Biology subjects

Maier, B.

Publications and source records attributed to Maier, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Differential active adhesion and a capillary instability drive global eversion and dissemination of bacterial colonies

Attractive forces between cells determine the shape and sorting behaviour of bacterial colonies. During colony development, chemical gradients form within the colony but it is unclear how they affect cohesion. Here, we discover that such gradients trigger global eversion of proliferating colonies formed by the human pathogen Neisseria gonorrhoeae. Like a jet, the inner core flows towards the periphery where it is partially dispersed and partially spreads around the core of the colony. Living dispersed cells reform colonies leading to rapid dissemination. The eversion depends on local oxygen depletion, which reduces the activity of the molecular motors that govern self-attraction: before the eversion the colony consists of a weakly cohesive spherical core surrounded by a strongly cohesive shell. An idealized computational model reveals that in this configuration a non-linear instability occurs, akin to a capillary instability, when the thickness of the strongly interacting shell falls below a critical value. We show that the probability for eversion strongly depends on the motor-generated attractive force between bacteria. Overall, our results indicate that chemical gradients induce spontaneous symmetry breaking in a mechanically active colony, thereby triggering a non-linear shape instability. This instability generates large-scale cellular fluxes that redistribute bacteria toward environments more favourable for their growth.

biophysics↗

bioRxiv2025

Hair test reveals plasticity of human chronotype

Circadian clocks govern daily physiological and behavioral processes and are crucial for health, yet disruptions can lead to various diseases. Chronotype, the state of circadian timing, varies between individuals and is reflected in behaviors such as sleep-wake patterns, cognitive performance, and physical activity. This interindividual variability is influenced by both genetic factors and environmental cues, but the relative contributions of each remain unclear, particularly in terms of plasticity - how much chronotype can shift in response to lifestyle and environmental factors. The gold standard for chronotype assessment, dim-light melatonin onset (DLMO), is invasive and impractical for large-scale studies, while blood-based molecular biomarker tests, which estimate internal time, show promise but are limited by practicality. Here, we introduce HairTime, a novel assay that estimates chronotype from a single hair sample collected at one point during the day. HairTime was developed and evaluated in two studies: a training study and a validation study, where it demonstrated a strong ability to predict chronotype, with DLMO as the comparison. This non-invasive method is suitable for large-scale, longitudinal studies and clinical practice. We assessed HairTime using over 4,000 samples, observing a normal distribution of chronotype across the population, with its estimation associating with age, sex, and notably, work schedules. The association with work schedules reveals the plasticity of chronotype, as workdays circadian timing earlier, highlighting that societal factors can influence and modify an individuals internal rhythm. Additionally, we explore the concept of circadian amplitude, finding that lower amplitude rhythms in hair follicle cells are linked to reduced chronotype prediction accuracy. Our results highlight that both intrinsic circadian mechanisms and external factors, such as lifestyle and work schedules, shape chronotype. HairTime offers an innovative tool for understanding circadian rhythms, facilitating personalized chronotherapy to improve health outcomes by aligning treatments with an individuals biological rhythms.

systems biology↗

bioRxiv2025

Gonococcal polarization dynamics during adaptation to low oxygen levels

Neisseria gonorrhoeae can switch between aerobic and microaerophilic lifestyles, but little is known about the dynamics of this transition. In particular, switching from respiration to partial denitrification is likely to affect the electrophysiology of these bacteria. Here, we use a Nernstian dye to measure the membrane potential of single planktonic cells while they continuously consume the oxygen in the growth medium. We show that cells undergo a characteristic pattern of transient depolarization followed by transient hyperpolarization at a critical oxygen concentration, reminiscent of the response to sudden changes in membrane voltage driven by gated ion-channels. Subsequently, the cells depolarize strongly to a near-constant membrane potential. In the presence of nitrite, the cells repolarize after a delay and the repolarization depends on the oxygen-dependent regulator fnr required for denitrification. The temporal behaviour of planktonic cells explains the complex spatio-temporal polarization pattern of the colonies formed by N. gonorrhoeae. This sexually transmitted human pathogen experiences different growth environments during transmission. Our results are an important step towards understanding how electrophysiology adapts to changing environments.

biophysics↗

bioRxiv2025

Gonococcal aggregation causes upregulation of genes involved in antibiotic tolerance

Aggregation and biofilm formation can increase the tolerance of bacteria to external stressors, including antibiotic treatment. While resistant bacteria grow at an elevated drug dose, tolerant bacteria survive longer-term treatment. The mechanisms by which aggregation confers tolerance are insufficiently characterized for most organisms, including the human pathogen Neisseria gonorrhoeae. We hypothesize that bacterial aggregation causes upregulation of genes involved in tolerance and that deletion of these genes increases killing rates during antibiotic treatment. To test this hypothesis and identify genes involved in gonococcal tolerance, we compared the transcriptome of aggregating and planktonic N. gonorrhoeae strains. In general, the transcriptome analysis shows that aggregation causes a strong upregulation of prophage-related genes and a shift towards anaerobic respiration. We generated deletion strains for the twenty most upregulated genes and measured their killing kinetics during treatment with the clinically relevant antibiotics ceftriaxone or ciprofloxacin. We identified five genes and one multigene segment that are involved in gonococcal antibiotic tolerance. These include prophage genes whose deletion affects tolerance differently in aggregating and planktonic strains. Furthermore, deletion of genes encoding a putative multi-drug efflux pump, an alcohol dehydrogenase, and a DNA repair protein reduces tolerance. In summary, we have identified multiple genes that affect antibiotic tolerance and are upregulated in response to aggregation. Author summaryOften bacterial infections recur after antibiotic treatment because not all of the bacteria were killed. The ability to survive treatment by bactericidal drugs is termed tolerance. It is well established that aggregation can increase tolerance by reducing growth and metabolism. However, the genes involved in tolerance are not well characterized, especially in the human pathogen Neisseria gonorrhoeae. Here, we aim to identify such genes by following the hypothesis that aggregation upregulates genes that cross-protect N. gonorrhoeae from antibiotic treatment. We show that prophage-associated genes are strongly upregulated in aggregates and that deletion of various phage genes affects tolerance to the currently administered drug, ceftriaxone. We identify three additional genes belonging to different functional classes whose deletion reduces tolerance to ciprofloxacin. Our study is an important step towards understanding the molecular mechanisms of gonococcal antibiotic tolerance. In particular, we propose that prophages could serve as a target for the treatment of tolerant gonococcal infections.

microbiology↗

bioRxiv2024

Hypusinated and unhypusinated isoforms of eIF5A exert distinct effects in models of pancreas development and function

Hypusination of eukaryotic translation initiation factor 5A (eIF5A) is essential for its role in translation elongation and termination. Although the function of hypusinated eIF5A (eIF5AHyp) in cellular proliferation is well-characterized, the role of its unhypusinated form (eIF5ALys) remains unclear. We hypothesized that eIF5ALys exerts independent effects on cellular replication and metabolism distinct from the loss of eIF5AHyp. To test this hypothesis, we utilized zebrafish and mouse models with inducible knockdowns of deoxyhypusine synthase (DHPS) and eIF5A to investigate their roles in cellular growth. Gene expression analysis via RNA sequencing and morphometric measurements of pancreas and {beta}-cell mass were performed to assess phenotypic changes and identify affected biological pathways. Loss of DHPS in zebrafish resulted in significant defects in pancreatic growth, accompanied by the dysregulation of mRNA translation, neurogenesis, and stress pathways. By contrast, knockdown of eIF5A had minimal impact on pancreas development, suggesting that the effects of DHPS loss are not solely due to the lack of eIF5AHyp. In mice, {beta} cell-specific deletion of DHPS impaired {beta} cell mass expansion and glucose tolerance, while eIF5A deletion had no statistically significant effects. These findings reveal an independent role for eIF5ALys in regulating developmental and functional responses and that a balance in levels of the hypusinated and unhypusinated isoforms of eIF5A may be pivotal in cellular phenotypes in health and disease.

cell biology↗

bioRxiv2024

Collective β-lactam resistance in Escherichia coli due to β-lactamase release upon cell death

Collective antibiotic resistance occurs when populations of bacteria survive antibiotic treatments that are lethal to individual bacteria, which affects the efficacy of drug therapies. An important mechanism of collective resistance against widely used {beta}-lactams is the production of drug-degrading {beta}-lactamases. Here, we integrate experiments with mathematical modeling to understand the collective survival of Escherichia coli challenged with cefotaxime. At near-lethal cefotaxime concentrations, we observe complex dynamics, involving initial biomass growth due to filamentation, followed by death, and subsequently growth recovery. We show that production of AmpC, a chromosomal {beta}-lactamase, is responsible for cefotaxime degradation, allowing the resumption of cell division in surviving filaments. The detoxification of the environment proceeds through CTX hydrolysis by AmpC in the periplasm of intact cells, as well as extracellularly after cell lysis. Our model predicts the recovery time from molecular parameters, and quantifies the relative roles of periplasmic and extracellular degradation for two strains of E. coli that differ in the degree of privatization of AmpC hydrolysis. Our findings suggest that {beta}-lactam survival of bacterial infections depends on a combination of intra- and extracellular {beta}-lactamase activity, which will likely vary among isolates.

microbiology↗

bioRxiv2023

Inflammation primes the kidney for recovery by activating AZIN1 A-to-I editing

The progression of kidney disease varies among individuals, but a general methodology to quantify disease timelines is lacking. Particularly challenging is the task of determining the potential for recovery from acute kidney injury following various insults. Here, we report that quantitation of post-transcriptional adenosine-to-inosine (A-to-I) RNA editing offers a distinct genome-wide signature, enabling the delineation of disease trajectories in the kidney. A well-defined murine model of endotoxemia permitted the identification of the origin and extent of A-to-I editing, along with temporally discrete signatures of double-stranded RNA stress and Adenosine Deaminase isoform switching. We found that A-to-I editing of Antizyme Inhibitor 1 (AZIN1), a positive regulator of polyamine biosynthesis, serves as a particularly useful temporal landmark during endotoxemia. Our data indicate that AZIN1 A-to-I editing, triggered by preceding inflammation, primes the kidney and activates endogenous recovery mechanisms. By comparing genetically modified human cell lines and mice locked in either A-to-I edited or uneditable states, we uncovered that AZIN1 A-to-I editing not only enhances polyamine biosynthesis but also engages glycolysis and nicotinamide biosynthesis to drive the recovery phenotype. Our findings implicate that quantifying AZIN1 A-to-I editing could potentially identify individuals who have transitioned to an endogenous recovery phase. This phase would reflect their past inflammation and indicate their potential for future recovery.

molecular biology↗

bioRxiv2023

Antigenic variation impacts gonococcal lifestyle and antibiotic tolerance by modulating interbacterial forces

Type 4 pili (T4P) are multifunctional filaments involved in adhesion, surface motility, colony formation, and horizontal gene transfer. These extracellular polymers are surface-exposed and, therefore, act as antigens. The human pathogen Neisseria gonorrhoeae uses pilin antigenic variation to escape immune surveillance, yet it is unclear how antigenic variation impacts other functions of T4P. Here, we addressed this question by replacing the major pilin of a laboratory strain of N. gonorrhoeae with pilins from clinical isolates. Structural predictions reveal filament features that vary from one strain to the next, with the potential to impact pilus:pilus interactions. Using a combination of laser tweezers, electron microscopy, and advanced image analysis, we explore the phenotypic consequences of these structural changes. We reveal that strains differing only in their major pilin sequence vary substantially in their attractive forces, which we attribute to variations in the stereochemistry of the T4P filament. In liquid culture, strongly interacting bacteria form colonies while weakly interacting bacteria retain a planktonic lifestyle. We show that lifestyle strongly affects growth kinetics and antibiotic tolerance. In the absence of external stresses, planktonic bacteria grow faster than colony-forming bacteria. In the presence of the antibiotics ceftriaxone and ciprofloxacin, the killing kinetics indicate strongly increased tolerance of colony-forming strains. We propose that pilin antigenic variation produces a mixed population containing variants optimized for growth, colonization, or survivability under external stress. Different environments select different variants, ensuring the survival and reproduction of the population as a whole. Significance statementNeisseria are highly successful human pathogens that continuously vary their surface structures to escape immune surveillance. Antigenic variation of the major pilin subunit causes variations of the structure of the Type 4 pilus, a surface exposed virulence factor. Here, we investigate the effect of pilin antigenic variation on bacterial lifestyle and tolerance against antibiotics. We find that pilin antigenic variation causes changes in the physical interactions between the bacteria, resulting in distinct aggregating and planktonic phenotypes. During treatment with antibiotics, aggregating strains are more tolerant than planktonic strains by an order of magnitude. Since tolerance tends to facilitate resistance development, pilin antigenic variation reduces the efficiency of antibiotic treatment.

microbiology↗

bioRxiv2023

Genome-wide transformation reveals extensive exchange across closely related Bacillus species

Bacterial transformation is an important mode of horizontal gene transfer that helps spread genetic material across species boundaries. Yet, the factors that pose barriers to genome-wide cross-species gene transfer are poorly characterized. Here, we develop a replacement accumulation assay to study the effects of genomic distance on transfer dynamics. Using Bacillus subtilis as recipient and various species of the genus Bacillus as donors, we find that the rate of orthologous replacement decreases exponentially with the divergence of their core genomes. We reveal that at least 96 % of the B. subtilis core genes are accessible to replacement by alleles from Bacillus spizizenii. For the more distantly related Bacillus atrophaeus, gene replacement events cluster at genomic locations with high sequence identity and preferentially replace ribosomal genes. Orthologous replacement also creates mosaic patterns between donor and recipient genomes, rearranges the genome architecture, and governs gain and loss of accessory genes. We conclude that cross-species gene transfer is dominated by orthologous replacement of core genes which occurs nearly unrestricted between closely related species. At a lower rate, the interplay between the core and accessory genomes gives rise to more complex genome dynamics.

genomics↗

bioRxiv2022

Collective polarization dynamics in gonococcal colonies

Membrane potential in bacterial systems has been shown to be dynamic and tightly related to survivability at the single cell level. However, little is known about spatio-temporal patterns of membrane potential in bacterial colonies and biofilms. Here, we discovered a switch from uncorrelated to collective dynamics within colonies formed by the human pathogen Neisseria gonorrhoeae. In freshly assembled colonies, polarization is heterogeneous with instances of transient and uncorrelated hyper- or depolarization of individual cells. As colonies reach a critical size, the polarization behaviour switches to collective dynamics: A hyperpolarized shell forms at the centre, travels radially outward, and halts several micrometres from the colony periphery. Once the shell has passed, we detect an influx of potassium correlated with depolarisation. Transient hyperpolarization also demarks the transition from volume to surface growth. By combining simulations and the use of an alternative electron acceptor for the respiratory chain, we provide strong evidence that local oxygen gradients shape the collective polarization dynamics. Finally, we show that within the hyperpolarized shell, tolerance against aminoglycoside antibiotics but not against {beta}-lactam antibiotics is increased, suggesting that depolarization instantaneously protects cells, while the protective effect of growth arrest does not set in immediately. These findings highlight that the polarization pattern can demark the differentiation into distinct subpopulations with different growth rates and antibiotic tolerance. Significance statementAt the level of single bacteria, membrane potential is surprisingly dynamic and transient hyperpolarization has been associated with increased death rate. Yet, little is known about the spatiotemporal dynamics of membrane polarization during biofilm development. Here, we reveal a discrete transition from uncorrelated to collective polarization dynamics within spherical colonies. Suddenly, a shell of hyperpolarized cells forms at the colony centre and hyperpolarization travels radially outward. In the wake of this shell, bacteria depolarize, reduce their growth rate, and become tolerant against antibiotics, indicating the onset of habitat diversity. Single cell live imaging and modelling link hyperpolarization to an oxygen gradient formed within the colonies. We anticipate that dynamical polarization patterns are tightly connected to biofilm differentiation in various bacterial species.

biophysics↗

bioRxiv2022

A neutrophil-B-cell axis governs disease tolerance during sepsis via Cxcr4

Sepsis is a life-threatening condition characterized by uncontrolled systemic inflammation and coagulation, leading to multi-organ failure. Therapeutic options to prevent sepsis-associated immunopathology remain scarce. Here, we established a model of long-lasting disease tolerance during severe sepsis, manifested by diminished immunothrombosis and organ damage in spite of a high pathogen burden. We found that, both neutrophils and B cells emerged as key regulators of tissue integrity. Enduring changes in the transcriptional profile of neutrophils, included upregulated Cxcr4 expression in protected, tolerant hosts. Neutrophil Cxcr4 upregulation required the presence of B cells, suggesting that B cells promoted tissue tolerance by suppressing tissue damaging properties of neutrophils. Finally, therapeutic administration of a Cxcr4 agonist successfully promoted tissue tolerance and prevented liver damage during sepsis. Our findings highlight the importance of a critical B-cell/neutrophil interaction during sepsis and establish neutrophil Cxcr4 activation as a potential means to promote disease tolerance during sepsis. SummaryWe show that a B cell/neutrophil interaction in the bone marrow facilitates tissue tolerance during severe sepsis. By affecting neutrophil Cxcr4 expression, B cells can impact neutrophil effector functions. Finally, therapeutic activation of Cxcr4 successfully promoted tissue tolerance and prevented liver damage during sepsis.

immunology↗

bioRxiv2021

Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo

The eIF2 initiation complex is central to maintaining a functional translation machinery. Extreme stress such as life-threatening sepsis exposes vulnerabilities in this tightly regulated system, resulting in an imbalance between the opposing actions of kinases and phosphatases on the main regulatory subunit eIF2. Here, we report that translation shutdown is a hallmark of established sepsis-induced kidney injury brought about by excessive eIF2 phosphorylation and sustained by blunted expression of the counterregulatory phosphatase subunit Ppp1r15a. We determined that the blunted Ppp1r15a expression persists because of the presence of an upstream open reading frame (uORF). Overcoming this barrier with genetic approaches enabled the derepression of Ppp1r15a, salvaged translation and improved kidney function in an endotoxemia model. We also found that the loss of this uORF has broad effects on the composition and phosphorylation status of the immunopeptidome that extended beyond the eIF2 axis. Collectively, our findings define the breath and potency of the highly conserved Ppp1r15a uORF and provide a paradigm for the design of uORF-based translation rheostat strategies. The ability to accurately control the dynamics of translation during sepsis will open new paths for the development of therapies at codon level precision.

physiology↗

bioRxiv2021

An integrative omics approach reveals posttranscriptional mechanisms underlying circadian temperature compensation

A defining property of circadian clocks is temperature compensation, characterized by the resilience of circadian free-running periods against changes in environmental temperature. As an underlying mechanism, the balance or critical reaction hypothesis have been proposed. While the former supposes a temperature-dependent balancing of reactions with opposite effects on circadian period, the latter assumes an insensitivity of certain critical period determining regulations upon temperature changes. Posttranscriptional regulations such as temperature-sensitive alternative splicing or phosphorylation have been described as underlying reactions. Here, we show that knockdown of cleavage and polyadenylation specificity factor subunit 6 (CPSF6), a key regulator of 3-end cleavage and polyadenylation, abolishes circadian temperature compensation in U-2 OS cells. We apply a combination of 3-End-RNA-seq and mass spectrometry-based proteomics to globally quantify changes in 3 UTR length as well as gene and protein expression between wild type and CPSF6 knock-down cells and their dependency on temperature. Analyzing differential responses upon temperature changes in wild type and CPSF6 knockdown cells reveals candidate genes underlying circadian temperature compensation. We identify that eukaryotic translation initiation factor 2 subunit 1 (EIF2S1) is among these candidates. EIF2S1 is known as a master regulator of cellular stress responses that additionally regulates circadian rhythms. We show that knockdown of EIF2S1 furthermore impairs temperature compensation, suggesting that the role of CPSF6 in temperature compensation may be mediated by its regulation of EIF2S1.

genomics↗

bioRxiv2021

Spatio-temporal dynamics of growth and death within spherical bacterial colonies

Bacterial growth within colonies and biofilms is heterogeneous. Local reduction of growth rates has been associated with tolerance against various antibiotics. However, spatial gradients of growth rates are poorly characterized in three-dimensional bacterial colonies. Here, we report two spatially resolved methods for measuring growth rates in bacterial colonies. As bacteria grow and divide, they generate a velocity field that is directly related to the growth rates. We derive profiles of growth rates from the velocity field and show that they are consistent with the profiles obtained by single cell counting. Using these methods, we reveal that even small colonies comprising a few thousand cells of the human pathogen Neisseria gonorrhoeae develop a steep gradient of growth rates within two generations. Furthermore, we show that stringent response decelerates growth inhibition at the colony centre. Based on our results, we suggest that aggregation-related growth inhibition can protect gonococci from external stresses even at early biofilm stages.

biophysics↗

bioRxiv2021

Alterations in protein translation and carboxylic acid catabolic processes in diabetic kidney disease

Diabetic kidney disease (DKD) remains the leading cause of end stage kidney disease despite decades of study. Alterations in the glomerulus and kidney tubules both contribute to the pathogenesis of DKD although the majority of investigative efforts have focused on the glomerulus. We sought to examine the differential expression signature of human DKD in the glomerulus and proximal tubule and corroborate our findings in the db/db mouse model of diabetes. A transcriptogram network analysis of RNAseq data from laser microdissected (LMD) human glomerulus and proximal tubule of DKD and reference nephrectomy samples revealed enriched pathways including rhodopsin-like receptors, olfactory signaling, and ribosome (protein translation) in the proximal tubule of human DKD biopsy samples. The translation pathway was also enriched in the glomerulus. Increased translation in diabetic kidneys was validated using polyribosomal profiling in the db/db mouse model of diabetes. Using single nuclear RNA sequencing (snRNAseq) of kidneys from db/db mice, we prioritized additional pathways identified in human DKD. The top overlapping pathway identified in the murine snRNAseq proximal tubule clusters and the human LMD proximal tubule compartment was carboxylic acid catabolism. Using ultra-performance liquid chromatography-mass spectrometry, the fatty acid catabolism pathway was also found to be dysregulated in the db/db mouse model. The Acetyl-CoA metabolite was down-regulated in db/db mice, aligning with the human differential expression of the genes ACOX1 and ACACB. In summary, our findings demonstrate that proximal tubular alterations in protein translation and carboxylic acid catabolism are key features in both human and murine DKD.

systems biology↗

bioRxiv2020

Antibiotics modulate attractive interactions in bacterial colonies affecting survivability under combined treatment

Biofilm formation protects bacteria from antibiotics. Very little is known about the response of biofilm-dwelling bacteria to antibiotics at the single cell level. Here, we developed a cell-tracking approach to investigate how antibiotics affect structure and dynamics of colonies formed by the human pathogen Neisseria gonorrhoeae. Antibiotics targeting different cellular functions enlarge the cell volumes and modulate within-colony motility. Focusing on azithromycin and ceftriaxone, we identify changes in type 4 pilus (T4P) mediated cell-to-cell attraction as the molecular mechanism for different effects on motility. By using strongly attractive mutant strains, we reveal that the survivability under ceftriaxone treatment depends on motility. Combining our results, we find that sequential treatment with azithromycin and ceftriaxone is synergistic. Taken together, we demonstrate that antibiotics modulate T4P-mediated attractions and hence cell motility and colony fluidity. Author SummaryAggregation into colonies and biofilms can enhance bacterial survivability under antibiotic treatment. Aggregation requires modulation of attractive forces between neighboring bacteria, yet the link between attraction and survivability is poorly characterized. Here, we quantify these attractive interactions and show that different antibiotics enhance or inhibit them. Live-cell tracking of single cells in spherical colonies enables us to correlate attractive interactions with single cell motility and colony fluidity. Even moderate changes in cell-to-cell attraction caused by antibiotics strongly impact on within-colony motility. Vice versa, we reveal that motility correlates with survivability under antibiotic treatment. In summary, we demonstrate a link between cellular attraction, colony fluidity, and survivability with the potential to optimize the treatment strategy of commonly used drug combinations.

microbiology↗

bioRxiv2020

Human Microbial Transplant Restores T Cell Cytotoxicity and Anti-Tumor Response to PD-L1 Blockade in Gnotobiotic Mice

Recent studies demonstrate that gut microbiota regulate tumor response to immune checkpoint blockade. Still, the mechanisms by which microbiota control tumor response to immunotherapy remain unclear. We colonized germ-free mice with cultured human-derived microbiota prior to tumor inoculation. While no human donor microbiota altered tumor growth, two distinct gut microbiota inhibited tumor response to anti-PD-L1. Colonization with non-responder microbiota led to reduced tumor immune cell infiltration and modified antigen presenting cell phenotype. RNA sequencing of tumor-infiltrating CD8+ T cells revealed enrichment for stem cell-like genes in non-responders and reduced effector-like expression conferring cytotoxic potential. Antibiotic depletion and microbiota transplant restored anti-PD-L1 response in non-responders, with expansion of effector cells and cytotoxicity. Concomitant blockade of TNF similarly improved response to anti-PD-L1 and increased cytotoxicity. These results demonstrate inhibitory roles for the microbiota in checkpoint blockade and reveal the potential for microbiota transplant and TNF blockade to overcome microbiota-mediated resistance.

immunology↗

bioRxiv2020

CITEseq analysis of non-small-cell lung cancer lesions reveals an axis of immune cell activation associated with tumor antigen load and TP53 mutations

Immunotherapy is becoming a mainstay in the treatment of NSCLC. While tumor mutational burden (TMB) has been shown to correlate with response to immunotherapy, little is known about the relation of the baseline immune response with the tumor genotype. Here, we profiled 35 early stage NSCLC lesions using multiscale single cell sequencing. Unsupervised clustering identified in a subset of patients a key cellular module consisting of PDCD1+ CXCL13+ activated T cells, IgG+ plasma cells, and SPP1+ macrophages, referred to as the lung cancer activation module (LCAMhi). Transcriptional data from two NSCLC cohorts confirmed a subset of patients with LCAMhi enrichment, which was independent of overall immune cell content. The LCAMhi module strongly correlated with TMB, expression of cancer testis antigens, and with TP53 mutations in smokers and non-smokers. These data establish LCAM as a key mode of immune cell activation associated with high tumor antigen load and driver mutations.

immunology↗