Circadian control of tumor immunosuppression affects efficacy of immune checkpoint blockade.

The circadian clock is a critical regulator of immunity, and this circadian control of immune modulation has an essential function in host defense and tumor immunosurveillance. Here we use a single-cell RNA sequencing approach and a genetic model of colorectal cancer to identify clock-dependent changes to the immune landscape that control the abundance of immunosuppressive cells and consequent suppression of cytotoxic CD8+ T cells. Of these immunosuppressive cell types, PD-L1-expressing myeloid-derived suppressor cells (MDSCs) peak in abundance in a rhythmic manner. Disruption of the epithelial cell clock regulates the secretion of cytokines that promote heightened inflammation, recruitment of neutrophils and the subsequent development of MDSCs. We also show that time-of-day anti-PD-L1 delivery is most effective when synchronized with the abundance of immunosuppressive MDSCs. Collectively, these data indicate that circadian gating of tumor immunosuppression informs the timing and efficacy of immune checkpoint inhibitors.

Author Correction: Approaches and advances in the genetic causes of autoimmune disease and their implications.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Publisher Correction: Approaches and advances in the genetic causes of autoimmune disease and their implications.

In the version of this article initially published, the bibliographic information for reference 2 was incorrect in the reference list, and reference 2 was cited incorrectly at the end of the second sentence in the second paragraph ("...were identified2."). The correct reference 2 is as follows: "Kong, A. et al. The nature of nurture: Effects of parental genotypes. Science 359, 424-428 (2018)." The reference that should be cited at the end of the aforementioned sentence, which should be numbered '5' ("...were identified5."), is as follows: "Okada, Y. et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506, 376-381 (2014)." All subsequent references (5-161) should be renumbered accordingly (6-162) in the list and text. Also, several of the gene symbols in Table 2 were formatted incorrectly (without commas); the correct gene symbols are as follows: column 3 row 13, RBM17, IL2RA; column 3 row 30, DEXI, CLEC16A; column 3 row 39, UBASH3A, ICOSLG; column 4 row 15, PTEN, KLLN; column 4 row 21, CLEC7A, CLEC9A; and column 5 rows 7-9, AL391559.1, ENSG00000238747, RP11-63K6.7, RP3-512E2.2. The errors have been corrected in the HTML and PDF version of the article.

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are uncharted, constituting a major missing link in understanding genome control. Here, we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types. We show that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers. Promoter interactomes reflect lineage relationships of the hematopoietic tree, consistent with dynamic remodeling of nuclear architecture during differentiation. Interacting regions are enriched in genetic variants linked with altered expression of genes they contact, highlighting their functional role. We exploit this rich resource to connect non-coding disease variants to putative target promoters, prioritizing thousands of disease-candidate genes and implicating disease pathways. Our results demonstrate the power of primary cell promoter interactomes to reveal insights into genomic regulatory mechanisms underlying common diseases.

Approaches and advances in the genetic causes of autoimmune disease and their implications.

Genome-wide association studies are transformative in revealing the polygenetic basis of common diseases, with autoimmune diseases leading the charge. Although the field is just over 10 years old, advances in understanding the underlying mechanistic pathways of these conditions, which result from a dense multifactorial blend of genetic, developmental and environmental factors, have already been informative, including insights into therapeutic possibilities. Nevertheless, the challenge of identifying the actual causal genes and pathways and their biological effects on altering disease risk remains for many identified susceptibility regions. It is this fundamental knowledge that will underpin the revolution in patient stratification, the discovery of therapeutic targets and clinical trial design in the next 20 years. Here we outline recent advances in analytical and phenotyping approaches and the emergence of large cohorts with standardized gene-expression data and other phenotypic data that are fueling a bounty of discovery and improved understanding of human physiology.

Rare variant associations with plasma protein levels in the UK Biobank.

Integrating human genomics and proteomics can help elucidate disease mechanisms, identify clinical biomarkers and discover drug targets1-4. Because previous proteogenomic studies have focused on common variation via genome-wide association studies, the contribution of rare variants to the plasma proteome remains largely unknown. Here we identify associations between rare protein-coding variants and 2,923 plasma protein abundances measured in 49,736 UK Biobank individuals. Our variant-level exome-wide association study identified 5,433 rare genotype-protein associations, of which 81% were undetected in a previous genome-wide association study of the same cohort5. We then looked at aggregate signals using gene-level collapsing analysis, which revealed 1,962 gene-protein associations. Of the 691 gene-level signals from protein-truncating variants, 99.4% were associated with decreased protein levels. STAB1 and STAB2, encoding scavenger receptors involved in plasma protein clearance, emerged as pleiotropic loci, with 77 and 41 protein associations, respectively. We demonstrate the utility of our publicly accessible resource through several applications. These include detailing an allelic series in NLRC4, identifying potential biomarkers for a fatty liver disease-associated variant in HSD17B13 and bolstering phenome-wide association studies by integrating protein quantitative trait loci with protein-truncating variants in collapsing analyses. Finally, we uncover distinct proteomic consequences of clonal haematopoiesis (CH), including an association between TET2-CH and increased FLT3 levels. Our results highlight a considerable role for rare variation in plasma protein abundance and the value of proteogenomics in therapeutic discovery.

Plasma proteomic associations with genetics and health in the UK Biobank.

The Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. Here we provide a detailed summary of this initiative, including technical and biological validations, insights into proteomic disease signatures, and prediction modelling for various demographic and health indicators. We present comprehensive protein quantitative trait locus (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 81% are previously undescribed, alongside ancestry-specific pQTL mapping in non-European individuals. The study provides an updated characterization of the genetic architecture of the plasma proteome, contextualized with projected pQTL discovery rates as sample sizes and proteomic assay coverages increase over time. We offer extensive insights into trans pQTLs across multiple biological domains, highlight genetic influences on ligand-receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks, and illustrate long-range epistatic effects of ABO blood group and FUT2 secretor status on proteins with gastrointestinal tissue-enriched expression. We demonstrate the utility of these data for drug discovery by extending the genetic proxied effects of protein targets, such as PCSK9, on additional endpoints, and disentangle specific genes and proteins perturbed at loci associated with COVID-19 susceptibility. This public-private partnership provides the scientific community with an open-access proteomics resource of considerable breadth and depth to help to elucidate the biological mechanisms underlying proteo-genomic discoveries and accelerate the development of biomarkers, predictive models and therapeutics1.

Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Whole-genome sequencing of a sporadic primary immunodeficiency cohort.

Primary immunodeficiency (PID) is characterized by recurrent and often life-threatening infections, autoimmunity and cancer, and it poses major diagnostic and therapeutic challenges. Although the most severe forms of PID are identified in early childhood, most patients present in adulthood, typically with no apparent family history and a variable clinical phenotype of widespread immune dysregulation: about 25% of patients have autoimmune disease, allergy is prevalent and up to 10% develop lymphoid malignancies1-3. Consequently, in sporadic (or non-familial) PID genetic diagnosis is difficult and the role of genetics is not well defined. Here we address these challenges by performing whole-genome sequencing in a large PID cohort of 1,318 participants. An analysis of the coding regions of the genome in 886 index cases of PID found that disease-causing mutations in known genes that are implicated in monogenic PID occurred in 10.3% of these patients, and a Bayesian approach (BeviMed4) identified multiple new candidate PID-associated genes, including IVNS1ABP. We also examined the noncoding genome, and found deletions in regulatory regions that contribute to disease causation. In addition, we used a genome-wide association study to identify loci that are associated with PID, and found evidence for the colocalization of-and interplay between-novel high-penetrance monogenic variants and common variants (at the PTPN2 and SOCS1 loci). This begins to explain the contribution of common variants to the variable penetrance and phenotypic complexity that are observed in PID. Thus, using a cohort-based whole-genome-sequencing approach in the diagnosis of PID can increase diagnostic yield and further our understanding of the key pathways that influence immune responsiveness in humans.

Whole-genome sequencing of patients with rare diseases in a national health system.

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and causative genes for more than half such disorders remain to be discovered1. Here we used whole-genome sequencing (WGS) in a national health system to streamline diagnosis and to discover unknown aetiological variants in the coding and non-coding regions of the genome. We generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 extensively phenotyped participants. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed to be aetiological. By generating WGS data of UK Biobank participants2, we found that rare alleles can explain the presence of some individuals in the tails of a quantitative trait for red blood cells. Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.

A minimal role for synonymous variation in human disease.

Synonymous mutations change the DNA sequence of a gene without affecting the amino acid sequence of the encoded protein. Although some synonymous mutations can affect RNA splicing, translational efficiency, and mRNA stability, studies in human genetics, mutagenesis screens, and other experiments and evolutionary analyses have repeatedly shown that most synonymous variants are neutral or only weakly deleterious, with some notable exceptions. Based on a recent study in yeast, there have been claims that synonymous mutations could be as important as nonsynonymous mutations in causing disease, assuming the yeast findings hold up and translate to humans. Here, we argue that there is insufficient evidence to overturn the large, coherent body of knowledge establishing the predominant neutrality of synonymous variants in the human genome.

The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants.

Rare genetic diseases affect millions, and identifying causal DNA variants is essential for patient care. Therefore, it is imperative to estimate the effect of each independent variant and improve their pathogenicity classification. Our study of 140 214 unrelated UK Biobank (UKB) participants found that each of them carries a median of 7 variants previously reported as pathogenic or likely pathogenic. We focused on 967 diagnostic-grade gene (DGG) variants for rare bleeding, thrombotic, and platelet disorders (BTPDs) observed in 12 367 UKB participants. By association analysis, for a subset of these variants, we estimated effect sizes for platelet count and volume, and odds ratios for bleeding and thrombosis. Variants causal of some autosomal recessive platelet disorders revealed phenotypic consequences in carriers. Loss-of-function variants in MPL, which cause chronic amegakaryocytic thrombocytopenia if biallelic, were unexpectedly associated with increased platelet counts in carriers. We also demonstrated that common variants identified by genome-wide association studies (GWAS) for platelet count or thrombosis risk may influence the penetrance of rare variants in BTPD DGGs on their associated hemostasis disorders. Network-propagation analysis applied to an interactome of 18 410 nodes and 571 917 edges showed that GWAS variants with large effect sizes are enriched in DGGs and their first-order interactors. Finally, we illustrate the modifying effect of polygenic scores for platelet count and thrombosis risk on disease severity in participants carrying rare variants in TUBB1 or PROC and PROS1, respectively. Our findings demonstrate the power of association analyses using large population datasets in improving pathogenicity classifications of rare variants.

Unconventional localization of electrons inside of a nematic electronic phase.

The magnetotransport behavior inside the nematic phase of bulk FeSe reveals unusual multiband effects that cannot be reconciled with a simple two-band approximation proposed by surface-sensitive spectroscopic probes. In order to understand the role played by the multiband electronic structure and the degree of two-dimensionality, we have investigated the electronic properties of exfoliated flakes of FeSe by reducing their thickness. Based on magnetotransport and Hall resistivity measurements, we assess the mobility spectrum that suggests an unusual asymmetry between the mobilities of the electrons and holes, with the electron carriers becoming localized inside the nematic phase. Quantum oscillations in magnetic fields up to 38 T indicate the presence of a hole-like quasiparticle with a lighter effective mass and a quantum scattering time three times shorter, as compared with bulk FeSe. The observed localization of negative charge carriers by reducing dimensionality can be driven by orbitally dependent correlation effects, enhanced interband spin fluctuations, or a Lifshitz-like transition, which affect mainly the electron bands. The electronic localization leads to a fragile two-dimensional superconductivity in thin flakes of FeSe, in contrast to the two-dimensional high-[Formula: see text] induced with electron doping via dosing or using a suitable interface.

Controlling the Photophysical Properties of a Series of Isostructural d6 Complexes Based on Cr0, MnI, and FeII.

Development of first-row transition metal complexes with similar luminescence and photoredox properties as widely used RuII polypyridines is attractive because metals from the first transition series are comparatively abundant and inexpensive. The weaker ligand field experienced by the valence d-electrons of first-row transition metals challenges the installation of the same types of metal-to-ligand charge transfer (MLCT) excited states as in precious metal complexes, due to rapid population of energetically lower-lying metal-centered (MC) states. In a family of isostructural tris(diisocyanide) complexes of the 3d6 metals Cr0, MnI, and FeII, the increasing effective nuclear charge and ligand field strength allow us to control the energetic order between the 3MLCT and 3MC states, whereas pyrene decoration of the isocyanide ligand framework provides control over intraligand (ILPyr) states. The chromium(0) complex shows red 3MLCT phosphorescence because all other excited states are higher in energy. In the manganese(I) complex, a microsecond-lived dark 3ILPyr state, reminiscent of the types of electronic states encountered in many polyaromatic hydrocarbon compounds, is the lowest and becomes photoactive. In the iron(II) complex, the lowest MLCT state has shifted to so much higher energy that 1ILPyr fluorescence occurs, in parallel to other excited-state deactivation pathways. Our combined synthetic-spectroscopic-theoretical study provides unprecedented insights into how effective nuclear charge, ligand field strength, and ligand π-conjugation affect the energetic order between MLCT and ligand-based excited states, and under what circumstances these individual states become luminescent and exploitable in photochemistry. Such insights are the key to further developments of luminescent and photoredox-active first-row transition metal complexes.

Reversible Photoinduced Ligand Substitution in a Luminescent Chromium(0) Complex.

Light-triggered dissociation of ligands forms the basis for many compounds of interest for photoactivated chemotherapy (PACT), in which medicinally active substances are released or "uncaged" from metal complexes upon illumination. Photoinduced ligand dissociation is usually irreversible, and many recent studies performed in the context of PACT focused on ruthenium(II) polypyridines and related heavy metal complexes. Herein, we report a first-row transition metal complex, in which photoinduced dissociation and spontaneous recoordination of a ligand unit occurs. Two scorpionate-type tridentate chelates provide an overall six-coordinate arylisocyanide environment for chromium(0). Photoexcitation causes decoordination of one of these six ligating units and coordination of a solvent molecule, at least in tetrahydrofuran and 1,4-dioxane solvents, but far less in toluene, and below detection limit in cyclohexane. Transient UV-vis absorption spectroscopy and quantum chemical simulations point to photoinduced ligand dissociation directly from an excited metal-to-ligand charge-transfer state. Owing to the tridentate chelate design and the substitution lability of the first-row transition metal, recoordination of the photodissociated arylisocyanide ligand unit can occur spontaneously on a millisecond time scale. This work provides insight into possible self-healing mechanisms counteracting unwanted photodegradation processes and seems furthermore relevant in the contexts of photoswitching and (photo)chemical information storage.

Iron(III) Carbene Complexes with Tunable Excited State Energies for Photoredox and Upconversion.

Substituting precious elements in luminophores and photocatalysts by abundant first-row transition metals remains a significant challenge, and iron continues to be particularly attractive owing to its high natural abundance and low cost. Most iron complexes known to date face severe limitations due to undesirably efficient deactivation of luminescent and photoredox-active excited states. Two new iron(III) complexes with structurally simple chelate ligands enable straightforward tuning of ground and excited state properties, contrasting recent examples, in which chemical modification had a minor impact. Crude samples feature two luminescence bands strongly reminiscent of a recent iron(III) complex, in which this observation was attributed to dual luminescence, but in our case, there is clear-cut evidence that the higher-energy luminescence stems from an impurity and only the red photoluminescence from a doublet ligand-to-metal charge transfer (2LMCT) excited state is genuine. Photoinduced oxidative and reductive electron transfer reactions with methyl viologen and 10-methylphenothiazine occur with nearly diffusion-limited kinetics. Photocatalytic reactions not previously reported for this compound class, in particular the C-H arylation of diazonium salts and the aerobic hydroxylation of boronic acids, were achieved with low-energy red light excitation. Doublet-triplet energy transfer (DTET) from the luminescent 2LMCT state to an anthracene annihilator permits the proof of principle for triplet-triplet annihilation upconversion based on a molecular iron photosensitizer. These findings are relevant for the development of iron complexes featuring photophysical and photochemical properties competitive with noble-metal-based compounds.

Luminescence and Excited-State Reactivity in a Heteroleptic Tricyanido Fe(III) Complex.

Harnessing sunlight via photosensitizing molecules is key for novel optical applications and solar-to-chemical energy conversion. Exploiting abundant metals such as iron is attractive but becomes challenging due to typically fast nonradiative relaxation processes. In this work, we report on the luminescence and excited-state reactivity of the heteroleptic [FeIII(pzTp)(CN)3]- complex (pzTp = tetrakis(pyrazolyl)borate), which incorporates a σ-donating trispyrazolyl chelate ligand and three monodentate σ-donating and π-accepting cyanide ligands. Contrary to the nonemissive [Fe(CN)6]3-, a broad emission band centered at 600 nm at room temperature has been recorded for the heteroleptic analogue attributed to the radiative deactivation from a 2LMCT excited state with a luminescence quantum yield of 0.02% and a lifetime of 80 ps in chloroform at room temperature. Bimolecular reactivity of the 2LMCT excited state was successfully applied to different alcohol photo-oxidation, identifying a cyanide-H bonding as a key reaction intermediate. Finally, this research demonstrated the exciting potential of [Fe(pzTp)(CN)3]- as a photo-oxidant, paving the way for further exploration and development of emissive Fe-based photosensitizers competent for photochemical transformations.

Bifurcation of Excited-State Population Leads to Anti-Kasha Luminescence in a Disulfide-Decorated Organometallic Rhenium Photosensitizer.

We report a rhenium diimine photosensitizer equipped with a peripheral disulfide unit on one of the bipyridine ligands, [Re(CO)3(bpy)(S-Sbpy4,4)]+ (1+, bpy = 2,2'-bipyridine, S-Sbpy4,4 = [1,2]dithiino[3,4-c:6,5-c']dipyridine), showing anti-Kasha luminescence. Steady-state and ultrafast time-resolved spectroscopies complemented by nonadiabatic dynamics simulations are used to disclose its excited-state dynamics. The calculations show that after intersystem crossing the complex evolves to two different triplet minima: a (S-Sbpy4,4)-ligand-centered excited state (3LC) lying at lower energy and a metal-to-(bpy)-ligand charge transfer (3MLCT) state at higher energy, with relative yields of 90% and 10%, respectively. The 3LC state involves local excitation of the disulfide group into the antibonding σ* orbital, leading to significant elongation of the S-S bond. Intriguingly, it is the higher-lying 3MLCT state, which is assigned to display luminescence with a lifetime of 270 ns: a signature of anti-Kasha behavior. This assignment is consistent with an energy barrier ≥ 0.6 eV or negligible electronic coupling, preventing reaction toward the 3LC state after the population is trapped in the 3MLCT state. This study represents a striking example on how elusive excited-state dynamics of transition-metal photosensitizers can be deciphered by synergistic experiments and state-of-the-art calculations. Disulfide functionalization lays the foundation of a new design strategy toward harnessing excess energy in a system for possible bimolecular electron or energy transfer reactivity.

Fragmentation of Care in Patients with Peritoneal Metastases Undergoing Cytoreductive Surgery.

BACKGROUND: The delivery of multimodal treatment at a high-volume center is known to optimize the outcomes of gastrointestinal malignancies. However, patients undergoing cytoreductive surgery (CRS) for peritoneal metastases often must 'fragment' their surgical and systemic therapeutic care between different institutions. We hypothesized that this adversely affects outcomes. PATIENTS AND METHODS: Adults undergoing CRS for colorectal or appendiceal adenocarcinoma at our institution between 2016 and 2022 were identified retrospectively and grouped by care network: 'coordinated care' patients received exclusively in-network systemic therapy, while 'fragmented care' patients received some systemic therapy from outside-network providers. Factors associated with fragmented care were also ascertained. Overall survival (OS) from CRS and systemic therapy-related serious adverse events (SAEs) were compared across the groups. RESULTS: Among 85 (80%) patients, 47 (55%) had colorectal primaries and 51 (60%) received fragmented care. Greater travel distance [OR 1.01 (CI 1.00-1.02), p = 0.02] and educational status [OR 1.04 (CI 1.01-1.07), p = 0.01] were associated with receiving fragmented care. OS was comparable between patients who received fragmented and coordinated care in the colorectal [32.5 months versus 40.8 months, HR 0.95 (CI 0.43-2.10), p = 0.89] and appendiceal [31.0 months versus 27.4 months, HR 1.17 (CI 0.37-3.74), p = 0.55] subgroups. The frequency of SAEs (7.8% versus 17.6%, p = 0.19) was also similar. CONCLUSIONS: There were no significant differences in survival or SAEs based on the networks of systemic therapy delivery. This suggests that patients undergoing CRS at a high-volume center may safely receive systemic therapy at outside-network facilities with comparable outcomes.

Venous Thromboembolism in Peritoneal Mesothelioma: Uncovering the Hidden Risk.

INTRODUCTION: Venous thromboembolism (VTE) is a common complication in patients with abdominal malignancies. Despite known associations between pleural mesothelioma and increased VTE risk, the characteristics of VTE in patients with peritoneal mesothelioma (PeM) remain undescribed. METHODS: Patients treated for PeM were retrospectively identified from our institutional database. The frequency of VTE was assessed and logistic regression modeling was employed to assess VTE risk factors. The association between VTE and overall survival was also ascertained. Recommended thromboprophylaxis for patients who underwent surgery at our institution comprised a single preoperative dose of prophylactic anticoagulation, followed by daily dosing for four weeks postoperatively. RESULTS: Among 120 PeM patients, 26 (21.7%) experienced VTE, including 19/91 (20.9%) surgical patients, 4/23 (17.4%) patients who received systemic therapy, and 3/6 (50%) patients who underwent observation (p = 0.21). Most events were symptomatic (n = 16, 62%) and were attributable to pulmonary emboli (n = 16, 62%). The 90-day postoperative VTE rate was 4.4% (4/91), including 1 of 60 patients who underwent index surgical intervention at our institution and 3 patients with surgery elsewhere. A low serum albumin concentration was associated with VTE in non-surgical patients (odds ratio 0.12, confidence interval [CI] 0.02-0.72; p = 0.03). No significant difference in overall survival was observed between patients with and without VTE (median 46.0 months [CI 24.9-67.0] vs. 55.0 months [CI 27.5-82.5]; hazard ratio 0.98 [CI 0.54-1.81], p = 0.98). CONCLUSIONS: A high risk of VTE was observed in PeM patients, warranting suspicion throughout the disease trajectory. Postoperative VTE rates were within acceptable limits with 4-week thromboprophylaxis.