Comment in Nat Rev Neurosci. 2021 Mar;22(3):134-135.

Building tissues from scratch to explore entirely new cell configurations could revolutionize fundamental understanding in biology. Bioprinting is an emerging technology to do this. Although typically applied to engineer tissues for therapeutic tissue repair or drug screening, there are many opportunities for bioprinting within biology, such as for exploring cellular crosstalk or cellular morphogenesis. The overall goals of this Primer are to provide an overview of bioprinting with the biologist in mind, outline the steps in extrusion bioprinting (the most widely used and accessible technology), and discuss alternative bioprinting technologies and future opportunities for bioprinting in biology.

Update of bioRxiv. 2020 Oct 08;:

Comprehensively resolving neuronal identities in whole-brain images is a major challenge. We achieve this in C. elegans by engineering a multicolor transgene called NeuroPAL (a neuronal polychromatic atlas of landmarks). NeuroPAL worms share a stereotypical multicolor fluorescence map for the entire hermaphrodite nervous system that resolves all neuronal identities. Neurons labeled with NeuroPAL do not exhibit fluorescence in the green, cyan, or yellow emission channels, allowing the transgene to be used with numerous reporters of gene expression or neuronal dynamics. We showcase three applications that leverage NeuroPAL for nervous-system-wide neuronal identification. First, we determine the brainwide expression patterns of all metabotropic receptors for acetylcholine, GABA, and glutamate, completing a map of this communication network. Second, we uncover changes in cell fate caused by transcription factor mutations. Third, we record brainwide activity in response to attractive and repulsive chemosensory cues, characterizing multimodal coding for these stimuli.

Comment in Cell. 2021 Jan 7;184(1):15-17.

Update of bioRxiv. 2020 Oct 29;:

Author information: (1)MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK. Electronic address: e.volz@imperial.ac.uk. (2)Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. (3)School of Biosciences, Cardiff University, Cardiff, UK. (4)MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK. (5)School of Biosciences, Cardiff University, Cardiff, UK; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK. (6)Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK. (7)Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK. (8)MRC-University of Glasgow Centre for Virus Research, Glasgow, UK. (9)Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, UK. (10)https://www.cogconsortium.uk/. (11)Department of Pathology, University of Cambridge, Cambridge, UK. (12)Department of Zoology, University of Oxford, Oxford, UK; Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK. (13)Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. Electronic address: a.rambaut@ed.ac.uk. (14)School of Biosciences, Cardiff University, Cardiff, UK; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK; Quadram Institute Bioscience, Norwich, UK. Electronic address: connortr@cardiff.ac.uk.

Comment in Nat Rev Genet. 2021 Jan;22(1):1. Nat Rev Mol Cell Biol. 2021 Jan;22(1):2. Cell. 2021 Jan 7;184(1):15-17. J Infect. 2022 Mar;84(3):418-467.

Comment in Cancer Cell. 2021 Feb 8;39(2):142-144.

Wnts are evolutionarily conserved ligands that signal at short range to regulate morphogenesis, cell fate, and stem cell renewal. The first and essential steps in Wnt secretion are their O-palmitoleation and subsequent loading onto the dedicated transporter Wntless/evenness interrupted (WLS/Evi). We report the 3.2 Å resolution cryogenic electron microscopy (cryo-EM) structure of palmitoleated human WNT8A in complex with WLS. This is accompanied by biochemical experiments to probe the physiological implications of the observed association. The WLS membrane domain has close structural homology to G protein-coupled receptors (GPCRs). A Wnt hairpin inserts into a conserved hydrophobic cavity in the GPCR-like domain, and the palmitoleate protrudes between two helices into the bilayer. A conformational switch of highly conserved residues on a separate Wnt hairpin might contribute to its transfer to receiving cells. This work provides molecular-level insights into a central mechanism in animal body plan development and stem cell biology.

Erratum in Cell. 2021 Apr 1;184(7):1929-1939.

Comment on bioRxiv. 2020 Oct 08;: Cell. 2021 Jan 7;184(1):76-91.e13. Cell. 2021 Jan 7;184(1):92-105.e16. Cell. 2021 Jan 7;184(1):106-119.e14. Cell. 2021 Jan 7;184(1):133-148.e20.

Transcription of SARS-CoV-2 mRNA requires sequential reactions facilitated by the replication and transcription complex (RTC). Here, we present a structural snapshot of SARS-CoV-2 RTC as it transitions toward cap structure synthesis. We determine the atomic cryo-EM structure of an extended RTC assembled by nsp7-nsp82-nsp12-nsp132-RNA and a single RNA-binding protein, nsp9. Nsp9 binds tightly to nsp12 (RdRp) NiRAN, allowing nsp9 N terminus inserting into the catalytic center of nsp12 NiRAN, which then inhibits activity. We also show that nsp12 NiRAN possesses guanylyltransferase activity, catalyzing the formation of cap core structure (GpppA). The orientation of nsp13 that anchors the 5' extension of template RNA shows a remarkable conformational shift, resulting in zinc finger 3 of its ZBD inserting into a minor groove of paired template-primer RNA. These results reason an intermediate state of RTC toward mRNA synthesis, pave a way to understand the RTC architecture, and provide a target for antiviral development.

Comment in Nat Rev Genet. 2021 Jan;22(1):1. Cell. 2021 Jan 7;184(1):15-17.

2021 marks the 30th anniversary of the revelation that cyclosporin A and FK506 act in a way previously not seen-as "molecular glues" that induce neo-protein-protein associations. As a torrent of new molecular-glue probes and medicines are fueling interest in this field, I explore the arc of this story.

Craniosynostosis results from premature fusion of the cranial suture(s), which contain mesenchymal stem cells (MSCs) that are crucial for calvarial expansion in coordination with brain growth. Infants with craniosynostosis have skull dysmorphology, increased intracranial pressure, and complications such as neurocognitive impairment that compromise quality of life. Animal models recapitulating these phenotypes are lacking, hampering development of urgently needed innovative therapies. Here, we show that Twist1+/- mice with craniosynostosis have increased intracranial pressure and neurocognitive behavioral abnormalities, recapitulating features of human Saethre-Chotzen syndrome. Using a biodegradable material combined with MSCs, we successfully regenerated a functional cranial suture that corrects skull deformity, normalizes intracranial pressure, and rescues neurocognitive behavior deficits. The regenerated suture creates a niche into which endogenous MSCs migrated, sustaining calvarial bone homeostasis and repair. MSC-based cranial suture regeneration offers a paradigm shift in treatment to reverse skull and neurocognitive abnormalities in this devastating disease.

Comment in Cell. 2021 Jan 7;184(1):15-17.

Update of medRxiv. 2020 Aug 15;: Res Sq. 2020 Aug 13;:

Comment in Nat Rev Mol Cell Biol. 2021 Mar;22(3):164.

Comment on Cell. 2021 Jan 21;184(2):534-544.e11.

Comment on Cell. 2021 Jan 21;184(2):521-533.e14.

Comment in Trends Immunol. 2021 Mar;42(3):180-182.

Update of bioRxiv. 2020 Sep 16;:

Comment on Science. 2020 Oct 30;370(6516):609-613.

Comment on Cell. 2021 Jan 21;184(2):545-559.e22.

Despite considerable efforts, the mechanisms linking genomic alterations to the transcriptional identity of cancer cells remain elusive. Integrative genomic analysis, using a network-based approach, identified 407 master regulator (MR) proteins responsible for canalizing the genetics of individual samples from 20 cohorts in The Cancer Genome Atlas (TCGA) into 112 transcriptionally distinct tumor subtypes. MR proteins could be further organized into 24 pan-cancer, master regulator block modules (MRBs), each regulating key cancer hallmarks and predictive of patient outcome in multiple cohorts. Of all somatic alterations detected in each individual sample, >50% were predicted to induce aberrant MR activity, yielding insight into mechanisms linking tumor genetics and transcriptional identity and establishing non-oncogene dependencies. Genetic and pharmacological validation assays confirmed the predicted effect of upstream mutations and MR activity on downstream cellular identity and phenotype. Thus, co-analysis of mutational and gene expression profiles identified elusive subtypes and provided testable hypothesis for mechanisms mediating the effect of genetic alterations.

Comment in Cell. 2021 Jan 21;184(2):296-298.

Single-cell transcriptomics has been widely applied to classify neurons in the mammalian brain, while systems neuroscience has historically analyzed the encoding properties of cortical neurons without considering cell types. Here we examine how specific transcriptomic types of mouse prefrontal cortex (PFC) projection neurons relate to axonal projections and encoding properties across multiple cognitive tasks. We found that most types projected to multiple targets, and most targets received projections from multiple types, except PFC→PAG (periaqueductal gray). By comparing Ca2+ activity of the molecularly homogeneous PFC→PAG type against two heterogeneous classes in several two-alternative choice tasks in freely moving mice, we found that all task-related signals assayed were qualitatively present in all examined classes. However, PAG-projecting neurons most potently encoded choice in cued tasks, whereas contralateral PFC-projecting neurons most potently encoded reward context in an uncued task. Thus, task signals are organized redundantly, but with clear quantitative biases across cells of specific molecular-anatomical characteristics.

Comment on Cell. 2021 Jan 21;184(2):422-440.e17.

Comment in Cell. 2021 Jan 21;184(2):294-296. Sci Immunol. 2021 Feb 5;6(56): J Allergy Clin Immunol. 2021 Sep;148(3):708-709.

The escalating social and economic burden of an aging world population has placed aging research at center stage. The hallmarks of aging comprise diverse molecular mechanisms and cellular systems that are interrelated and act in concert to drive the aging process. Here, through the lens of telomere biology, we examine how telomere dysfunction may amplify or drive molecular biological processes underlying each hallmark of aging and contribute to development of age-related diseases such as neurodegeneration and cancer. The intimate link of telomeres to aging hallmarks informs preventive and therapeutic interventions designed to attenuate aging itself and reduce the incidence of age-associated diseases.

Comment in Immunity. 2021 Jan 12;54(1):11-13. Nat Cancer. 2021 Dec;2(12):1287.

Erratum in Cell. 2021 Feb 4;184(3):847.

Comment in Cell. 2021 Jan 21;184(2):299-301.

Comment in Cell Stress. 2021 Feb 18;5(3):37-39.

Comment in Hepatology. 2021 Nov;74(5):2891-2893.

The ultra-rare, pediatric premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS) is caused by mutation of LMNA, encoding the nuclear architectural protein lamin A. Patients develop atherosclerosis and typically die of heart failure in their teens. FDA-approved Zokinvy prevents farnesylation of lamin A, reduces vascular stiffness, and extends survival in HGPS patients. To view this Bench to Bedside, open or download the PDF.

Update of medRxiv. 2020 Oct 20;:

Comment in Cell. 2021 Jan 21;184(2):301-303. Nat Methods. 2021 Feb;18(2):120.

Proton-coupled monocarboxylate transporters MCT1-4 catalyze the transmembrane movement of metabolically essential monocarboxylates and have been targeted for cancer treatment because of their enhanced expression in various tumors. Here, we report five cryo-EM structures, at resolutions of 3.0-3.3 Å, of human MCT1 bound to lactate or inhibitors in the presence of Basigin-2, a single transmembrane segment (TM)-containing chaperon. MCT1 exhibits similar outward-open conformations when complexed with lactate or the inhibitors BAY-8002 and AZD3965. In the presence of the inhibitor 7ACC2 or with the neutralization of the proton-coupling residue Asp309 by Asn, similar inward-open structures were captured. Complemented by structural-guided biochemical analyses, our studies reveal the substrate binding and transport mechanism of MCTs, elucidate the mode of action of three anti-cancer drug candidates, and identify the determinants for subtype-specific sensitivities to AZD3965 by MCT1 and MCT4. These findings lay out an important framework for structure-guided drug discovery targeting MCTs.

Comment in Nat Rev Genet. 2021 Feb;22(2):69. Nature. 2021 May;593(7858):302-303.