartilage tissues from human embryonic stem cells. The resulting transcriptomic profiles of hESC-derived articular and growth plate chondrocytes were similar to fetal epiphyseal and growth plate chondrocytes, with respect to genes both known and previously unknown to cartilage biology. With the goal to characterize the regulatory landscapes accompanying these respective transcriptomes, we mapped chromatin accessibility in hESC-derived chondrocyte lineages, and mouse embryonic chondrocytes, using ATAC-sequencing. Integration of the expression dataset with the differentially accessible genomic regions revealed lineage-specific gene regulatory networks. We validated functional interactions of two transcription factors (RUNX2 in growth plate chondrocytes and RELA in articular chondrocytes) with their predicted genomic targets. The maps we provide thus represent a framework for probing regulatory interactions governing chondrocyte differentiation. This work constitutes a substantial step towards comprehensive and comparative molecular characterizations of distinct chondrogenic lineages, and sheds new light on human cartilage development and biology.

developmental biology↗

bioRxiv2018

Effective repair of joint cartilage using human pluripotent stem cell-derived tissue

Adult articular cartilage lacks significant regenerative capacity, and damage to this tissue often leads to progressive joint degeneration (osteoarthritis). We developed strategies to generate articular cartilage from human pluripotent stem cells (hPSCs) as a source of clinically relevant tissues for joint repair1. Previously, we demonstrated that these chondrocytes retain cartilage forming potential following subcutaneous implantation in mice. In this report, we evaluated the potential of human embryonic stem cell (hESC)-derived articular cartilage tissue to repair osteochondral defects created in the rat knee. Following implantation, the hESCderived cartilage maintained a proteoglycan and type II collagen-rich matrix, and was well integrated with native rat tissue at the basal and lateral surfaces. The ability to generate cartilage tissue with integrative and reparative properties from an unlimited and robust cell source represents a significant clinical advance for cartilage repair that can be applied to large animal models and ultimately to patient care.

developmental biology↗