2019 Highlights: What are the breakthroughs published in Cell?

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.

(Graphical Abstract; See article 9: Dong, Matthew B., et al.)

[1] HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA

Published in Cell, January 2019

Highlights: All known abasic site repair mechanisms operate only when the damage is in double-stranded DNA, while HMCES senses abasic sites in ssDNA to shield them and prevent genomic instability.

 All known abasic site repair mechanisms operate only when the damage is in double-stranded DNA. However, in this study, researchers from Vanderbilt University report the discovery of 5-hydroxymethylcytosine (5hmC) binding, ESC-specific (HMCES) as a sensor of abasic sites in single-stranded DNA. HMCES acts at replication forks, binds PCNA and single-stranded DNA, and generates a DNA-protein crosslink to shield abasic sites from error-prone processing. This unusual HMCES DNA-protein crosslink intermediate is resolved by proteasome-mediated degradation. Acting as a suicide enzyme, HMCES prevents translesion DNA synthesis and the action of endonucleases that would otherwise generate mutations and double-strand breaks. HMCES is evolutionarily conserved in all domains of life, and its biochemical properties are shared with its E. coli ortholog. Thus, HMCES is an ancient DNA lesion recognition protein that preserves genome integrity by promoting error-free repair of abasic sites in single-stranded DNA.

Reference: Mohni, Kareem N., et al. "HMCES maintains genome integrity by shielding abasic sites in single-strand DNA." Cell 176.1-2 (2019): 144-153.

[2] Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Published in Cell, January 2019

Highlights: Large-scale metagenomic assembly uncovered thousands of new human microbiome species. Many species (77%) were never described before, increase the mappability of metagenomes, and expand our understanding of global body-wide human microbiomes.

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. In this study, researchers from University of Trento, Italy, report that they leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. They recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). They annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. They thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.

Reference: Pasolli, Edoardo, et al. "Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle." Cell 176.3 (2019): 649-662.

[3] Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

Published in Cell, February 2019

Highlights: Early replicating control elements (ERCEs) regulate replication timing, A/B compartmentalization and TAD architecture, form CTCF-independent loops and have features of enhancer/promoters, and enable genetic dissection of large-scale chromosome structure and function.

In this study, researchers from Florida State University revealed the mechanism of DNA replication in mammalian cells. In the article, the researchers created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for replication timing (RT). CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these ‘‘early replication control elements’’ (ERCEs) was validated by deletions and inversions at additional domains. The results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.

Reference: Sima, Jiao, et al. "Identifying cis elements for spatiotemporal control of mammalian DNA replication." Cell 176.4 (2019): 816-830.

[4] The Landscape of Circular RNA in Cancer

Published in Cell, February 2019

Highlights: Using exome capture transcriptome sequencing, the researchers built the most comprehensive catalog of circRNA species to date: MiOncoCirc. Novel biomarkers can be nominated through MiOncoCirc.

In this study, researchers from the University of Michigan conducted preliminary studies of circRNA in a variety of cancers and found that these stable structures may serve as biomarkers for prostate cancers. They used an exome capture RNA sequencing protocol to detect and characterize circRNAs across >2,000 cancer samples and finally built the most comprehensive catalog of circRNA species to date: MiOncoCirc, the first database to be composed primarily of circRNAs directly detected in tumor tissues. Using MiOncoCirc, they identified candidate circRNAs to serve as biomarkers for prostate cancer and were able to detect circRNAs in urine. They further detected a novel class of circular transcripts, termed read-through circRNAs, that involved exons originating from different genes. MiOncoCirc will serve as a valuable resource for the development of circRNAs as diagnostic or therapeutic targets across cancer types.

Reference: Vo, Josh N., et al. "The landscape of circular RNA in cancer." Cell 176.4 (2019): 869-881.

[5] Mitochondrial Permeability Uncouples Elevated Autophagy and Lifespan Extension

Published in Cell, April 2019

Highlights: The role of autophagy in lifespan extension depends on modulation of mitochondrial permeability via the action of the kinase SGK1. Targeting mitochondrial permeability may maximize benefits of autophagy in aging.

Autophagy is required in diverse paradigms of lifespan extension, leading to the prevailing notion that autophagy is beneficial for longevity. However, why autophagy is harmful in certain contexts remains unexplained. In this study, researchers show that mitochondrial permeability defines the impact of autophagy on aging. Elevated autophagy unexpectedly shortens lifespan in C. elegans lacking serum/glucocorticoid regulated kinase-1 (sgk-1) because of increased mitochondrial permeability. In sgk-1 mutants, reducing levels of autophagy or mitochondrial permeability transition pore (mPTP) opening restores normal lifespan. Remarkably, low mitochondrial permeability is required across all paradigms examined of autophagy-dependent lifespan extension. Genetically induced mPTP opening blocks autophagy-dependent lifespan extension resulting from caloric restriction or loss of germline stem cells. Mitochondrial permeability similarly transforms autophagy into a destructive force in mammals, as liver-specific Sgk knockout mice demonstrate marked enhancement of hepatocyte autophagy, mPTP opening, and death with ischemia/reperfusion injury. Targeting mitochondrial permeability may maximize benefits of autophagy in aging.

Reference: Zhou, Ben, et al. "Mitochondrial permeability uncouples elevated autophagy and lifespan extension." Cell 177.2 (2019): 299-314.

[6] Human Pluripotency Is Initiated and Preserved by a Unique Subset of Founder Cells

Published in Cell, May 2019

Highlights: Human pluripotent founder cells (PFCs) within stem cell cultures share hallmark properties with primitive endoderm and reside exclusively at colony boundaries. The identification of PFCs may be key to further understanding and biological separation of these species’ distinctions.

In this study, the researchers identify human pluripotent founder cells (hPFCs) that initiate, preserve and establish, pluripotent stem cell (PSC) cultures. PFCs are marked by N-cadherin expression (NCAD+) and reside exclusively at the colony boundary of primate PSCs. As demonstrated by functional analysis, hPFCs harbor the clonogenic capacity of PSC cultures and emerge prior to commitment events or phenotypes associated with pluripotent reprogramming. Comparative single cell analysis with pre- and post-implantation primate embryos revealed hPFCs share hallmark properties with primitive endoderm (PrE) and can be regulated by non-canonical Wnt signaling. Uniquely informed by primate embryo organization in vivo, this study defines a subset of founder cells critical to the establishment pluripotent state. The identification of PFCs may be key to further understanding and biological separation of these species’ distinctions. As such, the identification of PFCs underscores an essential paradigm shift toward future approaches that fully consider primate-specific aspects of pluripotent biology. The authors suggest this will be critical for applications that inform human disease modeling and therapeutic use of PSCs for patients.

Reference: Nakanishi, Mio, et al. "Human Pluripotency Is Initiated and Preserved by a Unique Subset of Founder Cells." Cell 177.4 (2019): 910-924.

[7] Fc Glycan-Mediated Regulation of Placental Antibody Transfer

Published in Cell, June 2019

Highlights: Antibodies with a specific glycan modification and with the ability to activate NK cells are selectively transferred across the placenta to the neonate. This study provides insights for the development of next-generation maternal vaccines.

In the study published in Cell in June 2019, researchers used systems serology to define Fc features associated with antibody transfer. The Fc-profile of neonatal and maternal antibodies differed, skewed toward natural killer (NK) cell-activating antibodies. This selective transfer was linked to digalactosylated Fc-glycans that selectively bind FcRn and FCGR3A, resulting in transfer of antibodies able to efficiently leverage innate immune cells present at birth. Given emerging data that vaccination may direct antibody glycosylation, this study provides insights for the development of next-generation maternal vaccines designed to elicit antibodies that will most effectively aid neonates.

Reference: Jennewein, Madeleine F., et al. "Fc glycan-mediated regulation of placental antibody transfer." Cell (2019).

[8] Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies

Published in Cell, June 2019

Highlights: Analyses of human monoclonal antibodies against the Plasmodium falciparum protein PfRH5 identify a subset of non-neutralizing antibodies that synergize with a repertoire of other neutralizing antibodies by slowing the ability of malaria-causing parasites to invade red blood cells. The results provide a roadmap for structure-guided vaccine development to maximize antibody efficacy against blood-stage malaria.

PfRH5 protein is the leading target for next-generation vaccines against the disease causing blood-stage of malaria. In this study, researchers isolated a panel of human monoclonal antibodies (mAbs) against PfRH5 from peripheral blood B cells from vaccinees in the first clinical trial of a PfRH5-based vaccine. They identified a subset of mAbs with neutralizing activity that bind to three distinct sites and another subset of mAbs that are non-functional, or even antagonistic to neutralizing antibodies. They also identify the epitope of a novel group of non-neutralizing antibodies that significantly reduce the speed of red blood cell invasion by the merozoite, thereby potentiating the effect of all neutralizing PfRH5 antibodies as well as synergizing with antibodies targeting other malaria invasion proteins. The results provide a roadmap for structure-guided vaccine development to maximize antibody efficacy against blood-stage malaria.

Reference: Alanine, Daniel GW, et al. "Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies." Cell (2019).

[9] Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells

Published in Cell, September 2019

Highlights: Genome-wide CRISPR screening in CD8 T cells in the context of immunotherapy identifies genes that modulate T cell effector functions, including Dhx37, an RNA helicase that affects NF-kB signaling, T cell activation, and cytotoxicity.

In this study, researchers from Yale University performed genome scale CRISPR screens in CD8 T cells directly under cancer immunotherapy settings and identified regulators of tumor infiltration and degranulation. The in vivo screen robustly re-identified canonical immunotherapy targets such as PD-1 and Tim-3, along with genes that have not been characterized in T cells. The infiltration and degranulation screens converged on an RNA helicase Dhx37. Dhx37 knockout enhanced the efficacy of antigen-specific CD8 T cells against triple-negative breast cancer in vivo. Immunological characterization in mouse and human CD8 T cells revealed that DHX37 suppresses effector functions, cytokine production, and T cell activation. Transcriptomic profiling and biochemical interrogation revealed a role for DHX37 in modulating NF-κB. These data demonstrate high-throughput in vivo genetic screens for immunotherapy target discovery and establishes DHX37 as a functional regulator of CD8 T cells.

Reference: Dong, Matthew B., et al. "Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells." Cell 178.5 (2019): 1189-1204.

[10] Attacking Latent HIV with convertibleCAR-T Cells, a Highly Adaptable Killing Platform

Published in Cell, October 2019

Highlights: cCAR-T decreases tumor size in a mouse lymphoma model as efficiently as scFv CAR-T and kills HIV-infected primary cells with high efficiency and specificity.

In this study, researchers designed a universal CAR-T cell platform based on cytotoxic lymphocytes engineered to bind a variety of broadly neutralizing anti-HIV antibodies. This platform, convertibleCAR-T cells, effectively kills HIV-infected, but not uninfected, CD4 T cells from blood, tonsil, or spleen and only when armed with anti-HIV antibodies. convertibleCAR-T cells also kill within 48h more than half of the inducible reservoir found in blood of HIV-infected individuals on antiretroviral therapy. The modularity of convertibleCAR-T cell system, which allows multiplexing with several anti-HIV antibodies yielding greater breadth and control, makes it a promising tool for attacking the latent HIV reservoir.

Reference: Herzig, Eytan, et al. "Attacking Latent HIV with convertibleCAR-T Cells, a Highly Adaptable Killing Platform." Cell 179.4 (2019): 880-894.