2019 Highlights: What are the breakthroughs published in Science

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.

(Modified “Waddington valley” depicting T cell differentiation and the role of potassium in preserving T cell stemness. See article 2: Vodnala, Suman Kumar, et al.)

[1] Hachimoji DNA and RNA: A genetic system with eight building blocks

Published in Science, February 2019

Highlights: The study reports DNA- and RNA-like systems built from eight nucleotide “letters” (hence the name “hachimoji”) that form four orthogonal pairs, makes available a mutable genetic system built from eight different building blocks. With increased information density over standard DNA and predictable duplex stability, hachimoji DNA has great potential applications. In addition to its technical applications, this work expands the scope of the structures that might support life in the cosmos.

In this study, the researchers report DNA- and RNA-like systems built from eight nucleotide “letters” (hence the name “hachimoji”) that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to increase the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos.

Reference: Hoshika, Shuichi, et al. "Hachimoji DNA and RNA: A genetic system with eight building blocks." Science 363.6429 (2019): 884-887.

[2] T cell stemness and dysfunction in tumors are triggered by a common mechanism

Published in Science, March 2019

Highlights: The findings deepen our understanding of how cancer can progress despite the presence of T cells that continue to harbor the capacity for its destruction, and finally identify new therapeutic strategies to metabolically induce stemness programs in antitumor T cells that enhance cancer immunotherapies.

In this study, the researcher found that the overabundance of potassium in the tumor microenvironment trigger suppression of T cell effector function while preserve stemness. High levels of extracellular potassium constrain T cell effector programs by limiting nutrient uptake, thereby inducing autophagy and reduction of histone acetylation at effector and exhaustion loci, which in turn produces CD8+ T cells with improved in vivo persistence, multipotency, and tumor clearance. This mechanistic knowledge advances our understanding of T cell dysfunction and may lead to novel approaches that enable the development of enhanced T cell strategies for cancer immunotherapy.

Reference: Vodnala, Suman Kumar, et al. "T cell stemness and dysfunction in tumors are triggered by a common mechanism." Science 363.6434 (2019): eaau0135.

[3] Reactivation of PTEN tumor suppressor for cancer treatment through inhibition of a MYC-WWP1 inhibitory pathway

Published in Science, May 2019

Highlights: This study identified the MYCWWP1 axis as a fundamental and evolutionary conserved regulatory pathway for PTEN and PI3K signaling. This pathway emerges not only as a rheostat for growth control in physiological conditions but also as a critical vulnerability hijacked for neoplastic transformation, which may be reversed by WWP1 pharmacological inactivation. These findings pave the way toward a long-sought tumor suppressor “reactivation” approach to cancer treatment.

PTEN is a critical tumor suppressive phosphatase that is active in its dimer configuration at the plasma membrane. Polyubiquitination by the ubiquitin E3 ligase WWP1 (WW domain–containing ubiquitin E3 ligase 1) suppressed the dimerization, membrane recruitment, and function of PTEN. Either genetic ablation or pharmacological inhibition of WWP1 triggered PTEN reactivation and unleashed tumor suppressive activity. WWP1 appears to be a direct MYC (MYC proto-oncogene) target gene and was critical for MYC-driven tumorigenesis. This study identified indole-3-carbinol, a compound found in cruciferous vegetables, as a natural and potent WWP1 inhibitor. Thus, these findings unravel a potential therapeutic strategy for cancer prevention and treatment through PTEN reactivation.

Reference: Lee, Yu-Ru, et al. "Reactivation of PTEN tumor suppressor for cancer treatment through inhibition of a MYC-WWP1 inhibitory pathway." Science 364.6441 (2019): eaau0159.

[4] RNA-guided DNA insertion with CRISPR-associated transposases

Published in Science, July 2019

Highlights: This work identifies a function for CRISPR-Cas systems beyond adaptive immunity that does not require Cas nuclease activity and provides a strategy for targeted insertion of DNA without engaging homologous recombination pathways, with a particularly exciting potential for genome editing in eukaryotic cells.

CRISPR-Cas nucleases are powerful tools for manipulating nucleic acids; however, targeted insertion of DNA remains a challenge, as it requires host cell repair machinery. In this study, the researchers from Feng Zhang lab characterize a CRISPR-associated transposase from cyanobacteria Scytonema hofmanni (ShCAST) that consists of Tn7-like transposase subunits and the type V-K CRISPR effector (Cas12k). ShCAST catalyzes RNA-guided DNA transposition by unidirectionally inserting segments of DNA 60 to 66 base pairs downstream of the protospacer. ShCAST integrates DNA into targeted sites in the Escherichia coli genome with frequencies of up to 80% without positive selection. This work expands our understanding of the functional diversity of CRISPR-Cas systems and establishes a paradigm for precision DNA insertion.

Reference: Strecker, Jonathan, et al. "RNA-guided DNA insertion with CRISPR-associated transposases." Science (2019): eaax9181.

[5] Enhanced CAR-T cell activity against solid tumors by vaccine boosting through the chimeric receptor

Published in Science, July 2019

Highlights: It demonstrates an approach to enhance CAR-T function in solid tumors by directly vaccine-boosting donor cells through their chimeric receptor in vivo.

The researchers designed amphiphile CAR-T ligands (amph-ligands) that, upon injection, trafficked to lymph nodes and decorated the surfaces of antigen-presenting cells, thereby priming CAR-Ts in the native lymph node microenvironment. Amph-ligand boosting triggered massive CAR-T expansion, increased donor cell polyfunctionality, and enhanced antitumor efficacy in multiple immunocompetent mouse tumor models. The researchers demonstrate two approaches to generalizing this strategy to any chimeric antigen receptor, enabling this simple non-human leukocyte antigen-restricted approach to enhanced CAR-T functionality to be applied to existing CAR-T designs.

Reference: Ma, Leyuan, et al. "Enhanced CAR–T cell activity against solid tumors by vaccine boosting through the chimeric receptor." Science 365.6449 (2019): 162-168.

[6] Spatiotemporal immune zonation of the human kidney

Published in Science, September 2019

Highlights: This study provides a comprehensive description of immune topology in the human kidney, providing a resource that adds to the recently published murine kidney dataset, which will facilitate the future study of pathogenic mechanisms and the identification of therapeutic targets in immune and infectious kidney diseases.

In this study, the researchers use single-cell RNA sequencing to resolve the spatiotemporal immune topology of the human kidney. They reveal anatomically defined expression patterns of immune genes within the epithelial compartment, with antimicrobial peptide transcripts evident in pelvic epithelium in the mature, but not fetal, kidney. A network of tissue-resident myeloid and lymphoid immune cells was evident in both fetal and mature kidney, with postnatal acquisition of transcriptional programs that promote infection-defense capabilities. Epithelial-immune cross-talk orchestrated localization of antibacterial macrophages and neutrophils to the regions of the kidney most susceptible to infection. Overall, the study provides a global overview of how the immune landscape of the human kidney is zonated to counter the dominant immunological challenge.

Reference: Stewart, Benjamin J., et al. "Spatiotemporal immune zonation of the human kidney." Science 365.6460 (2019): 1461-1466.

[7] Control of aversion by glycine-gated GluN1/GluN3A NMDA receptors in the adult medial habenula

Published in Science, October 2019

Highlights: It discovers that GluN1/GluN3A receptors are operational in neurons of the mouse adult medial habenula (MHb), an epithalamic area controlling aversive physiological states. Reducing GluN1/GluN3A receptor levels in the MHb prevented place-aversion conditioning.

The unconventional N-methyl-D-aspartate (NMDA) receptor subunits GluN3A and GluN3B can, when associated with the other glycine-binding subunit GluN1, generate excitatory conductances purely activated by glycine. However, functional GluN1/GluN3 receptors have not been identified in native adult tissues. In this study, the researchers discovered that GluN1/GluN3A receptors are operational in neurons of the mouse adult medial habenula (MHb), an epithalamic area controlling aversive physiological states. In the absence of glycinergic neuronal specializations in the MHb, glial cells tuned neuronal activity via GluN1/GluN3A receptors. Reducing GluN1/GluN3A receptor levels in the MHb prevented place-aversion conditioning. This study extends the physiological and behavioral implications of glycine by demonstrating its control of negatively valued emotional associations via excitatory glycinergic NMDA receptors.

Reference: Otsu, Y., et al. "Control of aversion by glycine-gated GluN1/GluN3A NMDA receptors in the adult medial habenula." Science 366.6462 (2019): 250-254.

[8] A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses

Published in Science, October 2019

Highlights: It describes a new approach to define bnAb precursors for an epitope of interest and the design of vaccine priming immunogens that take advantage of that information. This approach lays out a generalizable pathway for the development and pre-clinical validation of germline-targeting immunogens for HCDR3-dependent antibody responses.

Vaccine induction of broadly neutralizing antibodies (bnAbs) to human immunodeficiency virus (HIV) remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity determining region 3 (HCDR3) is a major barrier. Exploiting ultra-deep human antibody sequencing data, the researchers identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. They then developed HIV envelope trimer-based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model, and in ex-vivo screens bound a range of potential bnAb-precursor human naive B cells. The repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs, and could be applied to most HCDR3-dominant antibodies from other pathogens.

Reference: Steichen, Jon M., et al. "A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses." Science 366.6470 (2019).