Biology subjects

Hoffmann, F.

Publications and source records attributed to Hoffmann, F..

15 recordsLinked to original sources

bioRxiv2026

A Perfect Soldier: the black soldier fly as a microbial-mediated physiological resilience model .

Understanding the complex interplay between a host, its diet, and its microbiome is crucial for comprehending an organisms health and adaptability. Diet impacts both the host and microbiome, which then influence each other. We used black soldier fly larvae (Hermetia illucens) as a model to investigate this tripartite interaction due to its resilience and bioconversion capabilities. We analyzed life-history traits and metatranscriptomics in larvae fed three diets: carbohydrate-rich, protein-rich, and balanced. Our results showed that dietary macronutrients correlated with shifts in the microbial community and gene expression. The carbohydrate-rich diet, in particular, led to increased microbial diversity and carbohydrate metabolism transcripts. However, this diet also negatively affected larval weight and development, suggesting potential host control over the microbiome. Overall, black soldier fly performance was highest on the balanced diet. This study highlights the black soldier flys resilience and its value as a model for exploring host-diet-microbe interactions. Significance StatementUnderstanding the intricate interplay between an organism, its diet, and its microbiome is fundamental to health and adaptability. This complex tripartite relationship, where dietary macronutrients influence microbial communities and their gene expression, while the host maintains control, is crucial for addressing global challenges from sustainable food systems to personalized medicine. Using the black soldier fly as a resilience model, our metatranscriptomic study reveals how specific dietary shifts impact both host and microbial gene expression, providing mechanistic insights into nutrient utilization and adaptability with broad implications for diverse biological systems, including animals and humans.

systems biology↗

bioRxiv2024

Synergistic cross-kingdom host cell damage between Candida albicans and Enterococcus faecalis

The fungus Candida albicans and the Gram-positive bacterium Enterococcus faecalis share mucosal niches in the human body. As opportunistic pathogens, both are found to expand population size during dysbiosis, and can cause severe systemic infections in susceptible individuals. Here, we show that the presence of C. albicans results in increased host cell damage by E. faecalis. Furthermore, E. faecalis aggravates oropharyngeal candidiasis in mice. Increased damage is mediated by enterococcal cytolysin, and involves both physical interaction and altered glucose availability. Physical interaction promotes accumulation of bacteria on host cells, facilitating contact of cytolysin with host cells. Glucose depletion by the metabolic activity of the fungus sensitized host cells to cytolysin. This work illustrates how a complex interplay between fungi and bacteria can result in detrimental consequences for the host.

microbiology↗

bioRxiv2024

Identification of a fungal antibacterial endopeptidase that modulates immune responses

Aspergillus fumigatus is a saprophytic fungus dwelling in soil and on decaying plant material, but also an opportunistic pathogen in immunocompromised patients. In its environmental niche, A. fumigatus faces competition from other microorganisms including bacteria. Here, we describe the discovery of the first secreted antibacterial protein in A. fumigatus. We identified a secreted fungal endopeptidase, designated CwhA, that cleaves peptidoglycan of Gram-positive bacteria at specific residues within the peptidoglycan stem peptide. Cleavage leads to bacterial lysis and the release of peptidoglycan cleavage products. Expression of cwhA is induced by the presence of bacteria. Furthermore, CwhA is highly abundant in murine lungs during invasive pulmonary aspergillosis and peptidoglycan cleavage products generated by CwhA stimulate cytokine production of human immune cells. Although CwhA does not affect human cells directly, this novel player in fungal-bacterial interactions could affect A. fumigatus infections by inhibiting Gram-positive bacteria in its vicinity, and modulating the immune system.

microbiology↗

bioRxiv2024

Activated Interferon Signaling Suppresses Age-Dependent Liver Cancer

Age is a major risk factor for liver cancer, as is the case for most adult human cancers. However, the underlying mechanisms are not well defined. A better understanding of the role of aging in liver and other cancers can facilitate approaches for risk assessment, early detection and prevention. We hypothesize that age-driven changes render aged liver more sensitive to oncogenic stress and hence tumorigenesis. To investigate how the liver changes with age, we documented the immune profile, transcriptome and epigenome of healthy livers from both young and aged mice, revealing pronounced alterations with aging. Notably, in aged hepatocytes, we identified heightened interferon (IFN) signaling, as well as simultaneous tumor suppressor and oncogene signaling at both bulk and single cell level, suggestive of an aged liver that is poised for neoplasia. To challenge this seemingly poised state, we employed adeno-associated virus (AAV)-mediated expression of a c-Myc oncogene in young and aged mouse liver hepatocytes in vivo. Analysis of aged hepatocytes expressing c-Myc revealed further elevated expression of IFN Stimulated Genes (ISGs). This ISG upregulation was evident in multiple models of oncogenic stress and transformation in older mice and also observed in aged humans with Metabolic dysfunction-Associated Steatohepatitis (MASH). We determined that Stat1 is both necessary and sufficient for the age specific elevated ISG expression in old wild type mice. Remarkably, inhibiting Jak/Stat signaling alongside ectopic c-Myc expression led to high-grade hepatocyte dysplasia and tumor formation, selectively in aged mice. Together, these results suggest that an aged liver is in a state of "precarious balance", due to concurrent activation of oncogenic and tumor suppressor pathways, but protected against neoplastic progression by IFN-signaling. Age-dependent activation of IFN signaling has been observed in many tissues and recent studies have demonstrated its detrimental consequences on aging, raising the question as to why IFN-signaling is activated during aging. We propose that aged tissues are intrinsically at higher risk of cancer and age-dependent activation of IFN-signaling is an adaptive process to protect from tumorigenesis, but one that also has maladaptive consequences.

cancer biology↗

bioRxiv2023

Multiomics atlas-assisted discovery of transcription factors enables specific cell state programming.

CD8+ T cells differentiate into diverse states that shape immune outcomes in cancer and chronic infection1-4. To systematically define the transcription factors (TFs) driving these states, we built a comprehensive atlas integrating transcriptional and epigenetic data across nine CD8+ T cell states and inferred TF activity profiles. Our analysis catalogued TF activity fingerprints, uncovering regulatory mechanisms governing selective cell state differentiation. Leveraging this platform, we focused on two transcriptionally similar but functionally opposing states critical in tumor and viral contexts: terminally exhausted T cells (TEXterm), which are dysfunctional5-8, and tissue-resident memory T cells (TRM), which are protective9-13. Global TF community analysis revealed distinct biological pathways and TF-driven networks underlying protective versus dysfunctional states. Through in vivo CRISPR screening integrated with single-cell RNA sequencing (in vivo Perturb-seq), we delineated several TFs that selectively govern TEXterm differentiation. We also identified HIC1 and GFI1 as shared regulators of TEXterm and TRM differentiation and KLF6 as a unique regulator of TRM. Importantly, we discovered novel TEXterm- selective TFs, including ZSCAN20 and JDP2, with no prior known function in T cells. Targeted deletion of these TFs enhanced tumor control and synergized with immune checkpoint blockade but did not interfere with TRM formation. Consistently, their depletion in human T cells reduces the expression of inhibitory receptors and improves effector function. By decoupling exhaustion TEX-selective from protective TRM programs, our platform enables more precise engineering of T cell states, accelerating the rational design of more effective cellular immunotherapies.

immunology↗

bioRxiv2022

Super-resolution STED imaging in the inner and outer whole-mount mouse retina

Since its invention in 1994, super-resolution microscopy has become a popular tool for advanced imaging of biological structures, allowing visualisation of subcellular structures at a spatial scale below the diffraction limit. Thus, it is not surprising that recently, different super-resolution techniques are being applied in neuroscience, e.g. to resolve the clustering of neurotransmitter receptors and protein complex composition in presynaptic terminals. Still, the vast majority of these experiments were carried out either in cell cultures or very thin tissue sections, while there are only a few examples of super-resolution imaging in thick (> ~50 m) biological samples. In that context, the mammalian whole-mount retina has rarely been studied with super-resolution microscopy. Here, we aimed at establishing a stimulated-emission-depletion (STED) microscopy protocol for imaging whole-mount retina. To this end, we developed sample preparation including horizontal slicing of retinal tissue, an immunolabeling protocol with STED-compatible fluorophores and optimised the STED microscopes settings. We labelled subcellular structures in somata, dendrites, and axons of retinal ganglion cells in the inner mouse retina. Under optimal conditions, we achieved a mean lateral spatial resolution of ~120 nm (using the full width of half-maximum as a proxy) for the thinnest filamentous structures in our preparation and a resolution enhancement of two or higher compared to conventional confocal images. When combined with horizontal slicing of the retina, these settings allowed us visualisation of putative GABAergic horizontal cell synapses in the outer retina with a similar resolution. Taken together, we successfully established a STED protocol for reliable super-resolution imaging in the whole-mount mouse retina, which enables investigating, for instance, protein complex composition and cytoskeletal ultrastructure at retinal synapses in health and disease.

neuroscience↗

bioRxiv2022

NeRFax: An efficient and scalable conversion from the internal representation to Cartesian space

MotivationAccurate modelling of protein ensembles requires sampling of a large number of 3D conformations. A number of sampling approaches that use internal coordinates have been proposed, yet poor performance in the conversion from internal to Cartesian coordinates limits their applicability. ResultsWe describe here NeRFax, an efficient method for the conversion from internal to Cartesian coordinates that utilizes the platform-agnostic JAX Python library. The relative benefit of NeRFax is demonstrated here, on peptide chain reconstruction tasks. Our novel approach offers 35-175x times performance gains compared to previous state-of-the-art methods, whereas >10,000x speedup is reported in a reconstruction of a biomolecular condensate of 1,000 chains. AvailabilityNeRFax has purely open-source dependencies and is available at https://github.com/PeptoneLtd/nerfax. Contactoliver@peptone.io

bioinformatics↗

bioRxiv2022

ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers

Intrinsically disordered proteins (IDP) are important for a broad range of biological functions and are involved in many diseases. An understanding of intrinsic disorder is key to develop compounds that target IDPs. Experimental characterization of IDPs is hindered by the very fact that they are highly dynamic. Computational methods that predict disorder from the amino acid sequence have been proposed. Here, we present ADOPT, a new predictor of protein disorder. ADOPT is composed of a self-supervised encoder and a supervised disorder predictor. The former is based on a deep bidirectional transformer, which extracts dense residue level representations from Facebooks Evolutionary Scale Modeling (ESM) library. The latter uses a database of NMR chemical shifts, constructed to ensure balanced amounts of disordered and ordered residues, as a training and test dataset for protein disorder. ADOPT predicts whether a protein or a specific region is disordered with better performance than the best existing predictors and faster than most other proposed methods (a few seconds per sequence). We identify the features which are relevant for the prediction performance and show that good performance can already gained with less than 100 features. ADOPT is available as a standalone package at https://github.com/PeptoneLtd/ADOPT.

bioinformatics↗

bioRxiv2022

A revised perspective on the evolution of troponin I and troponin T in vertebrates

The troponin (Tn) complex, responsible for the Ca2+ activation of striated muscle, is composed of three interacting protein subunits: TnC, TnI, and TnT, encoded by TNNC, TNNI, and TNNT genes. TNNI and TNNT are sister gene families, and in mammals the three TNNI paralogs (TNNI1, TNNI2, TNNI3), which encode proteins with tissue-specific expression, are each in close genomic proximity with one of the three TNNT paralogs (TNNT2, TNNT3, TNNT1, respectively). It has been widely presumed that all vertebrates broadly possess genes of these same three classes, although earlier work has overlooked jawless fishes (cyclostomes) and cartilaginous fishes (chimaeras, rays and sharks), which are distantly related to other jawed vertebrates. With a new phylogenetic and synteny analysis of a diverse array of vertebrates including these taxonomic groups, we define five distinct TNNI classes (TNNI1-5), with TNNI4 and TNNI5 being only present in non-mammalian vertebrates and typically found in tandem, and four classes of TNNT (TNNT1-4). These genes are located in four genomic loci that were generated by the 2R whole-genome duplication events. TNNI3, encoding cardiac TnI in mammals, was independently lost in cartilaginous and ray-finned fishes. Ray-finned fishes predominantly express TNNI1 in the heart. TNNI5 is highly expressed in shark hearts and contains an N-terminal extension similar to that of TNNI3 found in tetrapod hearts. Given that TNNI3 and TNNI5 are distantly related, this supports the hypothesis that the N-terminal extension may be an ancestral feature of vertebrate TNNI and not an innovation unique to TNNI3, as has been commonly believed.

evolutionary biology↗

bioRxiv2021

WDR31 is a novel ciliopathy protein displaying functional redundancy with GTPase-activating proteins ELMOD and RP2 in recruiting BBSome to cilium

The correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish and Caenorhabditis elegans reveals the role of WDR31 in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumulations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into cilia and exit from cilia are impacted. Furthermore, anterograde IFT in the middle segment travel at increased speed in wdr-31;rpi-2;elmd-1. Remarkably, a non-ciliary protein leaks into cilia of wdr-31;rpi-2;elmd-1 possible due to IFT defects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators.

genetics↗

bioRxiv2021

Whole genome duplications and the diversification of the Globin-X genes of vertebrates

The globin superfamily of vertebrate genes is a textbook example of how the interplay between local gene duplications, whole-genome duplications, and regulatory changes can facilitate the evolution of novel protein functions. Almost every vertebrate examined possesses copies of hemoglobin and myoglobin in their genomes, and both cytoglobin and neuroglobin are present in the vast majority of vertebrate genomes surveyed as well. The phylogenetic distribution of globin-E, globin-Y and globin-X (GbX), however, is more spotty, suggesting multiple independent gene losses. Globin-X is an enigmatic globin with a wide phyletic distribution that spans protostomes and deuterostomes. Unlike canonical globins such as hemoglobins and myoglobins, functional data suggest that GbX does not have a primary respiratory function. Instead, available evidence suggests that GbX may play a role in protecting cells from oxidative damage and in reducing nitrite and it is predicted to be bound to the cell membrane. Recently released genomes from key vertebrate taxa provide an excellent opportunity to address questions about the early stages of evolution of these genes in vertebrates. In the current study, we integrate bioinformatic, synteny and phylogenetic analyses to characterize the diversity of GbX genes in non-teleost ray-finned fishes, resolve relationships between the GbX genes of cartilaginous fish and the GbX genes of bony vertebrates, and demonstrate that the GbX genes of cyclostomes and gnathostomes have independent duplicative histories. Our study highlights the role that whole genome duplications (WGDs) have played in expanding the repertoire of genes in vertebrate genomes. Our results indicate that GbX paralogs have a remarkably high rate of retention following WGDs in comparison to other globin genes, and also provide an evolutionary framework for interpreting results of experiments that examine functional properties of GbX and patterns of tissue-specific expression. By identifying GbX genes products of different WGDs in the vertebrate tree of life, our results can guide the design of experimental work to explore whether gene duplicates that originate via WGDs have evolved novel functional properties or expression profiles relative to singleton or tandemly duplicated copies of GbX.

evolutionary biology↗

bioRxiv2020

Fitting side-chain NMR relaxation data using molecular simulations

Proteins display a wealth of dynamical motions that can be probed using both experiments and simulations. We present an approach to integrate side chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of these motions. The approach, which we term ABSURDer (Average Block Selection Using Relaxation Data with Entropy Restraints) can be used to find a set of trajectories that are in agreement with relaxation measurements. We apply the method to deuterium relaxation measurements in T4 lysozyme, and show how it can be used to integrate the accuracy of the NMR measurements with the molecular models of protein dynamics afforded by the simulations. We show how fitting of dynamic quantities leads to improved agreement with static properties, and highlight areas needed for further improvements of the approach.

biophysics↗

bioRxiv2019

Oxygenation properties of hemoglobin and the evolutionary origins of isoform multiplicity in an amphibious air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris)

Among the numerous lineages of teleost fish that have independently transitioned from obligate water-breathing to facultative air-breathing, evolved properties of hemoglobin (Hb)-O2 transport may have been shaped by the prevalence and severity of aquatic hypoxia (which influences the extent to which fish are compelled to switch to aerial respiration) as well as the anatomical design of air-breathing structures and the cardiovascular system. Here we examine the structure and function of Hbs in an amphibious, facultative air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris). We also characterized the genomic organization of the globin gene clusters of the species and we integrated phylogenetic and comparative genomic analyses to unravel the duplicative history of the genes that encode the subunits of structurally distinct mudskipper Hb isoforms (isoHbs). The B. pectinirostris isoHbs exhibit high intrinsic O2-affinities, similar to those of hypoxia-tolerant, water-breathing teleosts, and remarkably large Bohr effects. Genomic analysis of conserved synteny revealed that the genes that encode the -type subunits of the two main adult isoHbs are members of paralogous gene clusters that represent products of the teleost-specific whole-genome duplication. Experiments revealed no appreciable difference in the oxygenation properties of co-expressed isoHbs in spite of extensive amino acid divergence between the alternative -chain subunit isoforms. It therefore appears that the ability to switch between aquatic and aerial respiration does not necessarily require a division of labor between functionally distinct isoHbs with specialized oxygenation properties. Summary statementThe blue-spotted mudskipper routinely switches between aquatic and aerial respiration. This respiratory versatility is associated with properties of hemoglobin-oxygen transport that are similar to those found in hypoxia-adapted water-breathing fishes.

physiology↗

bioRxiv2019

The RAF oncogenes of vertebrates are ohnologs that derive from the two rounds of whole-genome duplications early in vertebrate evolution

The Rapidly Accelerated Fibrosarcoma (RAF) kinases are part of large group of serine/threonine-specific protein kinases that play important roles in cell differentiation and organism development. Animal RAF kinases are key connectors in the signaling cascade that links the small G protein RAS and the Mitogen-activated protein kinase phosphorylation pathway. Mutations in the RAF genes have been linked to a number of cancers including melanoma, lung cancer, colorectal cancer, thyroid cancer, and ovarian cancer. Most animals possess a single RAF gene, but vertebrates have three RAF genes in their genomes, named as A-, B-, and C-RAF, the latter also known as RAF-1. The emergence of the multiple copies of vertebrate RAFs is not well resolved, on the one hand, because of sequence and functional similarities, some authors speculate that vertebrate B-Raf is most closely related to the RAF genes of the fruit fly and Caenorhabditis elegans, whereas a competing hypothesis is that the A-, B- and C-RAF paralogs emerged from the two rounds of whole genome duplications that occurred early in the evolution of vertebrates. We applied a comparative approach grounded in synteny and phylogenetic analyses to evaluate these two scenarios. Our results are consistent with the hypothesis that the RAF genes of vertebrates are paralogs generated by whole genome duplications. Thus, the functional similarities between vertebrate B-RAF and invertebrate RAF probably reflect the retention of ancestral characters. Interestingly, data from the literature indicate that B-RAF is the paralog that associated with cancer more strongly, and also yields the most severe phenotypes when knocked out.

evolutionary biology↗

bioRxiv2019

Relocation of macrophages maintains the barrier function of the urothelium and protects against persistent infection

Macrophages perform essential functions during bacterial infections, such as phagocytosis of pathogens and elimination of neutrophils to reduce spreading of infection, inflammation and tissue damage. The spatial distribution of macrophages is critical to respond to tissue specific adaptations upon infections. Using a novel algorithm for correlative mass spectrometry imaging and state-of-the-art multiplex microscopy, we report here that macrophages within the urinary bladder are positioned in the connective tissue underneath the urothelium. Invading uropathogenic E.coli induced an IL-6-dependent CX3CL1 expression by urothelial cells, facilitating relocation of macrophages from the connective tissue into the urothelium. These cells phagocytosed UPECs and eliminated neutrophils to maintain barrier function of the urothelium, preventing persistent and recurrent urinary tract infection. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY GRAPHICAL ABSTRACT C_FIG_DISPLAY

immunology↗