The primary driver of type I diabetes is the autoimmune T cells that destroy insulin-producing β-cells within the islets of Langerhans in the pancreas1. Pancreatic islet macrophages have also been variably linked to disease onset and progression. As macrophage-mediated removal of dying cells through efferocytosis regulates tissue homeostasis and immune responses2, here we investigated how efferocytosis by intra-islet macrophages influences the immune environment of pancreatic islets. Using a series of complementary omics-based and functional approaches, we identify a subset of anti-inflammatory intra-islet efferocytic macrophages (e-Mac) within the pancreas of mice and humans. When limited β-cell apoptosis is induced in vivo in wild-type C57BL/6 mice and diabetic-prone NOD mice, islet macrophages adopt this e-Mac phenotype without an apparent increase in the total numbers of intra-islet macrophages. Such limited β-cell apoptosis and increase in e-Mac numbers led to long-term suppression of autoimmune diabetes in NOD mice. This e-Mac phenotype could also be recapitulated ex vivo by co-culturing macrophages with apoptotic β-cells. Mechanistically, the e-Mac-enriched populations imparted an anergic-like state on CD4+ T cells ex vivo and promoted accumulation of such anergic-like CD4+ T cells in vivo within the islets. Analysing macrophage-T cell interactions within pancreatic islets using NicheNet and targeted experimental validation, we identify the IGF-1-IGF1R axis as a contributor to the anergic-like T cell phenotype in the islets. Collectively, these data advance a concept that efferocytosis-associated reprogramming of the islet macrophages and the subsequent influence on the adaptive immune response could be beneficial in modulating diabetic autoimmunity.

Although autism has historically been conceptualized as a condition that emerges in early childhood1,2, many autistic people are diagnosed later in life3-5. It is unknown whether earlier- and later-diagnosed autism have different developmental trajectories and genetic profiles. Using longitudinal data from four independent birth cohorts, we demonstrate that two different socioemotional and behavioural trajectories are associated with age at diagnosis. In independent cohorts of autistic individuals, common genetic variants account for approximately 11% of the variance in age at autism diagnosis, similar to the contribution of individual sociodemographic and clinical factors, which typically explain less than 15% of this variance. We further demonstrate that the polygenic architecture of autism can be broken down into two modestly genetically correlated (rg = 0.38, s.e. = 0.07) autism polygenic factors. One of these factors is associated with earlier autism diagnosis and lower social and communication abilities in early childhood, but is only moderately genetically correlated with attention deficit-hyperactivity disorder (ADHD) and mental-health conditions. Conversely, the second factor is associated with later autism diagnosis and increased socioemotional and behavioural difficulties in adolescence, and has moderate to high positive genetic correlations with ADHD and mental-health conditions. These findings indicate that earlier- and later-diagnosed autism have different developmental trajectories and genetic profiles. Our findings have important implications for how we conceptualize autism and provide a model to explain some of the diversity found in autism.

Stem cell-based human embryo models offer a unique opportunity for functional studies of the human-specific features of development. Here we genetically and epigenetically manipulate human blastoids, a 3D embryo model of the blastocyst1, to investigate the functional effect of HERVK LTR5Hs, a hominoid-specific endogenous retrovirus, on pre-implantation development. We uncover a pervasive cis-regulatory contribution of LTR5Hs elements to the hominoid-specific diversification of the epiblast transcriptome in blastoids. Many of the LTR5Hs genomic insertions in the human genome are unique to our own species. We show that at least one such human-specific LTR5Hs element is essential for the blastoid-forming potential via enhancing expression of the primate-specific ZNF729 gene, encoding a KRAB zinc-finger protein. ZNF729 binds to GC-rich sequences, abundant at gene promoters associated with basic cellular functions, such as cell proliferation and metabolism. Despite mediating recruitment of TRIM28, at many of these promoters ZNF729 acts as a transcriptional activator. Together, our results illustrate how recently emerged transposable elements and genes can confer developmentally essential functions in humans.

Remote epitaxy, in which an epitaxial relation is established between a film and a substrate through remote interactions, enables the development of high-quality single crystalline epilayers and their transfer to and integration with other technologically crucial substates1,2. It is commonly believed that in remote epitaxy, the distance within which the remote interaction can play a leading part in the epitaxial process is less than 1 nm, as the atomically resolved fluctuating electric potential decays very rapidly to a negligible value after a few atomic distances3. Here we show that it is possible to achieve remote epitaxy when the epilayer-substrate distance is as large as 2-7 nm. We experimentally demonstrate long-distance remote epitaxy of CsPbBr3 film on an NaCl substrate, KCl film on a KCl substrate and ZnO microrods on GaN, and show that a dislocation in the GaN substrate exists immediately below every remotely epitaxial ZnO microrod. These findings indicate that remote epitaxy could be designed and engineered by means of harnessing defect-mediated long-distance remote interactions.

A fundamental question in physiology is understanding how tissues adapt and alter their cellular composition in response to dietary cues1-8. The mammalian small intestine is maintained by rapidly renewing LGR5+ intestinal stem cells (ISCs) that respond to macronutrient changes such as fasting regimens and obesogenic diets, yet how specific amino acids control ISC function during homeostasis and injury remains unclear. Here we demonstrate that dietary cysteine, a semi-essential amino acid, enhances ISC-mediated intestinal regeneration following injury. Cysteine contributes to coenzyme A (CoA) biosynthesis in intestinal epithelial cells, which promotes expansion of intraepithelial CD8αβ+ T cells and their production of interleukin-22 (IL-22). This enhanced IL-22 signalling directly augments ISC reparative capacity after injury. The mechanistic involvement of the pathway in driving the effects of cysteine is demonstrated by several findings: CoA supplementation recapitulates cysteine effects, epithelial-specific loss of the cystine transporter SLC7A11 blocks the response, and mice with CD8αβ+ T cells lacking IL-22 or a depletion of CD8αβ+ T cells fail to show enhanced regeneration despite cysteine treatment. These findings highlight how coupled cysteine metabolism between ISCs and CD8+ T cells augments intestinal stemness, providing a dietary approach that exploits ISC and immune cell crosstalk for ameliorating intestinal damage.

Squamates (lizards and snakes) comprise almost 12,000 living species, with wide ecological diversity and a crown group that originated around 190 million years ago1,2. Conflict between morphology and molecular phylogenies indicates a complex pattern of anatomical transformations during early squamate evolution, which remains poorly understood owing to the scarcity of early fossil taxa1,3. Here we present Breugnathair elgolensis gen. et sp. nov., based on a new skeleton from the Middle Jurassic epoch (167 million years ago) of Scotland, which is among the oldest relatively complete fossil squamates. Breugnathair is placed in a new family, Parviraptoridae, an enigmatic group with potential importance for snake origins, that was previously known from very incomplete remains. It displays a mosaic of anatomical traits that is not present in living groups, with head and body proportions similar to varanids (monitor lizards) and snake-like features of the teeth and jaws, alongside primitive traits shared with early-diverging groups such as gekkotans. Phylogenetic analyses of multiple datasets return conflicting results, with parviraptorids either as early toxicoferans (and potentially stem snakes) or as stem squamates that convergently evolved snake-like dental and mandibular traits related to feeding. These findings indicate high levels of homoplasy and experimentation during the initial radiation of squamates and highlight the potential importance of convergent morphological transformations during deep evolutionary divergences.

Metabolism enables life to sustain dynamics and to repeatedly interact with the environment by storing and consuming chemical energy. A major challenge for artificial molecular machines is to find a universal energy source akin to ATP for biological organisms and electricity for electromechanical machines. More than 20 years ago, DNA was first used as fuel to drive nanomechanical devices1,2 and catalytic reactions3. However, each system requires distinct fuel sequences, preventing DNA alone from becoming a universal energy source. Despite extensive efforts4, we still lack an ATP-like or electricity-like power supply to sustain diverse molecular machines. Here we show that heat can restore enzyme-free DNA circuits from equilibrium to out-of-equilibrium states. During heating and cooling, nucleic acids with strong secondary structures reach kinetically trapped states5,6, providing energy for subsequent computation. We demonstrate that complex logic circuits and neural networks, involving more than 200 distinct molecular species, can respond to a temperature ramp and recharge within minutes, allowing at least 16 rounds of computation with varying sequential inputs. Our strategy enables diverse systems to be powered by the same energy source without problematic waste build-up, thereby ensuring consistent performance over time. This scalable approach supports the sustained operation of enzyme-free molecular circuits and opens opportunities for advanced autonomous behaviours, such as iterative computation and unsupervised learning in artificial chemical systems.

Emergence of drug resistance is the main cause of therapeutic failure in patients with high-grade serous ovarian cancer (HGSOC)1. To study drug resistance in patients, we developed CloneSeq-SV, which combines single-cell whole-genome sequencing2 with targeted deep sequencing of clone-specific genomic structural variants in time-series cell-free DNA. CloneSeq-SV exploits tumour clone-specific structural variants as highly sensitive endogenous cell-free DNA markers, enabling the relative abundance measurements and evolutionary analysis of co-existing clonal populations over the therapeutic time course. Here, using this approach, we studied 18 patients with HGSOC over a multi-year period from diagnosis to recurrence and showed that drug resistance typically arose from selective expansion of a single or small subset of clones present at diagnosis. Drug-resistant clones frequently showed interpretable and distinctive genomic features, including chromothripsis, whole-genome doubling, and high-level amplifications of oncogenes such as CCNE1, RAB25, MYC and NOTCH3. Phenotypic analysis of matched single-cell RNA sequencing data3 indicated pre-existing and clone-specific transcriptional states such as upregulation of epithelial-to-mesenchymal transition and VEGF pathways, linked to drug resistance. In one notable case, clone-specific ERBB2 amplification affected the efficacy of a secondary targeted therapy with a positive patient outcome. Together, our findings indicate that drug-resistant states in HGSOC pre-exist at diagnosis, leading to positive selection and reduced clonal complexity at relapse. We suggest these findings motivate investigation of evolution-informed adaptive treatment regimens to ablate drug resistance in future HGSOC studies.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by a progressive loss of motor neurons. Neuroinflammation is apparent in affected tissues, including increased T cell infiltration and activation of microglia, particularly in the spinal cord1,2. Autoimmune responses are thought to have a key role in ALS pathology, and it is hypothesized that T cells contribute to the rapid loss of neurons during disease progression3,4. However, until now there has been no reported target for such an autoimmune response. Here we show that ALS is associated with recognition of the C9orf72 antigen, and we map the specific epitopes that are recognized. We show that these responses are mediated by CD4+ T cells that preferentially release IL-5 and IL-10, and that IL-10-mediated T cell responses are significantly greater in donors who have a longer predicted survival time. Our results reinforce the previous hypothesis that neuroinflammation has an important role in ALS disease progression, possibly because of a disrupted balance of inflammatory and counter-inflammatory T cell responses4. These findings highlight the potential of therapeutic strategies aimed at enhancing regulatory T cells5, and identify a key target for antigen-specific T cell responses that could enable precision therapeutics in ALS.

Chronic infections and cancer cause T cell dysfunction known as exhaustion. This cell state is caused by persistent antigen exposure, suboptimal co-stimulation and a plethora of hostile factors that dampen protective immunity and limit the efficacy of immunotherapies1-4. The mechanisms that underlie T cell exhaustion remain poorly understood. Here we analyse the proteome of CD8+ exhausted T (Tex) cells across multiple states of exhaustion in the context of both chronic viral infections and cancer. We show that there is a non-stochastic pathway-specific discordance between mRNA and protein dynamics between T effector (Teff) and Tex cells. We identify a distinct proteotoxic stress response (PSR) in Tex cells, which we term Tex-PSR. Contrary to canonical stress responses that induce a reduction in protein synthesis5,6, Tex-PSR involves an increase in global translation activity and an upregulation of specialized chaperone proteins. Tex-PSR is further characterized by the accumulation of protein aggregates and stress granules and an increase in autophagy-dominant protein catabolism. We establish that disruption of proteostasis alone can convert Teff cells to Tex cells, and we link Tex-PSR mechanistically to persistent AKT signalling. Finally, disruption of Tex-PSR-associated chaperones in CD8+ T cells improves cancer immunotherapy in preclinical models. Moreover, a high Tex-PSR in T cells from patients with cancer confers poor responses to clinical immunotherapy. Collectively, our findings indicate that Tex-PSR is a hallmark and a mechanistic driver of T cell exhaustion, which raises the possibility of targeting proteostasis pathways as an approach for cancer immunotherapy.

Bacteria combat phage infection using antiphage systems and many systems generate nucleotide-derived second messengers upon infection that activate effector proteins to mediate immunity1. Phages respond with counter-defences that deplete these second messengers, leading to an escalating arms race with the host. Here we outline an antiphage system we call Panoptes that indirectly detects phage infection when phage proteins antagonize the nucleotide-derived second-messenger pool. Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence. Crystal structures show that OptS is a minimal CRISPR polymerase (mCpol) domain, a version of the polymerase domain found in type III CRISPR systems (Cas10). OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2',3'-cyclic diadenosine monophosphate (2',3'-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector. Panoptes potently restricted phage replication, but phages that had loss-of-function mutations in anti-cyclic oligonucleotide-based antiphage signalling system (CBASS) protein 2 (Acb2) escaped defence. These findings were unexpected because Acb2 is a nucleotide 'sponge' that antagonizes second-messenger signalling. Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence. These data demonstrate a sophisticated immune strategy that bacteria use to guard their second-messenger pool and turn immune evasion against the virus.

In Gram-negative bacteria, the outer membrane is the first line of defence against antimicrobial agents and immunological attacks1. A key part of outer membrane biogenesis is the insertion of outer membrane proteins by the β-barrel-assembly machinery (BAM)2-4. Here we report the cryo-electron microscopy structure of a BAM complex isolated from Flavobacterium johnsoniae, a member of the Bacteroidota, a phylum that includes key human commensals and major anaerobic pathogens. This BAM complex is extensively modified from the canonical Escherichia coli system and includes an extracellular canopy that overhangs the substrate folding site and a subunit that inserts into the BAM pore. The novel BamG and BamH subunits that are involved in forming the extracellular canopy are required for BAM function and are conserved across the Bacteroidota, suggesting that they form an essential extension to the canonical BAM core in this phylum. For BamH, isolation of a suppressor mutation enables the separation of its essential and non-essential functions. The need for a highly remodelled and enhanced BAM complex reflects the unusually complex membrane proteins found in the outer membrane of the Bacteroidota.

The 'silent pandemic' caused by antimicrobial resistance requires innovative therapeutic approaches. Human monoclonal antibodies (mAbs), which are among the most transformative and safe drugs in oncology1 and autoimmunity2, are rarely used for infectious diseases and not yet used for antimicrobial resistance3. Here we applied an antigen-agnostic strategy to isolate extremely potent human mAbs against Klebsiella pneumoniae sequence type 147 (ST147), a hypervirulent and pandrug-resistant lineage that is spreading globally. Isolated mAbs target the KL64 capsule and the O-antigen. However, although mAbs displayed bactericidal activity in the picomolar range in vitro, only the capsule-specific mAbs were protective against fulminant bloodstream infection by ST147 and two geographically and genetically distant carbapenem-resistant KL64-bearing K. pneumoniae. Protection observed in vivo correlated with in vitro bacterial uptake by macrophages and enchained bacterial growth. Our study thus describes a mAb that protects against pandrug-resistant K. pneumoniae and provides a strategy to isolate mAbs and identify mAbs that confer protection against bacteria with antimicrobial resistance.

Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signalling that share mechanistic features with human antiviral systems1. In these pathways, including cyclic oligonucleotide-based antiphage signalling systems (CBASSs) and type III CRISPR systems in bacteria and cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) in humans, oligonucleotide synthesis occurs upon detection of virus or foreign genetic material in the cell, triggering the antiviral response2-4. Here, in an unexpected inversion of this process, we show that the CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as part of an active mechanism that represses a toxic effector. Cell-based experiments demonstrated that the absence or loss of mCpol-produced cyclic oligonucleotides triggers cell death, preventing the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Structural and mechanistic investigation revealed mCpol to be a di-adenylate cyclase whose product, c-di-AMP, prevents toxic oligomerization of the effector protein 2TMβ. Analysis of cells by fluorescence microscopy showed that lack of mCpol allows 2TMβ-mediated cell death due to inner membrane collapse. These findings unveil a powerful defence strategy against virus-mediated immune suppression, expanding our understanding of the role of oligonucleotides in immunity.