bluuebunny/crossref_metadata_2025 huggingface dataset:
Colorectal cancer detection and treatment with engineered probiotics
Authors: Gurbatri Candice R. , Radford Georgette , Vrbanac Laura , Coker Courtney , Im Jong-won , Taylor Samuel R. , Jang YoungUk , Sivan Ayelet , Rhee Kyu , Saleh Anas A. , Chien Tiffany , Zandkarimi Fereshteh , Lia Ioana , Lannagan Tamsin RM , Wang Tongtong , Wright Josephine A , Thomas Elaine , Kobayashi Hiroki , Ng Jia Q , Lawrence Matt , Sammour Tarik , Thomas Michelle , Lewis Mark , Papanicolas Lito , Perry Joanne , Fitzsimmons Tracy , Kaazan Patricia , Lim Amanda , Marker Julie , Ostroff Cheri , Rogers Geraint , Arpaia Nicholas , Worthley Daniel L , Woods Susan L , Danino Tal
Published: April 2023

Bioengineered probiotics enable new opportunities to improve colorectal cancer (CRC) screening, prevention and treatment strategies. Here, we demonstrate the phenomenon of selective, long-term colonization of colorectal adenomas after oral delivery of probioticE. coliNissle 1917 (EcN) to a genetically-engineered murine model of CRC predisposition. We show that, after oral administration, adenomas can be monitored over time by recovering EcN from stool. We also demonstrate specific colonization of EcN to solitary neoplastic lesions in an orthotopic murine model of CRC. We then exploit this neoplasia-homing property of EcN to develop early CRC intervention strategies. To detect lesions, we engineer EcN to produce a small molecule, salicylate, and demonstrate that oral delivery of this strain results in significantly increased levels of salicylate in the urine of adenoma-bearing mice, in comparison to healthy controls. We also assess EcN engineered to locally release immunotherapeutics at the neoplastic site. Oral delivery to mice bearing adenomas, reduced adenoma burden by ∼50%, with notable differences in the spatial distribution of T cell populations within diseased and healthy intestinal tissue, suggesting local induction of robust anti-tumor immunity. Together, these results support the use of EcN as an orally-delivered platform to detect disease and treat CRC through its production of screening and therapeutic molecules.
In vitrolymph node-mimicking 3D model displays long-term T cell-dependent CLL proliferation and survival
Authors: Haselager Marco Vincent , van Driel Bianca Francisca , Perelaer Eduard , de Rooij Dennis , Lashgari Danial , Loos Remco , Kater Arnon P. , Moerland Perry D. , Eldering Eric
Published: April 2023

Chronic lymphocytic leukemia (CLL) cells are highly dependent on microenvironmental cells and signals. The lymph node (LN) is the critical site ofin vivoCLL proliferation and development of resistance to both chemotherapy and targeted agents. We present a new model that incorporates key aspects of the CLL LN which enables investigation of CLL cells in the context of a protective niche. We describe a 3Din vitroculture system utilizing ultra-low attachment (ULA) plates to create spheroids of CLL cells derived from peripheral blood (PB). Starting from CLL:T cell ratios as observed in LN samples, CLL activation was induced by either direct stimulation and/or indirectly via T cells. Compared to 2D cultures, 3D cultures promoted CLL proliferation in a T cell-dependent manner, and enabled expansion for up to 7 weeks, including the formation of follicle-like structures after several weeks of culture. Addition of LN-derived stromal cells further enhanced the proliferative capacity. This model enables high-throughput drug screening, of which we describe response to Btk inhibition, venetoclax resistance, and T cell-mediated cytotoxicity as examples. In summary, we present the first LN-mimickingin vitro3D culture for primary CLL, which enables readouts such as real-time drug screens, kinetic growth assays and spatial localization. This is the firstin vitroCLL system that allows testing of response and resistance to venetoclax and Btk inhibitors in the context of the tumor microenvironment, thereby opening up new possibilities for clinically useful applications.
Potential Immunomodulatory Role of Lead in Monocyte/Macrophage Differentiation
Authors: Nicholson Stacia M. , Schanne Francis A.X.
Published: April 2023

Lead (Pb) is a pernicious toxic metal and public health hazard, as it persists in the environment contaminating soil, food, and drinking water. Lead exerts its toxic effect on numerous organ systems, with the abundance of focus on the red blood cells and neurons of the hematopoietic and central nervous systems. However, insufficient investigation has been conducted on the effect of Pb on immune cells. In the current study, the toxic effects of Pb on immune cells of monocyte/macrophage lineage are described. Pb exerts a dose-dependent alteration in differentiation of monocyte/macrophage cells that retain some plasticity in development. Pb induces a bifurcation in differentiation of monocyte/macrophage cells, resulting in inhibition of osteoclastogenesis and induction of dendritic cells (DC). This phenomenon was demonstrated in RAW 264.7 murine monocyte/macrophage cell line and was consistent with response in rat bone-marrow derived macrophage (Sprague-Dawley). Pb primarily produced this response through induction of GM-CSF production and inhibition of p38/MAPK activity. Long-term exposure to physiologically relevant concentrations of Pb has the potential to modulate the immune system through altering the cell-lineage commitment of monocyte/macrophage lineage cells in a dose-dependent manner. Thus, Pb may function as an immunomodulator.
Pelvic spine reduction affects diet but not gill raker morphology in two polymorphic brook stickleback (Culaea inconstans) populations
Authors: Mee Jonathan A. , Yap Emily , Wuitchik Daniel M.
Published: April 2023

Pelvic spine polymorphism occurs in several species in the stickleback family (Gasterosteidae). Given the similar phenotypic polymorphisms in multiple stickleback species, we sought to determine the extent of parallelism in the ecological correlates of pelvic spine reduction. Based on a metabarcoding analysis of brook stickleback gut contents in two polymorphic populations, we found significant diet differences were associated with pelvic spine reduction, but we found no clear or consistent trend supporting a tendency for benthic feeding in pelvic-reduced brook stickleback. These results contrast with those found in threespine stickleback where pelvic spine reduction is often associated with a benthic diet. Hence, we found non-parallel consequences of spine polymorphism across species. Furthermore, a difference in gill raker morphology has been frequently observed between ecomorphs with differen diets in many fish species. But, we found no evidence of any difference in gill raker morphology associated with pelvic spine polymorphism in brook stickleback.
BNP-Track: A framework for multi-particle superresolved tracking
Authors: Xu Lance W.Q. , Sgouralis Ioannis , Kilic Zeliha , Presse Steve
Published: April 2023

When tracking fluorescently labeled molecules (termed "emitters") under widefield microscopes, point spread function overlap of neighboring molecules is inevitable in both dilute and especially crowded environments. In such cases, superresolution methods leveraging rare photophysical events to distinguish static targets nearby in space introduce temporal delays that compromise tracking. As we have shown in a companion manuscript, for dynamic targets, information on neighboring fluorescent molecules is encoded as spatial intensity correlations across pixels and temporal correlations in intensity patterns across time frames. We then demonstrated how we used all spatiotemporal correlations encoded in the data to achieve superresolved tracking. That is, we showed the results of full posterior inference over both the number of emitters and their associated tracks simultaneously and self-consistently through Bayesian nonparametrics. In this companion manuscript we focus on testing the robustness of our tracking tool, BNP-Track, across sets of parameter regimes and compare BNP-Track to competing tracking methods in the spirit of a prior Nature Methods tracking competition. We explore additional features of BNP-Track including how a stochastic treatment of background yields greater accuracy in emitter number determination and how BNP-Track corrects for point spread function blur (or "aliasing") introduced by intraframe motion in addition to propagating error originating from myriad sources (such as criss-crossing tracks, out-of-focus particles, pixelation, shot and detector noise, stochastic background) in posterior inference over emitter numbers and their associated tracks. While head-to-head comparison with other tracking methods is not possible (as competitors cannot simultaneously learn molecule numbers and associated tracks), we can give competing methods some advantages in order to perform approximate head-to-head comparison. We show that even under such optimistic scenarios, BNP-Track is capable of tracking multiple diffraction-limited point emitters conventional tracking methods cannot resolve thereby extending the superresolution paradigm to dynamical targets.
Circulating exosomes from Alzheimer’s disease suppress VE-cadherin expression and induce barrier dysfunction in recipient brain microvascular endothelial cell
Authors: Bei Jiani , Miranda-Morales Ernesto G. , Gan Qini , Qiu Yuan , Husseinzadeh Sorosh , Liew Jia Yi , Chang Qing , Krishnan Balaji , Gaitas Angelo , Yuan Subo , Felicella Michelle , Qiu Wei Qiao , Fang Xiang , Gong Bin
Published: April 2023

Background

Blood-brain barrier (BBB) breakdown is a component of the progression and pathology of Alzheimer’s disease (AD). BBB dysfunction is primarily caused by reduced or disorganized tight junction or adherens junction proteins of brain microvascular endothelial cell (BMEC). While there is growing evidence of tight junction disruption in BMECs in AD, the functional role of adherens junctions during BBB dysfunction in AD remains unknown. Exosomes secreted from senescent cells have unique characteristics and contribute to modulating the phenotype of recipient cells. However, it remains unknown if and how these exosomes cause BMEC dysfunction in AD.

Objectives

This study aimed to investigate the potential roles of AD circulating exosomes and their RNA cargos in brain endothelial dysfunction in AD.

Methods

We isolated exosomes from sera of five cases of AD compared with age- and sex-matched cognitively normal controls using size-exclusion chromatography technology. We validated the qualities and particle sizes of isolated exosomes with nanoparticle tracking analysis and atomic force microscopy. We measured the biomechanical natures of the endothelial barrier of BMECs, the lateral binding forces between live BMECs, using fluidic force miscopy. We visualized the paracellular expressions of the key adherens junction protein VE-cadherin in BMEC cultures and a 3D BBB model that employs primary human BMECs and pericytes with immunostaining and evaluated them using confocal microscopy. We also examined the VE-cadherin signal in brain tissues from five cases of AD and five age- and sex-matched cognitively normal controls.

Results

We found that circulating exosomes from AD patients suppress the paracellular expression levels of VE-cadherin and impair the barrier function of recipient BMECs. Immunostaining analysis showed that AD circulating exosomes damage VE-cadherin integrity in a 3D model of microvascular tubule formation. We found that circulating exosomes in AD weaken the BBB depending on the RNA cargos. In parallel, we observed that microvascular VE-cadherin expression is diminished in AD brains compared to normal controls.

Conclusion

Usingin vitroandex vivomodels, our study illustrates that circulating exosomes from AD patients play a significant role in mediating the damage effect on adherens junction of recipient BMEC of the BBB in an exosomal RNA-dependent manner. This suggests a novel mechanism of peripheral senescent exosomes for AD risk.
Detecting Anomalous Proteins Using Deep Representations
Authors: Michael-Pitschaze Tomer , Cohen Niv , Ofer Dan , Hoshen Yedid , Linial Michal
Published: April 2023

Many advances in biomedicine can be attributed to identifying unusual proteins and genes. Many of these proteins’ unique properties were discovered by manual inspection, which is becoming infeasible at the scale of modern protein datasets. Here, we propose to tackle this challenge using anomaly detection methods that automatically identify unexpected properties. We adopt a state-of-the-art anomaly detection paradigm from computer vision, to highlight unusual proteins. We generate meaningful representations without labeled inputs, using pretrained deep neural network models. We apply these protein language models (pLM) to detect anomalies in function, phylogenetic families, and segmentation tasks. We compute protein anomaly scores to highlight human prion-like proteins, distinguish viral proteins from their host proteome, and mark non-classical ion/metal binding proteins and enzymes. Other tasks concern segmentation of protein sequences into folded and unstructured regions. We provide candidates for rare functionality (e.g., prion proteins). Additionally, we show the anomaly score is useful in 3D folding-related segmentation. Our novel method shows improved performance over strong baselines and has objectively high performance across a variety of tasks. We conclude that the combination of pLM and anomaly detection techniques is a valid method for discovering a range of global and local protein characteristics.
SFyNCS detects oncogenic fusions involving non-coding sequences in cancer
Authors: Zhong Xiaoming , Luan Jingyun , Yu Anqi , Lee-Hassett Anna , Miao Yuxuan , Yang Lixing
Published: April 2023

Fusion genes are well-known cancer drivers. However, very few known oncogenic fusions involve non-coding sequences. We develop SFyNCS with superior performance to detect fusions of both protein-coding genes and non-coding sequences from transcriptomic sequencing data. We validate fusions using somatic structural variations detected from the genomes. This allows us to comprehensively evaluate various fusion detection and filtering strategies and parameters. We detect 165,139 fusions in 9,565 tumor samples across 33 tumor types in the Cancer Genome Atlas cohort. Among them, 72% of the fusions involve non-coding sequences and many are recurrent. We discover two long non-coding RNAs recurrently fused with various partner genes in 32% of dedifferentiated liposarcomas and experimentally validated the oncogenic functions in mouse model.
Implementation considerations for deep learning with diffusion MRI streamline tractography
Authors: Cai Leon Y. , Lee Ho Hin , Newlin Nancy R. , Kim Michael E. , Moyer Daniel , Rheault François , Schilling Kurt G. , Landman Bennett A.
Published: April 2023

One area of medical imaging that has recently experienced innovative deep learning advances is diffusion MRI (dMRI) streamline tractography with recurrent neural networks (RNNs). Unlike traditional imaging studies which utilize voxel-based learning, these studies model dMRI features at points in continuous space off the voxel grid in order to propagate streamlines, or virtual estimates of axons. However, implementing such models is nontrivial, and an open-source implementation is not yet widely available. Here, we describe a series of considerations for implementing tractography with RNNs and demonstrate they allow one to approximate a deterministic streamline propagator with comparable performance to existing algorithms. We release this trained model and the associated implementations leveraging popular deep learning libraries. We hope the availability of these resources will lower the barrier of entry into this field, spurring further innovation.
Automated tumor immunophenotyping predicts clinical benefit from anti-PD-L1 immunotherapy
Authors: Li Xiao , Eastham Jeffrey , Giltnane Jennifer M. , Zou Wei , Zijlstra Andries , Tabatsky Evgeniy , Banchereau Romain , Chang Ching-Wei , Nabet Barzin , Patil Namrata , Molinero Luciana , Chui Steve , Peterson Maureen , Lau Shari , Rangell Linda , Waumans Yannick , Kockx Mark , Orlova Darya , Koeppen Hartmut
Published: April 2023

Background

Cancer immunotherapy has transformed the clinical approach to patients with malignancies as profound benefits can be seen in a subset of patients. To identify this subset, biomarker analyses increasingly focus on phenotypic and functional evaluation of the tumor microenvironment (TME) to determine if density, spatial distribution, and cellular composition of immune cell infiltrates can provide prognostic and/or predictive information. Attempts have been made to develop standardized methods to evaluate immune infiltrates in the routine assessment of certain tumor types; however, broad adoption of this approach in clinical decision-making is still missing.

Methods

We developed approaches to categorize solid tumors into “Desert”, “Excluded” and “Inflamed” types according to the spatial distribution of CD8+ immune effector cells to determine the prognostic and/or predictive implications of such labels. To overcome the limitations of this subjective approach we incrementally developed four automated analysis pipelines of increasing granularity and complexity for density and pattern assessment of immune effector cells.

Results

We show that categorization based on “manual” observation is predictive for clinical benefit from anti-programmed cell death ligand-1 (PD-L1) therapy in two large cohorts of patients with non-small cell lung cancer (NSCLC) or triple-negative breast cancer (TNBC). For the automated analysis we demonstrate that a combined approach outperforms individual pipelines and successfully relates spatial features to pathologist-based read-outs and patient response to therapy.

Conclusions

Our findings suggest tumor immunophenotype (IP) generated by automated analysis pipelines should be evaluated further as potential predictive biomarkers for cancer immunotherapy.

What is already known on this topic

Clinical benefit from checkpoint inhibitor-targeted therapies is realized only in a subset of patients. Robust biomarkers to identify patients who may respond to such therapies are needed.

What this study adds

We have developed manual and automated approaches to categorize tumors into immunophenotypes based on the spatial distribution of CD8+ T effector cells that predict clinical benefit from anti-PD-L1 immunotherapy for patients with advanced non-small cell lung cancer or triple-negative breast cancer.

How this study might affect research, practice or policy

Tumor immunophenotypes should be further validated as predictive biomarker for checkpoint inhibitor-targeted therapies in prospective clinical studies.
Untangling the mechanisms of pulmonary hypertension-induced right ventricular stiffening in a large animal model
Authors: Kakaletsis Sotirios , Malinowski Marcin , Mathur Mrudang , Sugerman Gabriella P. , Lucy Jeff J. , Snider Caleb , Jazwiec Tomasz , Bersi Matthew , Timek Tomasz A. , Rausch Manuel K.
Published: April 2023

Background

Pulmonary arterial hypertension (PHT) is a devastating disease with low survival rates. In PHT, chronic pressure overload leads to right ventricle (RV) remodeling and stiffening; thus, impeding diastolic filling and ventricular function. Multiple mechanisms contribute to RV stiffening, including wall thickening, microstructural disorganization, and myocardial stiffening. The relative importance of each mechanism is unclear. Our objective is to use a large animal model as well as imaging, experimental, and computational approaches to untangle these mechanisms.

Methods

We induced PHT in eight sheep via pulmonary artery banding. After eight weeks, the hearts underwent anatomic and diffusion tensor MRI to characterize wall thickening and microstructural disorganization. Additionally, myocardial samples underwent histological and gene expression analyses to quantify compositional changes and mechanical testing to quantify myocardial stiffening. All findings were compared to 12 control animals. Finally, we used computational modeling to disentangle the relative importance of each stiffening mechanism.

Results

First, we found that the RVs of PHT animals thickened most at the base and the free wall. Additionally, we found that PHT induced excessive collagen synthesis and microstructural disorganization, consistent with increased expression of fibrotic genes. We also found that the myocardium itself stiffened significantly. Importantly, myocardial stiffening correlated significantly with excess collagen synthesis. Finally, our model of normalized RV pressure-volume relationships predicted that myocardial stiffness contributes to RV stiffening significantly more than other mechanisms.

Conclusions

In summary, we found that PHT induces wall thickening, microstructural disorganization, and myocardial stiffening. These remodeling mechanisms were both spatially and directionally dependent. Using modeling, we show that myocardial stiffness is the primary contributor to RV stiffening. Thus, myocardial stiffening may be an important predictor for PHT progression. Given the significant correlation between myocardial stiffness and collagen synthesis, collagen-sensitive imaging modalities may be useful for non-invasively estimating myocardial stiffness and predicting PHT outcomes.
Resolvin D2-GPR18 Signaling on Myeloid Cells Limits Plaque Necrosis
Authors: Lipscomb Masharh , Walis Sean , Marinello Michael , Mena Hebe Agustina , Spite Matthew , Fredman Gabrielle
Published: April 2023

Introduction/Objective

Dysregulated inflammation-resolution programs are associated with atherosclerosis progression. Inflammation-resolution is in part mediated by Resolvins, including Resolvin D2 (RvD2). RvD2, which activates a G-protein coupled receptor (GPCR) called GPR18, limits plaque progression. Cellular targets of RvD2 are not known.

Approach and Results

Here we developed humanized GPR18 floxed (“fl/fl”) and a myeloid (Lysozyme M Cre) GPR18 knockout (mKO) mouse. We functionally validated this model by assessing efferocytosis in bone marrow derived macrophages (BMDMs) and found that RvD2 enhanced efferocytosis in the fl/fl, but not in the mKO BMDMs. We employed two different models to evaluate the role of GPR18 in atherosclerosis. We first used the PCSK9-gain of function approach and found increased necrosis in the plaques of the mKO mice compared with fl/fl mice. Next, we performed a bone marrow transfer of fl/fl or mKO bone marrow intoLdlr-/-recipients. For these experiments, we treated each genotype with either Veh or RvD2 (25 ng/mouse, 3 times/week for 3 weeks). Myeloid loss of GPR18 resulted in significantly more necrosis and cleaved caspase-3+cells compared with fl/fl transplanted mice. RvD2 treatment decreased plaques necrosis and cleaved caspase-3+cells in fl/fl, but not in the mKO transplanted mice.

Conclusions

These results are the first to suggest a causative role for endogenous RvD2 signaling on myeloid cells in limiting plaque necrosis. Moreover, these results provide a mechanistic basis for RvD2 as a therapy limiting plaque necrosis.
Assessment of the normal cell contamination impact on tumour sample analysed with SNP arrays: The signal confusion nightmare
Authors: Poulet Christophe B. , Swingland James T. , Botta Vincent , Robe Pierre , Herens Christian , Turkheimer Federico , Bours Vincent
Published: April 2023

Recent advances in high-throughput technologies enable a more comprehensive interpretation of the tumour evolution through the study of the intra-tumour heterogeneity. Several algorithms, however, often relies on the use of models that described the top of the iceberg regarding the stromal contamination of the samples, making diagnosis difficult to assess. Indeed, such as radio wave receivers, tools to analyse high-throughput technologies data, are used to enable the discrimination between multiple signals differing in frequencies. However, such tools often look at the average frequency more than distinct signals, leading to analyse a confused signal. This confusion could dramatically lead to a mis–interpretation of the real data, especially during the diagnosis as it relies on the choice of a unique scenario among many others. Here, we describe how this signal confusion occurs in the most classical DNA microarray analysis of tumours and we provide statistics to determine how many other possible scenario can lead the same signals, in order to improve the robustness of pigeon hole logic based analysis. Based on simulations, where a unique tumour population was diluted by an increasing gradient of normal cells, we underline the causes and consequences of such signal confusion for up to five allelic copies. Despite the removal of all technical biaises and background noise, we show how the signal confusion remains systematically present in the commonly used DNA microarray analysis, especially for the genotypes AAAAB, AAAB and AAB for copy numbers 5, 4 and 3 respectively, as well as their symmetric combinations for the B allele.
PPIAT: Target Mass Spectrometry-based Protein-Protein Interaction Analytics Tool
Authors: Park Jongham , Son Ahrum , Kim Hyunsoo
Published: April 2023

Motivation

The formation of protein networking is critical for understanding the biological functions of proteins and the underlying mechanisms of disease. To gain insights into target proteins that interact with a particular disease, we need to profiling all the proteins involved in the disease beforehand. However, the profiling results may not necessarily match with an experimental target protein. Therefore, it is necessary to identify physical protein-protein interactions (PPIs) using various methods. The cross-linking mass spectrometry (XL-MS) method is a representative approach to identify physical interactions between proteins, but there are many challenges in calculating theoretical mass values for application to target mass spectrometry.

Results

The research team developed PPIAT, which integrates information on reviewed human proteins, protein-protein interactions, cross-linkers, enzymes, and modifications. All functions are available for free on the web application.

Availability and implementation

The PPIAT is available atwww.ppiat.cnu.ac.kr

Contact

kimlab@cnu.ac.kr
Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response
Authors: Chen Jonathan H. , Nieman Linda T. , Spurrell Maxwell , Jorgji Vjola , Richieri Peter , Xu Katherine H. , Madhu Roopa , Parikh Milan , Zamora Izabella , Mehta Arnav , Nabel Christopher S. , Freeman Samuel S. , Pirl Joshua D. , Lu Chenyue , Meador Catherine B. , Barth Jaimie L. , Sakhi Mustafa , Tang Alexander L. , Sarkizova Siranush , Price Colles , Fernandez Nicolas F. , Emanuel George , He Jiang , Raay Katrina Van , Reeves Jason W. , Yizhak Keren , Hofree Matan , Shih Angela , Sade-Feldman Moshe , Boland Genevieve M. , Pelka Karin , Aryee Martin , Korsunsky Ilya , Mino-Kenudson Mari , Gainor Justin F. , Hacohen Nir
Published: April 2023

The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially-localized multicellular ‘immunity hubs’ defined by expression of the T cell-attracting chemokinesCXCL10/CXCL11and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens, and found that they were associated with beneficial responses to PD-1-blockade. Immunity hubs were enriched for many interferon-stimulated genes, T cells in multiple differentiation states, andCXCL9/10/11+ macrophages that preferentially interact with CD8 T cells. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcomes, distinct from mature tertiary lymphoid structures, and enriched for stem-like TCF7+PD-1+ CD8 T cells and activatedCCR7+LAMP3+ dendritic cells, as well as chemokines that organize these cells. These results elucidate the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model
Authors: Han Yunheng , Molloy Erin K.
Published: April 2023

Cancer progression and treatment can be informed by reconstructing its evolutionary history from tumor cells. However, traditional methods assume the input data are error-free and the output tree is fully resolved. These assumptions are challenged in tumor phylogenetics because single-cell sequencing produces sparse, error-ridden data and because tumors evolve clonally. Here, we find that methods based on quartets (four-leaf, unrooted trees) withstand these barriers. We consider a popular tumor phylogenetics model, in which mutations arise on a (highly unresolved) tree and then (unbiased) errors and missing values are introduced. Quartets are implied by mutations present in two cells and absent from two cells. Our main result is that the most probable quartet identifies the unrooted model tree on four cells. This motivates seeking a tree such that the number of quartets shared between it and the input mutations is maximized. We prove an optimal solution is a consistent estimator of the unrooted cell lineage tree; this guarantee includes the case where the model tree is highly unresolved, with error defined as the number of false negative branches. Lastly, we outline how quartet-based methods might be employed when there are copy number aberrations and other challenges specific to tumor phylogenetics.
tauFisher accurately predicts circadian time from a single sample of bulk and single-cell transcriptomic data
Authors: Duan Junyan , Ngo Michelle N. , Karri Satya Swaroop , Tsoi Lam C. , Gudjonsson Johann E. , Shahbaba Babak , Lowengrub John , Andersen Bogi
Published: April 2023

As the circadian clock regulates fundamental biological processes, disrupted clocks are often observed in patients and diseased tissues. Determining the circadian time of the patient or the tissue of focus is essential in circadian medicine and research. Here we present tau-Fisher, a computational pipeline that accurately predicts circadian time from a single transcriptomic sample by finding correlations between rhythmic genes within the sample. We demonstrate tauFisher’s out-standing performance in both bulk and single-cell transcriptomic data collected from multiple tissue types and experimental settings. Application of tauFisher at a cell-type level in a single-cell RNA-seq dataset collected from mouse dermal skin implies that greater circadian phase heterogeneity may explain the dampened rhythm of collective core clock gene expression in dermal immune cells compared to dermal fibroblasts. Given its robustness and generalizability across assay platforms, experimental setups, and tissue types, as well as its potential application in single-cell RNA-seq data analysis, tauFisher is a promising tool that facilitates circadian medicine and research.
A photoreceptor-based hydrogel with red light-responsive reversible sol-gel transition as transient cellular matrix
Authors: Hörner Maximilian , Becker Jan , Bohnert Rebecca , Baños Miguel , Jerez-Longres Carolina , Mühlhäuser Vanessa , Härrer Daniel , Wong Tin Wang , Meier Matthias , Weber Wilfried
Published: April 2023

Hydrogels with adjustable mechanical properties have been engineered as matrices for mammalian cells and allow the dynamic, mechano-responsive manipulation of cell fate and function. Recent research yielded hydrogels, where biological photoreceptors translated optical signals into a reversible and adjustable change in hydrogel mechanics. While their initial application provided important insights into mechanobiology, broader implementation is limited by a small dynamic range of addressable stiffness. Here, we overcome this limitation by developing a photoreceptor-based hydrogel with reversibly adjustable stiffness from 800 Pa to the sol state. The hydrogel is based on star-shaped polyethylene glycol, functionalized with the red/far-red light photoreceptor phytochrome B (PhyB), or phytochrome-interacting factor 6 (PIF6). Upon illumination with red light, PhyB heterodimerizes with PIF6, thus crosslinking the polymers and resulting in gelation. However, upon illumination with far-red light, the proteins dissociate and trigger a complete gel-to-sol transition. We comprehensively characterize the hydrogel’s light-responsive mechanical properties and apply it as reversible extracellular matrix for the spatiotemporally controlled deposition of mammalian cells within a microfluidic chip. We anticipate that this technology will open new avenues for the site- and time-specific positioning of cells and will contribute to overcome spatial restrictions.
Dolphin social phenotypes vary in response to food availability but not the North Atlantic Oscillation index
Authors: Fisher David N. , Cheney Barbara J.
Published: April 2023

Social behaviours can allow individuals to flexibly respond to environmental change, potentially buffering adverse effects. However, individuals may respond differently to the same environmental stimulus, complicating predictions for population-level response to environmental change. Here we show that bottlenose dolphins (Tursiops truncatus) alter their social behaviour at yearly and monthly scales in response to a proxy for food availability (salmon abundance) but do not respond to variation in a proxy for climate (the North Atlantic Oscillation index). There was also individual variation in plasticity for gregariousness and connectedness to distant parts of the social network, although these traits showed limited repeatability. In contrast, individuals showed consistent differences in clustering with their immediate social environment at the yearly scale but no individual variation in plasticity for this trait at either time scale. These results indicate that social behaviour in free-ranging cetaceans can be highly resource dependent with individuals increasing their connectedness over short timescales but possibly reducing their wider range of connection at longer timescales. Some social traits showed more individual variation in plasticity or mean behaviour than others, highlighting how predictions for the responses of populations to environmental variation must consider the type of individual variation present in the population.
Targeting Myeloma Essential Genes using NOT Gated CAR- T Cells, a computational approach
Authors: Walker Ieuan G , Roy James , Anderson Georgina , Lopez Jose Guerrereo , Chapman Michael A
Published: April 2023

Sensitive cell surface proteomics studies have shown that the number of completely tumour-specific targets for adoptive cellular immunotherapy is extremely low. Even approved CAR T-cell targets appear to have expression in the central nervous system, leading to long-term neurological complications. We propose that this toxicity could be significantly improved by adoption of NOT-gates, which have been shown to limit CAR T-cell activity against healthy tissue expressing a second target that is absent on the tumour. Furthermore, the approach could also target essential, but non-specific proteins on tumour cells. The use of a NOT gate confers the specificity, whilst targeting the essential protein limits antigen escape. Here we explore the feasibility of such an approach for CAR T-cell targeting of primary myeloma. We show that none of the 45 most essential proteins are unique to the myeloma cell. However, whilst widely expressed, one of the most important proteins for myeloma cell survival, the transferrin receptor, could safely be targeted by a NOT-gate approach. Exploring co-expression patterns demonstrate 26 proteins that are not expressed on myeloma cells, but which are coexpressed with the transferrin receptor in all healthy tissues. We also describe a web app, NOTATER, which can be used by scientists with no bioinformatic capabilities to explore potential NOT-gate combinations in myeloma.
Inhibition of miR-214 expression by small molecules alleviates head and neck cancer metastasis by targeting ALCAM/TFAP2 signaling
Authors: Agarwal Anshu , Kansal Vikash , Farooqi Humaira , Prasad Ram , Singh Vijay Kumar
Published: April 2023

Predominantly, head and neck cancer (HNC) is considered a regional disease and develops in the nasal cavity, oral cavity, tongue, pharynx, and larynx. In the advanced stage, the HNC spread into distant organs. By the time head and neck cancer diagnosed, the estimated metastasis is occurred in 10-40% cases. The most important vital organs affected by distant metastasis are the lungs, bones, and liver. Despite several advancements in chemotherapies, no significant changes are observed as 5-year survival rate remains the same. Therefore, it is crucial to decipher molecular mechanisms contributing to the metastatic dissemination of head and neck cancer. Here, we tested a novel ALCAM/TFAP2 signaling by targeting multidisciplinary miR-214 expression in head and cancer cells. Our results revealed that HNC cell lines (CAL27, SCC-9, SCC-4, and SCC-25) exhibit higher expression of miR-214 compared with normal human bronchial epithelial (NHBE) cells. Higher expression of miR-214 drives the invasive potential of these cell lines. Down-regulation of miR-214 in CAL27 and SCC-9 cells either using an anti-miR-214 inhibitor (50nM) or a small molecule of green tea (EGCG) inhibited cell invasion. Treating CAL27 and SCC-9 cells with EGCG also reduces ALCAM expression, a key activated leukocyte cell adhesion molecule, potentially blocking mesenchymal phenotype. Dietary administration of EGCG significantly inhibits distant metastasis of SCC-9 cells into the lungs, liver, and kidneys. Our results also demonstrate that the reduction of miR-214 expression influences in vitro cell movement and extravasation, as evident by reduced CD31 expression, a neovascularization marker. Together, these studies suggest that identifying bioactive molecules that can inhibit distant metastasis regulated by the miRNAs may provide potent interventional approaches and a better understanding of the complex functions of miRNAs and their therapeutic targets for clinical application.
Hepatocyte Dedifferentiation Profiling In Alcohol-Related Liver Disease Identifies CXCR4 As A Driver Of Cell Reprogramming
Authors: Aguilar-Bravo Beatriz , Ariño Silvia , Blaya Delia , Pose Elisa , Martinez García de la Torre Raquel A. , Latasa María U , Martínez-Sánchez Celia , Zanatto Laura , Sererols-Viñas Laura , Cantallops Paula , Affo Silvia , Coll Mar , Thillen Xavier , Dubuquoy Laurent , Avila Matías A , Argemi Josep Maria , Paz Arantza Lamas , Nevzorova Yulia A. , Cubero Javier , Bataller Ramon , Lozano Juan José , Ginès Pere , Mathurin Philippe , Sancho-Bru Pau
Published: April 2023

Background and Aims

Loss of hepatocyte identity is associated with impaired liver function in alcohol-related hepatitis (AH). In this context, hepatocyte dedifferentiation gives rise to cells with a hepatobiliary (HB) phenotype expressing biliary and hepatocytes markers and showing immature features. However, the mechanisms and the impact of hepatocyte dedifferentiation in liver disease are poorly understood.

Methods

HB cells and ductular reaction (DR) cells were quantified and microdissected from liver biopsies from patients with alcohol-related liver disease (ALD). Hepatocyte- specific overexpression or deletion of CXCR4, and CXCR4 pharmacological inhibition were assessed in mouse liver injury. Patient-derived and mouse organoids were generated to assess plasticity.

Results

Here we show that HB and DR cells are increased in patients with decompensated cirrhosis and AH, but only HB cells correlate with poor liver function and patients’ outcome. Transcriptomic profiling of HB cells revealed the expression of biliary-specific genes and a mild reduction of hepatocyte metabolism. Functional analysis identified pathways involved in hepatocyte reprogramming, inflammation, stemness and cancer gene programs. CXCR4 pathway was highly enriched in HB cells, and correlated with disease severity and hepatocyte dedifferentiation.In vitro, CXCR4 was associated with biliary phenotype and loss of hepatocyte features. Liver overexpression of CXCR4 in chronic liver injury decreased hepatocyte specific gene expression profile and promoted liver injury. CXCR4 deletion or its pharmacological inhibition ameliorated hepatocyte dedifferentiation and reduced DR and fibrosis progression.

Conclusions

This study shows the association of hepatocyte dedifferentiation with disease progression and poor outcome in AH. Moreover, the transcriptomic profiling of HB cells revealed CXCR4 as a new driver of hepatocyte-to-biliary reprogramming and as a potential therapeutic target to halt hepatocyte dedifferentiation in AH.

Lay summary

Here we describe that hepatocyte dedifferentiation is associated with disease severity and a reduced synthetic capacity of the liver. Moreover, we identify the CXCR4 pathway as a driver of hepatocyte dedifferentiation and as a therapeutic target in alcohol-related hepatitis.
Hydramorphogenesis as phase-transition dynamics
Authors: Agam Oded , Braun Erez
Published: April 2023

We utilize whole-bodyHydraregeneration from a small tissue segment to develop a physics framework for animal morphogenesis. Introducing experimental controls over this process, an external electric field and a drug that blocks gap junctions, allows us to characterize the essential step in the morphological transition - from a spherical shape to an elongated spheroid. We find that spatial fluctuations of the Ca2+distribution in theHydra’stissue drive this transition and construct a field-theoretic model that explains the morphological transition as a first-order-like phase transition resulting from the coupling of the Ca2+field and the tissue’s local curvature. Various predictions of this model are verified experimentally.
Combination CDC-like kinase inhibition (CLK)/Dual-specificity tyrosine-regulated kinase (DYRK) and taxane therapy inCTNNB1-mutated endometrial cancer
Authors: Corr Bradley R , Moroney Marisa R , Woodruff Elizabeth , Watson Zachary L , Jordan Kimberly R. , Danhorn Thomas , Bailey Courtney , Wolsky Rebecca J , Bitler Benjamin G
Published: April 2023

SM08502 (cirtuvivint) is a novel pan CDC-like kinase (CLK) and Dual specificity tyrosine kinase (DYRK) inhibitor that targets mRNA splicing and is optimized for Wnt pathway inhibition. Previous evaluation of single agent CLK/DYRK inhibition (SM04690) demonstrated inhibition of tumor progression and β-catenin/TCF transcriptional activity inCTNNB1-mutant endometrial cancer (EC).In-vitroanalysis of SM08502 similarly decreases Wnt transcriptional activity and cellular proliferation while increasing cellular apoptosis. SM08502 is an active single-agent therapy with IC50’s in the nanomolar range for all EC cell lines evaluated. Combination of SM08502 with paclitaxel has synergistic effectin vitro, as demonstrated by Combination Index <1, and inhibits tumor progression in four endometrial cancer models (HEC265, Ishikawa, Ishikawa-S33Y, and SNGM). In ourin vivomouse models, Ishikawa demonstrated significantly lower tumor volumes of combination vs SM08502 alone (Repeated Measures one-way ANOVA, p = 0.04), but not vs paclitaxel alone. HEC265, SNGM, and Ishikawa-S33Y tumors all had significantly lower tumor volumes with combination SM08502 and paclitaxel compared to single-agent paclitaxel (Repeated Measures one-way ANOVA, p = 0.01, 0.004, and 0.0008, respectively) or single-agent SM08502 (Repeated Measures one-way ANOVA, p = 0.002, 0.005, and 0.01, respectively) alone. Mechanistically, treatment with SM08502 increases alternative splicing (AS) events compared to treatment with paclitaxel. AS regulation is an important post-transcriptional mechanism associated with the oncogenic process in many cancers, including EC. Results from these studies have led to a Phase I evaluation of this combination in recurrent EC.
Cell surface proteomics reveal a strategy for targeting myeloma through combinatorial targeting of TNFRSF8 and TMPRSS11E
Authors: Anderson Georgina S.F. , Walker Ieuan G. , Roy James P. , Chapman Michael A.
Published: April 2023

Chimeric antigen receptor (CAR) T-cell therapy is a highly effective novel treatment in haematological malignancies that has shown promise as a therapeutic option in multiple myeloma. However, widespread adoption of CAR T-cell therapy in myeloma has been hindered by the challenge of unbiased target antigen identification and selection. As activation of CAR T-cells requires minimal antigen on the cell surface, a major risk of toxicity is destruction of healthy tissue expressing the target protein, i.e. on-target, off-tumour toxicity. Indeed, examination of the myeloma surface proteome demonstrated that there was no single target that was completely unique to myeloma cells. One approach to achieve target specificity is to require simultaneous expression of two proteins on the target cells, so-called AND-gate targeting. To identify potential AND-gate combinations for myeloma, we devised an algorithm to prioritise pairings that exhibited pan-myeloma expression and no overlapping expression in vital healthy tissue, as predicted by proteomics. Through this approach, we identified over 600 combinations. To minimise the risk of exhaustion or priming by CAR T-cells, any combination whereby one of the two antigens was expressed in T-cells was also excluded, leading to the prioritisation of 144 candidate pairings. This demonstrates the potential for AND-gating to expand the repertoire of CAR T-cell targets for myeloma. We evaluated one of these candidate pairings, TMPRSS11E and TNFRSF8,in vitro. Activation in the Jurkat cell line co-expressing a suboptimal CAR against TNFRSF8 and a chimeric costimulatory receptor (CCR) against TMPRSS11E was markedly enhanced following co-culture with a dual-target positive myeloma cell line compared with single-target positive K562, demonstrating improved discrimination between tumour and non-tumour cells.
Telling mutualistic and antagonistic ecological networks apart by learning their multiscale structure
Authors: Pichon Benoît , Goff Rémy Le , Morlon Hélène , Perez-Lamarque Benoît
Published: April 2023

Characterizing and understanding the processes that shape the structure of ecological networks, which represent who interacts with whom in a community, has many implications in ecology, evolutionary biology, and conservation. A highly debated question is whether and how the structure of a bipartite ecological network differs between antagonistic (e.g., herbivory) and mutualistic (e.g., pollination) interaction types.

Here, we tackle this question by using a multiscale characterization of network structure, machine learning tools, and a large database of empirical and simulated bipartite networks.

Contrary to previous studies focusing on global structural metrics, such as nestedness and modularity, which concluded that antagonistic and mutualistic networks cannot be told apart from only their structure, we find that they can be told apart by combining a meso-scale characterization of their structure and supervised machine learning. Motif frequencies appear particularly informative, with an over-representation of densely connected motifs in antagonistic networks and of motifs with asymmetrical specialization in mutualistic networks. These characteristics can be used to predict interaction types with relatively good confidence. Beyond this classical mutualism/antagonism dichotomy, we also find significant structural uniqueness linked to specific ecologies (e.g., pollination, parasitism).

Our results clarify structural differences between antagonistic and mutualistic networks and suggest the investigation of the structural uniqueness of specific ecologies as a promising approach for characterizing interactions beyond the coarse antagonistic/mutualistic dichotomy.