Programming human cell fate: overcoming challenges and unlocking potential through technological breakthroughs.

In recent years, there have been notable advancements in the ability to programme human cell identity, enabling us to design and manipulate cell function in a Petri dish. However, current protocols for generating target cell types often lack efficiency and precision, resulting in engineered cells that do not fully replicate the desired identity or functional output. This applies to different methods of cell programming, which face similar challenges that hinder progress and delay the achievement of a more favourable outcome. However, recent technological and analytical breakthroughs have provided us with unprecedented opportunities to advance the way we programme cell fate. The Company of Biologists' 2023 workshop on 'Novel Technologies for Programming Human Cell Fate' brought together experts in human cell fate engineering and experts in single-cell genomics, manipulation and characterisation of cells on a single (sub)cellular level. Here, we summarise the main points that emerged during the workshop's themed discussions. Furthermore, we provide specific examples highlighting the current state of the field as well as its trajectory, offering insights into the potential outcomes resulting from the application of these breakthrough technologies in precisely engineering the identity and function of clinically valuable human cells.

Recognition of the Diglycine C-End Degron by CRL2KLHDC2 Ubiquitin Ligase.

Aberrant proteins can be deleterious to cells and are cleared by the ubiquitin-proteasome system. A group of C-end degrons that are recognized by specific cullin-RING ubiquitin E3 ligases (CRLs) has recently been identified in some of these abnormal polypeptides. Here, we report three crystal structures of a CRL2 substrate receptor, KLHDC2, in complex with the diglycine-ending C-end degrons of two early-terminated selenoproteins and the N-terminal proteolytic fragment of USP1. The E3 recognizes the degron peptides in a similarly coiled conformation and cradles their C-terminal diglycine with a deep surface pocket. By hydrogen bonding with multiple backbone carbonyls of the peptides, KLHDC2 further locks in the otherwise degenerate degrons with a compact interface and unexpected high affinities. Our results reveal the structural mechanism by which KLHDC2 recognizes the simplest C-end degron and suggest a functional necessity of the E3 to tightly maintain the low abundance of its select substrates.

C-Terminal End-Directed Protein Elimination by CRL2 Ubiquitin Ligases.

The proteolysis-assisted protein quality control system guards the proteome from potentially detrimental aberrant proteins. How miscellaneous defective proteins are specifically eliminated and which molecular characteristics direct them for removal are fundamental questions. We reveal a mechanism, DesCEND (destruction via C-end degrons), by which CRL2 ubiquitin ligase uses interchangeable substrate receptors to recognize the unusual C termini of abnormal proteins (i.e., C-end degrons). C-end degrons are mostly less than ten residues in length and comprise a few indispensable residues along with some rather degenerate ones. The C-terminal end position is essential for C-end degron function. Truncated selenoproteins generated by translation errors and the USP1 N-terminal fragment from post-translational cleavage are eliminated by DesCEND. DesCEND also targets full-length proteins with naturally occurring C-end degrons. The C-end degron in DesCEND echoes the N-end degron in the N-end rule pathway, highlighting the dominance of protein "ends" as indicators for protein elimination.

The C-degron pathway eliminates mislocalized proteins and products of deubiquitinating enzymes.

Protein termini are determinants of protein stability. Proteins bearing degradation signals, or degrons, at their amino- or carboxyl-termini are eliminated by the N- or C-degron pathways, respectively. We aimed to elucidate the function of C-degron pathways and to unveil how normal proteomes are exempt from C-degron pathway-mediated destruction. Our data reveal that C-degron pathways remove mislocalized cellular proteins and cleavage products of deubiquitinating enzymes. Furthermore, the C-degron and N-degron pathways cooperate in protein removal. Proteome analysis revealed a shortfall in normal proteins targeted by C-degron pathways, but not of defective proteins, suggesting proteolysis-based immunity as a constraint for protein evolution/selection. Our work highlights the importance of protein termini for protein quality surveillance, and the relationship between the functional proteome and protein degradation pathways.

Lineage recording in human cerebral organoids.

Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enable highly resolved descriptions of cell states within these systems; however, approaches are needed to directly measure lineage relationships. Here we establish iTracer, a lineage recorder that combines reporter barcodes with inducible CRISPR-Cas9 scarring and is compatible with single-cell and spatial transcriptomics. We apply iTracer to explore clonality and lineage dynamics during cerebral organoid development and identify a time window of fate restriction as well as variation in neurogenic dynamics between progenitor neuron families. We also establish long-term four-dimensional light-sheet microscopy for spatial lineage recording in cerebral organoids and confirm regional clonality in the developing neuroepithelium. We incorporate gene perturbation (iTracer-perturb) and assess the effect of mosaic TSC2 mutations on cerebral organoid development. Our data shed light on how lineages and fates are established during cerebral organoid formation. More broadly, our techniques can be adapted in any iPSC-derived culture system to dissect lineage alterations during normal or perturbed development.

A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons.

Ambiguity in genetic codes exists in cases where certain stop codons are alternatively used to encode non-canonical amino acids. In selenoprotein transcripts, the UGA codon may either represent a translation termination signal or a selenocysteine (Sec) codon. Translating UGA to Sec requires selenium and specialized Sec incorporation machinery such as the interaction between the SECIS element and SBP2 protein, but how these factors quantitatively affect alternative assignments of UGA has not been fully investigated. We developed a model simulating the UGA decoding process. Our model is based on the following assumptions: (1) charged Sec-specific tRNAs (Sec-tRNASec) and release factors compete for a UGA site, (2) Sec-tRNASec abundance is limited by the concentrations of selenium and Sec-specific tRNA (tRNASec) precursors, and (3) all synthesis reactions follow first-order kinetics. We demonstrated that this model captured two prominent characteristics observed from experimental data. First, UGA to Sec decoding increases with elevated selenium availability, but saturates under high selenium supply. Second, the efficiency of Sec incorporation is reduced with increasing selenoprotein synthesis. We measured the expressions of four selenoprotein constructs and estimated their model parameters. Their inferred Sec incorporation efficiencies did not correlate well with their SECIS-SBP2 binding affinities, suggesting the existence of additional factors determining the hierarchy of selenoprotein synthesis under selenium deficiency. This model provides a framework to systematically study the interplay of factors affecting the dual definitions of a genetic codon.

NGN2 induces diverse neuron types from human pluripotency.

Human neurons engineered from induced pluripotent stem cells (iPSCs) through neurogenin 2 (NGN2) overexpression are widely used to study neuronal differentiation mechanisms and to model neurological diseases. However, the differentiation paths and heterogeneity of emerged neurons have not been fully explored. Here, we used single-cell transcriptomics to dissect the cell states that emerge during NGN2 overexpression across a time course from pluripotency to neuron functional maturation. We find a substantial molecular heterogeneity in the neuron types generated, with at least two populations that express genes associated with neurons of the peripheral nervous system. Neuron heterogeneity is observed across multiple iPSC clones and lines from different individuals. We find that neuron fate acquisition is sensitive to NGN2 expression level and the duration of NGN2-forced expression. Our data reveal that NGN2 dosage can regulate neuron fate acquisition, and that NGN2-iN heterogeneity can confound results that are sensitive to neuron type.

Combination of inductive effect of lipopolysaccharide and in situ mechanical conditioning for forming an autologous vascular graft in vivo.

Autologous vascular grafts have the advantages of better biocompatibility and prognosis. However, previous studies that implanted bare polymer tubes in animals to grow autologous tubular tissues were limited by their poor yield rates and stability. To enhance the yield rate of the tubular tissue, we employed a design with the addition of overlaid autologous whole blood scaffold containing lipopolysaccharides (LPS). Furthermore, we applied in vivo dynamic mechanical stimuli through cyclically inflatable silicone tube to improve the mechanical properties of the harvested tissues. The effectiveness of the modification was examined by implanting the tubes in the peritoneal cavity of rats. A group without mechanical stimuli served as the controls. After 24 days of culture including 16 days of cyclic mechanical stimuli, we harvested the tubular tissue forming on the silicone tube for analysis or further autologous interposition vascular grafting. In comparison with those without cyclic dynamic stimuli, tubular tissues with this treatment during in vivo culture had stronger mechanical properties, better smooth muscle differentiation, and more collagen and elastin expression by the end of incubation period in the peritoneal cavity. The grafts remained patent after 4 months of implantation and showed the presence of endothelial and smooth muscle cells. This model shows a new prospect for vascular tissue engineering.

SELENOPROTEINS. CRL2 aids elimination of truncated selenoproteins produced by failed UGA/Sec decoding.

Selenocysteine (Sec) is translated from the codon UGA, typically a termination signal. Codon duality extends the genetic code; however, the coexistence of two competing UGA-decoding mechanisms immediately compromises proteome fidelity. Selenium availability tunes the reassignment of UGA to Sec. We report a CRL2 ubiquitin ligase-mediated protein quality-control system that specifically eliminates truncated proteins that result from reassignment failures. Exposing the peptide immediately N-terminal to Sec, a CRL2 recognition degron, promotes protein degradation. Sec incorporation destroys the degron, protecting read-through proteins from detection by CRL2. Our findings reveal a coupling between directed translation termination and proteolysis-assisted protein quality control, as well as a cellular strategy to cope with fluctuations in organismal selenium intake.

New abietane and seco-abietane diterpenes from the roots of Taiwania cryptomerioides.

Four new diterpenes, 3-oxosaprorthoquinone (1), 3-oxomicrostegiol (2), 3-oxoisotaxodione (3), and taiwaninal (4), together with two known compounds, 3-oxosapriparaquinone (5) and 6-dehydrohinokiol (6), were isolated from the roots of Taiwania cryptomerioides. The structures of 1-4 were principle elucidated based on spectral evidence.

Cadinane-type sesquiterpenes from the roots of Taiwania cryptomerioides Hayata.

Five new cadinane-type sesquiterpenes, 15-acetoxy-T-muurolol (1), isokhusinodiol (2), cadin-10(14)-ene-4beta,5alpha-diol (3), cadinane-4beta,5alpha,10beta-triol (4), and muurolane-4beta,5beta,10beta-triol (5), together with five known compounds, T-cadinol (6), T-muurolol (7), alpha-cadinol (8), delta-cadinol (9), and khusinodiol (10), were isolated from the roots of Taiwania cryptomerioides. The structure of the new constituents were elucidated through chemical and spectral studies.

New abietane-type diterpenes from the heartwood of Picea morrisonicola.

New abietane-type diterpenes, 15-acetoxy-7-oxodehydroabietic acid (1), picealactones A (2), B (3), and C (4), together with the known 7-oxodehydroabietic acid (5) were isolated and identified from the heartwood of Picea morrisonicola. The structures of 1-4 were determined on the basis of spectral data explanation. Compounds 2-4 possessed a rare 5-dehydro-18, 6-olide functionality. Compounds 1 and 2 were first isolated from natural source.

Novel diterpenes from the heartwood of Chamaecyparis obtusa var. formosana.

Two novel diterpenes, obtusanal B (1) and obtusadione (2), along with obtusanal A (3), obtunone (4), 12-hydroxy-6,7-secoabieta-8,11,13-triene-6,7-dial, 8,12-dihydroxydielmentha-5,9-diene-7,11-dione and myrcene, isolated from the heartwood of Chamaecyparis obtusa var. formosana, were characterized by spectroscopic means, including 2D-NMR techniques. Compounds 1 and 2 are 7(6-->2)abeoabietane and 14(8-->9)abeoabietane type diterpenes, respectively. Their biosyntheses were proposed.