vascular-organoid-generation-from-human-induced-pluripotent-stem-cells

Vascular Organoid Generation from Human-Induced Pluripotent Stem Cells

Vascular organoids derived from human induced pluripotent stem cells (hiPSCs) recapitulate the cell type diversity and complex architecture of human ...

Columbia University

For patients carrying  mutations, at least one-third develop triple negative breast cancer (TNBC). Not only is TNBC difficult to treat due to the lack of molecular target receptors, but  mutations (BRCA1m) also result in chemotherapeutic resistance, making disease recurrence more likely. Although BRCA1m are highly heterogeneous and therefore difficult to target,  gene's synthetic lethal pair, , is conserved in BRCA1m cancer cells. Therefore, we hypothesize that targeting  might be a fruitful direction to sensitize BRCA1m cancer cells to chemotherapy. We used CRISPR/Cas9 technology to generate  deficiency in two TNBC cell lines, MDA-MB-231 ( wild-type) and MDA-MB-436 (BRCA1m). We explored whether this  disruption (PARP1m) could significantly lower the chemotherapeutic dose necessary to achieve therapeutic efficacy in both a 2D and 3D tumor-on-a-chip model. With both BRCA1m and PARP1m, the TNBC cells were more sensitive to three representative chemotherapeutic breast cancer drugs, doxorubicin, gemcitabine and docetaxel, compared with the  wild-type counterpart in the 2D culture environment. However, PARP1m did not result in this synergy in the 3D tumor-on-a-chip model, suggesting that drug dosing in the tumor microenvironment may influence the synergy. Taken together, our results highlight a discrepancy in the efficacy of the combination of PARP1 inhibition and chemotherapy for TNBC treatment, which should be clarified to justify further clinical testing.

CRISPR/Cas9-mediated mutagenesis to validate the synergy between PARP1 inhibition and chemotherapy in -mutated breast cancer cells.

Chocolate bloom is an off-white coating on the surface of chocolate products due to the altered distribution of the ingredients. Bloom reduces the shelf-life of chocolate and affects its visual and tactile quality, all of which are serious concerns for chocolate manufacturers and consumers. The automated, rapid, and noninvasive point-of-care detection of chocolate bloom has been an essential but challenging problem. The ability to detect and characterize chocolate bloom using portable laser spectroscopy could be used to develop in-situ quality control sensors. In this work, a handheld Raman spectrometer was used to detect chocolate bloom. Raman spectra acquired from bloomed HERSHEY'S milk chocolate, Hawaiian Host milk chocolate covered macadamia nuts, and Babayevsky Russian dark chocolate were used to characterize the type of bloom. The 1064 nm laser beam of the handheld Raman instrument was used to partially remove the fat bloom of the dark chocolate and to induce sugar bloom on the milk chocolate. The handheld Raman approach has a high potential for industrial and consumer applications for the on-site chemical analysis of chocolate bloom and as an alternative laser-based chocolate decoration.

Point-of-care detection, characterization, and removal of chocolate bloom using a handheld Raman spectrometer.

Atherosclerosis begins with the accumulation of cholesterol-carrying lipoproteins on blood vessel walls and progresses to endothelial cell dysfunction, monocyte adhesion, and foam cell formation. Endothelialized tissue-engineered blood vessels (TEBVs) have previously been fabricated to recapitulate artery functionalities, including vasoconstriction, vasodilation, and endothelium activation. Here, the initiation of atherosclerosis is emulated by designing branched TEBVs (brTEBVs) of various geometries treated with enzyme-modified low-density-lipoprotein (eLDL) and TNF-α to induce endothelial cell dysfunction and adhesion of perfused human monocytes. Locations of monocyte adhesion under pulsatile flow are identified, and the hemodynamics in the brTEBVs are characterized using particle image velocimetry (PIV) and computational fluid dynamics (CFD). Monocyte adhesion is greater at the side outlets than at the main outlets or inlets, and is greatest at larger side outlet branching angles (60° or 80° vs 45°). In PIV experiments, the branched side outlets are identified as atherosclerosis-prone areas where fluorescent particles show a transient swirling motion following flow pulses; in CFD simulations, side outlets with larger branching angles show higher vorticity magnitude and greater flow disturbance than other areas. These results suggest that the branched TEBVs with eLDL/TNF-α treatment provide a physiologically relevant model of early atherosclerosis for preclinical studies.

Emulating Early Atherosclerosis in a Vascular Microphysiological System Using Branched Tissue-Engineered Blood Vessels.

Chemotherapy, although effective against primary tumors, may promote metastasis by causing the release of proinflammatory factors from damaged cells. Here, polymeric nanoparticles that deliver chemotherapeutics and scavenge proinflammatory factors simultaneously to inhibit chemotherapy-induced breast cancer metastasis are developed. The cationic nanoparticles can adsorb cell-free nucleic acids (cfNAs) based on charge-charge interaction, which downregulates the expression of Toll-like receptors and then reduces the secretion of inflammatory cytokines. Through in vitro structural optimization, cationic polyamidoamine (PAMAM) dendrimers modified with drug-binding dodecyl groups and diethylethanolamine surface groups (PAMAM-G3-C12 -DEEA ) exhibit the most desirable combination of nanoparticle size (≈140 nm), drug loading, cytotoxicity, cfNA binding, and anti-inflammatory activity. In the mouse models of breast cancer metastasis, paclitaxel-loaded nanoparticles reduce serum levels of cfNAs and inflammatory cytokines compared with paclitaxel treatment alone and inhibit both primary tumor growth and tumor metastasis. Additionally, no significant side effects are detected in the serum or major organs. These results provide a strategy to deliver chemotherapeutics to primary tumors while reducing the prometastatic effects of chemotherapy.

Therapeutic Nanocarriers Inhibit Chemotherapy-Induced Breast Cancer Metastasis.

Single-cell genomics enables dissection of tumor heterogeneity and molecular underpinnings of drug response at an unprecedented resolution. However, broad clinical application of these methods remains challenging, due to several practical and preanalytical challenges that are incompatible with typical clinical care workflows, namely the need for relatively large, fresh tissue inputs. In the present study, we show that multimodal, single-nucleus (sn)RNA/T cell receptor (TCR) sequencing, spatial transcriptomics and whole-genome sequencing (WGS) are feasible from small, frozen tissues that approximate routinely collected clinical specimens (for example, core needle biopsies). Compared with data from sample-matched fresh tissue, we find a similar quality in the biological outputs of snRNA/TCR-seq data, while reducing artifactual signals and compositional biases introduced by fresh tissue processing. Profiling sequentially collected melanoma samples from a patient treated in the KEYNOTE-001 trial, we resolved cellular, genomic, spatial and clonotype dynamics that represent molecular patterns of heterogeneous intralesional evolution during anti-programmed cell death protein 1 therapy. To demonstrate applicability to banked biospecimens of rare diseases, we generated a single-cell atlas of uveal melanoma liver metastasis with matched WGS data. These results show that single-cell genomics from archival, clinical specimens is feasible and provides a framework for translating these methods more broadly to the clinical arena.

Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens.

Gene editing in the mammalian brain has been challenging because of the restricted transport imposed by the blood-brain barrier (BBB). Current approaches rely on local injection to bypass the BBB. However, such administration is highly invasive and not amenable to treating certain delicate regions of the brain. We demonstrate a safe and effective gene editing technique by using focused ultrasound (FUS) to transiently open the BBB for the transport of intravenously delivered CRISPR/Cas9 machinery to the brain.

Focused ultrasound-mediated brain genome editing.

Gene editing in the brain has been challenging because of the restricted transport imposed by the blood-brain barrier (BBB). Current approaches mainly rely on local injection to bypass the BBB. However, such administration is highly invasive and not amenable to treating certain delicate regions of the brain. We demonstrate a safe and effective gene editing technique by using focused ultrasound (FUS) to transiently open the BBB for the transport of intravenously delivered CRISPR/Cas9 machinery to the brain.

Cosmic radiation is the most serious risk that will be encountered during the planned missions to the Moon and Mars. There is a compelling need to understand the effects, safety thresholds, and mechanisms of radiation damage in human tissues, in order to develop measures for radiation protection during extended space travel. As animal models fail to recapitulate the molecular changes in astronauts, engineered human tissues and "organs-on-chips" are valuable tools for studying effects of radiation in vitro. We have developed a bioengineered tissue platform for studying radiation damage in individualized settings. To demonstrate its utility, we determined the effects of radiation using engineered models of two human tissues known to be radiosensitive: engineered cardiac tissues (eCT, a target of chronic radiation damage) and engineered bone marrow (eBM, a target of acute radiation damage). We report the effects of high-dose neutrons, a proxy for simulated galactic cosmic rays, on the expression of key genes implicated in tissue responses to ionizing radiation, phenotypic and functional changes in both tissues, and proof-of-principle application of radioprotective agents. We further determined the extent of inflammatory, oxidative stress, and matrix remodeling gene expression changes, and found that these changes were associated with an early hypertrophic phenotype in eCT and myeloid skewing in eBM. We propose that individualized models of human tissues have potential to provide insights into the effects and mechanisms of radiation during deep-space missions and allow testing of radioprotective measures.

Modeling and countering the effects of cosmic radiation using bioengineered human tissues.

The effects of immunotherapeutics on interactions between immune and cancer cells are modulated by multiple components in the tumour microenvironment (TME), including endothelium and tumour stroma, which provide both a physical barrier and immunosuppressive stimuli. Herein, we report a recirculating chip to enable continuous immune cell recirculation through a microfluidic cell array to include these crucial players. This system consists of a three-layered cell array (μFCA) spatially emulating the TME, with tailored fluidic circuits establishing T cell recirculation. This platform enables the study of dynamics among the TME, immune cells in a circulatory system and cancer cell responses thereof. Through this system, we found that tumour endothelium hindered T cell infiltration into the reconstructed breast cancer tumour compartment. This negative effect was alleviated when treated with anti-human PD-L1 (programmed cell death ligand 1) antibody. Another key stromal component - cancer associated fibroblasts - attenuated T cell infiltration, compared against normal fibroblasts, and led to reduced apoptotic activity in cancer cells. These results confirm the capability of our tumour-on-a-chip system in identifying some key axes to target in overcoming barriers to immunotherapy by recapitulating immune cell interactions with the reconstructed TME. Our results also attest to the feasibility of scaling up this system for high-throughput cancer immunotherapeutic screening.

Enabling continuous immune cell recirculation on a microfluidic array to study immunotherapeutic interactions in a recapitulated tumour microenvironment.

Vascular malformation, a key clinical phenotype of Proteus syndrome, lacks effective models for pathophysiological study and drug development due to limited patient sample access. To bridge this gap, we built a human vascular organoid model replicating Proteus syndrome's vasculature. Using CRISPR/Cas9 genome editing and gene overexpression, we created induced pluripotent stem cells (iPSCs) embodying the Proteus syndrome-specific AKT point mutation for organoid generation. Our findings revealed that AKT overactivation in these organoids resulted in smaller sizes yet increased vascular connectivity, although with less stable connections. This could be due to the significant vasculogenesis induced by AKT overactivation. This phenomenon likely stems from boosted vasculogenesis triggered by AKT overactivation, leading to increased vascular sprouting. Additionally, a notable increase in dysfunctional PDGFR+ mural cells, impaired in matrix secretion, was observed in these AKT-overactivated organoids. The application of AKT inhibitors (ARQ092, AZD5363, or GDC0068) reversed the vascular malformations; the inhibitors' effectiveness was directly linked to reduced connectivity in the organoids. In summary, our study introduces an innovative in vitro model combining organoid technology and gene editing to explore vascular pathophysiology in Proteus syndrome. This model not only simulates Proteus syndrome vasculature but also holds potential for mimicking vasculatures of other genetically driven diseases. It represents an advance in drug development for rare diseases, historically plagued by slow progress.

Human vascular organoids with a mosaic  mutation recapitulate Proteus syndrome.

Spatially resolved gene expression profiling provides insight into tissue organization and cell-cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell resolution. Current ST analysis methods require single-cell RNA sequencing data as a reference for rigorous interpretation of cell states, mostly do not use associated histology images and are not capable of inferring shared neighborhoods across multiple tissues. Here we present Starfysh, a computational toolbox using a deep generative model that incorporates archetypal analysis and any known cell type markers to characterize known or new tissue-specific cell states without a single-cell reference. Starfysh improves the characterization of spatial dynamics in complex tissues using histology images and enables the comparison of niches as spatial hubs across tissues. Integrative analysis of primary estrogen receptor (ER)-positive breast cancer, triple-negative breast cancer (TNBC) and metaplastic breast cancer (MBC) tissues led to the identification of spatial hubs with patient- and disease-specific cell type compositions and revealed metabolic reprogramming shaping immunosuppressive hubs in aggressive MBC.

Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs.

Understanding the impact of long-term opioid exposure on the embryonic brain is critical due to the surging number of pregnant mothers with opioid dependency. However, this has been limited by human brain inaccessibility and cross-species differences in animal models. Here, a human midbrain model is established that uses hiPSC-derived midbrain organoids to assess cell-type-specific responses to acute and chronic fentanyl treatment and fentanyl withdrawal. Single-cell mRNA sequencing of 25,510 cells from organoids in different treatment groups reveals that chronic fentanyl treatment arrests neuronal subtype specification during early midbrain development and alters synaptic activity and neuron projection. In contrast, acute fentanyl treatment increases dopamine release but does not significantly alter gene expression related to cell lineage development. These results provide the first examination of the effects of opioid exposure on human midbrain development at the single-cell level.

Article	Year
CRISPR/Cas9-mediated mutagenesis to validate the synergy between PARP1 inhibition and chemotherapy in -mutated breast cancer cells. Bioengineering & translational medicine\| PubMed ID: 31989039	2020
Point-of-care detection, characterization, and removal of chocolate bloom using a handheld Raman spectrometer. Scientific reports\| PubMed ID: 32555247	2020
Emulating Early Atherosclerosis in a Vascular Microphysiological System Using Branched Tissue-Engineered Blood Vessels. Advanced biology\| PubMed ID: 33852179	2021
Therapeutic Nanocarriers Inhibit Chemotherapy-Induced Breast Cancer Metastasis. Advanced science (Weinheim, Baden-Wurttemberg, Germany)\| PubMed ID: 36220339	2022
Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens. Nature genetics\| PubMed ID: 36624340	2023
Focused ultrasound-mediated brain genome editing. Research square\| PubMed ID: 36712096	2023
Focused ultrasound-mediated brain genome editing. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 37579143	2023
Modeling and countering the effects of cosmic radiation using bioengineered human tissues. Biomaterials\| PubMed ID: 37633022	2023
Enabling continuous immune cell recirculation on a microfluidic array to study immunotherapeutic interactions in a recapitulated tumour microenvironment. Lab on a chip\| PubMed ID: 38180130	2024
Human vascular organoids with a mosaic mutation recapitulate Proteus syndrome. bioRxiv : the preprint server for biology\| PubMed ID: 38328122	2024
Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs. Nature biotechnology\| PubMed ID: 38514799	2024
Chronic Opioid Treatment Arrests Neurodevelopment and Alters Synaptic Activity in Human Midbrain Organoids. Advanced science (Weinheim, Baden-Wurttemberg, Germany)\| PubMed ID: 38549185	2024
Encoding spatial tumour dynamics with Starfysh. Nature reviews. Cancer\| PubMed ID: 39394485	2024

Siyu He

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