bluuebunny/crossref_metadata_2025 huggingface dataset:
LncRNA HLA-F-AS1 attenuates the ovarian cancer development by targeting miR-21-3p/PEG3 axis
Authors: Fang Wenhong , Xia Yufang
Published: March 2022

Dysregulated long noncoding RNA (lncRNA) HLA-F-AS1 is depicted in numerous cancers. However, its function in ovarian cancer has yet to be clarified. LncRNA HLA-F-AS1, miR-21-3p, and PEG3 expressions in ovarian cancer tissues and cells were measured via reverse transcription quantitative PCR. Scratch and CCK8 assays were performed to evaluate the cells’ migratory and proliferative abilities, respectively. To assess the expressions of the apoptosis-related proteins Bax and Bcl-2, Western blotting was conducted. Anti-AGO2 RNA immunoprecipitation (RIP) and dual-luciferase reporter assays were executed to study lncRNA HLA-F-AS1’s and PEG3 3′UTR’s interactions to miR-21-3p. Finally, the tumor growth in vivo was inspected by performing a xenograft experiment. Among the ovarian cancer tissues and cells, the expressions of PEG3 and lncRNA HLA-F-AS1 were depleted while an elevated miR-21-3p expression was observed. HLA-F-AS1’s overexpression attenuated ovarian cancer development in vivo and in vitro. MiR-21-3p targeted PEG3 3′UTR while HLA-F-AS1 targeted miR-21-3p. HLA-F-AS1 overexpression mitigated the enhancement brought about by miR-21-3p mimic on ovarian cancer cells’ proliferation and migration. Meanwhile, PEG3 overexpression abrogated miR-21-3p mimic’s function as an oncogene in the progression of ovarian cancer. Ovarian cancer development is suppressed when lncRNA HLA-F-AS1 targets the miR-21-3p/PEG3 axis. This may possibly be a novel therapeutic target for ovarian cancer.
Factors associated with burden among male caregivers for people with dementia
Authors: Tsai Chia-Fen , Huang Mao-Hsuan , Lee Jun-Jun , Jhang Kai-Ming , Huang Ling-Chun , Huang Li-Kai , Lee Wei-Ju , Sung Pi-Shan , Liu Yi-Chien , Ouyang Wen-Chen , Cheng Chih-Ming , Hsu Chih-Cheng , Fuh Jong-Ling
Published: March 2022

Background:

There is a dearth of information on male dementia caregivers in Asia and, in particular, on the factors relating to caregiver burden. We aimed to identify factors that may be associated with burden among male caregivers of people with dementia (PWD).

Methods:

Data were collected from a national dementia registration survey. The caregiver burden was measured with the short version of the Zarit Burden Interview (ZBI). We analyzed the correlation between ZBI scores and variables, such as demographic data of PWD and their male caregivers, caregivers’ monthly income, the relationship between PWD and caregivers, the severity of dementia, physical comorbidities and activities of daily living (ADL) of PWD, and neuropsychiatric symptoms assessed by the Neuropsychiatric Inventory (NPI).

Results:

A total of 509 PWD and their male caregivers were included. The majority of caregivers were sons (72.1%) and husbands (22.0%). Sons had higher ZBI scores than husbands (28.5 ± 15.2 vs 22.0 ± 17.0; p < 0.001). Multivariable linear regression showed that sons as caregivers (β = 7.44, p = 0.034), ADL (β = 0.52, p = 0.002) and NPI_severity subscore of apathy (β = 2.74, p = 0.001) were positively associated with ZBI scores.

Conclusion:

Poor ADL and apathy in PWD and being a patient's son were associated with higher levels of burden among male dementia caregivers. Effective interventions are needed to assist male caregivers in accomplishing their caregiving role and at the same time to alleviate their caregiver burden.
The Effects of Instrumental Balance Training on Balance in Individuals with Unilateral Transtibial Amputation: A Pilot Study
Authors: Kirdi Elif , Yalcin Ali , Keklicek Hilal , Topuz Semra , Ulger Ozlem , Yazicioglu Gul
Published: March 2022

Introduction

With the loss of a lower limb, an individual with amputation may face impaired gait and balance. Different rehabilitation techniques can be used to deal with those functional disabilities. The purpose of this study was to determine whether computerized balance training could have any possible effects on balance in individuals with unilateral transtibial amputation.

Materials and Methods

A total of 16 subjects who used a prosthesis in their daily life and were between 18 and 65 years of age were included in the study. Individuals were randomly divided into two groups: control group (CG) (n = 7) trained with traditional prosthetic rehabilitation and the experimental group (EG) (n = 9) trained with computerized balance training for five sessions for 2 weeks. Percentage of prosthetic weight bearing (PWB) timed up and go test (TUG), single-leg stance test (SLST), postural sway score, and limits of stability (LoS) were evaluated at baseline and posttreatment.

Results

No significant differences were observed in between-group comparisons after treatment. Within-group comparison showed that PWB, SLST, and LoS score increased in EG, whereas only PWB increased in CG.

Conclusions

Similar results were revealed with both computerized and traditional prosthetic training. Although there were no significant differences in between-group comparisons, computerized balance training improved the amputated side single-leg stance and stability limits, which are highly related to fall risk in individuals with amputation.

Clinical Relevance

Clinical relevance: Usage of computerized balance training can be helpful to improve single-leg stance and LoS in individuals with transtibial amputation.
Percent Agreement Between Immunohistochemistry and Next-Generation Sequencing in Testing Patients for Mismatch Repair Deficiency
Authors: Lawrence Lauren , Longacre Teri , Saleem Atif , Kunder Christian
Published: March 2022

The presence of mismatch repair deficiency is frequently assessed in gastrointestinal and gynecologic neoplasms by surgical pathologists using immunohistochemical methods. Targeted next-generation sequencing (NGS) covering some genes in the mismatch repair complex is used with increasing frequency, however, the percent positive and negative agreement of immunohistochemical methods and NGS of mismatch repair genes is not well-described in the literature. We sought to compare performance of immunohistochemistry (IHC) and NGS of mismatch repair genes on our institutional targeted panel. We evaluated the concordance of immunohistochemical and panel-based gene sequencing methods in a retrospective cohort study of patients evaluated at our center with both immunohistochemical and panel-based sequencing. Our NGS panel covers only MLH1 and MSH2, whereas our immunohistochemical panel assesses for expression of MLH1, PMS2, MSH2, and MSH6. We identified 68 unique patients with both immunohistochemical evaluation of mismatch repair protein expression and NGS panel sequencing, of which 67 were suitable for analysis given the patterns of immunohistochemical loss of expression observed. The percent positive agreement for NGS with IHC was 50%, albeit with very rare positive cases (n=2/4). Percent negative agreement was also high at 100% (n=63/63). One case with loss of MLH1, PMS2, and MSH6 expression by IHC and no pathogenic variants by NGS exhibited MLH1 promoter hypermethylation. Percent negative agreement between immunohistochemical and NGS gene sequencing is high, although firm conclusions regarding percent positive agreement between NGS and IHC are limited by low numbers of positive cases in our cohort. In general, we consider the findings to support continued use of immunohistochemical methods to screen for the presence of mismatch repair deficiency and consider additional testing by NGS likely to add little diagnostic value in the context of intact immunohistochemical expression of mismatch repair proteins.
Transient hypoalgesia after COVID-19 infection
Authors: Becker Juliane , Papagianni Aikaterini , Herrmann Eva , Nöller Frank , Sommer Claudia , Rittner Heike L.
Published: March 2022

Introduction:

Loss of smell or taste are often-cited complications during COVID-19 disease, but there is no clear evidence for affection of the peripheral nervous system.

Methods:

Here, we report a 48-year-old man presenting with persistent dysgeusia and hypoalgesia of the lower legs, hands, and cheeks after COVID-19 infection in Spring 2020.

Results:

Upon clinical examination 7 months after the infection, the patient could not feel pain after pinprick stimuli. Quantitative sensory testing revealed increased thermal detection thresholds at the face but no changes at the foot. Electrical C-fiber stimulation elicited lower pain ratings at the distal leg compared with the proximal leg, but overall higher pain ratings than in healthy control subjects. The axon flare reaction in response to histamine and acetylcholine was almost absent with no pain sensation. Skin punch biopsy revealed a reduced intraepidermal nerve fiber density at the lower leg, and transient receptor potential vanilloid 1 and calcitonin gene-related peptide immunoreactivity were similar to a healthy control. Symptoms and positive tests improved 5 months later.

Conclusion:

In summary, we describe a case of hypoalgesia after COVID-19 disease. Studies investigating long-COVID syndrome should test not only for painful neuropathic symptoms but also for hypoalgesia, especially in patients with prolonged dysgeusia.
Influence of Nonsyndromic Bicoronal Synostosis and Syndromic Influences on Orbit and Periorbital Malformation
Authors: Lu Xiaona , Forte Antonio Jorge , Dinis Jacob , Junn Alexandra , Alperovich Michael , Alonso Nivaldo , Persing John A.
Published: March 2022

Background:

Oculoorbital disproportion in patients with craniosynostosis has similarities and dissimilarities between syndromic and nonsyndromic cases. The authors hypothesized that these two conditions have specific individual influences as they relate to development of the orbital and periorbital skeletons.

Methods:

A total of 133 preoperative computed tomography scans (nonsyndromic bicoronal synostosis, n = 38; Apert syndrome bicoronal synostosis subtype, n = 33; Crouzon syndrome bicoronal synostosis subtype, n = 10; controls, n = 52) were included. Craniometric and volumetric analyses related to the orbit and periorbital anatomy were performed.

Results:

Orbital cavity volume was mildly restricted in nonsyndromic bicoronal synostosis (7 percent, p = 0.147), but more so in Apert and Crouzon syndromes [17 percent (p = 0.002) and 21 percent (p = 0.005), respectively]. The sphenoid side angle in Apert syndrome was wider than when compared to Crouzon syndrome (p = 0.043). The ethmoid side angle in Apert patients, however, was narrower (p = 0.066) than that in Crouzon patients. Maxilla anteroposterior length was more restricted in Apert syndrome than Crouzon syndrome (21 percent, p = 0.003) and nonsyndromic cases (26 percent, p < 0.001). The posterior nasal spine position was retruded in Crouzon syndrome (39 percent, p < 0.001), yet the anterior nasal spine position was similar in Apert and Crouzon syndromes.

Conclusions:

Orbit and periorbital malformation in syndromic craniosynostosis is likely the combined influence of syndromic influences and premature suture fusion. Apert syndrome expanded the anteriorly contoured lateral orbital wall associated with bicoronal synostosis, whereas Crouzon syndrome had more infraorbital rim retrusion, resulting in more severe exorbitism. Apert syndrome developed maxillary hypoplasia, in addition to the maxillary retrusion, observed in Crouzon syndrome and nonsyndromic bicoronal synostosis patients.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Risk, II.
Coronary Computed Tomography Angiography Results in More Computed Tomography Chest Follow-up for Incidental Findings at 1 Year Relative to Stress-perfusion Cardiac Magnetic Resonance Imaging
Authors: Smith Ben C. , Allen Bradley D.
Published: March 2022

Rationale and Objectives:

The aim of this study is to elucidate the prevalence and factors associated with follow-up chest computed tomography (CT) imaging in patients undergoing stress-perfusion cardiac magnetic resonance imaging (sCMR) and coronary CT angiography (cCTA).

Materials and Methods:

Cardiac imaging encounters between January 1, 2015 and May 16, 2020 were selected for analysis. Follow-up was tracked within 1-year of initial cardiac imaging, up to May 16, 2021. Patient demographics, comorbidities, and cardiopulmonary outcomes were also analyzed.

Results:

Between 2015 and 2020, there were 4024 cCTA and 837 sCMR imaging procedures on unique patients with 1.1% and 0.5% of patients having follow-up CT chest studies within 1 year, respectively. When controlling for patient demographic factors, body mass index, insurance status, smoking history, and comorbid diagnostic codes, there was statistically significant increased odds (adjusted odds ratio [95% confidence interval]: 2.864 [1.129-7.265]) of undergoing follow-up within the cCTA cohort. Pulmonary nodules represented the most common incidental finding, with cCTA associated with higher rates of pulmonary nodules detected on imaging (adjusted odds ratio [95% confidence interval]: 5.947 [4.136-8.552]). sCMR was associated with higher rates of MI, percutaneous coronary intervention, and lung malignancy within 1 year, with no difference in all-cause mortality.

Conclusions:

Patients undergoing either cCTA and sCMR demonstrated a low prevalence of follow-up CT chest imaging; however, follow-up was 2 times greater after cCTA due to greater pulmonary nodule detection. Potential for follow-up should be considered when evaluating the comparative effectiveness of these modalities, including the impact of follow-up imaging on cost and patient outcomes. Strategies to improve lung nodule detection and characterization at the time of sCMR may provide added value in these patients.
Cosmological milestones, conformal frameworks and quiescent cosmology
Authors: Scott Susan M. , Threlfall Philip
Published: March 2022

To understand the nature of the birth of our Universe and its eventual demise is a driving force in theoretical physics and astronomy and, indeed, for humanity. A zoo of definitions has appeared in the literature to catalogue different types of cosmological milestones such as ‘Big Bangs’, ‘Big Crunches’, ‘Big Rips’, ‘Sudden Singularities’, ‘Bounces’ and ‘Turnarounds’.
Quiescent cosmology
is the notion that the Universe commenced in a Big Bang that was highly regular and smooth, and evolved away from this initial isotropy and homogeneity due to gravitational attraction. The
quiescent cosmology
concept meshes well with Penrose’s ideas regarding gravitational entropy and the clumping of matter, and the associated Weyl Curvature Hypothesis. Conformal frameworks, such as the Isotropic Past Singularity (IPS), have been devised to encapsulate initial and final states for the Universe which are in accordance with these programmes. These geometric definitions are independent of models, coordinates and the equation of state of the source of the gravitational field. Much of the research on cosmological milestones has been focussed on the FRW solutions, many of which possess initial singularities which are isotropic Big Bangs. We analyse here the relationship between cosmological milestones and conformal frameworks for these solutions. We establish the general properties of FRW models which admit these conformal frameworks, including whether they satisfy various energy conditions, and are therefore physically reasonable. These results inform future development of the
quiescent cosmology
program.

This article is part of the theme issue ‘The future of mathematical cosmology, Volume 1’.
On stable exponential cosmological solutions with two factor spaces in (1+ m + 2)-dimensional Einstein–Gauss–Bonnet model with
Λ
-term
Authors: Ivashchuk V. D. , Kobtsev A. A.
Published: March 2022

A

(
m
+
3
)

-dimensional Einstein–Gauss–Bonnet gravitational model including the Gauss–Bonnet term and the cosmological term

Λ

is considered. Exact solutions with exponential time dependence of two scale factors, governed by two Hubble-like parameters

H
>
0

and

h
≠
H

, corresponding to factor spaces of dimensions

m
>
2

and

l
=
2

, respectively, are found. Under certain restrictions on

x
=
h

/

H

, the stability of the solutions in a class of cosmological solutions with diagonal metrics is proved. A subclass of solutions with small enough variation of the effective gravitational constant

G

is considered and the stability of all solutions from this subclass is shown.

This article is part of the theme issue ‘The future of mathematical cosmology, Volume 1’.
Trajectories of gene expression, seasonal influenza, and within-host seasonal immunity: transfer value to covid-19
Authors: Lund Eiliv , Holden Marit , Busund Lill-Tove Rasmussen , Snapkov Igor , Shvetsov Nikita , Holden Lars
Published: March 2022

As a novel approach we will combine trajectories or longitudinal studies of gene expression with information on annual influenza epidemics. Seasonality of gene expression in immune cells from blood could be a consequence of within-host seasonal immunity interacting with the seasonal pandemics of influenza (flu) in temperate regions and, thus, with potential valuable analogy transfer to the proposed seasonal development of covid-19.

Here we operationalized within-host immunity as genes with both a significant seasonal term and a significant flu term in the sine-cosine model. Information on gene expression was based on microarray using RNase buffered blood samples collected randomly from a population-based cohort of Norwegian middle-aged women in 2003-2006, The Norwegian Women and Cancer (NOWAC) study. The unique discovery (N=425) and replication (N=432) design were based on identical sampling and preprocessing. Data on proportion of sick leaves due to flu, and the flu intensities per week was obtained from the National Institute of Public Health, giving a semi-ecological analysis.

The discovery analysis found 2942 (48.1%) significant genes in a generalized seasonal model over four years. For 1051 within-host genes both the seasonal and the flu term were significant. These genes followed closely the flu intensities. The trajectories showed slightly more genes with a maximum in early winter than in late summer. Moving the flu intensity forward in time indicated a better fit 3-4 weeks before the observed influenza. In the replication analyses, 369 genes (35.1% of 1051) were significant. Exclusion of genes with unknown functions and with more than a season in difference reduced the number of genes in the discovery dataset to 305, illustrating the variability in the measurements and the problem in assessing weak biological relationships. Thus, we found for the first time a clear seasonality in gene expression with marked responses to the annual seasonal influenza in a unique discovery – replication design. Hypothetically, this could support the within-host seasonal immunity concept.
Polygenic risk vectors (PRV) improve genetic risk stratification for cardio-metabolic diseases
Authors: Li Ruowang , Zhang Xinyuan , Li Binglan , Feng Qiping , Kottyan Leah , Luo Yuan , Sawicki Konrad Teodor , Khan Atlas , Limdi Nita , Puckelwartz Megan , Wei Wei-Qi , Weng Chunhua , Chen Yong , Ritchie Marylyn D. , Moore Jason H.
Published: March 2022

1.

Accurate disease risk stratification can lead to more precise and personalized prevention and treatment of diseases. As an important component to disease risk, genetic risk factors can be utilized as an early and stable predictor for disease onset. Recently, the polygenic risk score (PRS) method has combined the effects from hundreds to millions of single nucleotide polymorphisms (SNPs) into a score that can be used for genetic risk stratification. However, current PRS approaches only utilize the additive associations between SNPs and disease risk in a one-dimensional score. Here, we show that leveraging multiple types of genetic effects in multi-dimensional risk vectors, or a polygenic risk vector (PRV), can improve the stratification of cardio-metabolic diseases risks. Using data from UK Biobank (UKBB) and Electronic Medical Records and Genomics (eMERGE) Network biobank linked electronic health records (EHR) as development and evaluation data, we found that the combined effects between the additive PRS and the dominant PRS outperformed either one in terms of disease risk stratification, especially for the individuals in the high-risk group. Our results demonstrate that disease risks are likely to be influenced by multiple types of genetic effects, and PRV could utilize these effects for better risk stratification while retaining the simplicity of the PRS method.
Hippocampal gamma and sharp wave/ripples mediate bidirectional interactions with cortical networks during sleep
Authors: Pedrosa Rafael , Nazari Mojtaba , Mohajerani Majid H. , Knöpfel Thomas , Stella Federico , Battaglia Francesco
Published: March 2022

Hippocampus-neocortex interactions during sleep are critical for memory processes: hippocampally-initiated replay contributes to memory consolidation in the neocortex and hippocampal sharp wave/ripples are linked to generalized increases in neocortical cell activity and DOWN-UP state transitions. Yet, the spatial and temporal patterns of this exchange are unknown. With voltage imaging, electrocorticography, and laminarly-resolved hippocampal potentials, we characterized cortico-hippocampal interactions during anesthesia and NREM sleep. We observed neocortical activation transients spanning multiple spatial scales hinting at a quasi-critical regime. Transients were organized in a small number of functional networks matching known anatomical connectivity. A network overlapping with the default mode network and centered on retrosplenial cortex was the most associated with the hippocampus. Interestingly, hippocampal slow gamma was the oscillation that best correlated with this neocortical network, outpacing ripples. In fact, neocortical activity predicted hippocampal slow gamma and followed ripples, suggesting that consolidation processes rely on bi-directional exchanges between hippocampus and neocortex.
Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution
Authors: Stuart Tim , Hao Stephanie , Zhang Bingjie , Mekerishvili Levan , Landau Dan A , Maniatis Silas , Satija Rahul , Raimondi Ivan
Published: March 2022

Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility, and other factors. However, most current single-cell-resolution methods are unable to measure more than one aspect of chromatin state in a single experiment, limiting our ability to accurately measure chromatin states. Here, we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), a new assay capable of measuring the genome-wide presence of multiple histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq utilizes recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk- and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and in cells of the human immune system, demonstrating the high accuracy and sensitivity of the method. We further extend NTT-seq to enable simultaneous profiling of cell-surface protein expression alongside multimodal chromatin states to study cells of the immune system.
Reorganization of F-actin nanostructures is required for the late phases of SARS-CoV-2 replication in pulmonary cells
Authors: Swain Jitendriya , Merida Peggy , Rubio Karla , Bracquemond David , Aguilar-Ordoñez Israel , Günther Stefan , Barreto Guillermo , Muriaux Delphine
Published: March 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is worldwide the main cause of the COVID-19 pandemic. After infection of human pulmonary cells, intracellular viral replication take place in different cellular compartments resulting in the destruction of the host cells and causing severe respiratory diseases. Although cellular trafficking of SARS-CoV-2 have been explored, little is known about the role of the cytoskeleton during viral replication in pulmonary cells. Here we show that SARS-CoV-2 infection induces dramatic changes of F-actin nanostructures overtime. Ring-like actin nanostructures are surrounding viral intracellular organelles, suggesting a functional interplay between F-actin and viral M clusters during particle assembly. Filopodia-like structures loaded with viruses to neighbour cells suggest these structures as mechanism for cell-to-cell virus transmission. Strikingly, gene expression profile analysis and PKN inhibitor treatments of infected pulmonary cells reveal a major role of alpha-actinins superfamily proteins in SARS-CoV-2 replication. Overall, our results highlight cell actors required for SARS-CoV2 replication that are promises for antiviral targets.

Teaser

Impairing regulation of actin filaments inhibits SARS-CoV-2 particle production in human pulmonary cells.
Comparative host-pathogen dynamics of Snake Fungal Disease in sympatric species of water snakes (Nerodia)
Authors: Harding Stephen F. , Becker C. Guilherme , Yates Jessica , Crump Paul , Forstner Michael R. J. , Mullin Stephen J. , Rodriguez David
Published: March 2022

The ascomycete fungus Ophidiomyces ophiodiicola (Oo) is the causative agent of ophidiomycosis (Snake Fungal Disease), which has been detected globally. However, surveillance efforts in the central U.S., specifically Texas, have been minimal. The threatened and rare Brazos water snake (Nerodia harteri harteri) is one of the most range restricted snakes in the U.S. and is sympatric with two wide-ranging congeners, N. erythrogaster transversa and N. rhombifer, in north central Texas; thus, providing an opportunity to test comparative host-pathogen dynamics in this system. To accomplish this, we surveyed a portion of the Brazos river drainage (~400 river km) over 29 months and tested 150 Nerodia spp. for the presence of Oo via quantitative PCR and recorded any potential signs of Oo infection. We found Oo was distributed across the entire range of N. h. harteri, Oo prevalence was 46 % overall, and there was a significant association between Oo occurrence and signs of infection in our sample. Models indicated adults had a higher probability of Oo infection than juveniles and subadults, and adult N. h. harteri had a higher probability of infection than adult N. rhombifer but not higher than adult N. e. transversa. High Oo prevalence estimates (94.4%) in adult N. h. harteri has implications for their conservation and management owing to their patchy distribution, comparatively low genetic diversity, and threats from anthropogenic habitat modification.
Lrig3 restricts the size of the colon stem cell compartment
Authors: Stevenson Janelle G. , Sayegh Ryan , Pedicino Natalie , Pellitier Natalie A. , Wheeler Tim , Bechard Matthew E. , Huh Won Jae , Coffey Robert J. , Zemper Anne E.
Published: March 2022

The cellular census of the colonic crypt is tightly regulated, yet the molecular mechanisms that regulate this census are not fully understood. Lrig3, a transmembrane protein, is expressed in colonic crypt epithelial cells, including the stem, progenitor, and differentiated cell types. Mice missing Lrig3 have a disruption in their cellular census: using a novel Lrig3-/- mouse we demonstrate that Lrig3-/- mice have more cells per crypt, a greater mucosal area, and longer colons compared to wildtype mice, suggesting the expression of Lrig3 is required for both the total number of epithelial cells in the mouse colon, as well as colon length. In addition, we show Lrig3-/- mice have significantly more stem, progenitor, and deep crypt secretory cells, yet harbor a normal complement of enteroendocrine, Tuft, and absorptive cells. Lrig3-/- mice also have a concomitant decrease in phosphorylated Extracellular signal-related kinases, indicating the loss of Lrig3 leads to an expansion of the colonic stem cell compartment, in an Erk-dependent manner. Our study describes the expression of Lrig3 within the colon, defines perturbations in mice lacking Lrig3, and supports a role for Lrig3 in the establishment of both colonic crypt structure and cellular census, defined as the epithelial cell type and number in colon crypts.

Graphical Abstract
Dynamic Network Curvature Analysis of RNA-Seq Data in Sarcoma
Authors: Elkin Rena , Oh Jung Hun , Cruz Filemon Dela , Deasy Joseph O. , Kung Andrew L. , Tannenbaum Allen R.
Published: March 2022

In this work, we utilized network features of cancer gene interactomes to cluster pediatric sarcoma tumors and identify candidate therapeutic targets in an unsupervised manner. RNA-Seq data were mapped to protein-level interactomes to construct weighted networks for mathematical analysis. We employed a geometric approach centered on a discrete notion of curvature, which provides a measure of the functional association between genes in the context of their connectivity. Specifically, we adopted a recently proposed dynamic extension of graph curvature to extract features of the non-Euclidean, multiscale structure of genomic networks. We propose a hierarchical clustering approach to reveal preferential gene clustering according to their geometric cooperation which captured the characteristicEWSR1-FLI1fusion in Ewing sarcoma. We also performedin silicoedge perturbations to assess systemic response to simulated interventions quantified by changes in curvature. These results demonstrate that geometric network-based features can be useful for identifying non-trivial gene associations in an agnostic manner.
Cross-generational heritability analysis of physiological traits in Porites astreoides across an inshore-offshore gradient in the Lower Florida Keys
Authors: Zhang Yingqi , Barnes Shelby J. , Kenkel Carly D.
Published: March 2022

Estimating the heritable genetic variation in fitness-related traits is key to projecting the adaptive evolution of organisms in response to a changing environment. While heritability studies on reef-building corals to date support adaptive capacity, little is known about the dynamics of trait heritability across life stages in which distinct selective pressures can have long-lasting effects both within and across generations. In this study, we obtained heritability estimates for energetic and thermal stress response traits in larval, recruit, and adult Porites astreoides from two populations in the Lower Florida Keys. To induce bleaching phenotypes among individual families, larvae were exposed to a 4-day thermal stress at 32 °C, whereas adults and recruits received the same treatment for 22 days. Origin-dependent tolerance was observed in two life stages where offshore recruits lost more symbiont cells under heat than inshore recruits compared to their respective controls and heat-treated offshore adults suffered a greater loss in total protein content. Surprisingly, larvae appeared to be largely insensitive to heat regardless of origin. Broad sense heritability (H2) estimates varied greatly among traits and life stages, which may reflect changes in the relative importance of genetic and environmental variation throughout development. Notably, more than 80% of the variation in larval chlorophyll a concentration was attributed to genetic factors. The overall moderate to high H2 estimates measured here suggest these corals have considerable potential to adapt to environmental change.
WDR82 mediated H3K4me3 is associated with tumor proliferation and therapeutic efficacy in pediatric high-grade gliomas
Authors: Wadhwani Nitin , Nayak Sonali , Wang Yufen , Hashizume Rintaro , Jie Chunfa , Mania-Farnell Barbara , James Charles David , Xi Guifa , Tomita Tadanori
Published: March 2022

Pediatric high-grade gliomas (pHGGs) are common malignant brain tumors without effective treatment and poor patient survival. Abnormal posttranslational modification at the histone H3 tail plays critical roles in tumor cell malignancy. We have previously shown that trimethylation of lysine 4 at histone H3 (H3K4me3) plays a significant role in pediatric ependymoma malignancy and is associated with tumor therapeutic sensitivity. Here, we show that H3K4me3 and its methyltransferase WDR82 are elevated in pHGGs. Reduction of H3K4me3 by downregulating WDR82 decreases H3K4me3 promoter occupancy and expression of genes associated with stem cell features, cell proliferation, the cell cycle and DNA damage repair. Reduction of WDR82 mediated H3K4me3 increases the response of pediatric glioma cells to chemotherapy. These findings suggest that WDR82 mediated H3K4me3 is an important determinant of pediatric glioma malignancy and therapeutic response. This highlights the need for a more thorough understanding of the potential of WDR82 as an epigenetic target to increase therapeutic efficacy and improve prognosis for children with malignant gliomas.
HOIL1 regulates group 2 innate lymphoid cell numbers and type 2 inflammation in the small intestine
Authors: Wood Matthew J. , Marshall Jeffrey N. , Hartley Victoria L. , Liu Ta-Chiang , Iwai Kazuhiro , Stappenbeck Thaddeus S. , MacDuff Donna A.
Published: March 2022

Patients with mutations in HOIL1 experience a complex immune disorder including intestinal inflammation. To investigate the role of HOIL1 in regulating intestinal inflammation, we employed a mouse model of HOIL1 deficiency. The ileum of Hoil1−/− mice displayed features of type 2 inflammation including tuft cell and goblet cell hyperplasia, and elevated expression of Il13, Il5 and Il25 mRNA. Inflammation persisted in the absence of T and B cells, and bone marrow chimeric mice revealed a requirement for HOIL1 expression in radiation-resistant cells to regulate inflammation. Although disruption of IL-4 receptor alpha (IL4Rα) signaling on intestinal epithelial cells ameliorated tuft and goblet cell hyperplasia, expression of Il5 and Il13 mRNA remained elevated. KLRG1hi CD90lo group 2 innate lymphoid cell (ILC2) were increased independent of IL4Rα signaling, tuft cell hyperplasia and IL-25 induction. Antibiotic treatment dampened intestinal inflammation indicating commensal microbes as a contributing factor. We have identified a key role for HOIL1, a component of the Linear Ubiquitin Chain Assembly Complex, in regulating type 2 inflammation in the small intestine. Understanding the mechanism by which HOIL1 regulates type 2 inflammation will advance our understanding of intestinal homeostasis and inflammatory disorders and may lead to the identification of new targets for treatment.
ID1 and CEBPA Coordinate Epidermal Progenitor Cell Differentiation
Authors: Kantzer Christina Geraldine , Yang Wei , Grommisch David , Patil Kim Vikhe , Mak Kylie Hin-Man , Genander Maria
Published: March 2022

The regulatory circuits that coordinate epidermal differentiation during development are still not fully understood. Here we report that the transcriptional regulator ID1 is enriched in basal epidermal progenitor cells and find ID1 expression to be diminished upon differentiation. In utero silencing of Id1 impairs progenitor cell proliferation, leads to precocious delamination of targeted progenitor cells and enables differentiated keratinocytes to retain progenitor markers and characteristics. Transcriptional profiling suggests ID1 acts by mediating adhesion to the basement membrane while inhibiting spinous layer differentiation. Co-immunoprecipitation reveals ID1 binding to transcriptional regulators of the class I bHLH family. We localize bHLH Tcf3, Tcf4 and Tcf12 to epidermal progenitor cells during epidermal stratification and established TCF3 as a downstream effector of ID1-mediated epidermal proliferation. Finally, we identify crosstalk between CEBPA, a known mediator of epidermal differentiation, and Id1 and demonstrate that CEBPA antagonizes BMP-induced activation of Id1. Our work establishes ID1 as a key coordinator of epidermal development, acting to balance progenitor proliferation with differentiation and unveils how functional crosstalk between CEBPA and Id1 orchestrates epidermal lineage progression.
Genome-wide base editor screen identifies regulators of protein abundance in yeast
Authors: Schubert Olga T. , Bloom Joshua S. , Sadhu Meru J. , Kruglyak Leonid
Published: March 2022

Abundance of proteins is extensively regulated both transcriptionally and post-transcriptionally. To systematically characterize how regulation of protein abundance is encoded in the genome and identify protein regulators on a genome-wide scale, we developed a genetic screen that uses a CRISPR base editor. We examined the effects of 16,452 genetic perturbations on the abundance of eleven yeast proteins representing a variety of cellular functions. Thereby, we uncovered hundreds of regulatory relationships, including a novel link between the GAPDH isoenzymes Tdh1/2/3 and the Ras/PKA pathway. Many of the identified regulators are specific to one of the eleven proteins, but we also found genes that, upon perturbation, affected the abundance of most of the tested proteins. While the more specific regulators usually act transcriptionally, broad regulators often have roles in protein translation. Our results provide unprecedented insights into the components, scale and connectedness of the protein regulatory network.
Ambient RNA analysis reveals misinterpreted and masked cell types in brain single-nuclei datasets
Authors: Caglayan Emre , Liu Yuxiang , Konopka Genevieve
Published: March 2022

Ambient RNA contamination in single-cell RNA sequencing (RNA-seq) is a significant problem, but its consequences are poorly understood. Here, we show that ambient RNAs in brain single-nuclei RNA-seq can have a nuclear or extra-nuclear origin with distinct gene set signatures. Both ambient RNA signatures are predominantly neuronal and we find that some previously annotated neuronal cell types are distinguished by ambient RNA. Strikingly, we also detect pervasive neuronal ambient RNA contamination in all glial cell types unless glia and neurons are physically separated prior to sequencing. We demonstrate that this contamination can be removedin silico. We also show that previous annotations of immature oligodendrocytes are likely glial cells contaminated with ambient RNAs. After ambient RNA removal, we detect extremely rare, committed oligodendrocyte progenitor cells, which were infrequently annotated in previous adult human brain datasets. Together, these results provide an in-depth analysis of ambient RNA contamination in brain single-cell datasets.
A Strategy to Quantify Myofibroblast Activation on a Continuous Spectrum
Authors: Hillsley Alexander , Santoso Matthew , Engels Sean M. , Contreras Lydia M. , Rosales Adrianne M.
Published: March 2022

Myofibroblasts are a highly secretory and contractile phenotype most commonly identified by the de novo expression and assembly of alpha-smooth muscle actin stress fibers. Traditionally, this activation process has been thought of as a binary process, with cells being labeled as “activated” or “quiescent (non-activated)”. More recently, this view has been expanded to consider activation on a continuous spectrum. However, there is no established method to quantify a cell’s position on this spectrum, and as a result, the binary labeling system is still widely used. While transcriptomic analyses provide a continuous measure of myofibroblast markers, a faster and more facile screening method is needed. To this end, we utilized optical microscopy and machine learning methods to quantify myofibroblast activation on a spectrum. We first measured size and shape features of over 1,000 individual cardiac fibroblasts and found that these features provide enough information to predict activation state, on the binary scale, with 94% accuracy as compared to manual classification. We next performed dimensionality reduction techniques on these features to create a continuous scale of activation. Importantly, this new classification system captures a range of fibroblast activation states, but still possesses inherent bias due to choice of morphological features. Thus, we next used self-supervised machine learning to create a second continuous labeling system free from biases associated with the manually measured features. Lastly, we compared our findings for mechanically activated cardiac fibroblasts to a distribution of cell phenotypes generated from transcriptomic data using single-cell RNA sequencing. Altogether, these results demonstrate a continuous spectrum of activation from fibroblast to myofibroblast and provide a strategy to quantify a cell’s position on that spectrum.
A deep unsupervised language model for protein design
Authors: Ferruz Noelia , Schmidt Steffen , Höcker Birte
Published: March 2022

Protein design aims to build new proteins from scratch thereby holding the potential to tackle many environmental and biomedical problems. Recent progress in the field of natural language processing (NLP) has enabled the implementation of ever-growing language models capable of understanding and generating text with human-like capabilities. Given the many similarities between human languages and protein sequences, the use of NLP models offers itself for predictive tasks in protein research. Motivated by the evident success of generative Transformer-based language models such as the GPT-x series, we developed ProtGPT2, a language model trained on protein space that generatesde novoprotein sequences that follow the principles of natural ones. In particular, the generated proteins display amino acid propensities which resemble natural proteins. Disorder and secondary structure prediction indicate that 88% of ProtGPT2-generated proteins are globular, in line with natural sequences. Sensitive sequence searches in protein databases show that ProtGPT2 sequences are distantly related to natural ones, and similarity networks further demonstrate that ProtGPT2 is sampling unexplored regions of protein space. AlphaFold prediction of ProtGPT2-sequences yielded well-folded non-idealized structures with embodiments as well as large loops and revealed new topologies not captured in current structure databases. ProtGPT2 has learned to speak the protein language. It has the potential to generatede novoproteins in a high throughput fashion in a matter of seconds. The model is easy-to-use and freely available.
Fabrication of Conductive Hollow Microfibers for Encapsulation of Astrocyte Cells
Authors: Alimoradi Nima , Nasirian Vahid , Aykar Saurabh S. , McNamara Marilyn C. , Niaraki-Asli Amir Ehsan , Montazami Reza , Makowski Andrew , Hashemi Nicole N.
Published: March 2022

The manufacturing of 3D cell scaffoldings provides advantages for modeling diseases and injuries by physiologically relevant platforms. A triple-flow microfluidic device was developed to rapidly fabricate alginate/graphene hollow microfibers based on the gelation of alginate induced with CaCl2. This five-channel pattern actualized continuous mild fabrication of hollow fibers under an optimized flowing rate ratio of 300: 200: 100 μL.min−1. The polymer solution was 2.5% alginate in 0.1% graphene, and a 30% polyethylene glycol solution was used as the sheath and core solutions. The morphology and physical properties of microstructures were investigated by scanning electron microscopy, electrochemical, and surface area analyzers. Subsequently, these conductive microfibers’ biocompatibility was studied by encapsulating mouse astrocyte cells within these scaffolds. The cells could successfully survive both the manufacturing process and prolonged encapsulation for up to 8 days. These unique 3D hollow scaffolds could significantly enhance the available surface area for nutrient transport to the cells. In addition, these conductive hollow scaffolds illustrated unique advantages such as 0.728 cm3.gr−1 porosity and twice more electrical conductivity in comparison to alginate scaffolds. The results confirm the potential of these scaffolds as a microenvironment that supports cell growth.
Effects of disease emergence on invasive grass impacts
Authors: Kendig Amy E. , Adhikari Ashish , Lane Brett R. , Wojan Christopher M. , Kortessis Nicholas , Simon Margaret W. , Barfield Michael , Harmon Philip F. , Holt Robert D. , Clay Keith , Goss Erica M. , Flory S. Luke
Published: March 2022

Invasive species impact ecosystems through their large abundances and strong per capita effects. Enemies can regulate abundances and per capita effects, but are notably absent for many new invaders. However, invaders acquire enemies over time and as they spread; processes hypothesized to mitigate negative invader impacts by reducing abundance or per capita effects. Alternatively, properties of invaders or acquired enemies, such as an enemy’s ability to attack multiple species, may hinder enemy mitigation of invader impacts. We used field experiments to evaluate disease mitigation of invader impacts using the invasive grassMicrostegium vimineum, which hosts an emerging fungal disease, and a native grass competitor,Elymus virginicus. We manipulated competition through density gradients of each plant species, and we reduced ambient foliar diseases with fungicide and autoclaving. We then modeled long-term population dynamics with field-estimated parameters. In the field, disease did not reduce invader abundance or per capita effects. The invader amplified disease on itself and the competitor, and disease reduced invader and competitor fitness components (e.g., germination). The dynamical model predicted that disease impacts on the competitor are greater than on the invader, such that disease will reduce invader abundance by 18%, and competitor abundance by 88%, over time. Our study suggests that enemies acquired by invaders will not necessarily mitigate invader impacts if the invader amplifies the enemy and the enemy attacks and suppresses competitor species.
The Musashi proteins are post-transcriptional activators of protein expression and alternative exon splicing in vertebrate photoreceptors
Authors: Matalkah Fatimah , Jeong Bohye , Sheridan Macie , Horstick Eric , Ramamurthy Visvanathan , Stoilov Peter
Published: March 2022

The Musashi proteins, MSI1 and MSI2, are conserved RNA binding proteins with a role in the maintenance and renewal of stem cells. Contrasting with this role, retina and terminally differentiated photoreceptor cells express high levels of MSI1 and MSI2, indicating that the two proteins have a role unrelated to maintaining undifferentiated cell state. Here we show that the Musashi proteins are essential in mature photoreceptors. Combined knockout of Msi1 and Msi2 lead to loss of the retina response to light and progressive photoreceptor cell death. The two proteins are fully redundant as individual deletion of Msi1 or Msi2 did not produce a phenotype. To define the molecular functions underlying the requirement for Musashi in photoreceptors, we delineated their RNA targets and analyzed the effect of the combined Msi1/Msi2 knockout on transcript levels, pre-mRNA splicing, and protein expressions. We show distinct nuclear and cytoplasmic functions for the Musashi proteins in photoreceptor cells. In the nucleus, Musashi binding to the downstream proximal intron promotes splicing of alternative exons. Surprisingly, four conserved photoreceptor-specific alternative exons in genes critical for vision proved to be dispensable, leaving open questions about the selective pressures that lead to the conservation of these exons and the contribution of alternative splicing to the phenotype of the Musashi knockout. In the photoreceptor cell cytoplasm MSI1 and MSI2 act as activators of protein expression. The combined knockout of Msi1 and Msi2 reduced the levels of multiple proteins including proteins required for vision and photoreceptor survival.