bluuebunny/crossref_metadata_2025 huggingface dataset:
Vaccine-elicited B and T cell immunity to SARS-CoV-2 is impaired in chronic lung disease patients
Authors: Liu Haolin , Aviszus Katja , Zelarney Pearlanne , Liao Shu-Yi , Gerber Anthony N. , Make Barry , Wechsler Michael E. , Marrack Philippa , Reinhardt R. Lee
Published: January 2023

The protection afforded by vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to individuals with chronic lung disease is not well established. To understand how chronic lung disease impacts SARS-CoV-2 vaccine-elicited immunity we performed deep immunophenotyping of the humoral and cell mediated SARS-CoV-2 vaccine response in an investigative cohort of vaccinated patients with diverse pulmonary conditions including asthma, chronic obstructive pulmonary disease (COPD), and interstitial lung disease (ILD). Compared to healthy controls, 48% of vaccinated patients with chronic lung diseases had reduced antibody titers to the SARS-CoV-2 vaccine antigen as early as 3-4 months after vaccination, correlating with decreased vaccine-specific memory B cells. Vaccine-specific CD4 and CD8 T cells were also significantly reduced in patients with asthma, COPD, and a subset of ILD patients compared to healthy controls. These findings reveal the complex nature of vaccine-elicited immunity in high-risk patients with chronic lung disease.
Efficacy of recombinant human epidermal growth factor (rhEGF) incorporated in an absorbable collagen membrane for the management of gingival recession defects
Authors: Chandra Rampalli Viswa , Bindu Kotha Sushmitha , Reddy Aileni Amarendhar
Published: January 2023

Aim & Objectives

The aim of the present study is to evaluate the regeneration efficacy of rhEGF impregnated in collagen membrane for the management of Millers class I & class II gingival recession defects.

Patients and methods

18 patients with 30 Millers class I & class II gingival recession defects were treated with one of the following interventions and randomly allocated into each of the following experimental groups; Test group: rhEGF impregnated in collagen membrane, Control group: plain collagen membrane. Clinical measurements at baseline, 3 months and 6 months included decreased probing depth, recession depth and increase in width of keratinized gingiva.

Results

There was an improvement in tissue biotype in test group and statistically significant increase in KGW from baseline to 3 months which remained constant from 3 months to 6 months(p≤0.001) in both the groups. Similarly, RD shows constant increase from baseline to 6 months in test group whereas there is reduction in control group (p≤0.003). There was significant difference in clinical parameters in both test and control groups. All the patients had an uneventful healing phase.

Conclusion

The beneficial effects of rhEGF resulted in healthy wound healing process with less scarring offers more potential properties showed promising results over collagen membrane. Further larger samples are required to confirm the efficacy of rhEGF in root coverage for soft tissue regeneration.
Expected reduction in obesity of a 20% and 30% tax to Sugar-Sweetened-Beverages in Brazil: a modeling study
Authors: Basto-Abreu Ana , Torres-Alvarez Rossana , Barrientos-Gutierrez Tonatiuh , Pereda Paula , Duran Ana Clara
Published: January 2023

Background

The consumption of sugar-sweetened beverages (SSB) is associated with obesity, metabolic diseases, and incremental healthcare costs. Given their health consequences, the World Health Organization (WHO) recommended that countries implement taxes to SSB. Over the last 10 years, Brazil has almost doubled its obesity prevalence, yet, in 2016, the Brazilian government cut 23 percentage points to existing federal SSB taxes to their current 4%. To simulate the potential impact of updating the fiscal policy towards SSB in Brazil, we aimed to estimate the price-elasticity of SSB and model the potential impact of a new 20 or 30% excise SSB tax on consumption, obesity prevalence, and healthcare costs.

Methods and Findings

Using household purchases data from the Brazilian Household Budget Survey (POF) from 2017/2018, we estimated constant elasticity regressions using a log-log specification by income level for all beverage categories: (1) sugar-sweetened beverages, (2) alcoholic beverages, (3) other beverages, and (4) low-calorie sweetened beverages. We estimated baseline intake for each beverage group using 24h dietary recall data from POF 2017/2018. Applying the price and cross-price elasticities to the baseline intake, we obtained changes in caloric intake. The caloric reduction was introduced into an individual dynamic model to estimate changes in weight and obesity prevalence. By multiplying the reduction in obesity cases during 10 years by the obesity costs per capita, we predicted the reduction in obesity costs attributable to the sweetened beverage tax. SSB price elasticities were higher in the low (−1.24) than in the high-income tertile (−1.13); cross-price elasticities suggest SSB were weakly substituted by milk, water, and 100% fruit juices. We estimated a caloric change of -17.3 kcal/day/person under a 20% excise tax and -25.9 kcal/day/person for a 30% tax. 10 years after implementation, a 20% tax is expected to reduce obesity prevalence by 6.7% and 9.1% for a 30% tax. These reductions translate into a -2.8 million and -3.8 million obesity cases for a 20 and 30% tax, respectively, and a reduction of $US -257.4 million and $US -345.9 million obesity costs over 10 years for a 20 and 30% tax, respectively.

Conclusions

Adding a 20 to 30% excise tax on top of Brazil’s current federal tax in Brazil could help reduce the consumption of ultra-processed beverages, empty calories, and body weight while avoiding large health-related costs. Given the recent cuts to SSB taxes in Brazil, a program to revise and implement excise taxes could prove beneficial for the Brazilian population.
Altered sex differences in hippocampal subfield volumes in schizophrenia
Authors: Barth Claudia , Nerland Stener , Jørgensen Kjetil N. , Haatveit Beathe , Wortinger Laura A. , Melle Ingrid , Haukvik Unn K. , Ueland Torill , Andreassen Ole A. , Agartz Ingrid
Published: January 2023

Objective

The hippocampus is a heterogenous brain structure that differs between the sexes and has been implicated in the pathophysiology of psychiatric illnesses. Here, we explored sex and diagnostic group differences in hippocampal subfield volumes, in individuals with schizophrenia spectrum disorder (SZ), bipolar disorders (BD) and healthy controls.

Methods

1,521 participants underwent T1-weighted magnetic resonance imaging (SZ, n = 452, mean age 30.7 ± 9.2 [SD] years, males 59.1%; BD, n = 316, 33.7 ± 11.4, 41.5%; healthy controls, n = 753, 34.1 ± 9.1, 55.6%). Total hippocampal, subfield, and intracranial volumes were estimated with Freesurfer (v6.0.0). Analysis of covariance and multiple regression models were fitted to examine sex-by-diagnostic (sub)group interactions in volume. In SZ and BD, separately, associations between volumes and clinical as well as cognitive measures were examined between the sexes using regression models.

Results

Significant sex-by-group interactions were found for the total hippocampus, dentate gyrus, molecular layer, presubiculum, fimbria, HATA, and CA4, indicating a larger volumetric deficit in male patients relative to female patients when compared with same-sex healthy controls. Subgroup analyses revealed that this interaction was driven by males with schizophrenia. Effect sizes were overall small (partial η2< 0.02). We found no significant sex differences in the associations between hippocampal volumes and clinical or cognitive measures in SZ and BD.

Conclusions

Using a well-powered sample, our findings indicate that the pattern of morphological sex differences in hippocampal subfields is altered in individuals with schizophrenia relative to healthy controls, due to higher volumetric deficits in males.
scMINER: a mutual information-based framework for identifying hidden drivers from single-cell omics data
Authors: Ding Liang , Shi Hao , Qian Chenxi , Burdyshaw Chad , Veloso Joao Pedro , Khatamian Alireza , Pan Qingfei , Dhungana Yogesh , Xie Zhen , Risch Isabel , Yang Xu , Huang Xin , Yan Lei , Rusch Michael , Brewer Michael , Yan Koon-Kiu , Chi Hongbo , Yu Jiyang
Published: January 2023

The sparse nature of single-cell omics data makes it challenging to dissect the wiring and rewiring of the transcriptional and signaling drivers that regulate cellular states. Many of the drivers, referred to as “hidden drivers”, are difficult to identify via conventional expression analysis due to low expression and inconsistency between RNA and protein activity caused by post-translational and other modifications. To address this issue, we developed scMINER, a mutual information (MI)-based computational framework for unsupervised clustering analysis and cell-type specific inference of intracellular networks, hidden drivers and network rewiring from single-cell RNA-seq data. We designed scMINER to capture nonlinear cell-cell and gene-gene relationships and infer driver activities. Systematic benchmarking showed that scMINER outperforms popular single-cell clustering algorithms, especially in distinguishing similar cell types. With respect to network inference, scMINER does not rely on the binding motifs which are available for a limited set of transcription factors, therefore scMINER can provide quantitative activity assessment for more than 6,000 transcription and signaling drivers from a scRNA-seq experiment. As demonstrations, we used scMINER to expose hidden transcription and signaling drivers and dissect their regulon rewiring in immune cell heterogeneity, lineage differentiation, and tissue specification. Overall, activity-based scMINER is a widely applicable, highly accurate, reproducible and scalable method for inferring cellular transcriptional and signaling networks in each cell state from scRNA-seq data. The scMINER software is publicly accessible via:https://github.com/jyyulab/scMINER.
The LCLAT1/LYCAT acyltransferase is required for EGF-mediated phosphatidylinositol-3,4,5-trisphosphate generation and Akt signalling
Authors: Chan Victoria , Camardi Cristina , Zhang Kai , Orofiamma Laura A. , Anderson Karen E. , Hoque Jafarul , Bone Leslie N. , Awadeh Yasmin , Lee Daniel K. C. , Fu Norman J. , Chow Jonathan T. S. , Salmena Leonardo , Stephens Len R. , Hawkins Phillip T. , Antonescu Costin N. , Botelho Roberto J.
Published: January 2023

Receptor tyrosine kinases such as epidermal growth factor receptor (EGFR) stimulate phosphoinositide 3-kinases (PI3Ks) to convert phosphatidylinositol-4,5-bisphosophate [PtdIns(4,5)P2] into phosphatidylinositol-3,4,5-trisphosphate [PtdIns(3,4,5)P3]. PtdIns(3,4,5)P3then remodels actin and gene expression, and boosts cell survival and proliferation. PtdIns(3,4,5)P3partly achieves these functions by triggering activation of the kinase Akt, which phosphorylates targets like Tsc2 and GSK3β. Consequently, unchecked upregulation of PtdIns(3,4,5)P3-Akt signalling promotes tumour progression. Interestingly, 50-70% of PtdIns and PtdInsPs have stearate and arachidonate atsn-1 andsn-2 positions of glycerol, respectively, forming a species known as 38:4-PtdIns/PtdInsPs. LCLAT1 and MBOAT7 acyltransferases partly enrich PtdIns in this acyl format. We previously showed that disruption of LCLAT1 lowered PtdIns(4,5)P2levels and perturbed endocytosis and endocytic trafficking. However, the role of LCLAT1 in receptor tyrosine kinase and PtdIns(3,4,5)P3signaling was not explored. Here, we show that LCLAT1 silencing in MDA-MB-231 and ARPE-19 cells abated the levels of PtdIns(3,4,5)P3in response to EGF signalling. Importantly, LCLAT1-silenced cells were also impaired for EGF-driven and insulin-driven Akt activation and downstream signalling. Thus, our work provides first evidence that the LCLAT1 acyltransferase is required for receptor tyrosine kinase signalling.
Adaptation of Graph Convolutional Neural Networks and Graph Layer-wise Relevance Propagation to the Spektral library with application to gene expression data of Colorectal Cancer patients
Authors: Lutz Sebastian , Auer Florian , Hartmann Dennis , Chereda Hryhorii , Beißbarth Tim , Kramer Frank
Published: January 2023

Motivation

Colorectal Cancer has the second-highest mortality rate worldwide, which requires advanced diagnostics and individualized therapies to be developed. Information about the interactions between molecular entities provides valuable information to detect the responsible genes driving cancer progression. Graph Convolutional Neural Networks are able to utilize the prior knowledge provided by interaction networks and the Spektral library adds a performance increase in contrast to standard implementations. Furthermore, machine learning technology shows great potential to assist medical professionals through guided clinical decision support. However, the deep learning models are limited in their application in precision medicine due to their lack to explain the factors contributing to a prediction. Adaption of the Graph Layer-Wise Relevance Propagation methodology to graph-based deep learning models allows to attribute the learned outcome to single genes and determine their relevance. The resulting patient-specific subnetworks then can be used to identify potentially targetable genes.

Results

We present an implementation of Graph Convolutional Neural Networks using the Spektral library in combination with adapted functions for Graph Layer-Wise Relevance Propagation. Deep learning models were trained on a newly composed large gene expression dataset of Colorectal Cancer patients with different molecular interaction networks as prior knowledge: Protein-protein interactions from the Human Protein Reference Database and STRING, and pathways from the Reactome database. Our implementation performs comparably with the original implementation while reducing the computation time, especially for large networks. Further, the generated subnetworks are similar to those of the initial implementation and reveal possible, and even more distant, biomarkers and drug targets.

Availability

The implementation details and corresponding dataset including their visualizations can be found athttps://github.com/frankkramer-lab/spektral-gcnn-glrp-on-crc-data

Contact

sebastian.lutz@uni-a.de
Prediction of brain age using structural magnetic resonance imaging: A comparison of accuracy and test-retest reliability of publicly available software packages
Authors: Dörfel Ruben P. , Arenas-Gomez Joan M. , Fisher Patrick M. , Ganz Melanie , Knudsen Gitte M. , Svensson Jonas , Plavén-Sigray Pontus
Published: January 2023

Background

Brain age prediction algorithms using structural magnetic resonance imaging (MRI) aim to assess the biological age of the human brain. The difference between a person’s chronological age and the estimated brain age is thought to reflect deviations from a normal aging trajectory, indicating a slower, or accelerated, biological aging process. Several pre-trained software packages for predicting brain age are publicly available. In this study, we perform a head-to-head comparison of such packages with respect to 1) predictive accuracy, 2) test-retest reliability, and 3) the ability to track age progression over time.

Methods

We evaluated the six brain age prediction packages: brainageR, DeepBrainNet, brainage, ENIGMA, pyment, and mccqrnn. The accuracy and test-retest reliability were assessed on MRI data from 372 healthy people aged between 18.4 and 86.2 years (mean 38.7 ± 17.5 years).

Results

All packages showed significant correlations between predicted brain age and chronological age (r = 0.66 to 0.97, p < 0.001), with pyment displaying the strongest correlation. The mean absolute error was between 3.56 (pyment) and 9.54 years (ENIGMA). brainageR, pyment, and mccqrnn were superior in terms of reliability (ICC values between 0.94 - 0.98), as well as predicting age progression over a longer time span.

Conclusion

Of the six packages, pyment and brainageR consistently showed the highest accuracy and test-retest reliability.
The sequence of regional structural disconnectivity due to multiple sclerosis lesions
Authors: Tozlu Ceren , Olafson Emily , Jamison Keith , Demmon Emily , Kaunzner Ulrike , Marcille Melanie , Zinger Nicole , Michaelson Nara , Safi Neha , Nguyen Thanh , Gauthier Susan , Kuceyeski Amy
Published: January 2023

Objective

Prediction of disease progression is challenging in multiple sclerosis (MS) as the sequence of lesion development and retention of inflammation within a subset of chronic lesions is heterogeneous among patients. We investigated the sequence of lesion-related regional structural disconnectivity across the spectrum of disability and cognitive impairment in MS.

Methods

In a full cohort of 482 patients, the Expanded Disability Status Scale was used to classify patients into (i) no or mild vs (ii) moderate or severe disability groups. In 363 out of 482 patients, Quantitative Susceptibility Mapping was used to identify paramagnetic rim lesions (PRL), which are maintained by a rim of iron-laden innate immune cells. In 171 out of 482 patients, Brief International Cognitive Assessment was used to identify subjects with cognitive impairment. Network Modification Tool was used to estimate the regional structural disconnectivity due to MS lesions. Discriminative event-based modeling was applied to investigate the sequence of regional structural disconnectivity due to all representative lesions across the spectrum of disability and cognitive impairment.

Results

Structural disconnection in the ventral attention and subcortical networks was an early biomarker of moderate or severe disability. The earliest biomarkers of disability progression were structural disconnections due to PRL in the motor-related regions. Subcortical structural disconnection was an early biomarker of cognitive impairment.

Interpretation

MS lesion-related structural disconnections in the subcortex is an early biomarker for both disability and cognitive impairment in MS. PRL-related structural disconnection in the motor cortex may identify the patients at risk for moderate or severe disability in MS.
Deep learning enables fast, gentle STED microscopy
Authors: Ebrahimi Vahid , Stephan Till , Kim Jiah , Carravilla Pablo , Eggeling Christian , Jakobs Stefan , Han Kyu Young
Published: January 2023

STED microscopy is widely used to image subcellular structures with super-resolution. Here, we report that denoising STED images with deep learning can mitigate photobleaching and photodamage by reducing the pixel dwell time by one or two orders of magnitude. Our method allows for efficient and robust restoration of noisy 2D and 3D STED images with multiple targets and facilitates long-term imaging of mitochondrial dynamics.
Multi-Omic Signatures of Sarcoidosis and Progression in Bronchoalveolar Lavage Cells
Authors: Konigsberg Iain R. , Lin Nancy W. , Liao Shu-Yi , Liu Cuining , MacPhail Kristyn , Mroz Margaret M. , Davidson Elizabeth , Restrepo Clara I. , Sharma Sunita , Li Li , Maier Lisa A. , Yang Ivana V.
Published: January 2023

Introduction

Sarcoidosis is a heterogeneous, granulomatous disease that can prove difficult to diagnose, with no accurate biomarkers of disease progression. Therefore, we profiled and integrated the DNA methylome, mRNAs, and microRNAs to identify molecular changes associated with sarcoidosis and disease progression that might illuminate underlying mechanisms of disease and potential genomic biomarkers.

Methods

Bronchoalveolar lavage cells from 64 sarcoidosis subjects and 16 healthy controls were used. DNA methylation was profiled on Illumina HumanMethylationEPIC arrays, mRNA by RNA-sequencing, and miRNAs by small RNA-sequencing. Linear models were fit to test for effect of diagnosis and phenotype, adjusting for age, sex, and smoking. We built a supervised multi-omics model using a subset of features from each dataset.

Results

We identified 46,812 CpGs, 1,842 mRNAs, and 5 miRNAs associated with sarcoidosis versus controls and 1 mRNA,SEPP1- a protein that supplies selenium to cells, associated with disease progression. Our integrated model emphasized the prominence of the PI3K/AKT1 pathway in sarcoidosis, which is important in T cell and mTOR function. Novel immune related genes and miRNAs includingLYST, RGS14, SLFN12L, and hsa-miR-199b-5p, distinguished sarcoidosis from controls. Our integrated model also demonstrated differential expression/methylation ofIL20RB, ABCC11, SFSWAP, AGBL4, miR-146a-3p, and miR-378b between non-progressive and progressive sarcoidosis.

Conclusions

Leveraging the DNA methylome, transcriptome, and miRNA-sequencing in sarcoidosis BAL cells, we detected widespread molecular changes associated with disease, many which are involved in immune response. These molecules may serve as diagnostic/prognostic biomarkers and/or drug targets, although future testing will be required for confirmation.
Hyperextended telomeres promote C-circle formation in telomerase positive human cells
Authors: Jones Celina Y. , Williams Christopher L. , Moreno Sara P. , Morris Danna K. , Mondello Chiara , Karlseder Jan , Bertuch Alison A.
Published: January 2023

Telomere length maintenance is crucial to cancer cell immortality. Up to 15% of cancers utilize a telomerase-independent, recombination-based mechanism termed alternative lengthening of telomeres (ALT). The primary ALT biomarker is the C-circle, a type of circular DNA with extrachromosomal telomere repeats (cECTRs). How C-circles form is not well characterized. To investigate C-circle formation in telomerase+ cells, we studied the human cen3tel cell line, in which telomeres progressively hyper-elongated postTERT-immortalization. cECTR signal was observed in 2D gels and C-circle assays but not t-circle assays, which also detect cECTRs. Telomerase activity and C-circle signal were not separable in the analysis of clonal populations, consistent with C-circle production occurring within telomerase+ cells. Two other long telomere, telomerase+ (LTT+) cell lines, HeLa1.3 (~23 kb telomeres) and HeLaE1 (~50 kb telomeres), had similar cECTR properties. Telomerase activity did not directly impact C-circle signal in LTT+ cells; instead, C-circle signal correlated with telomere length. LTT+ lines were less sensitive to hydroxyurea than an ALT+ cell line, suggesting that ALT status is a stronger contributor to replication stress levels than telomere length. Additionally, FANCM did not suppress C-circles in LTT+ cells as it does in ALT+ cells. Thus, C-circle formation may be driven by telomere length, independently of telomerase and replication stress, highlighting limitations of C-circles as a stand-alone ALT biomarker.
Drosophila activins adapt gut size to food intake and promote regenerative growth
Authors: Christensen Christian F. , Laurichesse Quentin , Loudhaief Rihab , Colombani Julien , Andersen Ditte S.
Published: January 2023

Rapidly renewable tissues adapt different strategies to cope with environmental insults. While tissue repair is associated with increased ISC proliferation and accelerated tissue turnover rates, reduced calorie intake triggers a homeostasis-breaking process causing adaptive resizing of the gut. Here we show that activins are key drivers of both adaptive and regenerative growth. Activin-β (Act-β) is produced by progenitor cells in response to intestinal infections and stimulates ISC proliferation and turnover rates to promote tissue repair. Dawdle (Daw), a divergent Drosophila activin, signals through its receptor, BaboC, in progenitor cells to promote their maturation into enterocytes (ECs). Daw is dynamically regulated during starvation-refeeding cycles, where it couples nutrient intake with progenitor maturation and adaptive resizing of the gut. Our results highlight an activin-dependent mechanism coupling nutrient intake with progenitor-to-EC maturation to promote adaptive resizing of the gut and further establish activins as key regulators of adult tissue plasticity.
Activated Oncostatin M signaling drives cancer-associated skeletal muscle wasting
Authors: Domaniku Aylin , Agca Samet , Toledo Batu , Bilgic Sevval Nur , Kashgari Aynur Erkin , Kir Serkan
Published: January 2023

Progressive weakness and muscle loss are associated with multiple chronic conditions including muscular dystrophy and cancer. Cancer-associated cachexia, characterized by dramatic weight loss and fatigue, leads to reduced quality of life and poor survival. Inflammatory cytokines have been implicated in muscle atrophy, however, available anti-cytokine therapies failed to prevent muscle wasting in cancer patients. We previously reported that muscle-specific deletion of the Oncostatin M (OSM) receptor (OSMR) preserved muscle mass and function in tumor-bearing mice. Here, we show that OSM is a potent inducer of muscle atrophy. OSM triggers cellular atrophy in primary myotubes utilizing the JAK/STAT3 pathway. Identification of OSM targets by RNA sequencing revealed the induction of various muscle atrophy-related genes, includingAtrogin1. OSM overexpression in mice caused muscle wasting while the neutralization of circulating OSM protected from tumor-driven loss of muscle mass and function. Our results indicate that activated OSM/OSMR signaling drives muscle atrophy, and the therapeutic targeting of this pathway may be useful in preventing muscle wasting.
Sequential restoring O2then unloading CO2is beneficial against reperfusion injury: role of CO2in metabolism
Authors: Liu Nan , Wang Lv , Xing Ying , Wang Chen
Published: January 2023

CO2is one of main byproducts during mitochondrial oxidation. Under the acute occlusion of coronary artery situation, the intra-tissue pCO2of heart could be extremely high. This CO2accumulation will be acutely unloaded and discharged by blood reperfusion. However, the effect of this intra-tissue CO2accumulation then unloading process on cardiac ischemic reperfusion injury has not been well investigated yet. In the present study, we show that the perfusion with a high level of pCO2and normal pO2in the initial 30min followed by a 30min normal pCO2and normal pO2is better than the perfusion with 1h normal pCO2and normal pO2simultaneously during the reperfusion after a 45min global ischemia in isolated rat hearts. To observe the effect of high pCO2on cellular metabolism, we exposed C2C12 cells under about 370mmHg pCO2to observe the mitochondrial substrate switch and TCA cycle flux change, by using13C tracers. We show that a short time exposure to the extremely high level of pCO2is not completely destructive for cellular metabolism but has specific effects. The high pCO2inhibits pyruvate transport into mitochondria and the next oxidation, switching to more reliance on fatty acid oxidation and enhancing the glutamine oxidation to maintain the TCA cycle. Intriguingly, the high pCO2significantly activates the reductive carboxylation from glutamine, fixation of mitochondrial excessive CO2. The mechanism under the beneficial effect of the high-then-low CO2sequential reperfusion strategy is discussed further.
Early whole-body mutant huntingtin lowering averts changes in proteins and lipids important for synapse function and white matter maintenance in the LacQ140 mouse model
Authors: Shing Kai , Sapp Ellen , Boudi Adel , Liu Sophia , Seeley Connor , Marchionini Deanna , DiFiglia Marian , Kegel-Gleason Kimberly B.
Published: January 2023

Background

Expansion of a triplet repeat tract in exon1 of the HTT gene causes Huntington’s disease (HD). The mutant HTT protein (mHTT) has numerous aberrant interactions with diverse, pleiomorphic effects. No disease modifying treatments exist but lowering mutant huntingtin (mHTT) by gene therapy is a promising approach to treat Huntington’s disease (HD). It is not clear when lowering should be initiated, how much lowering is necessary and for what duration lowering should occur to achieve benefits. Furthermore, the effects of mHTT lowering on brain lipids have not been assessed.

Methods

Using a mHtt-inducible mouse model we analyzed whole body mHtt lowering initiated at different ages and sustained for different time-periods. Subcellular fractionation (density gradient ultracentrifugation), protein chemistry (gel filtration, western blot, and capillary electrophoresis immunoassay), liquid chromatography and mass spectrometry of lipids, and bioinformatic approaches were used to test effects of mHTT transcriptional lowering.

Results

mHTT protein in cytoplasmic and synaptic compartments of the caudate putamen, which is most affected in HD, was reduced 38-52%. Little or no lowering of mHTT occurred in nuclear and perinuclear regions where aggregates formed at 12 months of age. mHtt transcript repression partially or fully preserved select striatal proteins (SCN4B, PDE10A). Total lipids in striatum were reduced in LacQ140 mice at 9 months and preserved by early partial mHtt lowering. The reduction in total lipids was due in part to reductions in subclasses of ceramide (Cer), sphingomyelin (SM), and monogalactosyldiacylglycerol (MGDG), which are known to be important for white matter structure and function. Lipid subclasses phosphatidylinositol (PI), phosphatidylserine (PS), and bismethyl phosphatidic acid (BisMePA) were also changed in LacQ140 mice. Levels of all subclasses other than ceramide were preserved by early mHtt lowering. Pathway enrichment analysis of RNAseq data imply a transcriptional mechanism is responsible in part for changes in myelin lipids, and some but not all changes can be rescued by mHTT lowering.

Conclusions

Our findings suggest that early and sustained reduction in mHtt can prevent changes in levels of select striatal proteins and most lipids but a misfolded, degradation-resistant form of mHTT hampers some benefits in the long term.
PortPred: exploiting deep learning embeddings of amino acid sequences for the identification of transporter proteins and their substrates
Authors: Anteghini Marco , dos Santos Vitor AP Martins , Saccenti Edoardo
Published: January 2023

The physiology of every living cell is regulated at some level by transporter proteins which constitute a relevant portion of membrane-bound proteins and are involved in the movement of ions, small and macromolecules across bio-membranes. The importance of transporter proteins is unquestionable. The prediction and study of previously unknown transporters can lead to the discovery of new biological pathways, drugs and treatments. Here we present PortPred, a tool to accurately identify transporter proteins and their substrate starting from the protein amino acid sequence. PortPred successfully combines pre-trained deep learning-based protein embeddings and machine learning classification approaches and outperforms other state-of-the-art methods. In addition, we present a comparison of the most promising protein sequence embeddings (Unirep, SeqVec, ProteinBERT, ESM-1b) and their performances for this specific task.
Building a Pangenome Alignment Index via Recursive Prefix-Free Parsing
Authors: Oliva Marco , Gagie Travis , Boucher Christina
Published: January 2023

Motivation

Pangenomics alignment has emerged as an opportunity to reduce bias in biomedical research. Traditionally, short read aligners—such as Bowtie and BWA—were used to index a single reference genome, which was then used to find approximate alignments of reads to that genome. Unfortunately, these methods can only index a small number of genomes due to the linear-memory requirement of the algorithms used to construct the index. Although there are a couple of emerging pangenome aligners that can index a larger number of genomes more algorithmic progress is needed to build an index for all available data.

Results

Emerging pangenomic methods include VG, Giraffe, and Moni, where the first two methods build an index a variation graph from the multiple alignment of the sequences, and Moni simply indexes all the sequences in a manner that takes the repetition of the sequences into account. Moni uses a preprocessing technique calledprefix-free parsingto build a dictionary and parse from the input—these, in turn, are used to build the main run-length encoded BWT, and suffix array of the input. This is accomplished in linear space in the size of the dictionary and parse. Therein lies the open problem that we tackle in this paper. Although the dictionary scales nicely (sub-linear) with the size of the input, the parse becomes orders of magnitude larger than the dictionary. To scale the construction of Moni, we need to remove the parse from the construction of the RLBWT and suffix array. We accomplish this, in this paper by applying prefix-free parsing recursively on the parse. Although conceptually simple, this leads to an algorithmic challenge of constructing the RLBWT and suffix array without access to the parse. We solve this problem, implement it, and demonstrate that this improves the construction time by a factor of 8.9 the running time and by a factor of 2.7 the memory required.

Availability

Our implementation is open source and available athttps://github.com/marco-oliva/r-pfbwt.

Contact

Marco Oliva atmarco.oliva@ufl.edu
Electrophysiological signatures of veridical head direction in humans
Authors: Griffiths Benjamin J. , Schreiner Thomas , Schaefer Julia K. , Vollmar Christian , Kaufmann Elisabeth , Quach Stefanie , Remi Jan , Noachtar Soheyl , Staudigl Tobias
Published: January 2023

Information about heading direction is critical for navigation as it provides the means to orient ourselves in space. However, given that veridical head direction signals require physical rotation of the head and most human neuroimaging experiments depend upon fixing the head in position, little is known about how the human brain is tuned to such heading signals. To address this, we asked fifty-two healthy participants undergoing simultaneous EEG and motion tracking recordings (split into two experiments) and ten patients undergoing simultaneous intracranial EEG and motion tracking recordings to complete a series of orientation tasks in which they made physical head rotations to target positions. We then used a series of forward encoding models and linear mixed-effects models to isolate electrophysiological activity that was specifically tuned to heading direction. We identified a robust posterior central signature that predicts changes in veridical head orientation after regressing out confounds including sensory input and muscular activity. Both source localisation and intracranial analysis implicated the medial temporal lobe as the origin of this effect. Subsequent analyses disentangled head direction signatures from signals relating to head rotation and those reflecting location-specific effects. Lastly, when directly comparing head direction and eye gaze-related tuning, we found that the brain maintains both codes while actively navigating, with stronger tuning to head direction in the medial temporal lobe. Together, these results reveal a taxonomy of population-level head direction signals within the human brain that is reminiscent of those reported in the single units of rodents.
Costimulatory domains direct distinct fates of CAR-driven T cell dysfunction
Authors: Selli Mehmet Emrah , Landmann Jack H. , Terekhova Marina , Lattin John , Heard Amanda , Hsu Yu-Sung , Chang Tien-Ching , Chang Jufang , Warrington John , Ha Helen , Kingston Natalie , Hogg Graham , Slade Michael , Berrien-Elliot Melissa M. , Foster Mark , Kersting-Schadek Samantha , Gruszczynska Agata , DeNardo David , Fehniger Todd A. , Artyomov Maxim , Singh Nathan
Published: January 2023

Chimeric antigen receptor (CAR) engineered T cells often fail to enact effector functions after infusion into patients. Understanding the biological pathways that lead CAR T cells to failure is of critical importance in the design of more effective therapies. We developed and validated anin vitromodel that drives T cell dysfunction through chronic CAR activation and interrogated how CAR costimulatory domains contribute to T cell failure. We found that dysfunctional CD28-based CARs targeting CD19 bear hallmarks of classical T cell exhaustion while dysfunctional 41BB-based CARs are phenotypically, transcriptionally and epigenetically distinct. We confirmed activation of this unique transcriptional program in CAR T cells that failed to control clinical disease. Further, we demonstrate that 41BB-dependent activation of the transcription factor FOXO3 is a significant contributor to this dysfunction and disruption ofFOXO3improves CAR T cell function. These findings identify that chronic activation of 41BB leads to novel state of T cell dysfunction that can be alleviated by genetic modification of FOXO3.

Chronic stimulation of CARs containing the 41BB costimulatory domain leads to a novel state of T cell dysfunction that is distinct from T cell exhaustion.
Cytokines reprogram airway sensory neurons in asthma
Authors: Crosson Théo , Bhat Shreyas , Wang Jo-Chiao , Salaun Clara , Fontaine Eleanne , Roversi Katiane , Herzog Herbert , Rafei Moutih , Blunck Rikard , Talbot Sebastien
Published: January 2023

Nociceptor neurons play a crucial role in maintaining the body’s homeostasis by detecting and responding to potential dangers in the environment. However, this function can be detrimental during allergic reactions, since vagal nociceptors can contribute to immune cell infiltration, bronchial hypersensitivity, and mucus imbalance, in addition to causing pain and coughing. Despite this, the specific mechanisms by which nociceptors acquire pro-inflammatory characteristics during allergic reactions are not yet fully understood. In this study, we aimed to investigate the molecular profile of airway nociceptor neurons during allergic airway inflammation and identify the signals driving such reprogramming. Using retrograde tracing and lineage reporting, we identified a unique class of inflammatory vagal nociceptor neurons that exclusively innervate the airways. In the ovalbumin mouse model of airway inflammation, these neurons undergo significant reprogramming characterized by the upregulation of the NPY receptorNpy1r. A screening of cytokines and neurotrophins revealed that IL-1β, IL-13 and BDNF drive part of this reprogramming. IL-13 triggeredNpy1roverexpression in nociceptors via the JAK/STAT6 pathway. In parallel, sympathetic neurons and macrophages release NPY in the bronchoalveolar fluid of asthmatic mice, which limits the excitability of nociceptor neurons. Single-cell RNA sequencing of lung immune cells has revealed that a cell-specific knockout of Npy1r in nociceptor neurons in asthmatic mice leads to an increase in airway inflammation mediated by T cells. Opposite findings were observed in asthmatic mice in which nociceptor neurons were chemically ablated. In summary, allergic airway inflammation reprograms airway nociceptor neurons to acquire a pro-inflammatory phenotype, while a compensatory mechanism involving NPY1R limits nociceptor neurons’ activity.
PP1β opposes classic PP1 function, inhibiting spine maturation and promoting LTP
Authors: Foley Karl , McKee Cody , Mayer Abigail , Ganguly Archan , Barnett Daniel , Ward Nancy , Zhang Yu , Nairn Angus C. , Xia Houhui
Published: January 2023

Protein phosphatase 1 (PP1) regulates synaptic plasticity and has been described as a molecular constraint on learning and memory. There are three neuronal isoforms, PP1α, PP1β, and PP1γ, but little is known about their individual functions. PP1α and PP1γ are assumed to mediate the effects of PP1 on learning and memory based on their enrichment at dendritic spines and their preferential binding to neurabin and spinophilin, major PP1 synaptic scaffolding proteins. However, it was recently discovered that human de novo PP1β mutations cause intellectual disability, suggesting an important but ill-defined role for PP1β. In this study, we investigated the functions of each PP1 isoform in hippocampal synaptic physiology using conditional CA1-specific knockout mice. In stark contrast to classic PP1 function, we found that PP1β promotes synaptic plasticity as well as spatial memory. These changes in synaptic plasticity and memory are accompanied by changes in GluA1 phosphorylation, GluN2A levels, and dendritic spine density and morphology, including silent synapse number. These functions of PP1β reveal a previously unidentified signaling pathway regulating spine maturation and plasticity, broadening our understanding of the complex role of PP1 in synaptic physiology.
Senescence of cortical neurons following persistent DNA double-strand breaks induces cerebrovascular lesions
Authors: Kopsidas Caroline A. , Lowe Clara C. , Zhang Jun , Kang Wenjun , Zhou Xiaoming , Feng Yuanyi
Published: January 2023

DNA double strand breaks (DSBs), neuroinflammation, and vascular alterations in the brain are all associated with neurodegenerative disorders. However, the interconnections between these neuropathological changes and how they act synergistically to promote irreversible neurodegeneration remain unclear. Here we show that abrogating the BRCA1-associated protein Brap in cerebral cortical neurons, as opposed to vascular endothelium cells, causes cerebrovascular defects. This non-cell autonomous effect is mediated by cellular senescence resulting from persistent neuronal DSBs. We show that in the state of senescence, there is a massive upregulation of genes involved in cell secretion, inflammatory responses, and vascular changes, which coincides with cerebral microclots and microbleeds. The vascular lesions intertwine with neuroinflammation and exacerbate neuronal DSBs, culminating in oxidative stress, metabolic alteration, and downregulation of genes essential for neuronal function. By demonstrating the cerebrovascular impact of cortical neuronal DSBs, our data suggest that senescence-associated secretory phenotype can initiate brain-wide neurodegeneration.
The impact of extracellular matrix on the precision medicine utility of pancreatic cancer patient-derived organoids
Authors: Lumibao Jan C. , Okhovat Shira R. , Peck Kristina L. , Lin Xiaoxue , Lande Kathryn , Zou Jingjing , Engle Dannielle D.
Published: January 2023

The use of patient-derived organoids (PDOs) to characterize therapeutic sensitivity and resistance (pharmacotyping) is a promising precision medicine approach. The potential of this approach to inform clinical decisions is now being tested in several large multi-institutional clinical trials. PDOs are cultivated in extracellular matrix from basement membrane extracts (BMEs) that are most commonly acquired commercially. Each clinical site utilizes distinct BME lots and may be restricted due to the availability of commercial BME sources. However, the impact of different sources and lots of BMEs on organoid drug response is unknown. Here, we tested the impact of BME source and lot on proliferation, chemotherapy and targeted therapy drug response, and gene expression in mouse and human pancreatic ductal adenocarcinoma (PDA) organoids. Both human and mouse organoids displayed increased proliferation in Matrigel (Corning) compared to Cultrex (RnD) and UltiMatrix (RnD). However, we observed no substantial impact on drug response when oragnoids were cultured in Matrigel, Cultrex, or UltiMatrix. We also did not observe major shifts in gene expression across the different BME sources, and PDOs maintained their Classical or Basal-like designation. Overall, we find that BME source (Matrigel, Cultrex, UltiMatrix) does not shift PDO dose-response curves and drug testing results, indicating that PDO pharmacotyping is a robust approach for precision medicine.
Time to degree, identity, and grant writing: Lessons learned from a mixed-methods longitudinal case study
Authors: Alvero AJ , Peña Courtney , Moore Amber R , Luqueno Leslie , Barron Cisco B. , Steele Latishya , Eberle Stevie , Botham Crystal M.
Published: January 2023

Time to degree completion is an important metric of academic progress and success for doctoral students. It is also a common way for educational stakeholders to compare programs even if the content of the degree programs varies. But what types of behaviors and experiences are associated with faster times to degree? In this education article, we examine the relationship between receiving competitive research awards (e.g. grant writing) and time to degree for PhD students. We organize our analyses by student identities, specifically gender and underrepresented minority (URM) status, to examine differences in time to degree based on student demographics. Our dataset included students that graduated between academic years 2008-09 through 2018-19. We also interviewed students currently enrolled in these same programs. We find that URM women who won competitive research awards graduate faster than all other students who also won awards but also report lower levels of advisor support. We also find that URM women and all URM students tended to graduate faster compared to other groups of students who did not win awards. Students who reported feeling supported by their advisors, most of which reflected hands-on guidance through the writing process, in the interviews were more likely to apply for grants. Combined, these results highlight that writing grants and specific types of advisor support may influence faster times to degree for bioscience PhD students. This study suggests similar introspective analyses at other institutions and databases are needed.
Autoinhibited kinesin-1 adopts a hierarchical folding pattern
Authors: Tan Zhenyu , Yue Yang , Leprevost Felipe da Veiga , Haynes Sarah E. , Basrur Venkatesha , Nesvizhskii Alexey I. , Verhey Kristen J. , Cianfrocco Michael A.
Published: January 2023

Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine cross-linking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer [kinesin-1 heavy chain (KHC)] and kinesin-1 heterotetramer [KHC bound to kinesin light chain 1 (KLC1)]. Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.