Easy and Accessible Workflow for Label-Free Single-Cell Proteomics.

Single-cell proteomics (SCP) can provide information that is unattainable through either bulk-scale protein measurements or single-cell profiling of other omes. Maximizing proteome coverage often requires custom instrumentation, consumables, and reagents for sample processing and separations, which has limited the accessibility of SCP to a small number of specialized laboratories. Commercial platforms have become available for SCP cell isolation and sample preparation, but the high cost of these platforms and the technical expertise required for their operation place them out of reach of many interested laboratories. Here, we assessed the new HP D100 Single Cell Dispenser for label-free SCP. The low-cost instrument proved highly accurate and reproducible for dispensing reagents in the range from 200 nL to 2 µL. We used the HP D100 to isolate and prepare single cells for SCP within 384-well PCR plates. When the well plates were immediately centrifuged following cell dispensing and again after reagent dispensing, we found that ∼97% of wells that were identified in the instrument software as containing a single cell indeed provided the proteome coverage expected of a single cell. This commercial dispenser combined with one-step sample processing provides a very rapid and easy-to-use workflow for SCP with no reduction in proteome coverage relative to a nanowell-based workflow, and the commercial well plates also facilitate autosampling with unmodified instrumentation. Single-cell samples were analyzed using home-packed 30 µm i.d. nanoLC columns as well as commercially available 50 µm i.d. columns. The commercial columns resulted in ∼35% fewer identified proteins. However, combined with the well plate-based preparation platform, the presented workflow provides a fully commercial and relatively low-cost alternative for SCP sample preparation and separation, which should greatly broaden the accessibility of SCP to other laboratories.

Suppression of Ah Receptor (AhR) increases the aggressiveness of TNBC cells and 11-Cl-BBQ-activated AhR inhibits their growth.

Triple-negative breast cancer (TNBC) represents around 15% of the 2.26 million breast cancers diagnosed worldwide annually and has the worst outcome. Despite recent therapeutic advances, there remains a lack of targeted therapies for this breast cancer subtype. The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor with biological roles in regulating development, xenobiotic metabolism, cell cycle progression and cell death. AhR activation by select ligands can promote tumor suppression in multiple cancer types. AhR can negatively regulate the activity of different oncogenic signaling pathways and can directly upregulate tumor suppressor genes such as p27Kip1. To determine the role of AhR in TNBC, we generated AhR-deficient cancer cells and investigated the impact of AhR loss on TNBC cell growth phenotypes. We found that AhR-deficient MDA-MB-468 TNBC cells have increased proliferation and formed significantly more colonies compared to AhR expressing cells. These cells without AhR expression grew aggressively in vivo. To determine the molecular targets driving this phenotype, we performed transcriptomic profiling in AhR expressing and AhR knockout MDA-MB-468 cells and identified tyrosine receptor kinases, as well as other genes involved in proliferation, survival and clonogenicity that are repressed by AhR. In order to determine therapeutic targeting of AhR in TNBC, we investigated the anti-cancer effects of the novel AhR ligand 11-chloro-7H-benzimidazo[2,1-a]benzo[de]iso-quinolin-7-one (11-Cl-BBQ), which belongs to a class of high affinity, rapidly metabolized AhR ligands called benzimidazoisoquinolines (BBQs). 11-Cl-BBQ induced AhR-dependent cancer cell-selective growth inhibition and strongly inhibited colony formation in TNBC cells.

The cyclin-dependent kinase inhibitor p27Kip1 interacts with the aryl hydrocarbon receptor and negatively regulates its transcriptional activity.

p27Kip1 functions to coordinate cell cycle progression through the inhibition of cyclin-dependent kinase (CDK) complexes. p27Kip1 also exerts distinct activities beyond CDK-inhibition, including functioning as a transcriptional regulator. The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor with diverse biological roles. The regulatory inputs that control AhR-mediated transcriptional responses are an active area of investigation. AhR was previously established as a direct regulator of p27Kip1 transcription. Here, we report the physical interaction of AhR and p27Kip1 and show that p27Kip1 expression negatively regulates AhR-mediated transcription. p27Kip1 knockout cells display increased AhR nuclear localisation and significantly higher expression of AhR target genes. This work thus identifies new regulatory cross-talk between p27Kip1 and AhR.

An Evaluation of Human Induced Pluripotent Stem Cells to Test for Cardiac Developmental Toxicity.

To prevent congenital defects arising from maternal exposure, safety regulations require pre-market developmental toxicity screens for industrial chemicals and pharmaceuticals. Traditional embryotoxicity approaches depend heavily on the use of low-throughput animal models which may not adequately predict human risk. The validated embryonic stem cell test (EST) developed in murine embryonic stem cells addressed the former problem over 15 years ago. Here, we present a proof-of-concept study to address the latter challenge by updating all three endpoints of the classic mouse EST with endpoints derived from human induced pluripotent stem cells (hiPSCs) and human fibroblasts. Exposure of hiPSCs to selected test chemicals inhibited differentiation at lower concentrations than observed in the mouse EST. The hiPSC-EST also discerned adverse developmental outcomes driven by novel environmental toxicants. Evaluation of the early cardiac gene TBX5 yielded similar toxicity patterns as the full-length hiPSC-EST. Together, these findings support the further development of hiPSCs and early molecular endpoints as a biologically relevant embryotoxicity screening approach for individual chemicals and mixtures.

Cardiac differentiation potential of human induced pluripotent stem cells in a 3D self-assembling peptide scaffold.

In the past decade, various strategies for cardiac reparative medicine involving stem cells from multiple sources have been investigated. However, the intra-cardiac implantation of cells with contractile ability may seriously disrupt the cardiac syncytium and de-synchronize cardiac rhythm. For this reason, bioactive cardiac implants, consisting of stem cells embedded in biomaterials that act like band aids, have been exploited to repair the cardiac wall after myocardial infarction. For such bioactive implants to function properly after transplantation, the choice of biomaterial is equally important as the selection of the stem cell source. While adult stem cells have shown promising results, they have various disadvantages including low proliferative potential in vitro, which make their successful usage in human transplants difficult. As a first step towards the development of a bioactive cardiac patch, we investigate here the cardiac differentiation properties of human induced pluripotent stem cells (hiPSCs) when cultured with and without ascorbic acid (AA) and when embedded in RAD16-I, a biomaterial commonly used to develop cardiac implants. In adherent cultures and in the absence of RAD16-I, AA promotes the cardiac differentiation of hiPSCs by enhancing the expression of specific cardiac genes and proteins and by increasing the number of contracting clusters. In turn, embedding in peptide hydrogel based on RAD16-I interferes with the normal cardiac differentiation progression. Embedded hiPSCs up-regulate genes associated with early cardiogenesis by up to 105 times independently of the presence of AA. However, neither connexin 43 nor troponin I proteins, which are related with mature cardiomyocytes, were detected and no contraction was noted in the constructs. Future experiments will need to focus on characterizing the mature cardiac phenotype of these cells when implanted into infarcted myocardia and assess their regenerative potential in vivo.

Online monitoring of myocardial bioprosthesis for cardiac repair.

BACKGROUND/OBJECTIVES: The aim of this study was to develop a myocardial bioprosthesis for cardiac repair with an integrated online monitoring system. Myocardial infarction (MI) causes irreversible myocyte loss and scar formation. Tissue engineering to reduce myocardial scar size has been tested with variable success, yet scar formation and modulation by an engineered graft is incompletely characterized. METHODS: Decellularized human pericardium was embedded using self-assembling peptide RAD16-I with or without GFP-labeled mediastinal adipose tissue-derived progenitor cells (MATPCs). Resulting bioprostheses were implanted over the ischemic myocardium in the swine model of MI (n=8 treated and n=5 control animals). For in vivo electrical impedance spectroscopy (EIS) monitoring, two electrodes were anchored to construct edges, covered by NanoGold particles and connected to an impedance-based implantable device. Histological evaluation was performed to identify and characterize GFP cells on post mortem myocardial sections. RESULTS: Pluripotency, cardiomyogenic and endothelial potential and migratory capacity of porcine-derived MATPCs were demonstrated in vitro. Decellularization protocol efficiency, biodegradability, as well as in vitro biocompatibility after recellularization were also verified. One month after myocardial bioprosthesis implantation, morphometry revealed a 36% reduction in infarct area, Ki67(+)-GFP(+)-MATPCs were found at infarct core and border zones, and bioprosthesis vascularization was confirmed by presence of Griffonia simplicifolia lectin I (GSLI) B4 isolectin(+)-GFP(+)-MATPCs. Electrical impedance measurement at low and high frequencies (10 kHz-100 kHz) allowed online monitoring of scar maturation. CONCLUSIONS: With clinical translation as ultimate goal, this myocardial bioprosthesis holds promise to be a viable candidate for human cardiac repair.

Self-assembling peptide scaffolds as innovative platforms for drug and cell delivery systems in cardiac regeneration.

Today, the use of biomaterials in many biomedical platforms is becoming increasingly popular due to their high diversity, infinite mimicking capacity, and emerging functions. Applications currently cover diverse areas in biomedicine including systems for cell isolation, expansion and maintenance, platforms for drug and cell delivery, scaffolds for tissue engineering, tissue regeneration and repair, cancer therapy, etc. Biomaterials in general can be: (1) natural in origin such as many proteins from the extracellular matrix, natural polysaccharides or scaffolds presented in a blood clot or (2) synthetic, including polymers, ceramics, or peptides. In this review, we focus on the use of self-assembling peptide scaffolds as an innovative and reliable strategy to obtain platforms for cell and drug delivery to injured or diseased tissues and organs. This type of material is molecular by design and it develops spontaneously into nanofiber scaffolds with multiple uses. In particular, examples are given for applications in the area of cardiac repair and regeneration.