bluuebunny/crossref_metadata_2025 huggingface dataset:
The arrow-of-time in neuroimaging time series identifies causal triggers of brain function
Authors: Bolton Thomas A. W. , Van De Ville Dimitri , Amico Enrico , Preti Maria G. , Liégeois Raphaël
Published: May 2022

Moving from association to causal analysis of neuroimaging data is crucial to advance our understanding of brain function. The arrow-of-time (AoT), i.e., the known asymmetric nature of the passage of time, is the bedrock of causal structures shaping physical phenomena. However, almost all current time series metrics do not exploit this asymmetry, probably due to the difficulty to account for it in modelling frameworks. Here, we introduce an AoT-sensitive metric that captures the intensity of causal effects in multivariate time series, and apply it to high-resolution functional neuroimaging data. We find that that causal effects underlying brain function are more clearly localized in space and time than functional activity or connectivity, thereby allowing us to trace neural pathways recruited in different conditions. Overall, we provide a mapping of the causal brain that challenges the association paradigm of brain function.
Shared and distinctive neighborhoods of emerin and LBR revealed by proximity labeling and quantitative proteomics
Authors: Cheng Li-Chun , Zhang Xi , Abhinav Kanishk , Nguyen Julie A , Baboo Sabyasachi , Martinez-Bartolomé Salvador , Branon Tess C , Ting Alice Y , Loose Esther , Yates John R , Gerace Larry
Published: May 2022

Emerin and LBR are abundant transmembrane proteins of the nuclear envelope (NE) that are concentrated at the inner nuclear membrane (INM). Although both proteins interact with chromatin and nuclear lamins, they have distinctive biochemical and functional properties. Here we have deployed proximity labeling using the engineered biotin ligase TurboID (TbID) and quantitative proteomics to compare the neighborhoods of emerin and LBR in cultured mouse embryonic fibroblasts (MEFs). Our analysis revealed 232 high confidence proximity partners (HCPP) that interact selectively with emerin and/or LBR, 49 of which are shared by both. These included previously characterized NE-concentrated proteins, as well as a host of additional proteins not previously linked to emerin or LBR functions. Many of these are TM proteins of the ER and include two E3 ubiquitin ligases. Using the proximity ligation assay as an orthogonal approach, we validated the interactions described by proximity labeling for 11/12 proteins analyzed, supporting the robustness of our analysis. Overall, this work presents methodology that may be used for large-scale mapping of the landscape of the INM and reveals a group of new proteins with potential functional connections to emerin and LBR.
Microbiome assembly and maintenance across the lifespan of bumble bee workers
Authors: Hammer Tobin J. , Easton-Calabria August , Moran Nancy A.
Published: May 2022

How a host’s microbiome changes over its lifespan can influence development and aging. As these temporal patterns have only been described in detail for humans and a handful of other hosts, an important next step is to compare microbiome dynamics across a broader array of host-microbe symbioses, and to investigate how and why they vary. Here we characterize the temporal dynamics and stability of the bumblebee worker gut microbiome. Bumblebees are a useful symbiosis model given their relatively well-understood life history and simple, host-specific gut bacterial communities. Furthermore, microbial dynamics may influence bumblebee health and pollination services. We combined high-temporal-resolution sampling with 16S rRNA gene sequencing, quantitative PCR, and shotgun metagenomics to characterize gut microbiomes over the adult lifespan of Bombus impatiens workers. To understand how hosts may control (or lose control of) the gut microbiome as they age, we also sequenced hindgut transcriptomes. We found that, at the community level, microbiome assembly is highly predictable and similar to patterns of primary succession observed in the human gut. At the same time, partitioning of strain-level bacterial variants among colonies suggests stochastic colonization events similar to those observed in flies and nematodes. We also find strong differences in temporal dynamics among symbiont species, suggesting ecological differences among microbiome members in colonization and persistence. Finally, we show that both the gut microbiome and host transcriptome—including expression of key immunity genes—stabilize, as opposed to senesce, with age. We suggest that in highly social groups such as bumblebees, maintenance of both microbiomes and immunity contribute to the inclusive fitness of workers, and thus remain under selection even in old age. Our findings provide a foundation for exploring the mechanisms and functional outcomes of bee microbiome succession, and for comparative analyses with other host-microbe symbioses.
Mechanism of Lys6 poly-ubiquitin specificity by the L. pneumophila deubiquitinase LotA
Authors: Warren Gus D. , Kitao Tomoe , Franklin Tyler G. , Nguyen Justine V. , Geurink Paul P. , Kubori Tomoko , Nagai Hiroki , Pruneda Jonathan N.
Published: May 2022

The versatility of ubiquitination to impose control over vast domains of eukaryotic biology is due, in part, to diversification through differently-linked poly-ubiquitin chains. Deciphering the signaling roles for some poly-ubiquitin chain types, including those linked via K6, has been stymied by a lack of stringent linkage specificity among the implicated regulatory proteins. Forged through strong evolutionary pressures, pathogenic bacteria have evolved intricate mechanisms to regulate host ubiquitin, and in some cases even with exquisite specificity for distinct poly-ubiquitin signals. Herein, we identify and characterize a deubiquitinase domain of the secreted effector protein LotA from Legionella pneumophila that specifically regulates K6-linked poly-ubiquitin during infection. We demonstrate the utility of LotA as a tool for studying K6 poly-ubiquitin. By determining apo and diUb-bound structures, we identify the mechanism of LotA activation and K6 poly-ubiquitin specificity, and identify a novel ubiquitin-binding domain utilized among bacterial deubiquitinases.
Phosphorylation Status of B Beta Subunit Controls PP2A activity in Ethylene-mediated Root Growth Inhibition
Authors: Shao Zhengyao , Zhao Bo , Kotla Prashanth , Burns Jackson G. , Tran Jaclyn , Ke Meiyu , Chen Xu , Browning Karen S. , Qiao Hong
Published: May 2022

The various combinations and regulations of different subunits of phosphatase PP2A holoenzymes underlie their functional complexity and importance. We found that phosphorylation status of Bβ of PP2A acts as a switch to regulate the activity of PP2A. In the absence of ethylene, phosphorylated Bβ leads to an inactivation of PP2A; the substrate EIR1 remains to be phosphorylated, preventing the EIR1 mediated auxin transport in epidermis, leading to normal root growth. Upon the ethylene treatment, the dephosphorylated Bβ mediates the formation of A2-C4-Bβ protein complex to activate PP2A, resulting in the dephosphorylation of EIR1 to promote auxin transport in epidermis of elongation zone, leading to root growth inhibition. Altogether, our research revealed a novel molecular mechanism by which the dephosphorylation of Bβ subunit switches on the PP2A activity to dephosphorylate EIR1 to establish EIR1 mediated auxin transport in epidermis in elongation zone for root growth inhibition in response to ethylene.

Significance Statement

Root growth is critical to the establishment of planted seedlings. Ethylene plays an important role in the root growth. Yet, the molecular mechanisms that how ethylene regulates the root growth are largely unexplored. This research sheds light on the molecular mechanisms of the determination of the functional specificity and activity of PP2A in response to stimulus in cell type specific manner and reveals the novel molecular mechanism through which ethylene signaling regulates EIR1 dephosphorylation through Bβ dephosphorylation to active EIR1 mediated auxin transport in epidermis in elongation zone, leading to root growth inhibition.
Drosophila melanogasteris a powerful host model to study mycobacterial virulence
Authors: Fuentes Esther , Sivakumar Niruja , Selvik Linn-Karina , Arch Marta , Cardona Pere Joan , Ioerger Thomas R. , Dragset Marte Singsås
Published: May 2022

Drosophila melanogaster(Drosophila), the common fruit fly, is one of the most extensively studied animal models we have, with a broad, advanced, and organized research community with tools and mutants readily available at low cost. Yet,Drosophilahas barely been exploited to understand the underlying mechanisms of mycobacterial infections, including those caused by the top-killer pathogenMycobacterium tuberculosis(Mtb). In this study, we aimed to investigate whetherDrosophilais a suitable host model to study mycobacterial virulence, usingMycobacterium marinum(Mmar) to model mycobacterial pathogens. First, we validated that an established mycobacterial virulence factor, EccB1 of the ESX-1 Type VII secretion system, is required forMmargrowth within the flies. Second, we identifiedMmarvirulence factors inDrosophilain a high-throughput genome-wide manner using transposon insertion sequencing (TnSeq). Of the 181 identified virulence genes, the vast majority (91%) had orthologs inMtb, suggesting that the encoded virulence mechanisms may be conserved acrossMmarandMtb. Finally, we validated one of the novelMmarvirulence genes we identified, a putative ATP-binding protein ABC transporter encoded bymmar_1660, as required for full virulence during bothDrosophilaand human macrophage infection. Together, our results show thatDrosophilais a powerful host model to study and identify novel mycobacterial virulence factors relevant to human infection.
Adult-born granule cells improve stimulus encoding and discrimination in the dentate gyrus
Authors: Arribas Diego M. , Marin-Burgin Antonia , Morelli Luis G.
Published: May 2022

Heterogeneity plays an important role in diversifying neural responses to support brain function. Adult neurogenesis provides the dentate gyrus with a heterogeneous population of granule cells (GCs) that were born and developed their properties at different times. Immature GCs have distinct intrinsic and synaptic properties than mature GCs and are needed for correct encoding and discrimination in spatial tasks. How immature GCs enhance the encoding of information to support these functions is not well understood. Here, we record the responses to fluctuating current injections of GCs of different ages to study how they encode stimuli. Immature GCs produce unreliable responses compared to mature GCs, exhibiting imprecise spike timings across repeated stimulation. We use a statistical model to describe the stimulus-response transformation performed by GCs of different ages. We fit this model to the data and obtain parameters that capture GCs encoding properties. Parameter values from this fit reflect the maturational differences of the population and indicate that immature GCs perform a differential encoding of stimuli. To study how this age heterogeneity influences encoding by a population, we perform stimulus decoding using populations that contain GCs of different ages. We find that, despite their individual unreliability, immature GCs enhance the fidelity of the signal encoded by the population and improve the discrimination of similar time dependent stimuli. Thus, the observed heterogeneity confers the population with enhanced encoding capabilities.
A human and rhesus macaque interferon-stimulated gene screen reveals ARHGEF3/XPLN as an antiviral gene against hepatitis C virus and other flaviviruses
Authors: G Bamford Connor G , Cortes Elihu-Aranday , Sanchez-Velazquez Ricardo , Mullan Catrina , Kohl Alain , Patel Arvind H. , Wilson Sam J. , McLauchlan John
Published: May 2022

Natural hepatitis C virus (HCV) infection is restricted to humans whereas in other primates such as rhesus macaques, the virus is non-permissive. To identify human and rhesus macaque genes that differ or share the ability to inhibit HCV replication, we conducted a medium-throughput screen of lentivirus-expressed host genes that disrupt replication of HCV subgenomic replicon RNA expressing secreted Gaussia luciferase. A combined total of >800 interferon-stimulated genes (ISGs) were screened. Our findings confirmed established anti-HCV ISGs, such as IRF1, PKR and DDX60. Novel species-specific inhibitors were also identified and independently validated. Using a cell-based system that recapitulates productive HCV infection, we identified the ‘Rho Guanine Nucleotide Exchange Factor 3’ gene (ARHGEF3) from both species as a restriction factor for full-length virus replication. Mechanistically, ARHGEF3-mediated inhibition was ablated by mutating a critical GEF active site residue and deleting the N-terminal portion of the protein. Additionally, replication of two mosquito-borne flaviviruses, yellow fever virus (YFV) and Zika virus (ZIKV), were reduced in ARHGEF3-expressing cell lines compared to controls. In conclusion, we ascribe novel antiviral activity to the cellular gene ARHGEF3 that inhibits replication of HCV and other important human viral pathogens belonging to the Flaviviridae, and is conserved between humans and rhesus macaques.
Induced pluripotent stem cells and cerebral organoids from the critically endangered Sumatran rhinoceros
Authors: Zywitza Vera , Frahm Silke , Krüger Norman , Weise Anja , Göritz Frank , Hermes Robert , Holtze Susanne , Colleoni Silvia , Galli Cesare , Drukker Micha , Hildebrandt Thomas B. , Diecke Sebastian
Published: May 2022

Less than 80 Sumatran rhinos (SR, Dicerorhinus sumatrensis) are left on earth. Habitat loss and limited breeding possibilities are the greatest threats for the species and lead to a continuous population decline. To stop erosion of genetic diversity, reintroduction of genetic material is indispensable. However, as the propagation rate of captive breeding is far too low, innovative technologies have to be developed. Induced pluripotent stem cells (iPSCs) are a powerful tool to fight extinction. They give rise to each cell within the body including gametes, and provide a unique modality to preserve genetic material across time. Additionally, they enable studying species-specific developmental processes.

Here, we generate iPSCs from the last male Malaysian SR Kertam, who died in 2019, and characterize them comprehensively. Differentiation in cells of the three germ layers and cerebral organoids demonstrate their high quality and great potential for supporting rescue of this critically endangered species.

HIGHLIGHTS

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Characterization of Sumatran Rhino (SR) fibroblasts

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Generation of SR induced pluripotent stem cells (SR-iPSCs)

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SR-iPSCs generate cells of the three germ layers

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SR-iPSCs give rise to cerebral organoids
Transretinal migration of astrocytes and brain/spinal cord-like cells arising from transplanted human retinal organoids
Authors: Liu Ying V. , Santiago Clayton P. , Sogunro Akin , Konar Gregory J. , Hu Ming-wen , McNally Minda M. , Lu Yu-chen , Li Zhuo-lin , Agakishiev Dzhalal , Hadyniak Sarah E. , Hussey Katarzyna A. , Creamer Tyler J. , Orzolek Linda D. , Teng Derek , Qian Jiang , Jiang Zheng , Johnston Robert J. , Blackshaw Seth , Singh Mandeep S.
Published: May 2022

Human retinal organoid transplantation can potentially restore vision in patients with degenerative retinal diseases. How the recipient retina regulates the maturation, fate specification, and migration of transplanted organoid cells is unknown. We transplanted human retinal organoid-derived cells into photoreceptor-deficient mice, conducted histology and single-cell RNA sequencing analyses, and observed two main classes of graft-derived cells. The first class consisted of retinal astrocytes and brain/spinal cord-like neural precursors, absent or rare in cultured organoids, that migrated into all recipient retinal layers and traveled long distances. The second class consisted of retinal progenitor-derived cells, including rods and cones, that remained in the subretinal space and matured more rapidly than photoreceptors in culture. These data suggest that the recipient subretinal space promotes the maturation of transplanted photoreceptors while inducing or expanding migratory cell populations that are not normally derived from retinal progenitors. These findings have important implications for cell-based treatment of retinal diseases.
Insights into the genomics of clownfish adaptive radiation: the genomic substrate of the diversification
Authors: Marcionetti Anna , Salamin Nicolas
Published: May 2022

Clownfishes are an iconic group of coral reef fishes that evolved a mutualistic interaction with sea anemones, which triggered the rapid diversification of the group. We investigated the genomic architecture underlying this process to determine the genomic characteristics associated with the adaptive radiation of the group and assess the mechanisms of parallel evolution in clownfishes.

We took advantage of the available genomic data of five pairs of closely related but ecologically divergent clownfish species to perform comparative genomic analyses. We found that clownfish genomes show two bursts of transposable elements, overall accelerated coding evolution, and topology inconsistencies potentially resulting from hybridization events. These characteristics possibly facilitated the rapid diversification of the group. We also detected a signature of positive selection throughout the radiation in 5.4 % of the clownfish genes. Among them, five presented functions associated with social behavior and ecology. They could have potentially played a role in the evolution of size-based hierarchical social structure so particular to clownfishes. Finally, we found genes with patterns of either relaxation or intensification of purifying selection and signals of positive selection linked with clownfish ecological divergence, suggesting some level of parallel evolution during the diversification of the group.

Altogether, these results provide the first insights into the genomic substrate of clownfish adaptive radiation. This work integrates the growing collection of studies investigating the genomic mechanisms governing species diversification, which brings us a step closer to understanding how biodiversity on Earth is created
Assessment of Human Renal Transporter Based Drug-Drug Interactions Using Proximal Tubule Kidney-Chip
Authors: Nookala Anantha Ram , Ronxhi Janey , Sliz Josiah , Jeanty Sauvear , Manatakis Dimitris V. , Jadalannagari Sushma , Hamilton Geraldine , Park Hyoungshin , He Yu , Lavarias Mitchell , Luo Gang , Jang Kyung-Jin , Mckenzie Donald
Published: May 2022

Study of renal transporters is crucial for understanding drug disposition and toxicity, and more importantly, predicting potential drug-drug interactions (DDIs). However, conventional in vitro models often fail to predict renal transporter activity and are not scalable to a predictive clinical outcome due to in vitro-in vivo discrepancy. Here, we successfully developed a human Proximal Tubule Kidney-Chip model that emulated in vivo renal physiology and function to assess renal transporter-based DDIs. Active and improved functionality of key renal transporters including p-glycoprotein (P-gp), multidrug and toxin extrusion (MATE) 1 and 2-K, organic anion transporter (OAT) 1 and 3, and organic cation transporter (OCT) 2 were demonstrated using appropriate probe substrates in Kidney-Chips compared to transwell controls. Moreover, comparative transcriptomic analysis revealed that key efflux and uptake transporters were expressed significantly higher in the Kidney-Chip compared to the transwell. Additionally, key parameters obtained from substrate-inhibitor interactions in the model were used to predict clinical DDIs as well as clearance values, which were closer to in vivo clearances. Overall, these results support that the human Proximal Tubule Kidney-Chip can reliably assess the role of human renal transporters in drug disposition and drug interactions, providing a critical tool to assess renal transport in vitro.
Longitudinal comparison of the developing gut virome in infants and their mothers
Authors: Granados Andrea C , Ley Catherine , Walters William A. , Federman Scot , Santos Yale , Haggerty Thomas , Sotomayor-Gonzalez Alicia , Servellita Venice , Ley Ruth E , Parsonnet Julie , Chiu Charles Y
Published: May 2022

The virome of the human gut and its development in early life are poorly understood. Here we performed viral metagenomic sequencing on stool samples from a multiethnic, socioeconomically diverse cohort of 53 infants collected longitudinally over their first 3 years of life and their mothers to investigate and compare their viromes. The asymptomatic infant virome consisted of bacteriophages, dietary/environmental viruses, and human pathogenic viruses, in contrast to the material virome, in which sequence reads from human pathogenic viruses were absent or present at extremely low levels. Picornaviruses and phages in the family Microviridae (microviruses) dominated the infant virome, while microviruses and tomato mosaic virus dominated the maternal virome. As the infants aged, the human pathogenic and dietary/environmental virus components remained distinct from the materal virome, while the phage component evolved to become more similar. However, the composition of the evolving infant virome was not determined by the mother and was still maturing to the adult virome at three years of age.

Importance

The development of the human gut virome in early childhood is poorly understood. Here we use viral metagenomic sequencing in a cohort of 53 infants to the characterize their gut viromes and compare them to their mothers’.. This study finds that the infant virome consists of phages and human pathogenic viruses in asymptomatic individuals and is still maturing into the adult virome at three years of age.
The Drosophila attP40 docking site and derivatives are insertion mutations of MSP300
Authors: van der Graaf Kevin , Srivastav Saurabh , Singh Pratibha , McNew James A , Stern Michael
Published: May 2022

The ϕC31 integrase system is widely used in Drosophila to allow transgene targeting to specific loci. Over the years, flies bearing any of more than 100 attP docking sites have been constructed. One popular docking site, termed attP40, is located close to the Nesprin-1 orthologue MSP300 and lies upstream of certain MSP300 isoforms and within the first intron of others. Here we show that attP40 causes larval muscle nuclear clustering, which is a phenotype also conferred by MSP300 mutations. We also show that flies bearing insertions within attP40 can exhibit decreased MSP300 transcript levels in third instar larvae. Finally, chromosomes carrying certain “transgenic RNAi project” (TRiP) insertions into attP40 can confer pupal or adult inviability, or infertility. These phenotypes do not require transcription from the insertions within attP40. These results demonstrate that attP40 and insertion derivatives act as MSP300 insertional mutations. These findings should be considered when interpreting data from attP40-bearing flies.
Multifunctional flexible electro-optical arrays for simultaneous spatiotemporal cardiac mapping and modulation
Authors: Obaid Sofian N. , Chen Zhiyuan , Madrid Micah , Lin Zexu , Tian Jinbi , Humphreys Camille , Adams Jillian , Daza Nicolas , Balansag Jade , Efimov Igor R. , Lu Luyao
Published: May 2022

Bioelectronic devices that allow simultaneous accurate monitoring and control of the spatiotemporal patterns of cardiac activity provide an effective means to understand the mechanisms and optimize therapeutic strategies for heart disease. Optogenetics is a promising technology for cardiac research due to its advantages such as cell-type selectivity and high space-time resolution, but its efficacy is limited by the insufficient number of modulation channels and lack of simultaneous spatiotemporal mapping capabilities in current cardiac optogenetics tools. Here we present soft implantable electro-optical cardiac devices integrating multilayered highly uniform arrays of transparent microelectrodes and multicolor micro-light-emitting-diodes in thin, flexible platforms for mechanically compliant high-content electrical mapping and single-/multi-site optogenetics and electrical stimulation without light-induced artifacts. Systematic benchtop characterizations, together with ex vivo and in vivo evaluations on healthy and diseased small animal and human hearts demonstrate their functionalities in real-time spatiotemporal mapping and control of cardiac rhythm and function, with broad applications in basic and ultimately clinical cardiology.
Comparing Heart Rate Variability in Canadian Armed Forces Patients to Control Participants without Chronic Pain/Mental Health Issues
Authors: Kamal Latifah , Minerbi Amir , Sahar Tali , Heilman Keri J. , Besemann LCol Markus , Sreenivasan Vidya , Aggerwal Salena , Gupta Gaurav
Published: May 2022

Background

The autonomic nervous system is subserved by the sympathetic and parasympathetic which regulate vital involuntary physiological functions like heart rate. Parasympathetic activity can be measured from the high-frequency component of heart rate variability (HRV), measured via the amplitude of RSA, as a possible predictor for mental health and chronic pain disorders. Therefore, investigators looked to correlate HRV with chronic pain when compared healthy controls.

Methods

As part of a larger ongoing study, patients complete pre-defined questionnaires on their pain condition, potential risk factors, and function. For patients and controls investigators collected performance and cardiac measures (RSA, LF-HRV, heart period) while at rest, walking and lifting tests. This analysis focused on differences in heart rate variability measures between 100 patients and 48 controls.

Results

Preliminary analysis revealed demographic and anthropometric variables varied significantly between groups. When comparing HRV measures, respiratory sinus arrhythmia (RSA) during lying and sitting were significantly decreased in patients compared to controls while heart period lying and walking were significantly increased in patients. Correlation analysis revealed significant positive correlation between RSA during lying and sitting when looking at age, gender, and weight. Heart periods during lying and walking were negatively correlated with gender and weight.

Discussion

To our knowledge it is the first study to look at chronic pain and HRV in the Canadian Forces, while also collecting data on patient reported outcomes, and during various resting and activities. Many potential limitations exist for this study including challenges with respect to controlling for known confounders of heart variability.

Conclusion

By establishing heart rate variability as a correlate of chronic pain, the outcome of this project could potentially improve quality of care for patients with these conditions. Further work controlling for confounders and relating HRV to pain severity, subtypes, patient reported outcomes and functional abilities will be required to determine the exact value for clinical decision making.
Pan-cancer scale screening reveals NRF2 associated immunoevasive characteristics in non-small cell lung cancer and squamous malignancies
Authors: Härkönen Jouni , Pölönen Petri , Jawahar Deen Ashik , Selvarajan Ilakya , Teppo Hanna-Riikka , Dimova Elitsa Y , Kietzmann Thomas , Ahtiainen Maarit , Eklund Tiia , Kuopio Teijo , Talvitie Eva-Maria , Taimen Pekka , Kallajoki Markku , Kaikkonen Minna U , Heinäniemi Merja , Levonen Anna-Liisa
Published: May 2022

The NRF2 pathway is frequently activated in various cancer types, yet a comprehensive analysis of its effects across different malignancies is currently lacking. We developed a robust NRF2 activity metric and utilized it to conduct a pan-cancer wide analysis of oncogenic NRF2 signaling. We identified a distinct immunoevasive phenotype where high NRF2 activity is associated with low interferon-gamma (IFNγ), HLA-I expression and T-cell infiltration spanning non-small cell lung cancer (NSCLC) and squamous malignancies of head and neck area, cervix and esophagus. In squamous cell cancers, NRF2 overactive tumors comprise a molecular phenotype with SOX2/TP63 amplification, TP53 mutation and CDKN2A loss. These immune-cold NRF2 hyperactive diseases are associated with upregulation of immunomodulatory NAMPT, WNT5A, SPP1, SLC7A11 and SLC2A1 that represent candidate NRF2 target genes, suggesting direct modulation of the tumor immune milieu. Based on single-cell mRNA data, coupled with a priori information on intercellular ligand-receptor interactions, cancer cells of this subtype exhibit decreased expression of IFNγ responsive ligands, and increased expression of immunosuppressive ligands NAMPT, SPP1 and WNT5A that mediate signaling in intercellular crosstalk. As we observed differential cytokine mRNA expression with IFNγ treatment in NSCLC adenocarcinoma subtype, we explored the cytokine secretome in vitro. We found that secreted neutrophil chemoattractants interleukin-8 (CXCL8) and ENA-78 (CXCL5) are elevated in NRF2 overactive cells, suggesting contribution of immunosuppressive neutrophils in NRF2 driven immune escape. Importantly, as overactive NRF2 is associated with immune-cold characteristics, our results highlight the utility of NRF2 pathway activation as a putative biomarker for stratifying immune-checkpoint blockade responders and non-responders across NSCLC and squamous cancers.

Abstract Figure
Alignment of Single-Molecule Sequencing Reads by Enhancing the Accuracy and Efficiency of Locality-Sensitive Hashing
Authors: Nikaein Hassan , Sharifi-Zarchi Ali
Published: May 2022

Aligning single-molecule sequencing (SMS) reads to a reference genome has been computationally challenging due to the high sequencing error rates in this technology. Short distances between consecutive errors in SMS reads confront finding seeds, subsequences of the reads with exact matches to the reference, that specifically target a unique genomic position. To overcome this issue, one can look for similarities, rather than exact matches. MinHash, a locality-sensitive hashing (LSH) scheme, measures the similarity of two sequences by listing all k-mers of each one and approximating the fraction of common k-mers between them using a family of hash functions, which usually includes hundreds to thousands of different hash functions in order to increase the measurement accuracy. MinHash is used to address various bioinformatics problems, including the assembly of SMS reads. Here, we enhance both the efficiency and accuracy of the MinHash scheme by algorithmic techniques. We use a single hash function, rather than hundreds or thousands of different hash functions as used in the other MinHash-based algorithms, without losing the accuracy. We also double the size of the seed sequences by allowing one sequencing error of any form inside a pair of k-mers, which has a significant impact on the accuracy. We show algorithm, called Aryana-LoR, outperforms the accuracy of the other existing SMS aligners in both E-coli and Human genomes.

Availability

Aryana-LoR is freely available at https://gitlab.com/hnikaein/aryana-LoR
Identifying Neural Correlates of Balance Deficits in Traumatic Brain Injury Using Partial Least Squares Correlation Analysis
Authors: Handiru Vikram Shenoy , Suviseshamuthu Easter S. , Saleh Soha , Su Haiyan , Yue Guang H. , Allexandre Didier
Published: May 2022

Background

Balance impairment is one of the most debilitating consequences of Traumatic Brain Injury (TBI). To study the neurophysiological underpinnings of balance impairment, the brain functional connectivity during perturbation tasks can provide new insights. To better characterize the association between the task-relevant functional connectivity and the degree of balance deficits in TBI, the analysis needs to be performed on the data stratified based on the balance impairment. However, such stratification is not straightforward, and it warrants a data-driven approach.

Approach

We conducted a study to assess the balance control using a computerized posturography platform in 17 individuals with TBI and 15 age-matched healthy controls. We stratified the TBI participants into balance-impaired and non-impaired TBI usingk-means clustering of either center of pressure (COP) displacement during a balance perturbation task or Berg Balance Scale (BBS) score as a functional outcome measure. We analyzed brain functional connectivity using the imaginary part of coherence across different cortical regions in various frequency bands. These connectivity features are then studied using the mean-centered partial least squares correlation (MC-PLSC) analysis, which is a multivariate statistical framework with the advantage of handling more features than the number of samples, thus making it suitable for a small-sample study.

Main Results

Based on the nonparametric significance testing using permutation and bootstrap procedure, we noticed that the theta-band connectivity strength in the following regions of interest significantly contributed to distinguishing balance impaired from non-impaired population, regardless of the type of strat-ification:left middle frontal gyrus, right paracentral lobule, precuneus, andbilateral middle occipital gyri.

Significance

Identifying neural regions linked to balance impairment enhances our understanding of TBI-related balance dysfunction and could inform new treatment strategies. Future work will explore the impact of balance platform training on sensorimotor and visuomotor connectivity.
Variation in the ACE2 receptor has limited utility for SARS-CoV-2 host prediction
Authors: Mollentze Nardus , Keen Deborah , Munkhbayar Uuriintuya , Biek Roman , Streicker Daniel G.
Published: May 2022

Transmission of SARS-CoV-2 from humans to other species threatens wildlife conservation and may create novel sources of viral diversity for future zoonotic transmission. A variety of computational heuristics have been developed to pre-emptively identify susceptible host species based on variation in the ACE2 receptor used for viral entry. However, the predictive performance of these heuristics remains unknown. Using a newly-compiled database of 96 species we show that, while variation in ACE2 can be used by machine learning models to accurately predict animal susceptibility to sarbecoviruses (accuracy = 80.2%, binomial confidence interval [CI]: 70.8 – 87.6%), the sites informing predictions have no known involvement in virus binding and instead recapitulate host phylogeny. Models trained on host phylogeny alone performed equally well (accuracy = 84.4%, CI: 75.5 – 91.0%) and at a level equivalent to retrospective assessments of accuracy for previously published models. These results suggest that the predictive power of ACE2-based models derives from strong correlations with host phylogeny rather than processes which can be mechanistically linked to infection biology. Further, biased availability of ACE2 sequences misleads projections of the number and geographic distribution of at-risk species. Models based on host phylogeny reduce this bias, but identify a very large number of susceptible species, implying that model predictions must be combined with local knowledge of exposure risk to practically guide surveillance. Identifying barriers to viral infection or onward transmission beyond receptor binding and incorporating data which are independent of host phylogeny will be necessary to manage the ongoing risk of establishment of novel animal reservoirs of SARS-CoV-2.
Choice of 3D morphometric method leads to diverging interpretations of form–function relationships in the carnivoran calcaneus
Authors: Wimberly Alexa N. , Natale Rossy , Higgins Robert , Slater Graham J.
Published: May 2022

Abstract

Three dimensional morphometric methods are a powerful tool for comparative analysis of shape. However, morphological shape is often represented using landmarks selected by the user to describe features of perceived importance, and this may lead to over confident prediction of form-function relationships in subsequent analyses. We used Generalized Procrustes Analysis (GPA) of 13 homologous 3D landmarks and spherical harmonics (SPHARM) analysis, a homology-free method that describes the entire shape of a closed surface, to quantify the shape of the calcaneus, a landmark poor structure that is important in hind-limb mechanics, for 111 carnivoran species spanning 12 of 13 terrestrial families. Both approaches document qualitatively similar patterns of shape variation, including a dominant continuum from short/stout to long/narrow calcanea. However, while phylogenetic generalized linear models indicate that locomotor mode best explains shape from the GPA, the same analyses find that shape described by SPHARM is best predicted by foot posture and body mass without a role for locomotor mode, though effect sizes for all are small. User choices regarding morphometric methods can dramatically impact macroevolutionary interpretations of shape change in a single structure, an outcome that is likely exacerbated when readily landmarkable features are few.
A D-2-Hydroxyglutarate dehydrogenase mutant reveals a critical role for ketone body metabolism in Caenorhabditis elegans development
Authors: Ponomarova Olga , Zhang Hefei , Li Xuhang , Nanda Shivani , Leland Thomas B. , Fox Bennett W. , Giese Gabrielle E. , Schroeder Frank C. , Yilmaz L. Safak , Walhout Albertha J.M.
Published: May 2022

In humans, mutations in D-2-hydroxyglutarate (D-2HG) dehydrogenase (D2HGDH) result in D-2HG accumulation, delayed development, seizures, and ataxia. While the mechanisms of 2HG-associated diseases have been studied extensively, the endogenous metabolism of D-2HG remains unclear in any organism. Here, we find that, in Caenorhabditis elegans, D-2HG is produced in the propionate shunt, which is transcriptionally activated when flux through the canonical, vitamin B12-dependent propionate breakdown pathway is perturbed. Deletion of the D2HGDH ortholog, dhgd-1, results in embryonic lethality, mitochondrial defects, and the upregulation of ketone body metabolism genes. Viability can be rescued by RNAi of hphd-1, which encodes the enzyme that produces D-2HG, or by supplementing either vitamin B12 or the ketone body 3-hydroxybutyrate (3HB). Altogether, our findings support a model in which C. elegans relies on ketone bodies for energy when vitamin B12 levels are low, and in which a loss of dhgd-1 causes lethality by limiting ketone body production.

HIGHLIGHTS

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D-2-hydroxyglutarate is produced by HPHD-1 in the propionate shunt pathway

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DHGD-1 recycles 2-hydroxyglutarate to sustain flux through the propionate shunt

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dhgd-1 loss perturbs ketone body metabolism and causes embryonic lethality

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3-Hydroxybutyrate, vitamin B12 or hphd-1 RNAi rescue dhgd-1 mutant lethality
Genomic screening reveals UBA1 as a potent and druggable target in c-MYC-high TNBC models
Authors: Jacob Sheeba , Turner Tia H. , Cai Jinyang , Floros Konstantinos V. , Yu Ann K. , Coon Colin M. , Khatri Rishabh , Alzubi Mohammad A. , Jakubik Charles T. , Bouck Ynes M. , Puchalapalli Madhavi , Shende Mayuri , Dozmorov Mikhail G. , Boikos Sosipatros A. , Hu Bin , Harrell J. Chuck , Benes Cyril H. , Koblinski Jennifer E. , Costa Carlotta , Faber Anthony C.
Published: May 2022

Triple negative breast cancer (TNBC) accounts for over 30% of all breast cancer-related deaths, despite accounting for only 10%–15% of total breast cancer cases. Targeted therapy development has largely stalled in TNBC, underlined by a lack of traditionally druggable addictions like receptor tyrosine kinases (RTKs). Here, through full genome CRISPR/Cas9 screening of TNBC models, we have uncovered the sensitivity of TNBCs to the depletion of the Ubiquitin-Like Modifier Activating Enzyme 1 (UBA1). Targeting UBA1 with the first in-class UBA1 inhibitor TAK-243 induced unresolvable ER-stress and activating transcription factor 4 (ATF4)-mediated upregulation of pro-apoptotic NOXA, leading to cell death. In five patient derived xenograft models (PDXs) of TNBC, TAK-243 therapy led to tumor inhibition or frank tumor regression. In an intracardiac metastatic model of TNBC, TAK-243 markedly reduced metastatic burden. Importantly, there was an order of magnitude greater sensitivity of TNBC lines to TAK-243 compared to normal tissue-derived cells. Lastly, c-MYC expression correlates with TAK-243 sensitivity and cooperates with TAK-243 to induce a stress response and cell death. We posit UBA1 is an important new target in TNBC expressing high levels of c-MYC.

Significance

Genomic screening of TNBC cell lines revealed broad sensitivity to depletion of the E1 ubiquitin enzyme, UBA1. Disrupting UBA1 with the first in-class inhibitor TAK-243 in TNBC models induces ER-stress through an ATF4-NOXA axis that is dependent on c-MYC, leading to apoptosis, in vitro and in vivo, primary tumor growth inhibition and metastatic inhibition.
Molecular analysis of a public cross-neutralizing antibody response to SARS-CoV-2
Authors: Yuan Meng , Wang Yiquan , Lv Huibin , Wilson Ian A. , Wu Nicholas C.
Published: May 2022

As SARS-CoV-2 variants of concerns (VOCs) continue to emerge, cross-neutralizing antibody responses become key towards next-generation design of a more universal COVID-19 vaccine. By analyzing published data from the literature, we report here that the combination of germline genes IGHV2-5/IGLV2-14 represents a public antibody response to the receptor-binding domain (RBD) that potently cross-neutralizes all VOCs to date, including Omicron and its sub-lineages. Detailed molecular analysis shows that the complementarity-determining region H3 sequences of IGHV2-5/IGLV2-14-encoded RBD antibodies have a preferred length of 11 amino acids and a conserved HxIxxI motif. In addition, these antibodies have a strong allelic preference due to an allelic polymorphism at amino-acid residue 54 of IGHV2-5, which locates at the paratope. These findings have important implications for understanding cross-neutralizing antibody responses to SARS-CoV-2 and its heterogenicity at the population level as well as the development of a universal COVID-19 vaccine.
stainlib: a python library for augmentation and normalization of histopathology H&E images
Authors: Otálora Sebastian , Marini Niccoló , Podareanu Damian , Hekster Ruben , Tellez David , Van Der Laak Jeroen , Müller Henning , Atzori Manfredo
Published: May 2022

Computational pathology is a domain of increasing scientific and social interest. The automatic analysis of histopathology images stained with Hematoxylin and Eosin (H&E) can help clinicians diagnose and quantify diseases. Computer vision methods based on deep learning can perform on par or better than pathologists in specific tasks [1, 2, 15]. Nevertheless, the visual heterogeneity in histopathology images due to batch effects, differences in preparation in different pathology laboratories, and the scanner can produce tissue appearance changes in the digitized whole-slide images. Such changes impede the application of the trained models in clinical scenarios where there is high variability in the images. We introduce stainlib, an easy-to-use and expandable python3 library that collects and unifies state-of-the-art methods for color augmentation and normalization of histopathology H&E images. stainlib also contains recent deep learning-based approaches that perform a robust stain-invariant training of CNN models. stainlib can help researchers build models robust to color domain shift by augmenting and harmonizing the training data, allowing the deployment of better models in the digital pathology practice.
Cartilage-penetrating hyaluronic acid hydrogel preserves tissue content and reduces chondrocyte catabolism
Authors: Kowalski Michael A. , Fernandes Lorenzo M. , Hammond Kyle E. , Labib Sameh , Drissi Hicham , Patel Jay M.
Published: May 2022

Articular cartilage injuries have a limited healing capacity and, due to inflammatory and catabolic activities, often experience progressive degeneration towards osteoarthritis. Current repair techniques generally provide short-term symptomatic relief; however, the regeneration of hyaline cartilage remains elusive, leaving both the repair tissue and surrounding healthy tissue susceptible to long-term wear. Therefore, methods to preserve cartilage following injury, especially from matrix loss and catabolism, are needed to delay, or even prevent, the deteriorative process. The goal of this study was to develop and evaluate a cartiage-penetrating hyaluronic-acid (HA) hydrogel to improve damaged cartilage biomechanics and prevent tissue degeneration. At time zero, the HA-based hydrogel provided a 46.5% increase in compressive modulus and a decrease in permeability after simulated degeneration of explants (collagenase application). Next, in a degenerative culture model (interleukin-1 β [IL-1β] for 2 weeks), hydrogel application prior to or midway through the culture mitigated detrimental changes to compressive modulus and permeability observed in non-treated explants. Furthermore, localized loss of proteoglycan was observed in degenerative culture conditions alone (non-treated), but hydrogel administration significantly improved the retention of matrix elements. Finally, NITEGE staining and gene expression analysis showed the ability of the HA gel to decrease chondrocyte catabolic activity. These results highlight the importance of reinforcing damaged cartilage with a biomaterial system to both preserve tissue content and reduce catabolism associated with injury and inflammation.
Benefits of global mutant huntingtin lowering diminish over time in a Huntington’s disease mouse model
Authors: Marchionini Deanna M. , Liu Jeh-Ping , Ambesi-Impiombato Alberto , Cox Kimberly , Cirillo Kim , Bansal Mukesh , Mushlin Rich , Brunner Daniela , Ramboz Sylvie , Kwan Mei , Kuhlbrodt Kirsten , Tillack Karsten , Peters Finn , Rauhala Leena , Obenauer John , Greene Jonathan R. , Hartl Christopher , Khetarpal Vinod , Lager Brenda , Rosinski Jim , Aaronson Jeff , Alam Morshed , Signer Ethan , Muñoz-Sanjuán Ignacio , Howland David , Zeitlin Scott O.
Published: May 2022

We have developed a novel inducible Huntington’s disease (HD) mouse model that allows temporal control of whole-body allele-specific mutant Huntingtin (mHtt) expression. We asked whether moderate global lowering of mHtt (∼50%) was sufficient for long-term amelioration of HD-related deficits and, if so, whether early mHtt lowering (before measurable deficits) was required. Both early and late mHtt lowering delayed behavioral dysfunction and mHTT protein aggregation, as measured biochemically. However, long-term follow up revealed that the benefits, in all mHtt lowering groups, attenuated by 12 months of age. While early mHtt lowering attenuated cortical and striatal transcriptional dysregulation evaluated at 6 months of age, the benefits diminished by 12- months of age and late mHtt lowering was unable to ameliorate striatal transcriptional dysregulation at 12 months of age. Only early mHtt lowering delayed the elevation in cerebrospinal fluid neurofilament light chain that we observed in our model starting at 9 months of age. As small-molecule HTT-lowering therapeutics progress to the clinic, our findings suggest that moderate mHtt lowering allows disease progression to continue, albeit at a slower rate, and could be relevant to the degree of mHTT lowering required to sustain long-term benefit in humans.