bims-pideca 2023-06-11 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2023–06–11
eleven papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

scTIE: data integration and inference of gene regulation using single-cell temporal multimodal data.
Template-jumping prime editing enables large insertion and exon rewriting in vivo.
Functional impact and molecular binding modes of drugs that target the PI3K isoform p110δ.
Unraveling the Link between Class 1A PI3-Kinase, Autophagy, and Myelodysplasia.
Studying stochastic systems biology of the cell with single-cell genomics data.
Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data.
LTK and ALK promote neuronal polarity and cortical migration by inhibiting IGF1R activity.
The technological landscape and applications of single-cell multi-omics.
Distinct longevity mechanisms across and within species and their association with aging.
CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression.
Insulin-like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth.

bioRxiv. 2023 May 22. pii: 2023.05.18.541381. [Epub ahead of print]

scTIE: data integration and inference of gene regulation using single-cell temporal multimodal data.

Yingxin Lin, Tung-Yu Wu, Xi Chen, Sheng Wan, Brian Chao, Jingxue Xin, Jean Y H Yang, Wing H Wong, Y X Rachel Wang.

Single-cell technologies offer unprecedented opportunities to dissect gene regulatory mecha-nisms in context-specific ways. Although there are computational methods for extracting gene regulatory relationships from scRNA-seq and scATAC-seq data, the data integration problem, essential for accurate cell type identification, has been mostly treated as a standalone challenge. Here we present scTIE, a unified method that integrates temporal multimodal data and infers regulatory relationships predictive of cellular state changes. scTIE uses an autoencoder to embed cells from all time points into a common space using iterative optimal transport, followed by extracting interpretable information to predict cell trajectories. Using a variety of synthetic and real temporal multimodal datasets, we demonstrate scTIE achieves effective data integration while preserving more biological signals than existing methods, particularly in the presence of batch effects and noise. Furthermore, on the exemplar multiome dataset we generated from differentiating mouse embryonic stem cells over time, we demonstrate scTIE captures regulatory elements highly predictive of cell transition probabilities, providing new potentials to understand the regulatory landscape driving developmental processes.

DOI: https://doi.org/10.1101/2023.05.18.541381
Nat Commun. 2023 Jun 08. 14(1): 3369

Template-jumping prime editing enables large insertion and exon rewriting in vivo.

Chunwei Zheng, Bin Liu, Xiaolong Dong, Nicholas Gaston, Erik J Sontheimer, Wen Xue.

Targeted insertion of large DNA fragments holds promise for genome engineering and gene therapy. Prime editing (PE) effectively inserts short (<50 bp) sequences. Employing paired prime editing guide RNAs (pegRNAs) has enabled PE to better mediate relatively large insertions in vitro, but the efficiency of larger insertions (>400 bp) remains low and in vivo application has not been demonstrated. Inspired by the efficient genomic insertion mechanism of retrotransposons, we develop a template-jumping (TJ) PE approach for the insertion of large DNA fragments using a single pegRNA. TJ-pegRNA harbors the insertion sequence as well as two primer binding sites (PBSs), with one PBS matching a nicking sgRNA site. TJ-PE precisely inserts 200 bp and 500 bp fragments with up to 50.5 and 11.4% efficiency, respectively, and enables GFP (~800 bp) insertion and expression in cells. We transcribe split circular TJ-petRNA in vitro via a permuted group I catalytic intron for non-viral delivery in cells. Finally, we demonstrate that TJ-PE can rewrite an exon in the liver of tyrosinemia I mice to reverse the disease phenotype. TJ-PE has the potential to insert large DNA fragments without double-stranded DNA breaks and facilitate mutation hotspot exon rewriting in vivo.

DOI: https://doi.org/10.1038/s41467-023-39137-6
Commun Biol. 2023 06 05. 6(1): 603

Functional impact and molecular binding modes of drugs that target the PI3K isoform p110δ.

Floyd Hassenrück, Maria Farina-Morillas, Lars Neumann, Francesco Landini, Stuart James Blakemore, Mina Rabipour, Juan Raul Alvarez-Idaboy, Christian P Pallasch, Michael Hallek, Rocio Rebollido-Rios, Günter Krause.

Targeting the PI3K isoform p110δ against B cell malignancies is at the mainstay of PI3K inhibitor (PI3Ki) development. Therefore, we generated isogenic cell lines, which express wild type or mutant p110δ, for assessing the potency, isoform-selectivity and molecular interactions of various PI3Ki chemotypes. The affinity pocket mutation I777M maintains p110δ activity in the presence of idelalisib, as indicated by intracellular AKT phosphorylation, and rescues cell functions such as p110δ-dependent cell viability. Resistance owing to this substitution consistently affects the potency of p110δ-selective in contrast to most multi-targeted PI3Ki, thus distinguishing usually propeller-shaped and typically flat molecules. Accordingly, molecular dynamics simulations indicate that the I777M substitution disturbs conformational flexibility in the specificity or affinity pockets of p110δ that is necessary for binding idelalisib or ZSTK474, but not copanlisib. In summary, cell-based and molecular exploration provide comparative characterization of currently developed PI3Ki and structural insights for future PI3Ki design.

DOI: https://doi.org/10.1038/s42003-023-04921-z
Autophagy. 2023 Jun 08.

Unraveling the Link between Class 1A PI3-Kinase, Autophagy, and Myelodysplasia.

Kristina Ames, Kira Gritsman.

  Myelodysplastic syndrome (MDS) is a clonal malignancy that develops from hematopoietic stem cells (HSCs), but the underlying mechanisms of MDS initiation are not well understood. The phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) pathway is often dysregulated in MDS. To investigate how PI3K inactivation affects HSC function, we generated a mouse model in which three Class IA PI3K genes were deleted in hematopoietic cells. Surprisingly, PI3K deficiency caused cytopenias, reduced survival, and multilineage dysplasia with chromosomal abnormalities, consistent with MDS initiation. PI3K-deficient HSCs had impaired autophagy, and pharmacologic treatment with autophagy-inducing reagents improved HSC differentiation. Furthermore, a similar autophagic degradation defect was observed in MDS patient HSCs. Therefore, our study uncovered a crucial protective role for Class IA PI3K in maintaining autophagic flux in HSCs to preserve the balance between self-renewal and differentiation.

Keywords:  Myelodysplastic syndrome; PI3K/AKT; autophagic flux; autophagosome; autophagy; differentiation; hematopoietic stem cells; lysosome; self-renewal

DOI:  https://doi.org/10.1080/15548627.2023.2221922
bioRxiv. 2023 May 29. pii: 2023.05.17.541250. [Epub ahead of print]

Studying stochastic systems biology of the cell with single-cell genomics data.

Gennady Gorin, John J Vastola, Lior Pachter.

Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.

DOI: https://doi.org/10.1101/2023.05.17.541250
Nat Commun. 2023 Jun 05. 14(1): 3244

Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data.

Alok K Maity, Andrew E Teschendorff.

Variations of cell-type proportions within tissues could be informative of biological aging and disease risk. Single-cell RNA-sequencing offers the opportunity to detect such differential abundance patterns, yet this task can be statistically challenging due to the noise in single-cell data, inter-sample variability and because such patterns are often of small effect size. Here we present a differential abundance testing paradigm called ELVAR that uses cell attribute aware clustering when inferring differentially enriched communities within the single-cell manifold. Using simulated and real single-cell and single-nucleus RNA-Seq datasets, we benchmark ELVAR against an analogous algorithm that uses Louvain for clustering, as well as local neighborhood-based methods, demonstrating that ELVAR improves the sensitivity to detect cell-type composition shifts in relation to aging, precancerous states and Covid-19 phenotypes. In effect, leveraging cell attribute information when inferring cell communities can denoise single-cell data, avoid the need for batch correction and help retrieve more robust cell states for subsequent differential abundance testing. ELVAR is available as an open-source R-package.

DOI: https://doi.org/10.1038/s41467-023-39017-z
EMBO Rep. 2023 Jun 09. e56937

LTK and ALK promote neuronal polarity and cortical migration by inhibiting IGF1R activity.

Tania Christova, Stephanie Ky Ho, Ying Liu, Mandeep Gill, Liliana Attisano.

  The establishment of axon-dendrite polarity is fundamental for radial migration of neurons, cortical patterning, and formation of neuronal circuits. Here, we show that the receptor tyrosine kinases, Ltk and Alk, are required for proper neuronal polarization. In isolated primary mouse embryonic neurons, the loss of Ltk and/or Alk causes a multiple axon phenotype. In mouse embryos and newborn pups, the absence of Ltk and Alk delays neuronal migration and subsequent cortical patterning. In adult cortices, neurons with aberrant neuronal projections are evident and axon tracts in the corpus callosum are disrupted. Mechanistically, we show that the loss of Alk and Ltk increases the cell-surface expression and activity of the insulin-like growth factor 1 receptor (Igf-1r), which activates downstream PI3 kinase signaling to drive the excess axon phenotype. Our data reveal Ltk and Alk as new regulators of neuronal polarity and migration whose disruption results in behavioral abnormalities.

Keywords:  ALK; IGF-1R; LTK; cortical migration; neuronal polarity

DOI:  https://doi.org/10.15252/embr.202356937
Nat Rev Mol Cell Biol. 2023 Jun 06.

The technological landscape and applications of single-cell multi-omics.

Alev Baysoy, Zhiliang Bai, Rahul Satija, Rong Fan.

Single-cell multi-omics technologies and methods characterize cell states and activities by simultaneously integrating various single-modality omics methods that profile the transcriptome, genome, epigenome, epitranscriptome, proteome, metabolome and other (emerging) omics. Collectively, these methods are revolutionizing molecular cell biology research. In this comprehensive Review, we discuss established multi-omics technologies as well as cutting-edge and state-of-the-art methods in the field. We discuss how multi-omics technologies have been adapted and improved over the past decade using a framework characterized by optimization of throughput and resolution, modality integration, uniqueness and accuracy, and we also discuss multi-omics limitations. We highlight the impact that single-cell multi-omics technologies have had in cell lineage tracing, tissue-specific and cell-specific atlas production, tumour immunology and cancer genetics, and in mapping of cellular spatial information in fundamental and translational research. Finally, we discuss bioinformatics tools that have been developed to link different omics modalities and elucidate functionality through the use of better mathematical modelling and computational methods.

DOI: https://doi.org/10.1038/s41580-023-00615-w
Cell. 2023 May 26. pii: S0092-8674(23)00476-2. [Epub ahead of print]

Distinct longevity mechanisms across and within species and their association with aging.

Alexander Tyshkovskiy, Siming Ma, Anastasia V Shindyapina, Stanislav Tikhonov, Sang-Goo Lee, Perinur Bozaykut, José P Castro, Andrei Seluanov, Nicholas J Schork, Vera Gorbunova, Sergey E Dmitriev, Richard A Miller, Vadim N Gladyshev.

  Lifespan varies within and across species, but the general principles of its control remain unclear. Here, we conducted multi-tissue RNA-seq analyses across 41 mammalian species, identifying longevity signatures and examining their relationship with transcriptomic biomarkers of aging and established lifespan-extending interventions. An integrative analysis uncovered shared longevity mechanisms within and across species, including downregulated Igf1 and upregulated mitochondrial translation genes, and unique features, such as distinct regulation of the innate immune response and cellular respiration. Signatures of long-lived species were positively correlated with age-related changes and enriched for evolutionarily ancient essential genes, involved in proteolysis and PI3K-Akt signaling. Conversely, lifespan-extending interventions counteracted aging patterns and affected younger, mutable genes enriched for energy metabolism. The identified biomarkers revealed longevity interventions, including KU0063794, which extended mouse lifespan and healthspan. Overall, this study uncovers universal and distinct strategies of lifespan regulation within and across species and provides tools for discovering longevity interventions.

Keywords:  Igf1, KU0063794; aging; bowhead whale; gene expression; lifespan extension; longevity; longevity signatures; mSALT; naked mole rat

DOI:  https://doi.org/10.1016/j.cell.2023.05.002
Nat Commun. 2023 Jun 03. 14(1): 3225

CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression.

Gemma Noviello, Rutger A F Gjaltema, Edda G Schulz.

Certain cellular processes are dose-dependent, requiring specific quantities or stoichiometries of gene products, as exemplified by haploinsufficiency and sex-chromosome dosage compensation. Understanding dosage-sensitive processes requires tools to quantitatively modulate protein abundance. Here we present CasTuner, a CRISPR-based toolkit for analog tuning of endogenous gene expression. The system exploits Cas-derived repressors that are quantitatively tuned by ligand titration through a FKBP12F36V degron domain. CasTuner can be applied at the transcriptional or post-transcriptional level using a histone deacetylase (hHDAC4) fused to dCas9, or the RNA-targeting CasRx, respectively. We demonstrate analog tuning of gene expression homogeneously across cells in mouse and human cells, as opposed to KRAB-dependent CRISPR-interference systems, which exhibit digital repression. Finally, we quantify the system's dynamics and use it to measure dose-response relationships of NANOG and OCT4 with their target genes and with the cellular phenotype. CasTuner thus provides an easy-to-implement tool to study dose-responsive processes in their physiological context.

DOI: https://doi.org/10.1038/s41467-023-38909-4
Dev Biol. 2023 Jun 06. pii: S0012-1606(23)00092-1. [Epub ahead of print]

Insulin-like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth.

Victor M Lewis, Heather K Le Bleu, Astra L Henner, Hannah Markovic, Amy E Robbins, Scott Stewart, Kryn Stankunas.

Zebrafish robustly regenerate fins, including their characteristic bony ray skeleton. Amputation activates intra-ray fibroblasts and dedifferentiates osteoblasts that migrate under a wound epidermis to establish an organized blastema. Coordinated proliferation and re-differentiation across lineages then sustains progressive outgrowth. We generate a single cell transcriptome dataset to characterize regenerative outgrowth and explore coordinated cell behaviors. We computationally identify sub-clusters representing most regenerative fin cell lineages, and define markers of osteoblasts, intra- and inter-ray fibroblasts and growth-promoting distal blastema cells. A pseudotemporal trajectory and in vivo photoconvertible lineage tracing indicate distal blastemal mesenchyme restores both intra- and inter-ray fibroblasts. Gene expression profiles across this trajectory suggest elevated protein production in the blastemal mesenchyme state. O-propargyl-puromycin incorporation and small molecule inhibition identify insulin growth factor receptor (IGFR)/mechanistic target of rapamycin kinase (mTOR)-dependent elevated bulk translation in blastemal mesenchyme and differentiating osteoblasts. We test candidate cooperating differentiation factors identified from the osteoblast trajectory, finding IGFR/mTOR signaling expedites glucocorticoid-promoted osteoblast differentiation in vitro. Concordantly, mTOR inhibition slows but does not prevent fin regenerative outgrowth in vivo. IGFR/mTOR may elevate translation in both fibroblast- and osteoblast-lineage cells during the outgrowth phase as a tempo-coordinating rheostat.

DOI: https://doi.org/10.1016/j.ydbio.2023.05.008