2019 Highlights: What are the breakthroughs published in Nature?

At the beginning of 2020, we look back to 2019 and sort out a collection of groundbreaking research published in Cell, Nature, and Science, hoping that the articles can help you stay connected with the latest research in molecular biology, gene editing technology, cell therapy, and immunology.

(a, Domain composition of CasX. b, Model of CasX ternary complex with 30-bp target DNA in state I, shown in side and top views. See article 2: Liu, Jun-Jie, et al.)

(a, Schematic of the ORBIT method. b, Atomic force microscopy images of DNA origami rotors. See article 8: Kosuri, Pallav, et al.)

[1] Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade

Published in Nature, January 2019

Highlights: Effective immunotherapy with checkpoint blockade is assumed to require recognition of tumour cells by cytotoxic CD8+ T cells, but this study shows that loss of function of ADAR1 restores sensitivity to immunotherapy in tumours with a B2m deletion. This suggests that recognition of tumours by CD8+ T cells is not an obligate part of an effective immune response against cancer cells. This finding suggests a strategy for effective immunotherapy even in the absence of a tumour-specific endogenous CD8+ T-cell response.Most patients with cancer either do not respond to immune checkpoint blockade or develop resistance to it, often because of acquired mutations that impair antigen presentation. In this study, the researchers show that loss of function of the RNA-editing enzyme ADAR1 in tumour cells profoundly sensitizes tumours to immunotherapy and overcomes resistance to checkpoint blockade. In the absence of ADAR1, A-to-I editing of interferon-inducible RNA species is reduced, leading to double stranded RNA ligand sensing by PKR and MDA5; this results in growth inhibition and tumour inflammation, respectively. Loss of ADAR1 overcomes resistance to PD-1 checkpoint blockade caused by inactivation of antigen presentation by tumour cells. Thus, effective anti-tumour immunity is constrained by inhibitory checkpoints such as ADAR1 that limit the sensing of innate ligands. The induction of sufficient inflammation in tumours that are sensitized to interferon can bypass the therapeutic requirement for CD8+ T cell recognition of cancer cells and may provide a general strategy to overcome immunotherapy resistance.

Reference: Ishizuka, Jeffrey J., et al. "Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade." Nature 565.7737 (2019): 43.

[2] CasX enzymes comprise a distinct family of RNA-guided genome editors

Published in Nature, February 2019

Highlights: The compact size, dominant RNA content and minimal trans-cleavage activity of CasX differentiate this enzyme family from Cas9 and Cas12a, and provide opportunities for therapeutic delivery and safety that may offer important advantages relative to existing genome-editing technologies.

In this study, the researchers from University of California, Berkeley, reveal the underlying mechanisms of a third, fundamentally distinct RNA-guided genome-editing platform named CRISPR–CasX, which uses unique structures for programmable double-stranded DNA binding and cleavage. Biochemical and in vivo data demonstrate that CasX is active for Escherichia coli and human genome modification. Eight cryo-electron microscopy structures of CasX in different states of assembly with its guide RNA and double-stranded DNA substrates reveal an extensive RNA scaffold and a domain required for DNA unwinding. The data demonstrate how CasX activity arose through convergent evolution to establish an enzyme family that is functionally separate from both Cas9 and Cas12a.

Reference: Liu, Jun-Jie, et al. "CRISPR-CasX is an RNA-dominated enzyme active for human genome editing." Nature 566.7743 (2019): 218.

[3] A new genomic blueprint of the human gut microbiota

Published in Nature, February 2019

Highlights: The researchers identify 1,952 uncultured candidate bacterial species by reconstructing 92,143 metagenome-assembled genomes from 11,850 human gut microbiomes. The work expands the known diversity of uncultured gut bacteria, which provides unprecedented resolution for taxonomic and functional characterization of the intestinal microbiota.

The composition of the human gut microbiota is linked to health and disease, the complete bacterial repertoire of the human gut microbiota remains undefined. In this study, the researchers identify 1,952 uncultured candidate bacterial species by reconstructing 92,143 metagenome-assembled genomes from 11,850 human gut microbiomes. These uncultured genomes substantially expand the known species repertoire of the collective human gut microbiota, with a 281% increase in phylogenetic diversity. Although the newly identified species are less prevalent in well-studied populations compared to reference isolate genomes, they improve classification of understudied African and South American samples by more than 200%. These candidate species encode hundreds of newly identified biosynthetic gene clusters and possess a distinctive functional capacity that might explain their elusive Nature. Their work expands the known diversity of uncultured gut bacteria, which provides unprecedented resolution for taxonomic and functional characterization of the intestinal microbiota.

Reference: Almeida, Alexandre, et al. "A new genomic blueprint of the human gut microbiota." Nature 568.7753 (2019): 499.

[4] High frequency of shared clonotypes in human B cell receptor repertoires

Published in Nature, February 2019

Highlights: The unexpectedly high prevalence of shared clonotypes in B cell repertoires, and identification of the sequences of these shared clonotypes, should enable better understanding of the role of B cell immune repertoires in health and disease.

In this study, the researchers sequence recombined and expressed B cell receptor genes in several individuals to determine the size of their B cell receptor repertoires, and the extent to which these are shared between individuals. Their experiments revealed that the circulating repertoire of each individual contained between 9 and 17 million B cell clonotypes. The three individuals that studied shared many clonotypes. Some of the B cell clonotypes had thousands of clones, or somatic variants, within the clonotype lineage. Although some of these shared lineages might be driven by exposure to common antigens, previous exposure to foreign antigens was not the only force that shaped the shared repertoires, as we also identified shared clonotypes in umbilical cord blood samples and all adult repertoires. The unexpectedly high prevalence of shared clonotypes in B cell repertoires, and identification of the sequences of these shared clonotypes, should enable better understanding of the role of B cell immune repertoires in health and disease. 

Reference: Soto, Cinque, et al. "High frequency of shared clonotypes in human B cell receptor repertoires." Nature 566.7744 (2019): 398.

[5] Stem cell competition orchestrates skin homeostasis and ageing

Published in Nature, April 2019

Highlights: Cell competition coupled with SCDs is crucial for mammalian epithelial organ youthfulness, homeostasis with quality control and eventual ageing, providing insights into other epithelial organs. Differential COL17A1 expression drives stem cell competition through COL17A1-dependent SCDs. Small molecules that stabilize COL17A1 promote skin wound healing, and may therefore be beneficial for organ integrity, regeneration and the reduction of ageing.

In this study, the researchers report that the expression of the hemidesmosome component collagen XVII (COL17A1) by epidermal stem cells fluctuates physiologically through genomic/oxidative stress-induced proteolysis, and that the resulting differential expression of COL17A1 in individual stem cells generates a driving force for cell competition. In vivo clonal analysis in mice and in vitro 3D modelling show that clones that express high levels of COL17A1, which divide symmetrically, outcompete and eliminate adjacent stressed clones that express low levels of COL17A1, which divide asymmetrically. Stem cells with higher potential or quality are thus selected for homeostasis, but their eventual loss of COL17A1 limits their competition, thereby causing ageing. The resultant hemidesmosome fragility and stem cell delamination deplete adjacent melanocytes and fibroblasts to promote skin ageing. Conversely, the forced maintenance of COL17A1 rescues skin organ ageing, thereby indicating potential angles for anti-ageing therapeutic intervention.

Reference: Liu, Nan, et al. "Stem cell competition orchestrates skin homeostasis and ageing." Nature 568.7752 (2019): 344.

[6] Charting cellular identity during human in vitro β-cell differentiation

Published in Nature, May 2019

Highlights: This study provides a perspective on human stem-cell differentiation, and will guide future endeavours that focus on the differentiation of pancreatic islet cells, and their applications in regenerative medicine.

In vitro differentiation of human stem cells can produce pancreatic β-cells; the loss of this insulin-secreting cell type underlies type 1 diabetes. To understand this differentiation process, this study report the transcriptional profiling of more than 100,000 human cells undergoing in vitro β-cell differentiation, and describe the cells that emerged. The researchers implement a scalable re-aggregation technique to deplete non-endocrine cells and identify CD49a (also known as ITGA1) as a surface marker of the β-cell population, which allows magnetic sorting to a purity of 80%. Finally, the researchers use a high-resolution sequencing time course to characterize gene-expression dynamics during the induction of human pancreatic endocrine cells, from which develop a lineage model of in vitro β-cell differentiation. This study provides a perspective on human stem-cell differentiation, and will guide future endeavours that focus on the differentiation of pancreatic islet cells, and their applications in regenerative medicine.

Reference: Veres, Adrian, et al. "Charting cellular identity during human in vitro β-cell differentiation." Nature 569.7756 (2019): 368.

[7] Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis

Published in Nature, July 2019

Highlights: This study quantitatively evaluated RNA single nucleotide variations (SNVs) that were induced by CBEs or ABEs, and also demonstrates that such effects can be eliminated by engineering deaminases.

The extent of potential RNA mutations induced by DNA base editors is of great concern. In this study, researchers quantitatively evaluated RNA single nucleotide variations (SNVs) that were induced by CBEs or ABEs. Both the cytosine base editor BE3 and the adenine base editor ABE7.10 generated tens of thousands of off-target RNA SNVs. Subsequently, by engineering deaminases, they found that three CBE variants and one ABE variant showed a reduction in off-target RNA SNVs to the baseline while maintaining efficient DNA on-target activity. This study reveals a previously overlooked aspect of off-target effects in DNA editing and also demonstrates that such effects can be eliminated by engineering deaminases.

Reference: Zhou, Changyang, et al. "Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis." Nature 571.7764 (2019): 275-278.

[8] Rotation tracking of genome-processing enzymes using DNA origami rotors

Published in Nature, July 2019

Highlights: This study introduces a method (origami-rotor-based imaging and tracking, ORBIT), that uses fluorescently labelled DNA origami rotors to track DNA rotation at the single-molecule level with a time resolution of milliseconds. We envisage that ORBIT will enable studies of a wide range of interactions between proteins and DNA.

In this study the researchers from Harvard University introduced origami-rotor-based imaging and tracking (ORBIT), a method that uses fluorescently labelled DNA origami rotors to track DNA rotation at the single-molecule level with a time resolution of milliseconds. They used ORBIT to track the DNA rotations that result from unwinding by the RecBCD complex, a helicase that is involved in DNA repair, as well as from transcription by RNAP. They characterized a series of events that occur during RecBCD-induced DNA unwinding-including initiation, processive translocation, pausing and backtracking-and revealed an initiation mechanism that involves reversible ATP-independent DNA unwinding and engagement of the RecB motor. During transcription by RNAP, they directly observed rotational steps that correspond to the unwinding of single base pairs. The researchers envisage ORBIT will enable studies of a wide range of interactions between proteins and DNA.

Reference: Kosuri, Pallav, et al. "Rotation tracking of genome-processing enzymes using DNA origami rotors." Nature 572.7767 (2019): 136-140.

[9] Niche stiffness underlies the ageing of central nervous system progenitor cells

Published in Nature, August 2019

Highlights: The study shows that tissue stiffness is a crucial regulator of ageing in OPCs, and provide insights into how the function of adult stem and progenitor cells changes with age. These findings could be important not only for the development of regenerative therapies, but also for understanding the ageing process itself.

In this study, the researchers show that the microenvironment of the central nervous system (CNS) multipotent stem cells known as oligodendrocyte progenitor cells (OPCs) stiffens with age, and this mechanical change is sufficient to cause age-related loss of function of OPCs.

Using biological and synthetic scaffolds to mimic the stiffness of young brains, they find that isolated aged OPCs cultured on these scaffolds are molecularly and functionally rejuvenated. When disrupt mechanical signalling, the proliferation and differentiation rates of OPCs are increased. They identify the mechanoresponsive ion channel PIEZO1 as a key mediator of OPC mechanical signalling. Inhibiting PIEZO1 overrides mechanical signals in vivo and allows OPCs to maintain activity in the ageing CNS. The researchers also show that PIEZO1 is important in regulating cell number during CNS development. Thus the study shows that tissue stiffness is a crucial regulator of ageing in OPCs, and provide insights into how the function of adult stem and progenitor cells changes with age.

Reference: Segel, Michael, et al. "Niche stiffness underlies the ageing of central nervous system progenitor cells." Nature 573.7772 (2019): 130-134.

[10] Decoding human fetal liver haematopoiesis

Published in Nature, October 2019

Highlights: Using single-cell transcriptome profiling technology, the researchers identify the repertoire of human blood and immune cells during development. The integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a reference for harnessing the therapeutic potential of HSC/MPPs.

Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells and multipotent progenitors (HSC/MPPs) but remains poorly defined in humans. In this study, using single-cell transcriptome profiling of approximately 140,000 liver and 74,000 skin, kidney and yolk sac cells, the researchers identify the repertoire of human blood and immune cells during development. They infer differentiation trajectories from HSC/MPPs and evaluate the influence of the tissue microenvironment on blood and immune cell development. They reveal physiological erythropoiesis in fetal skin and the presence of mast cells, natural killer and innate lymphoid cell precursors in the yolk sac, demonstrate a shift in the haemopoietic composition of fetal liver during gestation away from being predominantly erythroid, accompanied by a parallel change in differentiation potential of HSC/MPPs, which they functionally validate. The integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a reference for harnessing the therapeutic potential of HSC/MPPs.

Reference: Popescu, Dorin-Mirel, et al. "Decoding the development of the blood and immune systems during human fetal liver haematopoiesis." bioRxiv (2019): 654210.