Kim R, Yu J, Lim J
… +41 more, Oh BB, Nam SJ, Kim SW, Lee JE, Chae BJ, Kim JY, Park GE, Kang BJ, Paik PS, Bae SY, Yoon CI, Lee YJ, Kim D, Shin K, Lee JE, Kang J, Lee A, Connolly-Strong E, Lee S, Lee BR, Lee Y, Yi KJ, Kwon YO, Chun IH, Park J, Kim J, Choi C, Shin JY, Lee H, Kim M, Park H, Jeong I, Yi B, Lee WC, Lee JS, Park WC, Kim SH, Choi YL, Lee J, Ju YS, Park YH
Breast cancer remains a major global health challenge. Here, to comprehensively characterize its genomic landscape and the clinical significance of genomic characteristics, we analysed whole-genome sequences from 1,364 c...Breast cancer remains a major global health challenge. Here, to comprehensively characterize its genomic landscape and the clinical significance of genomic characteristics, we analysed whole-genome sequences from 1,364 clinically annotated breast cancers, with transcriptome data available for most cases. Our study expands the repertoire of oncogenic alterations and identifies novel driver genes, recurrent gene fusions, structural variants and copy number alterations. Timing analyses on copy number alterations suggest that genomic instability emerges decades before tumour diagnosis, and offer insights into early initiation of tumorigenesis. Pattern-driven genomic features, including mutational signatures, homologous recombination deficiency, tumour mutational burden and tumour heterogeneity scores, were associated with clinical outcomes, highlighting their potential utility as predictive biomarkers for clinical evaluation of treatments such as CDK4/6 and HER2 inhibitors, as well as adjuvant and neoadjuvant chemotherapy. These findings highlight the power of large-scale, clinically annotated whole-genome sequencing in advancing our understanding of how genomic alterations shape patient outcomes.
Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the var...Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans, in the human gut and on Earth, with compilations encompassing thousands of public datasets. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for NO emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.
Gut bacteriophages profoundly impact microbial ecology and health; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy...Gut bacteriophages profoundly impact microbial ecology and health; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.
Generative genomic models can design increasingly complex biological systems. However, controlling these models to generate novel sequences with desired functions remains challenging. Here, we show that Evo, a genomic la...Generative genomic models can design increasingly complex biological systems. However, controlling these models to generate novel sequences with desired functions remains challenging. Here, we show that Evo, a genomic language model, can leverage genomic context to perform function-guided design that accesses novel regions of sequence space. By learning semantic relationships across prokaryotic genes, Evo enables a genomic 'autocomplete' in which a DNA prompt encoding genomic context for a function of interest guides the generation of novel sequences enriched for related functions, which we refer to as 'semantic design'. We validate this approach by experimentally testing the activity of generated anti-CRISPR proteins and type II and III toxin-antitoxin systems, including de novo genes with no significant sequence similarity to natural proteins. In-context design of proteins and non-coding RNAs with Evo achieves robust activity and high experimental success rates even in the absence of structural priors, known evolutionary conservation or task-specific fine-tuning. We then use Evo to complete millions of prompts to produce SynGenome, a database containing over 120 billion base pairs of artificial intelligence-generated genomic sequences that enables semantic design across many functions. More broadly, these results demonstrate that generative genomics with biological language models can extend beyond natural sequences.
Organ shortage remains a major challenge in transplantation, and gene-edited pig organs offer a promising solution. Despite gene editing, the immune reactions following xenotransplantation can still cause transplant fail...Organ shortage remains a major challenge in transplantation, and gene-edited pig organs offer a promising solution. Despite gene editing, the immune reactions following xenotransplantation can still cause transplant failure. To understand the immunological response of a pig-to-human kidney xenotransplantation, we conducted large-scale multi-omics profiling of the xenograft and the host's blood over a 61-day procedure in a brain-dead human (decedent) recipient. Blood plasmablasts, natural killer cells and dendritic cells increased between postoperative day (POD) 10 and 28, concordant with an expansion of IgG and IgA B cell clonotypes and subsequent biopsy-confirmed antibody-mediated rejection (AMR) at POD33. Human T cell frequencies increased from POD14 and peaked between POD33 and POD49 in the blood and xenograft, which coincided with T cell receptor diversification, expansion of a restricted TRBV2 and TRBJ1 clonotype and histological evidence of combined AMR and cell-mediated rejection at POD49. At POD33, the most abundant human immune population in the graft was CXCL9 macrophages, which aligned with interferon-γ-driven inflammation and a T helper 1-type immune response. There was also evidence of interactions between activated pig-resident macrophages and infiltrating human immune cells. Xenograft tissue showed pro-fibrotic tubular and interstitial injury marked by S100A6 (ref. ), SPP1 (also known as osteopontin) and COLEC11 (ref. ) expression at POD21-POD33. Proteomic profiling revealed activation of human and pig complement, with a decreased human component after AMR therapy, in which complement was inhibited. Collectively, these data delineate the molecular orchestration of human immune responses to a porcine kidney and reveal potential immunomodulatory targets for improving xenograft survival.
Wang F, Sun C, Wu TW
… +25 more, Fu Y, Fan Y, Zhao S, Huang K, Pan Z, Lu Y, Han JR, Jia S, Zeng L, Zhang S, Chen T, An S, Meng SS, Guo X, Li W, Lian H, Sun X, Hu J, Yang C, Feng S, Li P, Du L, Liu X, Piatkevich KD, Zou Y
The number of spatial omics technologies being developed is increasing. However, a missing tool is one that can locate proteins in tissues in an untargeted manner at high spatial resolution and coverage. Here we present...The number of spatial omics technologies being developed is increasing. However, a missing tool is one that can locate proteins in tissues in an untargeted manner at high spatial resolution and coverage. Here we present in situ imaging proteomics via expansion (iPEX), which integrates isotropic tissue magnification with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging. iPEX provides scalable spatial resolution down to the micrometre scale and substantially increases the sensitivity of protein identification by 10-100-fold. Using the retina as a model, iPEX enabled the construction of spatial proteomic maps with high precision, the visualization of single-cell layers and extrasomatic structures and the identification of colocalized proteins. iPEX was readily applied to diverse tissues, including brain, intestine, liver and organoids, detecting 600-1,500 proteins at 1-5-µm effective pixel size. The application of iPEX to depict spatial proteomic maps in brains of mice with 5xFAD Alzheimer's disease revealed an early-onset mitochondrial aberrancy. Notably, in young mice, the peroxisomal acetyl-CoA acyltransferase ACAA1A-of which the N392S mutant is a monogenic risk factor in Alzheimer's disease-was downregulated. ACAA1 depletion blocked the biosynthesis of long-chain polyunsaturated fatty acids, including docosahexaenoic acid, in multiple cellular contexts. These lipidome alterations were restored in cells overexpressing wild-type ACAA1 but not ACAA1(N392S), which suggests that the dysregulation of long-chain polyunsaturated fatty acids has an early role in neurodegeneration. Together, these results demonstrate that iPEX facilitates untargeted spatial proteomics at micrometre resolution for diverse applications.
Rare diseases are collectively common, affecting approximately 1 in 20 individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in next-generation sequencing, devel...Rare diseases are collectively common, affecting approximately 1 in 20 individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in next-generation sequencing, development of new computational and functional genomics approaches to prioritize genes and variants and increased global sharing of clinical and genetic data. However, more than half of individuals suspected to have a rare disease lack a genetic diagnosis. The Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium was initiated to study thousands of challenging rare disease cases and families and apply, standardize and evaluate emerging genomics technologies and analytics to accelerate their adoption in clinical practice. Furthermore, all data generated, currently representing over 7,500 individuals from over 3,000 families, are rapidly made available to researchers worldwide through the Analysis, Visualization and Informatics Lab-space (AnVIL) to catalyse global efforts to develop approaches for genetic diagnoses in rare diseases. Most of these families have undergone previous clinical genetic testing but remained unsolved, with most being exome-negative. Here we describe the collaborative research framework, datasets and discoveries comprising GREGoR that will provide foundational resources and substrates for the future of rare disease genomics.
Gao Y, van Velthoven CTJ, Lee C
… +59 more, Thomas ED, Mathieu R, Ayala AP, Barta S, Bertagnolli D, Campos J, Cardenas T, Carey D, Casper T, Chakka AB, Chakrabarty R, Chiang M, Ching L, Clark M, Desierto MJ, Ferrer R, Gloe J, Goldy J, Guilford N, Guzman J, Halterman CR, Hastings SD, Hirschstein D, Ho W, James K, Juneau Z, Martin N, McCue R, Meyerdierks E, Mitchell AC, Nagra JS, Nguy B, Nguyen TN, Olsen P, Oyama AA, Pena N, Quon J, Ren Q, Ruiz A, Shapovalova NV, Sulc J, Torkelson A, Tran A, Tung H, Valera Cuevas N, Wang J, Ariza J, McMillen DAM, Waters J, Kunst M, Ronellenfitch K, Levi B, Hawrylycz MJ, Pagan C, Dee N, Smith KA, Tasic B, Yao Z, Zeng H
The mammalian cortex is composed of a highly diverse set of cell types and develops through a series of temporally regulated events. Single-cell transcriptomics enables a systematic study of cell types across the entire...The mammalian cortex is composed of a highly diverse set of cell types and develops through a series of temporally regulated events. Single-cell transcriptomics enables a systematic study of cell types across the entire timeline of cortical development. Here we present a comprehensive and high-resolution transcriptomic and epigenomic cell-type atlas of the developing mouse visual cortex. The atlas is built from a single-cell RNA sequencing dataset of 568,654 high-quality single-cell transcriptomes and a single-nucleus Multiome dataset of 200,061 high-quality nuclei, which were densely sampled across the embryonic and postnatal developmental stages (from embryonic day 11.5 to postnatal day 56). We computationally reconstructed a transcriptomic developmental trajectory map of all excitatory, inhibitory and non-neuronal cell types in the visual cortex. Branching points that mark the emergence of new cell types at specific developmental ages and molecular signatures of cellular diversification are identified. The trajectory map shows that neurogenesis, gliogenesis and early postmitotic maturation in the embryonic stage give rise to all cell classes and nearly all subclasses in a staggered parallel manner. Increasingly refined cell types emerge throughout the postnatal differentiation process, including the late emergence of many cell types during the eye-opening stage and the onset of critical period, suggesting that there is continuous cell-type diversification at different stages of cortical development. Throughout development, there are cooperative dynamic changes in gene expression and chromatin accessibility in specific cell types. We identify cell-type-specific and temporally resolved gene regulatory networks that link transcription factors and downstream target genes through accessible chromatin motifs. Collectively, our study provides a detailed dynamic molecular map directly associated with individual cell types and specific temporal events that can reveal the molecular logic underlying the complex and multifaceted cortical cell type and circuit development.
Somatic chromosome instability results in widespread structural and numerical chromosomal abnormalities (CAs) during cancer evolution. Although CAs have been linked to mitotic errors resulting in the emergence of nuclear...Somatic chromosome instability results in widespread structural and numerical chromosomal abnormalities (CAs) during cancer evolution. Although CAs have been linked to mitotic errors resulting in the emergence of nuclear atypia, the underlying processes and rates of spontaneous CA formation in human cells are underexplored. Here we introduce machine-learning-assisted genomics and imaging convergence (MAGIC)-an autonomously operated platform that integrates live-cell imaging of micronucleated cells, machine learning on-the-fly and single-cell genomics to systematically investigate CA formation. Applying MAGIC to near-diploid, non-transformed cell lines, we track de novo CAs over successive cell cycles, highlighting the common role of dicentric chromosomes as initiating events. We determine the baseline CA mutation rate, which approximately doubles in TP53-deficient cells, and observe that chromosome losses arise more frequently than gains. The targeted induction of DNA double-strand breaks along chromosome arms triggers distinct CA processes, revealing stable isochromosomes, coordinated segregation and amplification of isoacentric segments in multiples of two, as well as complex CA outcomes, influenced by the chromosomal break location. Our data contrast de novo CA spectra from somatic mutational landscapes after selection occurred. The experimentation enabled by MAGIC advances the dissection of DNA rearrangement processes, shedding light on fundamental determinants of chromosomal instability.
The generation and maintenance of immunity is a dynamic process that is dependent on age. Here, to better understand its progression, we profiled peripheral immunity in more than 300 healthy adults (25 to 90 years of age...The generation and maintenance of immunity is a dynamic process that is dependent on age. Here, to better understand its progression, we profiled peripheral immunity in more than 300 healthy adults (25 to 90 years of age) using single-cell RNA sequencing, proteomics and flow cytometry, following 96 adults longitudinally across 2 years with seasonal influenza vaccination. The resulting resource generated a single-cell RNA-sequencing dataset of more than 16 million peripheral blood mononuclear cells with 71 immune cell subsets from our Human Immune Health Atlas and enabled us to interrogate how immune cell composition and states shift with age, chronic viral infection and vaccination. From these data, we demonstrate robust, non-linear transcriptional reprogramming in T cell subsets with age that is not driven by systemic inflammation or chronic cytomegalovirus infection. This age-related reprogramming led to a functional T helper 2 (T2) cell bias in memory T cells that is linked to dysregulated B cell responses against highly boosted antigens in influenza vaccines. Collectively, this study reveals unique features of the immune ageing process that occur prior to advanced age and provides novel targets for age-related immune modulation. We provide interactive tools for exploring this extensive human immune health resource at https://apps.allenimmunology.org/aifi/insights/dynamics-imm-health-age/ .
Most stony corals are obligate symbionts that are dependent on nutrients provided by the photosynthetic activity of dinoflagellates residing within specialized cells. Disruption of this symbiotic consortium leads to cora...Most stony corals are obligate symbionts that are dependent on nutrients provided by the photosynthetic activity of dinoflagellates residing within specialized cells. Disruption of this symbiotic consortium leads to coral bleaching and, ultimately, mortality. However, a few coral species exhibit facultative symbiosis, allowing them to survive extended periods of bleaching. Despite this resilience, the underlying biological mechanisms remain poorly understood. Here we investigate the genomic and cellular basis of facultative symbiosis in Oculina patagonica, a thermotolerant Mediterranean coral. We sequenced and annotated a chromosome-scale genome of O. patagonica and built cell atlases for this species and two obligate symbiotic corals. Comparative genomic analysis revealed karyotypic and syntenic conservation across all scleractinians, with species-specific gene expansions primarily driven by tandem duplications. Single-cell transcriptomic profiling of symbiotic and naturally aposymbiotic wild specimens identified an increase in phagocytic immune cells and a metabolic shift in gastrodermal gene expression from growth-related functions to quiescent, epithelial-like states. Cross-species comparison of host cells uncovered Oculina-specific metabolic and signalling adaptations indicative of an opportunistic, dual-feeding strategy that decouples survival from symbiotic state.
Chen HH, Chen CH, Hou MC
… +126 more, Fu YC, Li LH, Chou CY, Yeh EC, Tsai MF, Chen CH, Yang HC, Huang YT, Liu YM, Wei CY, Su JP, Lin WJ, Wang EHF, Chiang CL, Jiang JK, Lee IH, Liang KH, Chen WS, Tsai HC, Lin SY, Chang FP, Ho HL, Yeh YC, Tseng WC, Lin MH, Chang HT, Tseng LM, Liang WY, Chen PC, Hsieh YC, Chen YM, Hsiao TH, Lin CH, Chen YJ, Chen IC, Mao CL, Chang SJ, Chang YL, Liao YJ, Lai CH, Lee WJ, Tung H, Yen TT, Yen HC, Chen MY, Lin YC, Kao YT, Kao BZ, Lee JE, Chung CL, Liu JC, Chan P, Lin CH, Chen CH, Wu IC, Lin LC, Wang JW, Shih SL, Hsieh SW, Hung CH, Li WM, Yang CJ, Yang CS, Weng RH, Chen YC, Chang CP, Wu TH, Lin YC, Sheen YJ, Wang SH, Chen SP, Raben T, Widen E, Hsu S, Hsieh FJ, Ho DR, Huang YH, Yang CH, Huang YS, Chen YF, Wu HM, Tsai PH, Huang KG, Chien CY, Ho YL, Wu MS, Kao JH, Liu YB, Juang JJ, Lin MH, Lin YH, Lee JY, Lu HJ, Lu CH, Feng AC, Liu JS, Chiang CP, Chu NF, Lin JC, Yeh YW, Meng E, Huang CY, Li CC, Wang TF, Su KY, Wang JK, Chen MH, Chen HF, Ma GC, Chang TY, Chiang FT, Chang HJ, Kao KJ, Hung CF, Tsai CY, Chen PY, Tsui K, Chen YT, Kwok PY, Sheu WH, Yang SF, Liou JM, Wang JY, Chiou JF, Wu JY, Fann CSJ
Predicting complex disease risks on the basis of individual genomic profiles is an advancing field in human genetics. However, most genetic studies have focused on populations of European ancestry, creating a global imba...Predicting complex disease risks on the basis of individual genomic profiles is an advancing field in human genetics. However, most genetic studies have focused on populations of European ancestry, creating a global imbalance in precision medicine and underscoring the need for genomic research in non-European groups. The Taiwan Precision Medicine Initiative recruited more than half a million Taiwanese residents, providing a large dataset of genetic profiles and electronic medical record data for people with Han Chinese ancestry. Using extensive phenotypic data, we conducted comprehensive genomic analyses across the medical phenome with individuals genetically similar to Han Chinese reference populations. These analyses identified population-specific genetic risk variants and new findings for various complex traits. We developed polygenic risk scores, demonstrating strong predictive performance for conditions such as cardiometabolic diseases, autoimmune disorders, cancers and infectious diseases. We observed consistent findings in an independent dataset, Taiwan Biobank, and among people of East Asian ancestry in the UK Biobank and the All of Us Project. The identified genetic risks accounted for up to 10.3% of the overall health variation in the Taiwan Precision Medicine Initiative cohort. Our approach of characterizing the phenome-wide genomic landscape, developing population-specific risk-prediction models, assessing their performance and identifying the genetic effect on health serves as a model for similar studies in other diverse study populations.
Han Chinese people comprise nearly 20% of the global population but remain under-represented in genetic studies, so there is an urgent need for large-scale cohorts to advance precision medicine. Here we present the Taiwa...Han Chinese people comprise nearly 20% of the global population but remain under-represented in genetic studies, so there is an urgent need for large-scale cohorts to advance precision medicine. Here we present the Taiwan Precision Medicine Initiative (TPMI), established by Academia Sinica in collaboration with 16 major medical centres around Taiwan, which has recruited 565,390 participants who consent to provide DNA samples for genetic profiling and grant access to their electronic medical records (EMRs) for research. EMR access is both retrospective and prospective, allowing longitudinal studies. Genetic profiling is done with population-optimized arrays of single-nucleotide polymorphisms for people of Han Chinese ancestry, which enable genome-wide association, phenome-wide association and polygenic risk score studies to be performed to evaluate common disease risk and pharmacogenetic response. Participants also agreed to be re-contacted for future research and receive personalized genetic risk profiles with health management recommendations. The TPMI has established the TPMI Data Access Platform, a central database and analysis platform that both safeguards the security of the data and facilitates academic research. As a large cohort of individuals with non-European ancestry that merges genetic profiles with EMR data and enables longitudinal follow-up, TPMI provides a unique resource that could be used to validate genetic risk prediction models, perform clinical trials of risk-based health management and inform health policies. Ultimately, the TPMI cohort will contribute to global genetic research and serve as a model for population-based precision medicine.
The doughnut-shaped framework of social and planetary boundaries (the 'Doughnut') provides a concise visual assessment of progress towards the goal of meeting the needs of all people within the means of the living planet...The doughnut-shaped framework of social and planetary boundaries (the 'Doughnut') provides a concise visual assessment of progress towards the goal of meeting the needs of all people within the means of the living planet. Here we present a renewed Doughnut framework with a revised set of 35 indicators that monitor trends in social deprivation and ecological overshoot over the 2000-2022 period. Although global gross domestic product (GDP) has more than doubled, our median results show a modest achievement in reducing human deprivation that would have to accelerate fivefold to meet the needs of all people by 2030. Meanwhile, the increase in ecological overshoot would have to stop immediately and accelerate nearly two times faster towards planetary boundaries to safeguard Earth-system stability by 2050. Disaggregating these global findings shows that the richest 20% of nations, with 15% of the global population, contribute more than 40% of annual ecological overshoot, whereas the poorest 40% of countries, with 42% of the global population, experience more than 60% of the social shortfall. These trends and inequalities reaffirm the case for overcoming the dependence of nations on perpetual GDP growth and reorienting towards regenerative and distributive economic activity-within and between nations-that assigns priority to human needs and planetary integrity.
Li H, Lan L, Chen H
… +17 more, Zaw Thin M, Ps H, Nelson JK, Evans IM, Ruiz EJ, Cheng R, Tran L, Allen M, Ma J, Yi T, Wang C, He Y, Guppy N, Sadanandam A, Lin SZ, Zhang C, Behrens A
Elucidating the complex network of communication between tumour cells is central to understanding cell fate decisions and progression of pancreatic ductal adenocarcinoma (PDAC). We previously showed that constant suppres...Elucidating the complex network of communication between tumour cells is central to understanding cell fate decisions and progression of pancreatic ductal adenocarcinoma (PDAC). We previously showed that constant suppression of BMP activity by the BMP antagonist GREM1 secreted by mesenchymal PDAC cells is essential for maintaining the fate of epithelial PDAC cells. Here we identify SPP1 (also known as osteopontin) as a key regulator of mesenchymal cell fate in pancreatic cancer. Proteomic analysis of plasma from patients with PDAC showed that SPP1 is substantially upregulated in late-stage disease. Inactivation of Spp1 led to a delay in tumorigenesis in mouse PDAC models and abolished metastasis formation. Spp1 was expressed in epithelial PDAC cells, and Spp1 inactivation resulted in a conversion of mesenchymal to epithelial PDAC cells. Mechanistically, SPP1 bound the CD61 receptor on mesenchymal PDAC cells to induce Bmp2 and Grem1 expression, and GREM1 inhibition of BMP signalling was required for Spp1 expression in epithelial cells, thereby forming an intercellular regulatory loop. Concomitant inactivation of Grem1 reverted the epithelial phenotype of Spp1 knockout to fully mesenchymal PDAC. Conversely, Grem1 heterozygosity combined with Spp1 knockout resulted in wild-type PDAC histology, a result that confirmed the direct antagonistic functions of these factors. Hence, mesenchymal and epithelial PDAC cell fates are determined by the reciprocal paracrine regulation of the soluble factors GREM1 and SPP1.
Prime editors make programmed genome modifications by writing new sequences into extensions of nicked DNA 3' ends. These edited 3' new strands must displace competing 5' strands to install edits, yet a bias towards retai...Prime editors make programmed genome modifications by writing new sequences into extensions of nicked DNA 3' ends. These edited 3' new strands must displace competing 5' strands to install edits, yet a bias towards retaining the competing 5' strands hinders efficiency and can cause indel errors. Here we discover that nicked end degradation, consistent with competing 5' strand destabilization, can be promoted by Cas9-nickase mutations that relax nick positioning. We exploit this mechanism to engineer efficient prime editors with strikingly low indel errors. Combining this error-suppressing strategy with the latest efficiency-boosting architecture, we design a next-generation prime editor (vPE). Compared with previous editors, vPE features comparable efficiency yet up to 60-fold lower indel errors, enabling edit:indel ratios as high as 543:1.
Bacteriophages are the most abundant entities on earth and exhibit vast genetic and phenotypic diversity. Exploitation of this largely unexplored molecular space requires identification and functional characterization of...Bacteriophages are the most abundant entities on earth and exhibit vast genetic and phenotypic diversity. Exploitation of this largely unexplored molecular space requires identification and functional characterization of genes that act at the phage-host interface. So far, this has been restricted to few model phage-host systems that are amenable to genetic manipulation. Here, to overcome this limitation, we introduce a non-genetic mRNA targeting approach using exogenous delivery of programmable antisense oligomers to silence genes of DNA and RNA phages. A systematic knockdown screen of core and accessory genes of the nucleus-forming jumbo phage ΦKZ, coupled to RNA-sequencing and microscopy analyses, reveals previously unrecognized proteins that are essential for phage propagation and that, upon silencing, elicit distinct phenotypes at the level of the phage and host response. One of these factors is the RNase H-like protein ΦKZ155 (also known as Nlp2), which acts at a major decision point during infection, linking the formation of the protective phage nucleus to phage genome amplification. This non-genetic antisense oligomer-based gene silencing method promises to be a versatile tool for molecular discovery in phage biology, will help to elucidate defence and anti-defence mechanisms in non-model phage-host pairs, and offers potential for optimizing phage therapy and biotechnological procedures.
Over time, cells in the brain and in the body accumulate damage, which contributes to the ageing process. In the human brain, the prefrontal cortex undergoes age-related changes that can affect cognitive functioning late...Over time, cells in the brain and in the body accumulate damage, which contributes to the ageing process. In the human brain, the prefrontal cortex undergoes age-related changes that can affect cognitive functioning later in life. Here, using single-nucleus RNA sequencing (snRNA-seq), single-cell whole-genome sequencing (scWGS) and spatial transcriptomics, we identify gene-expression and genomic changes in the human prefrontal cortex across lifespan, from infancy to centenarian. snRNA-seq identified infant-specific cell clusters enriched for the expression of neurodevelopmental genes, as well as an age-associated common downregulation of cell-essential homeostatic genes that function in ribosomes, transport and metabolism across cell types. Conversely, the expression of neuron-specific genes generally remains stable throughout life. These findings were validated with spatial transcriptomics. scWGS identified two age-associated mutational signatures that correlate with gene transcription and gene repression, respectively, and revealed gene length- and expression-level-dependent rates of somatic mutation in neurons that correlate with the transcriptomic landscape of the aged human brain. Our results provide insight into crucial aspects of human brain development and ageing, and shed light on transcriptomic and genomic dynamics.
Gomez JL, Magnus CJ, Bonaventura J
… +12 more, Solis O, Curry FP, Levinstein MR, Budinich RC, Carlton ML, Ventriglia EN, Lam S, Wang L, Schoenborn I, Dunne W, Michaelides M, Sternson SM
Chemical feedback is ubiquitous in physiology but is challenging to study without perturbing basal functions. One example is addictive drugs, which elicit a positive-feedback cycle of drug-seeking and ingestion by acting...Chemical feedback is ubiquitous in physiology but is challenging to study without perturbing basal functions. One example is addictive drugs, which elicit a positive-feedback cycle of drug-seeking and ingestion by acting on the brain to increase dopamine signalling. However, interfering with this process by altering basal dopamine also adversely affects learning, movement, attention and wakefulness. Here, inspired by physiological control systems, we developed a highly selective synthetic physiology approach to interfere with the positive-feedback cycle of addiction by installing a cocaine-dependent opposing signalling process into this body-brain signalling loop. We used protein engineering to create cocaine-gated ion channels that are selective for cocaine over other drugs and endogenous molecules. Expression of an excitatory cocaine-gated channel in the rat lateral habenula, a brain region that is normally inhibited by cocaine, suppressed cocaine self-administration without affecting food motivation. This artificial cocaine-activated chemogenetic process reduced the cocaine-induced extracellular dopamine rise in the nucleus accumbens. Our results show that cocaine chemogenetics is a selective approach for countering drug reinforcement by clamping dopamine release in the presence of cocaine. In the future, chemogenetic receptors could be developed for additional addictive drugs or hormones and metabolites, which would facilitate efforts to probe their neural circuit mechanisms using a synthetic physiology approach. As these chemogenetic ion channels are specific for cocaine over natural rewards, they may also offer a route towards gene therapies for cocaine addiction.
Nitrous oxide (NO), a driver of global warming and climate change, has reached unprecedented concentrations in Earth's atmosphere. Current NO sources outpace NO sinks, emphasizing the need for comprehensive understanding...Nitrous oxide (NO), a driver of global warming and climate change, has reached unprecedented concentrations in Earth's atmosphere. Current NO sources outpace NO sinks, emphasizing the need for comprehensive understanding of processes that consume NO. Microbes that express the enzyme NO reductase (NOR) convert NO to climate change-neutral dinitrogen (N). Known NORs belong to the canonical clade I and clade II NosZ reductases and are considered key enzymes for NO reduction. Here we report a previously unrecognized protein family with a role in NO reduction, clade III lactonase-type NOR (L-NOR), which diverges in sequence from canonical NosZ but conserves three-dimensional protein structural features. Integrated physiological, metagenomic, proteomic and structural modelling studies demonstrate that L-NORs catalyse NO reduction. L-NOR genes occur in several phyla, predominantly in uncultured taxa with broad geographic distribution. Our findings expand the known diversity of NORs and implicate previously unrecognized taxa (for example, Nitrospinota) in NO consumption. The expansion of NOR diversity and the identification of a novel type of catalyst for NO reduction advances the understanding of NO sinks, has implications for greenhouse gas emission and climate change modelling, and expands opportunities for innovative biotechnologies aimed at curbing NO emissions.