bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of volumetric brain analysis in subjects with rheumatoid arthritis and ulcerative colitis
Authors: Cox Jennifer G. , de Groot Marius , Kempton Matthew J. , Williams Steven C. R. , Cole James H.
Published: March 2023

Objectives

Rheumatoid arthritis (RA) and ulcerative colitis (UC) are two autoimmune diseases where patients report high levels of fatigue, pain, and depression. The effect of systemic inflammation from these diseases is likely affecting the brain, however, it is unknown whether there are measurable neuroanatomical changes and whether these are a contributing factor to these central symptoms.

Methods

We included 258 RA patients with 774 age and sex matched controls and 249 UC patients with 747 age and sex matched controls in a case control study utilising the UK Biobank dataset. We used imaging derived phenotypes (IDPs) to determine whether there were differences in (1) hippocampal volume and (2) additional subcortical brain volumes between patients compared to controls and if there were common regions affected between these two diseases.

Results

Patients with UC had moderately smaller hippocampi compared to age and sex matched controls (difference: 134.15 mm3, SD ± 64.76, p = 0.035). This result was not seen in RA patients. RA patients had a significantly smaller amygdala volume than age and sex matched controls (difference: 91.27 mm3, SD ± 30.85, p = 0.0021, adjusted p value = 0.012). This result was not seen in UC patients. All other subcortical structures analysed were comparable between the patients and control groups.

Conclusion

These results indicate there are subcortical brain differences between UC, RA and controls but different regions of the limbic system are preferentially affected by UC and RA. This study may provide evidence for different neurodegenerative mechanisms in distinct autoimmune diseases.

Key Messages

Central effects such as fatigue and pain place significant burden on patients with autoimmune diseases

Rheumatoid arthritis patients have smaller amygdala volumes compared to matched controls.

Ulcerative colitis patients have smaller hippocampal volumes compared to matched controls.
Medium-term scenarios of COVID-19 as a function of immune uncertainties and chronic disease
Authors: Saad-Roy Chadi M. , Morris Sinead E. , Baker Rachel E. , Farrar Jeremy , Graham Andrea L. , Levin Simon A. , Wagner Caroline E. , E. Metcalf C. Jessica. , Grenfell Bryan T.
Published: March 2023

As the SARS-CoV-2 trajectory continues, the longer-term immuno-epidemiology of COVID-19, the dynamics of Long COVID, and the impact of escape variants are important outstanding questions. We examine these remaining uncertainties with a simple modelling framework that accounts for multiple (antigenic) exposures via infection or vaccination. If immunity (to infection or Long COVID) accumulates rapidly with the valency of exposure, we find that infection levels and the burden of Long COVID are markedly reduced in the medium term. More pessimistic assumptions on host adaptive immune responses illustrate that the longer term burden of COVID-19 may be elevated for years to come. However, we also find that these outcomes could be mitigated by the eventual introduction of a vaccine eliciting robust (i.e. durable, transmission-blocking and/or ‘evolution-proof’) immunity. Overall, our work stresses the wide range of future scenarios that still remain, the importance of collecting real world epidemiological data to identify likely outcomes, and the crucial need for the development of a highly effective transmission-blocking, durable, and broadly-protective vaccine.
Characterization of skin- and intestine microbial communities in migrating high Arctic lake whitefish and cisco
Authors: Hamilton Erin F. , Juurakko Collin L. , Engel Katja , Groot Peter van C. de , Casselman John M. , Greer Charles W. , Neufeld Josh D. , Walker Virginia K.
Published: March 2023

At high latitudes, lake whitefish (Coregonus clupeaformis) and others in the closely relatedCoregonusspecies complex (CSC), including cisco (C. autumnalisandC. sardinella), can be diadromous, seasonally transitioning between freshwater lakes and the Arctic Ocean. CSC skin- and intestine microbiomes were collected, facilitated by Inuit fishers at sites on and around King William Island, Nunavut, at the northern range limits of lake whitefish. Community composition was explored using 16S rRNA gene sequencing, with significant differences in microbiota dispersions depending on fishing site salinity for lake whitefish intestine and skin, as well as cisco skin. Overall, lake whitefish intestine communities appeared more variable than cisco and had higher Shannon diversity, suggesting that lake whitefish and their microbiomes could be more susceptible to environmental stress possibly leading to dysbiosis. Although cisco condition was similar among distinct seasonal habitats, the higher average lake whitefish condition in freshwater rivers suggests that fishing these diadromous whitefish in estuaries may be optimal from a sustainable fishery perspective. Taken together, the impact of changing habitats on fish condition and different microbial composition may inform new approaches to CSC health in fisheries and aquaculture, in addition to being relevant for northern Indigenous peoples with subsistence and economic interests in these resources.
The Loss of the E3 ubiquitin ligase TRIP12 inhibits Pancreatic Acinar Cell Plasticity and Tumor Cell Metastatic Capacity
Authors: Brunet Manon , Vargas Claire , Fanjul Marjorie , Pieruccioni Laetitia , Varry Damien , Labrousse Guillaume , Lulka Hubert , Capilla Florence , Couvelard Anne , Gigoux Véronique , Guillermet-Guibert Julie , Torrisani Jérôme , Dufresne Marlène
Published: March 2023

Background & Aims

Although specialized and dedicated to the production of digestive enzymes, pancreatic acinar cells harbor a high plasticity and are able to modify their identity. They undergo reversible acinar-to-ductal cell metaplasia (ADM) through epigenetic silencing of the acinar lineage gene program mainly controlled by PTF1a (Pancreas Transcription Factor 1a). ADM becomes irreversible in the presence of oncogenic Kras mutations and leads to the formation of preneoplastic lesions. We investigated the role of the E3 ubiquitin ligase Thyroid hormone Receptor Interacting Protein 12 (TRIP12), involved in PTF1a degradation, in pancreatic carcinogenesis.

Methods

We used genetically engineered mouse models of pancreas-selective Trip12 deletion, mutant Kras (G12D) and mutant Trp53 (R172H). We performed RNA sequencing analysis from acinar cells and cell lines derived from mice models tumors. We investigated the impact of TRIP12 deficiency on acute pancreatitis, tumor formation and metastasis development.

Results

TRIP12 is overexpressed in human pancreatic preneoplastic lesions and tumors. We show that a conditional deletion of TRIP12 in the pancreas during murine embryogenesis alters pancreas homeostasis and acinar cell genes expression patterns in adults. EGF induced-ADM is suppressed in TRIP12-depleted pancreatic acini. In vivo, a loss of TRIP12 prevents acini to develop ADM in response to pancreatic injury, the formation of Kras-induced pancreatic preneoplastic lesions, and impairs tumors and metastasis formation in the presence of mutated Trp53. TRIP12 is required for Claudin18.2 isoform expression in pancreatic tumors cells.

Conclusions

Our study identifies TRIP12 as a novel regulator of acinar fate in the adult pancreas with an important dual role in pancreatic carcinogenesis, in initiation steps and in metastatic behavior of tumor cells.

Synopsis

This study shows that Thyroid hormone Receptor Interacting Protein 12 plays an important dual role in the initiation steps and invasion of pancreatic carcinogenesis. Moreover, expression of TRIP12 switches on the expression of Claudin-18, a targetable biomarker of pancreatic tumors.
KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation
Authors: Martins Filipe , Rosspopoff Olga , Carlevaro-Fita Joana , Forey Romain , Offner Sandra , Planet Evarist , Pulver Cyril , Pak HuiSong , Huber Florian , Michaux Justine , Bassani-Sternberg Michal , Turelli Priscilla , Trono Didier
Published: March 2023

Heterochromatin loss and genetic instability enhance cancer progression by favoring clonal diversity, yet uncontrolled replicative stress can lead to mitotic catastrophe and inflammatory responses promoting immune rejection. KRAB-containing zinc finger proteins (KZFPs) are epigenetic modulators, which for many control heterochromatin at transposable element (TE)-embedded regulatory sequences. We identified a cluster of 18 KZFPs associated with poor prognosis in diffuse large B cell lymphoma (DLBCL). We found their upregulation to correlate with increased copy number alterations and suppression of immune responses in tumor samples. Upon depleting two that target evolutionarily recent TEs, the primate-specific ZNF587 and ZNF417 paralogs, the proliferation of DLBCL cell lines was drastically impaired and replicative stress abruptly induced with marked alterations of the chromatin landscape and multiplication of DNA replication origins. Furthermore,ZNF587/417knockdown upregulated interferon/inflammatory-related genes through activation of the cGAS-STING DNA sensing pathway, augmented the susceptibility of tumor cells to macrophage-mediated phagocytosis, and modified their immunogenicity through an increased surface expression of HLA-I and reshuffling of their immunopeptidome. ZNF587 and ZNF417 are thus pro-oncogenic factors allowing for higher degrees of genetic instability through attenuation of replicative stress and secondary inflammation, an influence that likely facilitates the clonal expansion, diversification, and immune evasion of cancer cells.
A Poisson distribution-based general model of cancer rates and a cancer risk-dependent theory of aging
Authors: Yu Wenbo , Gargett Tessa
Published: March 2023

This article presents a formula for modeling the lifetime incidence of cancer in humans. The formula utilizes a Poisson distribution-based “np” model to predict cancer incidence, with “n” representing the effective number of cell turnover and “p” representing the probability of single-cell transformation. The model accurately predicts the observed incidence of cancer in humans when cell turnover reduction is taken into account. The model also suggests that cancer development is ultimately inevitable. The article proposes a theory of aging based on this concept, called the “np” theory (Nuts Poisoned). According to this theory, an organism maintains its order by balancing cellular entropy through continuous proliferation. However, cellular information entropy increases irreversibly over time, restricting the total number of cells an organism can generate throughout its lifetime. When cell division slows down and fails to compensate for the entropy increase of the system, aging occurs. Essentially, aging is the phenomenon of running out of predetermined cell resources. Different species have evolved separate strategies to utilize their limited cell resources throughout their life cycle.
Conserved cysteine residues in Kaposi’s sarcoma herpesvirus ORF34 are necessary for viral production and viral pre-initiation complex formation
Authors: Watanabe Tadashi , McGraw Aidan , Narayan Kedhar , Tibebe Hasset , Kuriyama Kazushi , Nishimura Mayu , Izumi Taisuke , Fujimuro Masahiro , Ohno Shinji
Published: March 2023

Kaposi’s sarcoma herpesvirus (KSHV) ORF34 plays a significant role as a component of the viral pre-initiation complex (vPIC), which is indispensable for late gene expression across beta and gamma herpesviruses. Although the key role of ORF34 within the vPIC and its function as a hub protein have been recognized, further clarification regarding its specific contribution to vPIC functionality and interactions with other components is required. This study employed a deep-learning algorithm-assisted structural model of ORF34, revealing highly conserved amino acid residues across human beta- and gamma-herpesviruses localized in structured domains. Thus, we engineered ORF34 alanine-scanning mutants by substituting conserved residues with alanine. These mutants were evaluated for their ability to interact with other vPIC factors and restore viral production in cells harboring the ORF34-deficient KSHV-BAC. Our experimental results highlight the crucial role of the 4 cysteine residues conserved in ORF34: a tetrahedral arrangement consisting of a pair of C-Xn-C consensus motifs. This suggests the potential incorporation of metal cations in interacting with ORF24 and ORF66 vPIC components, facilitating late gene transcription, and promoting overall virus production by capturing metal cations. In summary, our findings underline the essential role of conserved cysteines in KSHV ORF34 for effective vPIC assembly and viral replication, thereby enhancing our understanding of the complex interplay between the vPIC components.

IMPORTANCE

The initiation of late gene transcription is universally conserved across the gamma- and beta-herpesvirus families. This process employs a viral pre-initiation complex (vPIC), which is analogous to a cellular PIC. Although KSHV ORF34 is a critical factor for viral replication and is a component of the vPIC, the specifics of vPIC formation and the essential domains crucial for its function remain unclear. Structural predictions suggest that the 4 conserved cysteines (C170, C175, C256, and C259) form a tetrahedron that coordinates the metal cation. We further investigated the role of these conserved amino acids in interactions with other vPIC components, late gene expression, and virus production, to demonstrate for the first time that these cysteines are pivotal for these functions. This discovery not only deepens our comprehensive understanding of ORF34 and vPIC dynamics but also lays the groundwork for more detailed studies on herpesvirus replication mechanisms in future research.
Mutations inembB406 are associated with low-level ethambutol resistance in CanadianMycobacterium tuberculosisisolates
Authors: Hiebert Morgan R. , Sharma Meenu K. , Rabb Melissa J. , Karlowsky Lisa J. , Bergman Kiana S. , Soualhine Hafid
Published: March 2023

Background

InMycobacterium tuberculosis, molecular predictions of ethambutol resistance rely primarily on the detection of mutations withinembB. However, discordance betweenembB406 mutations and phenotypic drug sensitivity questions its clinical significance. This study aims to decipher the association ofembB406 mutations with ethambutol resistance inM. tuberculosis.

Methods

AllM. tuberculosisisolates from our culture collection containingembB406 mutations (n=16) and pan-sensitive control isolates (n=10) were selected for this study. Phenotypic drug susceptibility testing for ethambutol was performed in duplicate on the BACTEC™ MGIT™ 960 at concentrations of 2, 3, 4, and 5 μg/mL with strain H37Rv as assay control. Whole genome sequencing was performed on Illumina Miseq for drug resistance predictions (MyKrobe Predictor v.0.7.0), phylogenomics (SNVPhyl v.1.2.3) and single nucleotide polymorphism analysis (Snippy).

Results

TwoembB406 mutation subtypes were found among 16 strains: Gly406Asp and Gly406Ala. MyKrobe predicted all strains of either subtype to be ethambutol resistant. However, 12 of 16 strains appear phenotypically sensitive at 5 μg/mL but exhibit variable resistance between 2-4 μg/mL. Of these 12 strains, a newly described frameshift mutation in regulatorembR(Gln258fs) was found in 9 strains.

Conclusions

Mutations inembB406 are associated with low-level ethambutol resistance currently undetectable by the critical concentration of 5 μg/mL for ethambutol. Novel mutations are predicted to exacerbate variability in ethambutol resistance. We suggest amendment to molecular and phenotypic drug susceptibility testing to improve ethambutol DST sensitivity and specificity as well as concordance between rapid and gold standard methods.
Molecular pathology of acute respiratory distress syndrome, mechanical ventilation and abnormal coagulation in severe COVID-19
Authors: Soulé Antoine , Ma William , Liu Katelyn Yixiu , Allard Catherine , Qureshi Salman , Tremblay Karine , Emad Amin , Rousseau Simon
Published: March 2023

Systemic inflammation in critically ill patients can lead to serious consequences such as acute respiratory distress syndrome (ARDS), a condition characterized by the presence of lung inflammation, edema, and impaired gas exchange, associated with poor survival. Understanding molecular pathobiology is essential to improve critical care of these patients. To this end, we use multimodal profiles of SARS-CoV-2 infected hospitalized participants to the Biobanque Québécoise de la COVID-19 (BQC-19) to characterize endophenotypes associated with different degrees of disease severity. Proteomic, metabolomic, and genomic characterization supported a role for neutrophil-associated procoagulant activity in severe COVID-19 ARDS that is inversely correlated with sphinghosine-1 phosphate plasma levels. Fibroblast Growth Factor Receptor (FGFR) and SH2-containing transforming protein 4 (SHC4) signaling were identified as molecular features associated with endophenotype 6 (EP6). Mechanical ventilation in EP6 was associated with alterations in lipoprotein metabolism. These findings help define the molecular mechanisms related to specific severe outcomes, that can be used to identify early unfavorable clinical trajectories and treatable traits to improve the survival of critically ill patients.
Prevalence of anemia, associated risk factors and outcome in CHUK, Rwanda: a prospective observational study
Authors: Havugimana Phocas , Ndahimana Raphael , Babane Felix , Umutesi Ernestine , Ntihinyurwa Polyphile , Mushimiyimana Diane , Masaisa Florence , Ntabanganyimana Etienne
Published: March 2023

Background

Admitted patients with anemia are at increased morbidity and mortality risk as well as length of hospital stay. It affects more than 2 billion people worldwide and is causing significant morbidity and mortality. Its etiology is varying with many predisposing factors including nutritional deficiencies, infections, Malignancies, chronic inflammations and other chronic diseases like autoimmune diseases, chronic liver disease, and chronic kidney disease.

Methods

We performed a non-randomized, prospective observational study of 143 patients admitted in Internal Medicine between March and April 2021, we assessed their hemoglobin level in order to determine the prevalence of anemia. The demographic and clinical data were collected using a designed questionnaire. All patients found to have anemia were followed for outcome assessment (either discharge or died).

Results

The prevalence of anemia was high (52.4%) among 143 admitted patients in Internal Medicine, CHUK. Patients with HIV, cancer and chronic kidney disease had 5.84-, 4.11- and 3.79-times risk of having anemia respectively. In 75 patients who had anemia 10 patients died among them 5 patients were having severe anemia; 25 patients were 60 years old and above; 60 patients had normocytic anemia and they had an average of length of hospital stay of 20.6 days, patients with severe anemia, length of hospital stay was 28 days.

Conclusion

This study demonstrated a high prevalence of anemia which is associated with high mortality rate among admitted patients in CHUK. Priority should be given to the preventive medicine, optimal management of chronic disease and geriatric medicine.
Spatio-temporal distributions of COVID-19 vaccine doses uptake in the Netherlands: A Bayesian ecological modelling analysis
Authors: Wang Haoyi , Varol Tugce , Gültzow Thomas , Zimmermann Hanne M. L. , Ruiter Robert A.C. , Jonas Kai J.
Published: March 2023

Background

In the transitioning era towards the COVID-19 endemic, there is still a sizable population that has never been vaccinated against COVID-19 in the Netherlands. To identify regions and populations that have a lower chance of vaccination uptake, this study provides a spatio-temporal estimation of the relative chance of COVID-19 vaccination uptake for the first, second, and the booster doses in the Netherlands on both municipality level and the public health services (regional) level.

Methods

Data on COVID-19 vaccination uptake were retrieved from the publicly available national COVID-19 surveillance dataset. We used a Bayesian spatio-temporal modelling technique with the integrated nested Laplace approximation to account for the spatial structure and the space-time interaction. Additionally, we used an ecological regression modelling technique which takes into account areal level socio-demographic characteristics to adjust for their potential impact on the chance of the regional vaccination uptake.

Results

Our findings revealed a heterogenous spatio-temporal distribution of the relative chance of COVID-19 vaccination uptake with highly overlapping trends of all three vaccination doses. Internal heterogeneity of COVID-19 vaccination uptake within one public health services region on the municipality level was also identified. The Dutch main urban area and the most religiously conservative regions were identified to have a lower-than-average chance of COVID-19 vaccination uptake compared to the rest of the country. Ecological regression modelling analysis revealed that regions with a higher proportion of non-Western immigrants had a lower chance of COVID-19 vaccination uptake for all vaccination scenarios.

Conclusion

The obtained estimates should inform national and local COVID-19 vaccination policies and service strategies in the Netherlands for the ongoing COVID-19 campaign on the second booster. Namely, more regional efforts and services may be needed to close ‘vaccination gaps’ and optimise COVID-19 health-related outcomes, especially with regard to regions with a relatively higher proportion of marginalised populations.
Integrated metabolic and genetic analysis reveals distinct features of primary differentiated thyroid cancer and its metastatic potential in humans
Authors: Cararo-Lopes Eduardo , Sawant Akshada , Moore Dirk , Ke Hua , Shi Fuqian , Laddha Saurabh , Chen Ying , Sharma Anchal , Naumann Jake , Guo Jessie Yanxiang , Gomez Maria , Ibrahim Maria , Smith Tracey L , Riedlinger Gregory M. , Lattime Edmund C. , Trooskin Stanley , Ganesan Shridar , Su Xiaoyang , Pasqualini Renata , Arap Wadih , De Subhajyoti , Chan Chang S. , White Eileen
Published: March 2023

ABSTRACT

Differentiated thyroid cancer (DTC) affects thousands of lives worldwide every year. Typically, DTC is a treatable disease with a good prognosis. Yet, some patients are subjected to partial or total thyroidectomy and radioiodine therapy to prevent local disease recurrence and metastasis. Unfortunately, thyroidectomy and/or radioiodine therapy often worsen(s) the quality of life and might be unnecessary in indolent DTC cases. This clinical setting highlights the unmet need for a precise molecular diagnosis of DTC, which should dictate appropriate therapy. Here we propose a differential multi-omics model approach to distinguish normal gland from thyroid tumor and to indicate potential metastatic diseases in papillary thyroid cancer (PTC), a sub-class of DTC. Based on PTC patient samples, our data suggest that elevated nuclear and mitochondrial DNA mutational burden, intratumor heterogeneity, shortened telomere length, and altered metabolic profile reflect the potential for metastatic disease. Specifically, normal and tumor thyroid tissues from these patients had a distinct yet well-defined metabolic profile with high levels of anabolic metabolites and/or other metabolites associated with the energy maintenance of tumor cells. Altogether, this work indicates that a differential and integrated multi-omics approach might improve DTC management, perhaps preventing unnecessary thyroid gland removal and/or radioiodine therapy. Well-designed, prospective translational clinical trials will ultimately show the value of this targeted molecular approach.

TRANSLATIONAL RELEVANCE

In this article, we propose a new integrated metabolic, genomic, and cytopathologic methods to diagnose Differentiated Thyroid Cancer when the conventional methods failed. Moreover, we suggest metabolic and genomic markers to help predict high-risk Papillary Thyroid Cancer. Both might be important tools to avoid unnecessary surgery and/or radioiodine therapy that can worsen the quality of life of the patients more than living with an indolent Thyroid nodule.

Graphical Abstract
Estimation of the number of RSV-associated hospitalisations in adults in the European Union
Authors: Osei-Yeboah Richard , Spreeuwenberg Peter , Riccio Marco Del , Fischer Thea K. , Cavling Amanda , Boas Håkon , van Boven Michiel , Wang Xin , Lehtonen Toni , Bangert Mathieu , Campbell Harry , Paget John
Published: March 2023

Background

Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections in older adults that can result in hospitalisations and death. Estimating RSV- associated hospitalisation is critical for planning RSV-related healthcare needs for the ageing population across Europe.

Methods

We gathered national RSV-associated hospitalisation estimates from the REspiratory Syncytial virus Consortium in EUrope (RESCEU) for adults in Denmark, England, Finland, Norway, Netherlands, and Scotland from 2006 to 2017. We extrapolated these estimates to 28 EU countries using nearest-neighbour matching, multiple imputations, and two sets of 10 indicators.

Results

On average, 158 229 (95%CI: 140 865-175 592) RSV-associated hospitalisations occur annually among adults in the EU (above 18 years); 92% of these hospitalisations occur in adults over 65 years. Among 75-84 years old, the annual average is estimated at 74 519 (95%CI: 69 923-79 115) at a rate of 2.24 (95%CI: 2.10-2.38) per 1000 adults. Among adults aged ≥85 years, the annual average is estimated at 37 904 (95%CI: 32 444-43 363) at a rate of 2.99 (95%CI: 2.56-3.42).

Conclusion

Our estimates of RSV-associated hospitalisations in older adults are the first analysis integrating available data to provide estimates of the disease burden in this population across the EU. Importantly, for a condition which was considered in the past to be primarily a disease of young children, the average annual hospitalisation estimate in adults was lower but of a similar magnitude to the estimate in young children aged 0-4 years: 158 229 (95%CI: 140 865–175 592) versus 245 244 (95%CI: 224 688 –265 799).
Hybrid immunity elicits potent cross-variant ADCC against SARS-CoV-2 through a combination of anti-S1 and S2 antibodies
Authors: Grant Michael D. , Bentley Kirsten , Fielding Ceri A. , Hatfield Keeley M. , Ings Danielle P. , Harnum Debbie , Wang Eddie , Stanton Richard , Holder Kayla A.
Published: March 2023

Antibodies capable of neutralising SARS-CoV-2 have been well studied, but the Fc receptor-dependent antibody activities that also significantly impact the course of infection have not been studied in such depth. SARS-CoV-2 infection induces antibody-dependent NK cell responses targeting multiple antigens, however, as most vaccines induce only anti-spike antibodies, we investigated spike-specific antibody-dependent cellular cytotoxicity (ADCC). Vaccination produced antibodies that only weakly induced ADCC, however, antibodies from individuals who were infected prior to vaccination (‘hybrid’ immunity) elicited much stronger anti-spike ADCC. Quantitative and qualitative aspects of humoral immunity contributed to this capability, with infection skewing IgG antibody production towards S2, vaccination skewing towards S1 and hybrid immunity evoking strong responses against both domains. The capacity for hybrid immunity to provide superior spike-directed ADCC was associated with selectively increased antibody responses against epitopes within both S1 and S2. Antibodies targeting both spike domains were important for strong antibody-dependent NK cell activation, with three regions of antibody reactivity outside the receptor-binding domain (RBD) corresponding with potent anti-spike ADCC. Consequently, ADCC induced by hybrid immunity with ancestral antigen was conserved against variants containing neutralisation escape mutations in the RBD [Delta and Omicron (BA.1)]. Induction of antibodies recognizing a broad range of spike epitopes and eliciting strong and durable ADCC may partially explain why hybrid immunity provides superior protection against infection and disease than vaccination alone, and demonstrates that spike-only subunit vaccines would benefit from strategies to induce a combination of S1- and S2-specific antibody responses.

Significance

Neutralising antibodies prevent the entry of cell-free virus, however, antibodies that promote Fc-dependent activities such as ADCC are critical to control cell-associated virus. Although current SARS-CoV-2 vaccines induce potent neutralising antibodies, they fail to induce robust ADCC. Our demonstration that hybrid immunity induces superior ADCC with pan-variant activity may partially explain why hybrid immunity offers enhanced protection against reinfection. It also highlights that vaccine strategies based on expression of the spike subunit alone should not focus solely on inducing antibody responses targeting the receptor binding domain.
Identifying Fibrogenic Cells Following Salivary Gland Obstructive Injury
Authors: Altrieth Amber L. , O’Keefe Kevin J. , Gellatly Victoria A. , Tavarez Joey R. , Feminella Sage M. , Moskwa Nicholas L. , Cordi Carmalena V. , Turrieta Judy C. , Nelson Deirdre A. , Larsen Melinda
Published: March 2023

Fibrosis results from excess extracellular matrix accumulation, which alters normal tissue architecture and impedes function. In the salivary gland, fibrosis can be induced by irradiation treatment for cancer therapy, Sjögren’s Disease, and other causes; however, it is unclear which stromal cells and signals participate in injury responses and disease progression. As hedgehog signaling has been implicated in fibrosis of the salivary gland and other organs, we examined contributions of the hedgehog effector, Gli1, to fibrotic responses in salivary glands. To experimentally induce a fibrotic response in female murine submandibular salivary glands, we performed ductal ligation surgery. We detected a progressive fibrotic response where both extracellular matrix accumulation and actively remodeled collagen trended upwards at 7 days and significantly increased at 14 days post- ligation. Macrophages, which participate in extracellular matrix remodeling, Gli1+and PDGFRα+stromal cells, which may deposit extracellular matrix, both increased with injury. Using single-cell RNA-sequencing, we found that a majority ofGli1+cells at embryonic day 16 also expressPdgfraand/orPdgfrb.However, in adult mice, only a small subset of Gli1+cells express PDGFRα and/or PDGFRβ at the protein level. Using lineage-tracing mice, we found that Gli1-derived cells expand with ductal ligation injury. Although some of the Gli1 lineage-traced tdTomato+cells expressed vimentin and PDGFRβ following injury, there was no increase in the classic myofibroblast marker, smooth muscle alpha-actin. Additionally, there was little change in extracellular matrix area, remodeled collagen area, PDGFRα, PDGFRβ, endothelial cells, neurons, or macrophages in Gli1 null salivary glands following injury when compared with controls, suggesting that Gli1 signaling and Gli1+cells have only a minor contribution to mechanical injury-induced fibrotic changes in the salivary gland. We used scRNA-seq to examine cell populations that expand with ligation and/or showed increased expression of matrisome genes.Pdgfra+/Pdgfrb+stromal cell subpopulations both expanded in response to ligation, showed increased expression and a greater diversity of matrisome genes expressed, consistent with these cells being fibrogenic. Defining the signaling pathways driving fibrotic responses in stromal cell sub-types could reveal future therapeutic targets.
Hepatic Lipid Droplet-Associated Proteome Changes Distinguish Dietary-Induced Fatty Liver from Insulin Resistance in Male Mice
Authors: Woerkom Andries Van , Harney Dylan J , Nagarajan Shilpa R. , Hakeem-Sanni Mariam F. , Lin Jinfeng , Hooke Matthew , Pulpitel Tamara , Cooney Gregory J , Larance Mark , Saunders Darren N. , Brandon Amanda E , Hoy Andrew J.
Published: March 2023

Fatty liver is characterised by the expansion of lipid droplets and is associated with the development of many metabolic diseases, including insulin resistance, dyslipidaemia and cardiovascular disease. We assessed the morphology of hepatic lipid droplets and performed quantitative proteomics in lean, glucose-tolerant mice compared to high-fat diet (HFD) fed mice that displayed hepatic steatosis and glucose intolerance as well as high-starch diet (HStD) fed mice who exhibited similar levels of hepatic steatosis but remained glucose tolerant. Both HFD and HStD-fed mice had more and larger lipid droplets than Chow-fed animals. We observed striking differences in liver lipid droplet proteomes of HFD and HStD-fed mice compared to Chow-fed mice, with fewer differences between HFD and HStD. Taking advantage of our diet strategy, we identified a fatty liver lipid droplet proteome consisting of proteins common in HFD- and HStD-fed mice. Likewise, a proteome associated with glucose tolerance that included proteins common in Chow and HStD but not HFD-fed mice was identified. Notably, glucose intolerance was associated with changes in the ratio of adipose triglyceride lipase (ATGL) to perilipin 5 (PLIN5) in the lipid droplet proteome, suggesting dysregulation of neutral lipid homeostasis in glucose-intolerant fatty liver, which supports bioactive lipid synthesis and impairs hepatic insulin action. We conclude that our novel dietary approach uncouples ectopic lipid burden from insulin resistance-associated changes in the hepatic lipid droplet proteome.
Inducible expression of the restriction enzyme uncovered genome-wide distribution and dynamic behavior of histones H4K16ac and H2A.Z at DNA double-strand breaks inArabidopsis
Authors: Kawaguchi Kohei , Kazama Mei , Hata Takayuki , Matsuo Mitsuhiro , Obokata Junichi , Satoh Soichirou
Published: March 2023

DNA double-strand breaks (DSBs) are among the most serious types of DNA damage and cause mutations and chromosomal rearrangements. In eukaryotes, DSBs are immediately repaired in coordination with chromatin remodeling for the deposition of DSB-related histone modifications and variants. To elucidate the details of DSB-dependent chromatin remodeling throughout the genome, artificial DSBs need to be reproducibly induced at various genomic loci. Recently, in mammals, a comprehensive method for elucidating chromatin remodeling at multiple DSB loci via chemically induced expression of a restriction enzyme was developed. However, this DSB induction system is not suitable for investigating chromatin remodeling during and after DSB repair, and such approach has not been performed in plants. Here, we established a transgenicArabidopsisplant harboring a restriction enzyme geneSbfI driven by a heat-inducible promoter. Using this transgenic plant, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of histones H4K16ac and H2A.Z and investigated dynamics of these histone marks around the endogenous 623SbfI recognition sites. We also precisely quantified DSB efficiency at all cleavage sites using the DNA resequencing data obtained by ChIP-seq procedures. From the results,SbfI-induced DSBs were detected at 360 loci and induced the transient deposition of H4K16ac and H2A.Z around these regions. Interestingly, we also observed the co-localization of H4K16ac and H2A.Z at some DSB loci. Overall, DSB-dependent chromatin remodeling was found to be a highly conserved between plants and animals. These findings provide new insights into chromatin remodeling that occurs in response to DSBs inArabidopsis.
Flaviviruses alter endoplasmic reticulum-mitochondria contacts to regulate respiration and apoptosis
Authors: Freppel Wesley , Anton Anaïs , Nouhi Zaynab , Mazeaud Clément , Gilbert Claudia , Tremblay Nicolas , Torres Viviana Andrea Barragan , Sow Aïssatou Aïcha , Laulhé Xavier , Lamarre Alain , Rodrigue-Gervais Ian Gaël , Pichlmair Andreas , Scaturro Pietro , Hulea Laura , Chatel-Chaix Laurent
Published: March 2023

With no therapeutics available, there is an urgent need to better understand the pathogenesis of flaviviruses which constitute a threat to public health worldwide. During infection, dengue virus (DENV) and Zika virus (ZIKV), two flaviviruses induce alterations of mitochondria morphology to favor viral replication, suggesting a viral co-opting of mitochondria functions. Here, we performed an extensive transmission electron microscopy-based quantitative analysis to demonstrate that both DENV and ZIKV alter endoplasmic reticulum-mitochondria contacts (ERMC). This correlated at the molecular level with an impairment of ERMC tethering protein complexes located at the surface of both organelles. Furthermore, virus infection, as well as NS4B expression modulated the mitochondrial oxygen consumption rate. Consistently, metabolomic and mitoproteomic analyses revealed a decrease in the abundance of several metabolites of the Krebs cycle and changes in the stoichiometry of the electron transport chain. Most importantly, ERMC destabilization by protein knockdown increased virus replication while dampening ZIKV-induced apoptosis. Overall, our results support the notion that flaviviruses hijack ERMCs to generate a cytoplasmic environment beneficial for sustained and efficient replication.
A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses
Authors: Elek Claire K. A. , Brown Teagan L. , Viet Thanh Le , Evans Rhiannon , Baker David J. , Telatin Andrea , Tiwari Sumeet K. , Al-Khanaq Haider , Thilliez Gaëtan , Kingsley Robert A. , Hall Lindsay J. , Webber Mark A. , Adriaenssens Evelien M.
Published: March 2023

Bacteriophages (phages) within thePrzondovirusgenus are T7-like podoviruses belonging to theStudiervirinaesubfamily, within theAutographiviridaefamily and have a highly conserved genome organisation. The genome size of these phages ranges from 37 kb to 42 kb, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targetingKlebsiellaspp. We describe HYPPA – aHYbrid andPoly-polishPhageAssembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.

IMPACT STATEMENT

The current workflows employed for phage genome assembly are often error-prone and can lead to many incomplete phage genomes being deposited within databases. This can create challenges when performing comparative genomics, and may also lead to incorrect taxonomic assignment. To overcome these challenges we proposed HYPPA, a workflow that can produce complete and high-quality phage genomes without the need for laborious lab-based validation.

DATA SUMMARY

Phage raw reads are available from the National Centre for Biotechnology Information Sequence Read Archive (NCBI-SRA) under the BioProject number PRJNA914245. Phage annotated genomes have been deposited at GenBank under the accessionsOQ579023-OQ579032(Table 1). Bacterial WGS data for clinical preterm infant samples have been deposited at GenBank under BioProject accession PRJNA471164 (Table S1). Bacterial raw reads for food samples are available from NCBI-SRA with individual accessions (SAMN33593347-SAMN33593351), and can be found under the BioProject number PRJNA941224 (Table S1). Strain-specific details for bacteria and publicly-available phages used in these analyses, along with accessions for the latter can be found inTable S1andTable S6, respectively. The CL1-CL8 clinicalKlebsiellastrains (Table S1) were under a Materials Transfer Agreement, for which sequencing data and strain information is not available.
Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses
Authors: Maestri Renan , Perez-Lamarque Benoît , Zhukova Anna , Morlon Hélène
Published: March 2023

Several coronaviruses infect humans, with three, including the SARS-CoV2, causing diseases. While coronaviruses are especially prone to induce pandemics, we know little about their evolutionary history, host-to-host transmissions, and biogeography. One of the difficulties lies in dating the origination of the family, a particularly challenging task for RNA viruses in general. Previous cophylogenetic tests of virus-host associations, including in the Coronaviridae family, have suggested a virus-host codiversification history stretching many millions of years. Here, we establish a framework for robustly testing scenarios of ancient origination and codiversificationversusrecent origination and diversification by host switches. Applied to coronaviruses and their mammalian hosts, our results support a scenario of recent origination of coronaviruses in bats and diversification by host switches, with preferential host switches within mammalian orders. Hotspots of coronavirus diversity, concentrated in East Asia and Europe, are consistent with this scenario of relatively recent origination and localized host switches. Spillovers from bats to other species are rare, but have the highest probability to be towards humans than to any other mammal species, implicating humans as the evolutionary intermediate host. The high host-switching rates within orders, as well as between humans, domesticated mammals, and non-flying wild mammals, indicates the potential for rapid additional spreading of coronaviruses across the world. Our results suggest that the evolutionary history of extant mammalian coronaviruses is recent, and that cases of long-term virus–host codiversification have been largely over-estimated.
Single-cell time series analysis reveals the dynamics ofin vivoHSPC responses to inflammation
Authors: Bouman Brigitte Joanne , Demerdash Yasmin , Sood Shubhankar , Grünschläger Florian , Pilz Franziska , Itani Abdul Rahman , Kuck Andrea , Haas Simon , Haghverdi Laleh , Essers Marieke Alida Gertruda
Published: March 2023

Hematopoietic stem and progenitor cells (HSPCs) are known to respond to acute inflammation; however, little is understood about the dynamics and heterogeneity of these stress responses in HSPCs. Here, we performed single-cell sequencing of HSPCs during the sensing, response and recovery phases of the inflammatory response of HSPCs to treatment with the pro-inflammatory cytokine IFNα to investigate the HSPCs’ dynamic changes during acute inflammation. For the analysis of the resulting datasets, we developed a computational pipeline for single-cell time series. Using a semi-supervised response-pseudotime inference approach, we discover a variety of different gene responses of the HSPCs to the treatment. Interestingly, we were able to associate reduced myeloid differentiation programs in HSPCs with reduced myeloid progenitor and differentiated cells following IFNα treatment. Altogether, single-cell time series analysis have allowed us to unbiasedly study the heterogeneous and dynamic impact of IFNα on the HSPCs.
Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses
Authors: Park Seo-Young , Choi Dong-Hyuk , Song Jinsung , Park Uiseon , Cho Hyeran , Hong Bee Hak , Silberberg Yaron R. , Lee Dong-Yup
Published: March 2023

Designing and selecting cell culture media and feed are a key strategy to maximize culture performance in industrial biopharmaceutical processes. However, this is a major challenge for therapeutic proteins production since mammalian cells are very sensitive to their culture environment and require specific nutritional needs to grow and produce high-quality proteins such as antibodies. In this regard, in our previous study, we developed data-driven and in-silico model-guided systematic framework to investigate the effect of growth media on Chinese hamster ovary (CHO) cell culture performance, allowing us to design a new media formulation. To expand our exploration to feed, in this study, we evaluated two chemically defined feed media, A and B, in Ambr15 bioreactor runs using a monoclonal antibody-producing CHO K1 cell line. The feeds had a significant impact on cell growth, longevity, viability, and productivity and toxic metabolites production. Specifically, concentrated feed A was not sufficient to support prolonged cell culture and high titer compared to feed B. The framework systematically characterized the major metabolic bottlenecks in the TCA cycle and its related amino acid transferase reactions, and identified key design components, such as asparagine, aspartate, and glutamate, needed for highly productive cell cultures. From our results, we designed three new feeds by adjusting the levels of those amino acids and successfully validated their effectiveness in promoting cell growth and/or titer.
Self-assembly and contraction of micron-scale DNA rings
Authors: Illig Maja , Jahnke Kevin , Scheffold Marlene , Mersdorf Ulrike , Drechsler Hauke , Diez Stefan , Göpfrich Kerstin
Published: March 2023

Contractile rings formed from cytoskeletal filaments mediate the division of cells. The reverse-engineering of synthetic contractile rings could shed light on fundamental physical principles of the ring self-assembly and dynamics independent of the natural protein-based compounds. Here, we engineer DNA nanotubes and crosslink them with a synthetic peptide-functionalized star-PEG construct. The star-PEG construct induces the formation of DNA nanotube bundles composed of several tens of individual DNA nanotubes. Importantly, the DNA nanotube bundles curve into closed micron-scale DNA rings in a high-yield one-pot self-assembly process resulting in several thousand rings per microliter. The crosslinked DNA rings can undergo contraction to less than half of their initial diameter by two distinct mechanisms, triggered by increasing molecular crowding or temperature. DNA-based contractile rings expand the toolbox of DNA nanotechnology and could be a future element of an artificial division machinery in synthetic cells.