bluuebunny/crossref_metadata_2025 huggingface dataset:
Tensor decomposition based feature extraction and classification to detect natural selection from genomic data
Authors: Amin Md Ruhul , Hasan Mahmudul , Arnab Sandipan Paul , DeGiorgio Michael
Published: March 2023

Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under non-convex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data while preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termedT-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance ofT-RExon simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore,T-RExis a powerful addition to the toolkit for detecting adaptive processes from genomic data.
The genetic composition of hybridMangifera
Authors: Warschefsky Emily J. , von Wettberg Eric J.B.
Published: March 2023

Homoploid hybridization is known to play an important role in the evolution of plants, including many crop species, but can have different outcomes including introgression between parental taxa and the formation of new evolutionary lineages. We investigate the occurrence and consequences of hybridization between the economically important tree cropMangifera indica(mango) and two congeneric species in Southeast Asia. A total of 90 samples of the hybridM. odorataand its parental taxa,M. indica(mango) andM. foetida, along with 65 samples of a newly proposed hybrid,M. casturiand its putative parental taxa,M. indicaandM. quadrifida, were sampled and genotyped using restriction site associated DNA sequencing. For each hybrid, we assessed population structure and admixture and indices of genetic diversity, including multilocus linkage disequilibrium. We found no evidence of introgression betweenM. foetidaandM. indicacultivars from Southeast Asia, but find support for a hybrid origin ofM. casturi. Both hybrids show low levels of intraspecific genetic diversity and individuals have high genetic identity and significant multilocus linkage disequilibrium. For bothM. odorataandM. casturi, our results are consistent with hybrid lineages that have formed only a few times and have since been maintained clonally. While grafting may play a role in the continued propagation of these hybrids, we suggest that the ability ofM. odorataandM. casturito reproduce asexually through nucellar polyembryony has allowed the hybrids to persist independently of grafting.
EGFR inhibition in lung adenocarcinoma upregulates cell surface expression of the placental antigen ALPP and enhances efficacy of ALPP-ADC therapy
Authors: Chen Yihui , Hong Monica J. , Xu Hanwen , Vykoukal Jody , Park Soyoung , Cai Yining , León-Letelier Ricardo A. , Irajizad Ehsan , Hsiao Fu Chung , Dennison Jennifer B. , Ostrin Edwin J. , Fahrmann Johannes F. , Katayama Hiroyuki , Hanash Samir M.
Published: March 2023

Alkaline phosphatase placental type (ALPP) and ALPPL2 are closely related and regulated GPI anchored proteins that are known to be expressed on the cell surface in some cancers, whereas normal tissue expression is largely limited to the placenta. Clinical utility of ALPP is potentially limited by heterogenous expression in tumors. Here, we assessed ALPP and ALPPL2 surfaceome protein levels in 158 cancer cell lines and mRNA expression levels in 10,967 tumors representing 32 cancer types from The Cancer Genome Atlas (TCGA), which revealed ALPP, and to a lesser extent ALPPL2, to be variably expressed in several cancer types including lung adenocarcinoma (LUAD). Surface expression of ALPP was confirmed by tissue microarray analysis of 204 lung tumors. Using LUAD as a model system, we demonstrated that treatment with EGFR inhibitors, or induction of cancer cell quiescence via nutrient deprivation greatly enhanced ALPP surface expression. Mechanistic studies revealed that enhancement of surface ALPP expression in LUAD following gefitinib treatment was mediated through repression of EGFR signaling and activation of the transcription factor FoxO3a, which was identified as an upstream transcriptional regulator of ALPP. Using xenograft models of LUAD, we further demonstrated that gefitinib treatment upregulates surface expression of ALPP in LUAD cells but not in normal tissues. Combination therapy with gefitinib and an ALPP antibody conjugated with Monomethylauristatin F (ALPP-ADC-MAF) resulted in superior anti-cancer efficacy compared with gefitinib or ALPP-ADC-MAF alone. Our findings support a novel combination treatment modality that boosts the efficacy of ALPP-ADC directed therapy.
Transcription Factor Co-Expression Mediates Lineage Priming for Embryonic and Extra-Embryonic Differentiation
Authors: Redó-Riveiro Alba , Al-Mousawi Jasmina , Linneberg-Agerholm Madeleine , Proks Martin , Perera Marta , Brickman Joshua M.
Published: March 2023

In early mammalian development, cleavage stage blastomeres and cells of the inner cell mass (ICM) of the blastocyst co-express embryonic and extra-embryonic transcriptional determinants. Using a double protein-based reporter we identify embryonic stem cells (ESC) that co-express the extra-embryonic factor GATA6 alongside the embryonic factor SOX2 in specific conditions. Based on single cell transcriptomics we find these population resemble unsegregated ICM, exhibiting enhanced differentiation potential for endoderm while maintaining epiblast competence and suggesting they represent an ideal model to determine how GATA6 and SOX2 influence each other’s DNA binding. To relate this binding to future fate, we describe a complete enhancer set in both ESCs and naïve extraembryonic endoderm stem cells and ask whether SOX2 and GATA6 recognize these elements in ICM-like ESC sub-population. Both factors support cooperative recognition in these lineages, with GATA6 bound alongside SOX2 on a fraction of pluripotency enhancers and SOX2 alongside GATA6 more extensively on endoderm enhancers. Our findings suggest that cooperative binding between these antagonistic factors both supports self-renewal and prepares progenitor cells for later differentiation.
Quantitative determination of fluorescence labeling implemented in cell cultures
Authors: Spagnolo Chiara Schirripa , Moscardini Aldo , Amodeo Rosy , Beltram Fabio , Luin Stefano
Published: March 2023

Background

Labeling efficiency is a crucial parameter in fluorescence applications, especially when studying biomolecular interactions. Current approaches for estimating the yield of fluorescent labeling have critical drawbacks that usually lead them to be inaccurate or not quantitative.

Results

We present a method to quantify fluorescent-labeling efficiency that addresses the critical issues marring existing approaches. The method operates in the same conditions of the target experiments by exploiting a ratiometric evaluation with two fluorophores used in sequential reactions. We show the ability of the protocol to extract reliable quantification for different fluorescent probes, reagents concentrations, reaction timing and to optimize labeling performance. As paradigm, we consider the labeling of the membrane-receptor TrkA through 4’-phosphopantetheinyl transferase Sfp in living cells, visualizing the results by TIRF microscopy. This investigation allows us to find conditions for demanding single and multi-color single-molecule studies requiring high degrees of labeling.

Conclusions

The developed method allows the quantitative determination and the optimization of staining efficiency in any labeling strategy based on stable reactions.
People with a tobacco use disorder misattribute non-drug cues as worse predictors of positive outcomes compared to drug cues
Authors: Kalhan Shivam , Schwartenbeck Philipp , Hester Robert , Garrido Marta I.
Published: March 2023

Adaptive behaviours depend on dynamically updating internal representations of the world based on the ever-changing environmental contingencies. People with a substance use disorder (pSUD) show maladaptive behaviours with high persistence in drug-taking, despite severe negative consequences. We recently proposed a salience misattribution model for addiction (SMMA; Kalhan et al., (2021)), arguing that pSUD have aberrations in their updating processes where drug cues are misattributed as strong predictors of positive outcomes, but weaker predictors of negative outcomes. We also argue that conversely, non-drug cues are misattributed as weak predictors of positive outcomes, but stronger predictors of negative outcomes. However, these hypotheses need to be empirically tested. Here we used a multi-cue reversal learning task, with reversals in whether drug or non-drug cues are currently relevant in predicting the outcome (monetary win or loss). We show that compared to controls, people with a tobacco use disorder (pTUD), do form misaligned internal representations. We found that pTUD updated less towards learning the drug cue’s relevance in predicting a loss. Further, when neither drug nor non-drug cue predicted a win, pTUD updated more towards the drug cue being relevant predictors of that win. Our Bayesian belief updating model revealed that pTUD had a low estimated likelihood of non-drug cues being predictors of wins, compared to drug cues, which drove the misaligned updating. Overall, several hypotheses of the SMMA were supported, but not all. Our results implicate that strengthening the non-drug cue association with positive outcomes may help restore the misaligned internal representation in pTUD.
Comparative Genomics and Directed Evolution Reveal Genetic Determinants of Extreme UVC Radiation Tolerance in Bacteria Recovered from the Stratosphere
Authors: Ellington Adam J. , Schult Tyler J. , Reisch Christopher R. , Christner Brent C.
Published: March 2023

Aerosolized microbes surviving transport to and in the stratosphere endure extremes of low temperature, atmospheric pressure, and relative humidity, and high shortwave ultraviolet radiation flux. However, the genetic determinants for traits enabling resistance to the combination of stresses experienced by microbes in the high atmosphere have not been systematically investigated. In this study, we examined Proteobacteria and Actinobacteria isolated from the stratosphere (18 to 29 km ASL) and that demonstrated high tolerance to desiccation (15-25% RH) and UVC radiation (UVCR; λ= 254 nm). Closely related reference strains were more sensitive to UVCR than the stratospheric isolates, indicating that extreme resistance is not universally distributed in these phylogenetically related bacteria. Comparative genomic analyses revealed DNA repair and antioxidant defense genes in the isolates that are not possessed by the related reference strains, including genes encoding photolyase, DNA nucleases and helicases, and catalases. Directed evolution by repeated exposure to increasing doses of UVCR improved the LD90in a sensitive reference strain by ∼3.5-fold. The mutations acquired inCurtobacterium flaccumfaciens pv. flaccumfaciensstrain DSM 20129 incrementally increased its UVCR resistance, with the accumulation of 20 point mutations in protein coding genes increasing tolerance to a level approaching that of stratospheric isolateCurtobacteriumsp. L6-1. The genetic basis for the increased UVCR tolerance phenotypes observed is discussed, with a specific emphasis on the role of genes involved in DNA repair and detoxification of reactive oxygen species.

Importance

Ultraviolet radiation is omnipresent in sunlight and has important biological effects on organisms. The stratosphere is the only location on Earth where microbes receive natural exposure to highly mutagenic wavelengths (<280 nm) of ultraviolet radiation. Genetic studies of bacteria from an environment that selects for extreme ultraviolet radiation resistant phenotypes has expanded what is known from studies of model species (e.g.,E. coli) and identified potentially novel protection and repair strategies. In addition to deepening understanding of ultraviolet radiation photobiology in atmospheric microbes and bacteria in general, these advancements are also highly relevant to astrobiology and space biology. The cold, dry, hypobaric, and high radiation environment of the stratosphere provides an earthly analog for thin extraterrestrial atmospheres (e.g., Mars) and is ideal for bioprospecting extremophile phenotypes that enable engineering of genetic stability and functionality in bio-based space life-support systems or any application where long-term persistence is desirable (e.g., biocontrol).
CT-based Machine Learning for Donor Lung Screening Prior to Transplantation
Authors: Ram Sundaresh , Verleden Stijn E , Kumar Madhav , Bell Alexander J. , Pal Ravi , Ordies Sofie , Vanstapel Arno , Dubbeldam Adriana , Vos Robin , Galban Stefanie , Ceulemans Laurens J. , Frick Anna E. , Van Raemdonck Dirk E. , Verschakelen Johny , Vanaudenaerde Bart M. , Verleden Geert M. , Lama Vibha N , Neyrinck Arne P. , Galban Craig J.
Published: March 2023

Background

Assessment and selection of donor lungs remains largely subjective and experience based. Criteria to accept or decline lungs are poorly standardized and are not compliant with the current donor pool. Using ex vivo CT images, we investigated the use of a CT-based machine learning algorithm for screening donor lungs prior to transplantation.

Methods

Clinical measures and ex-situ CT scans were collected from 100 cases as part of a prospective clinical trial. Following procurement, donor lungs were inflated, placed on ice according to routine clinical practice, and imaged using a clinical CT scanner prior to transplantation while stored in the icebox. We trained and tested a supervised machine learning method calleddictionary learning, which uses CT scans and learns specific image patterns and features pertaining to each class for a classification task. The results were evaluated with donor and recipient clinical measures.

Results

Of the 100 lung pairs donated, 70 were considered acceptable for transplantation (based on standard clinical assessment) prior to CT screening and were consequently implanted. The remaining 30 pairs were screened but not transplanted. Our machine learning algorithm was able to detect pulmonary abnormalities on the CT scans. Among the patients who received donor lungs, our algorithm identified recipients who had extended stays in the ICU and were at 19 times higher risk of developing CLAD within 2 years post-transplant.

Conclusions

We have created a strategy to ex vivo screen donor lungs using a CT-based machine learning algorithm. As the use of suboptimal donor lungs rises, it is important to have in place objective techniques that will assist physicians in accurately screening donor lungs to identify recipients most at risk of post-transplant complications.
Prognostic factors of clinical responses in patients with advanced-stage intrahepatic cholangiocarcinoma followingAtractylodes lanceaadministration: A phase 2A clinical trial
Authors: Saeheng Teerachat , Karbwang Juntra , Cheomung Anurak , Tongsiri Nisit , Plengsuriyakarn Tullayakorn , Na-Bangchang Kesara
Published: March 2023

A statistical model is essential in determining the appropriate predictive indicators for therapies in many types of cancers. Predictors have been compared favorably to the traditional systems for many cancers. Thus, this study has been proposed as an alternative or a new standard approach. A recent study on the clinical efficacy ofAtractylodes lancea(Thunb) DC. (AL) revealed the higher clinical benefits in patients with advanced-stage intrahepatic cholangiocarcinoma (ICC) treated with AL compared with standard supportive care. we investigated the relationships between clinical efficacy and pharmacokinetic parameters of serum bioactivity of AL and its active constituent “atractylodin” and determined therapeutic ranges. Cox proportion hazard model and Receive Operating Characteristic (ROC) were applied to determine the cut-off values of AUC0-inf, Cmax, and Cavgassociated with therapeutic outcomes. Number-need to be treated (NNT) and relative risk (RR) was also applied to determine potential predictors. The AUC0-infof total AL bioactivity of> 96.71 µg*h/ml was identified as a promising predictor of disease prognosis,i.e., progression-free survival (PFS) and disease control rate (DCR). Cmaxof total AL bioactivity of>21.42 was identified as a predictor of the prognosis of death. The therapeutic range of total AL bioactivity for PFS and DCR is 14.48-65.8 µg/ml, and for overall survival is 10.97-65.8 µg/ml. The predictors of ICC disease prognosis were established based on the pharmacokinetics of total AL bioactivity. The information could be exploited to improve the clinical efficacy of AL in patients with advanced-stage ICC. These predictors will be validated in a phase 2B clinical study.
Insights into the comorbidity between type 2 diabetes and osteoarthritis
Authors: de S. V. Arruda Ana Luiza , Hartley April , Katsoula Georgia , Smith George Davey , Morris Andrew P. , Zeggini Eleftheria
Published: March 2023

Multimorbidity is a rising public health challenge with important implications for health management and policy. The most common multimorbidity pattern is for the combination of cardiometabolic and osteoarticular diseases. Here, we study the genetic underpinning of the comorbidity between type 2 diabetes and osteoarthritis. We find genome-wide genetic correlation between the two diseases, and robust evidence for association signal colocalization at 18 genomic regions. We integrate multi-omics and functional information to resolve the colocalizing signals, and identify high-confidence effector genes, includingFTOandIRX3, which provide proof-of-concept insights into the epidemiologic link between obesity and both diseases. We find enrichment for lipid metabolism and skeletal formation pathways for signals underpinning the knee and hip osteoarthritis comorbidities with type 2 diabetes, respectively. Causal inference analysis identifies complex effects of tissue-specific gene expression on comorbidity outcomes. Our findings provide insights into the biological basis for the type 2 diabetes-osteoarthritis disease co-occurrence.
Novel Use of ctDNA to Identify Muscle-Invasive and Non-Organ Confined Upper Tract Urothelial Carcinoma
Authors: Huelster Heather L , Gould Billie , Schiftan Elizabeth A , Camperlengo Lucia , Davaro Facundo , Rose Kyle M , Soupir Alex C , Jia Shidong , Zheng Tiantian , Sexton Wade J , Pow-Sang Julio , Spiess Philippe E , Grass G. Daniel , Wang Liang , Wang Xuefeng , Vosoughi Aram , Necchi Andrea , Meeks Joshua J , Faltas Bishoy M , Du Pan , Li Roger
Published: March 2023

PURPOSE

Optimal patient selection for neoadjuvant chemotherapy prior to surgical extirpation is limited by the inaccuracy of contemporary clinical staging methods in high-risk upper tract urothelial carcinoma (UTUC). We investigated whether the detection of plasma circulating tumor DNA (ctDNA) can predict muscle-invasive and non-organ confined (MI/NOC) UTUC.

PATIENTS AND METHODS

Plasma cell-free DNA was prospectively collected from chemotherapy-naïve, high-risk UTUC patients undergoing surgical extirpation and sequenced using a 152-gene panel and low-pass whole-genome sequencing. To test for concordance, whole exome sequencing was performed on matching tumor samples. The performance of ctDNA for predicting MI/NOC UTUC was summarized using area under a receiver-operating curve and the optimal variant count threshold determined using Younden’s J statistic. Kaplan-Meier methods estimated survival, and Mantel-Cox log-rank testing assessed the association between preoperative ctDNA positivity and clinical outcomes.

RESULTS

Of 30 patients prospectively enrolled, 14 were found to have MI/NOC UTUC. At least one ctDNA variant was detected from 21/30 (70%) patients with 52% concordance with matching tumor samples. Detection of at least two panel-based molecular alterations provided the optimal sensitivity and specificity to predict MI/NOC UTUC. Imposing this threshold in combination with a plasma copy number burden score >6.5 achieved a sensitivity of 79% and specificity of 94% in predicting MI/NOC UTUC. Furthermore, the presence of ctDNA was strongly prognostic for progression-free survival (1-yr PFS 69% vs. 100%, p<0.01) and overall survival (1-yr OS 56% vs. 100%, p<0.02).

CONCLUSION

The detection of plasma ctDNA prior to extirpative surgery was highly predictive of MI/NOC UTUC and strongly prognostic of PFS and OS. Preoperative ctDNA demonstrates promise as a biomarker for selecting patients to undergo neoadjuvant chemotherapy prior to nephroureterectomy.
Sex-specific difference of long-term mortality after transcatheter edge-to-edge repair for functional mitral regurgitation; Insights from the OCEAN-Mitral Registry
Authors: Hioki Hirofumi , Watanabe Yusuke , Kataoka Akihisa , Kozuma Ken , Shirai Shinichi , Naganuma Toru , Yamawaki Masahiro , Enta Yusuke , Mizuno Shingo , Ueno Hiroshi , Ohno Yohei , Nakajima Yoshifumi , Izumo Masaki , Bouta Hiroki , Kodama Kazuhisa , Yamaguchi Junichi , Kubo Shunsuke , Amaki Makoto , Asami Masahiko , Saji Mike , Mizutani Kazuki , Okazaki Shinya , Hachinohe Daisuke , Otsuka Toshiaki , Adachi Yuya , Yamamoto Masanori , Hayashida Kentaro
Published: March 2023

Background

Recent studies suggested short-term mortality after transcatheter edge-to-edge repair (TEER) was comparable between male and female. However, the sex-specific prognostic difference in long-term follow-up after TEER is still unknown. To evaluate the impact of sex on long-term mortality after TEER for functional mitral regurgitation (FMR) using multicenter registry data.

Methods

We retrospectively analyzed 1220 patients (male 60.3%) who underwent TEER for FMR at 24 centers. Impact of sex on all-cause death and hospitalization for heart failure (HF) after TEER was evaluated using multivariate regression analysis and propensity score (PS) matching methods.

Results

During the two-year follow-up, 205 all-cause death and 259 hospitalizations for HF were observed after TEER for FMR. Male had a significantly lower incidence of all-cause death than female (18.7% vs. 14.0%, log-rank p < 0.01). After adjustment by multivariate Cox-regression and PS matching, male was significantly associated with a higher incidence of all-cause mortality after TEER than female (hazard ratio [HR] 2.24, 95% confidence interval [CI] 1.48 to 3.39 in multivariate Cox-regression; HR 2.04, 95% CI 1.17 to 3.57 in PS matching). The sex-specific prognostic difference was even more pronounced after 1-year of TEER. On contrary, there was no sex-related difference in hospitalization for HF after TEER.

Conclusions

Male had a higher incidence of two-year all-cause death during after TEER for FMR than female, while this was not observed in hospitalization for HF. This result might indicate that female with FMR is more likely to benefit from TEER for better prognosis.

What is known?

There were conflicting results in sex-related prognostic difference after TEER for FMR.

What the study adds

During two-year follow-up period, male had higher increased risk of mortality after TEER than female in multivariate regression and propensity score matched analysis, while there was no sex-related difference in hospitalization for HF after TEER. Female with FMR might be likely to derived benefit from TEER concomitant with GDMT as compared to male.
Impact of Transjugular Intracardiac Echocardiography-Guided Self-Expandable Transcatheter Aortic Valve Implantation on Reduction of Conduction Disturbances
Authors: Ishizu Kenichi , Shirai Shinichi , Miyawaki Norihisa , Nakano Kenji , Fukushima Tadatomo , Ko Euihong , Tsuru Yasuo , Tashiro Hiroaki , Tabata Hiroyuki , Nakamura Miho , Morofuji Toru , Morinaga Takashi , Hayashi Masaomi , Isotani Akihiro , Ohno Nobuhisa , Kakumoto Shinichi , Ando Kenji
Published: March 2023

Background

A high permanent pacemaker implantation (PPI) risk remain a concern of self-expandable transcatheter aortic valve implantation (TAVI), despite continued improvements in implantation methodology. We aimed to assess the impact of real-time direct visualization of the membranous septum using transjugular intracardiac echocardiography (ICE) during TAVI on reducing the rates of conduction disturbances including the need for PPI.

Methods

Consecutive patients treated with Evolut R and Evolut PRO/PRO+ from February 2017 to September 2022 were included in this study. We compared outcomes between the conventional implantation method using the 3-cusps view (“3-cusps without ICE” group), the recent method using cusp-overlap view (“cusp-overlap without ICE” group), and our novel method using ICE (“cusp-overlap with ICE” group).

Results

Of the 446 patients eligible for analysis, 211 (47.3%) were categorized as the “3-cusps without ICE” group, 129 (28.9%) were in the “cusp-overlap without ICE” group, and 106 (23.8%) comprised the “cusp-overlap with ICE” group. Compared with the “3-cusps without ICE” group, the “cusp-overlap without ICE” group had a smaller implantation depth (2.2 [IQR 1.0–3.5] mm vs 4.3 [IQR: 3.3–5.4],P<0.001) and lower 30-day PPI rates (7.0% vs 14.2%,P= 0.035). Compared with the “cusp-overlap without ICE” group, the “cusp-overlap with ICE” group had lower 30-day PPI rates (1.0%,P= 0.014), albeit with comparable implantation depths (1.9 [IQR 0.9–2.9] mm,P= 0.150). Multivariable analysis showed that our novel method using ICE with the cusp-overlap view was independently associated with a 30-day PPI rate reduction. There were no group differences in 30-day all-cause mortality (1.4% vs 1.6% vs 0%;P= 0.254).

Conclusions

Our novel implantation method using transjugular ICE, which enabled a real-time direct visualization of the membranous septum, achieved a predictably high position of prostheses, resulting in a substantial reduction of conduction disturbances requiring PPI after TAVI.
Biochemical reactions between intra-articular tissues and joint instability in a rat model of osteoarthritis
Authors: Murata Kenji , Kawabata Sora , Kojima Takuma , Oka Yuichiro , Takasu Chiharu , Terada Hidenobu , Kanemura Naohiko
Published: March 2023

Aims

Joint instability is associated with various joint conditions including osteoarthritis (OA) and inflammation, and we have developed model which is determined to role of knee instability. Investigating cartilage maintenance factors such as hyaluronic acid (HA) and glycosaminoglycans (GAGs) can provide insights into the effect of the mechanical stress and the inhibitor used, with the following aims: 1) whether cartilage degeneration is inhibited in the new model, 2) whether combination TGF-β1 inhibition mitigates cartilage degeneration, and to determine the role of TGF-β1 in synovitis using fibroblasts.

Main methods

We used this novel model to investigate inhibition of OA progression with a focus on HA and GAGs, which help maintain the cartilage and synovial membrane. In detail, mechanical tests, X-ray, histological, and protein and mRNA expression analyses were used to determine the role of joint stability using in vivo model or fibroblast from synovial membrane.

Key findings

Joint stability mitigated cartilage degeneration loss, decreased osteophytes, increased the expression levels of HA and GAGs in the synovial membrane, and decreased the release of pro-inflammatory factors in rats. Moreover, injection of TGF-β1 inhibitor in an inflammatory synovial membrane promoted HA and GAGs expression. In synovial fibroblast cells, inhibition of TGF-β1 over expression significantly inhibited the downregulation of pro-inflammatory factors and promoted the upregulation of lubrification for cartilage.

Significance

Our results suggest that joint instability is an independent mechanical factor for OA progression. The results provide novel insights into the association between OA and joint instability, which has significant human sciences implications.

Research Highlights

• Established a new experimental rat model of the different joint instability for elucidate osteoarthritis onset/progression

• Using Histological staining to investigated the osteoarthritis including synovitis and osteophytes of the novel model

• Using fibroblast from synovial membrane to investigated the fibrosis

• Joint instability exacerbates articular cartilage degeneration and decreases HA and GAGs protein expressions in synovial membrane

• TGF-β1 inhibitor on early osteoarthritis joints may suppress synovial inflammation
Convolutional neural network approach for the automated identification ofin cellulocrystals
Authors: Kardoost Amirhossein , Schönherr Robert , Deiter Carsten , Redecke Lars , Lorenzen Kristina , Schulz Joachim , de Diego Iñaki
Published: March 2023

In cellulocrystallization is a rarely occurring event in nature. Recent advances, making use of heterologous overexpression, can promote the intracellular formation of protein crystals, but new tools are required to detect and to characterize these targets in the complex cell environment. In the present work we make use of Mask R-CNN, a Convolutional Neural Network (CNN) based instance segmentation method, for the identification of either single or multi-shaped crystals growing in living insect cells, using conventional bright field images. The algorithm can be rapidly adapted to recognize different targets, with the aim to extract relevant information to support a semi-automated screening pipeline, with the purpose to aid in the development of the intracellular protein crystallization approach.
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements
Authors: Chardon Florence M. , McDiarmid Troy A. , Page Nicholas F. , Daza Riza M. , Martin Beth , Domcke Silvia , Regalado Samuel G. , Lalanne Jean-Benoît , Calderon Diego , Li Xiaoyi , Starita Lea M. , Sanders Stephan J. , Ahituv Nadav , Shendure Jay
Published: March 2023

CRISPR-based gene activation (CRISPRa) is a promising therapeutic approach for gene therapy, upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsivecis-regulatory elements and the gene(s) they regulate. Random combinations of many gRNAs are introduced to each of many cells, which are then profiled and partitioned into test and control groups to test for effect(s) of CRISPRa perturbations of both enhancers and promoters on the expression of neighboring genes. Applying this method to a library of 493 gRNAs targeting candidatecis-regulatory elements in both K562 cells and iPSC-derived excitatory neurons, we identify gRNAs capable of specifically upregulating intended target genes and no other neighboring genes within 1 Mb, including gRNAs yielding upregulation of six autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD) risk genes in neurons. A consistent pattern is that the responsiveness of individual enhancers to CRISPRa is restricted by cell type, implying a dependency on either chromatin landscape and/or additionaltrans-acting factors for successful gene activation. The approach outlined here may facilitate large-scale screens for gRNAs that activate therapeutically relevant genes in a cell type-specific manner.
Stable mammalian serum albumins designed for bacterial expression
Authors: Khersonsky Olga , Goldsmith Moshe , Zaretsky Irina , Hamer-Rogotner Shelly , Dym Orly , Unger Tamar , Yona Meital , Fridmann-Sirkis Yael , Fleishman Sarel J.
Published: March 2023

Albumin is the most abundant protein in the blood serum of mammals and has essential carrier and physiological roles. Albumins are also used in a wide variety of molecular and cellular experiments and in the cultivated meat industry. Despite their importance, however, albumins are challenging for heterologous expression in microbial hosts, likely due to 17 conserved intramolecular disulfide bonds. Therefore, albumins used in research and biotechnological applications either derive from animal serum, despite severe ethical and reproducibility concerns, or from recombinant expression in yeast or rice. We use the PROSS algorithm to stabilize human and bovine serum albumins, finding that all are highly expressed inE. coli. Design accuracy is verified by crystallographic analysis of a human albumin variant with 16 mutations. This albumin variant exhibits ligand binding properties similar to those of the wild type. Remarkably, a design with 73 mutations relative to human albumin exhibits over 40°C improved stability and is stable beyond the boiling point of water. Our results suggest that proteins with many disulfide bridges have the potential to exhibit extreme stability when subjected to design. The designed albumins may be used to make economical, reproducible, and animal-free reagents for molecular and cell biology. They also open the way to high-throughput screening to study and enhance albumin carrier properties.

Graphical abstract

Highlights

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Computational design stabilized human and bovine serum albumins

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Designs express solubly inE. coliand exhibit up to 40 °C increased thermostability

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Some designs exhibit identical ligand binding properties

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Crystal structure confirms design accuracy

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Designs can be used in cell culture andin vitroapplications
Arabidopsis thalianaLSM7 is essential for auxin-mediated regulation ofSAURgenes and thermomorphogenesis
Authors: Nardeli Sarah Muniz , Zacharaki Vasiliki , Rojas-Murcia Nelson , Collani Silvio , Wang Kai , Bayer Martin , Schmid Markus , Goretti Daniela
Published: March 2023

Temperature affects plant growth by modulating the expression of genes and subsequent processing of RNAs that govern essential physiological processes. Here, we show thatArabidopsis thalianaSm-like7 (LSM7), a core component of the splicing and decapping machinery, is indispensable for embryogenesis and development. Hypomorphiclsm7-2mutants display severe developmental defects that are exacerbated by high temperatures. Transcriptome analysis verified LSM7’s extensive role in gene regulation. In particular, we found that the key regulator of thermomorphogenesis,PHYTOCHROME INTERACTING FACTOR 4(PIF4), and auxin-related genes, includingSMALL AUXIN UP-REGULATED(SAUR) genes, are misregulated inlsm7-2. Auxin metabolic profiling confirmed that auxin homeostasis was disturbed inlsm7-2. Importantly, overexpression of the auxin-responsiveSAUR19gene partially restored thermomorphogenesis defects inlsm7-2under high ambient temperature. Taken together, our research provides mechanistic insights into the interplay between RNA processing, hormone homeostasis, and the response to temperature regulation in plants and elucidates LSM7’s essential function in plant temperature acclimation and resilience.

Significance Statement

Given their sessile nature, plants cannot escape adverse environmental conditions such as cold or heat. Instead, they continuously adjust their gene expression and RNA processing to regulate growth and physiology in response to their surroundings. In this study, we investigated the role of the core RNA processing factor LSM7 in temperature acclimation inArabidopsis thaliana. We found that LSM7 knockdown mutants were impaired in thermomorphogenesis and, as a result, were hypersensitive to elevated temperatures. At the molecular level, we demonstrated that this temperature sensitivity was caused by the misregulation of key regulators of thermomorphogenesis, including PIF4, auxin homeostasis and signaling, and SAUR genes. Our findings provide valuable insights into the role of RNA processing in plant temperature acclimation.
The Road Less Traveled: Uncovering the Convergence Toward Specific Pleiotropic Phenotypes in Aging
Authors: Stoeger Thomas
Published: March 2023

Aging is a complex process influenced by a wide range of environmental and molecular factors. Despite this complexity, individuals tend to age in highly similar ways, leading to the question of what drives this convergence. Recent research, including my own discoveries, suggests that the length of transcript molecules plays a crucial role in age-dependent changes to the transcriptome. Drawing inspiration from the road trip analogy of cellular transcription, I propose that a non-linear scaling law drives convergence towards specific pleiotropic phenotypes in biological aging. This scaling law is based on the notion that molecular changes observed during aging may reflect unspecific damage to cellular physiology. By validating this hypothesis, I can improve our understanding of biological aging and identify new candidate compounds for anti-aging interventions, as well as re-identify one known intervention. This work has actionable implications for improving human health and extending lifespans.
Myc-regulated miRNAs modulate p53 expression and impact animal survival under nutrient deprivation
Authors: Gervé María P. , Sánchez Juan A. , Ingaramo María C. , Dekanty Andrés
Published: March 2023

The conserved transcription factor Myc regulates cell growth, proliferation and apoptosis, and its deregulation has been associated with human pathologies. Although specific miRNAs have been identified as fundamental components of the Myc tumorigenic program, how Myc regulates miRNA biogenesis remains controversial. Here we showed that Myc functions as an important regulator of miRNA biogenesis inDrosophilaby influencing both miRNA gene expression and processing. Through the analysis of ChIP-Seq datasets, we discovered that nearly 56% ofDrosophilamiRNA genes show dMyc binding, exhibiting either the canonical or non-canonical E-box sequences within the peak region. Consistently, reduction of dMyc levels resulted in widespread downregulation of miRNAs gene expression. dMyc also modulates miRNA processing and activity by controlling Drosha and AGO1 levels through direct transcriptional regulation. By usingin vivomiRNA activity sensors we demonstrated that dMyc promotes miRNA-mediated silencing in different tissues, including the wing primordium and the fat body. We also showed that dMyc-dependent expression of miR-305 in the fat body modulates Dmp53 levels depending on nutrient availability, having a profound impact on the ability of the organism to respond to nutrient stress. Indeed, dMyc depletion in the fat body resulted in extended survival to nutrient deprivation which was reverted by expression of either miR-305 or a dominant negative version of Dmp53. Our study reveals a previously unrecognized function of dMyc as an important regulator of miRNA biogenesis and suggests that Myc-dependent expression of specific miRNAs may have important tissue-specific functions.
TET2lesions enhance the aggressiveness ofCEBPA-mutant AML by rebalancingGATA2expression
Authors: Heyes Elizabeth , Wilhelmson Anna S. , Wenzel Anne , Manhart Gabriele , Eder Thomas , Schuster Mikkel B. , Rzepa Edwin , Pundhir Sachin , D’Altri Teresa , Gentil Coline , Meggendorfer Manja , Schwaller Jürg , Haferlach Torsten , Grebien Florian , Porse Bo T.
Published: March 2023

The myeloid transcription factor CEBPA is recurrently biallelically mutated (i.e., double mutated;CEBPADM) in acute myeloid leukemia (AML) with a combination of hypermorphic N-terminal mutations (CEBPANT), promoting expression of the leukemia-associated p30 isoform, and amorphic C-terminal mutations. The most frequently co-mutated genes inCEBPADMAML areGATA2andTET2, however the molecular mechanisms underlying this co-mutational spectrum are incomplete.

By combining transcriptomic and epigenomic analyses ofCEBPA-TET2co-mutated patients with models thereof, we identifyGATA2as a conserved target of theCEBPA-TET2mutational axis, providing a rationale for the mutational spectra inCEBPADMAML. Elevated CEBPA levels, driven byCEBPANT, mediate recruitment of TET2 to theGata2distal hematopoietic enhancer thereby increasingGata2expression. Concurrent loss of TET2 inCEBPADMAML induces a competitive advantage by increasingGata2promoter methylation, thereby rebalancing GATA2 levels. Of clinical relevance, demethylating treatment ofCebpa-Tet2co-mutated AML restoresGata2levels and prolongs disease latency.
aPEAR:an R package for autonomous visualisation of pathway enrichment networks
Authors: Kerseviciute Ieva , Gordevicius Juozas
Published: March 2023

The interpretation of pathway enrichment analysis (PEA) results is frequently complicated by an overwhelming and redundant list of significantly affected pathways. Here, we present an R packageaPEAR(Advanced Pathway Enrichment Analysis Representation) which leverages similarities between the pathway gene sets and represents them as a network of interconnected clusters. Each cluster is assigned a meaningful name which highlights the main biological themes in the experiment. Our approach enables automated and objective overview of the data without manual and time-consuming parameter tweaking.

Availability and implementation

The packageaPEARis implemented in R, published under the MIT open source licence. The source code, documentation, and usage instructions are available onhttps://gitlab.com/vugene/aPEARas well as on CRAN (https://CRAN.R-project.org/package=aPEAR).

Contact

kerseviciute.ieva@gmail.comorjuozas@vugene.com.

Supplementary information

The complete analysis used to evaluate the package can be found athttps://github.com/ievaKer/aPEAR-publication.
Inhibition of nonsense-mediated mRNA decay reduces the tumorigenicity of human fibrosarcoma cells
Authors: Nasif Sofia , Colombo Martino , Uldry Anne-Christine , Schröder Markus S. , de Brot Simone , Mühlemann Oliver
Published: March 2023

Nonsense-mediated mRNA decay (NMD) is a eukaryotic RNA degradation pathway that targets for degradation faulty mRNAs with premature termination codons as well as many physiological mRNAs encoding full-length proteins. Consequently, NMD functions in both, quality control and post-transcriptional regulation of gene expression, and it has been implicated in the modulation of cancer progression. To investigate the role of NMD in cancer, we knocked out SMG7 in the HT1080 human fibrosarcoma cell line. SMG7 is involved in deadenylation-coupled exonucleolytic mRNA decay, one of the two main degradation pathways in mammalian NMD. Genome-wide proteomic and transcriptomic analyses confirmed that NMD is severely compromised in these SMG7-knockout HT1080 cells. We compared the oncogenic properties between the parental, the SMG7-knockout, and a rescue cell line in which we re-introduced both isoforms of SMG7. In parallel, we tested the effect of a drug inhibiting the NMD factor SMG1 on the HT1080 cells to distinguish NMD-dependent effects from putative NMD-independent functions of SMG7. Using cell-based assays as well as a mouse xenograft tumor model, we show that the oncogenic properties of the parental HT1080 cells are severely compromised when NMD is inhibited. Molecular pathway analysis revealed a strong reduction of the matrix metalloprotease 9 (MMP9) gene expression in NMD-suppressed cells. Since MMP9 expression promotes cancer cell migration and invasion, metastasis and angiogenesis, its downregulation in NMD-suppressed cells explains, at least partially, their reduced tumorigenicity. Collectively, our findings emphasize the therapeutic potential of NMD inhibition for the treatment of certain types of cancer.

Significance

Nonsense-mediated mRNA decay (NMD) is a eukaryotic RNA decay pathway with reported roles in regulating cellular stress responses, differentiation, and viral defense. NMD has also emerged as a modulator of cancer progression, however, the available evidence supports both, a tumor suppressor as well as a pro-tumorigenic role for NMD. We discovered that NMD inhibition results in impaired tumorigenicity in the HT1080 human fibrosarcoma cell line and uncovered a direct correlation between NMD activity and the expression levels the pro-tumorigenic gene MMP9. Restoring MMP9 expression in NMD-suppressed cells partially improved their oncogenic properties. These results show that the tumorigenicity of the HT1080 fibrosarcoma cells relies on NMD activity and highlights the potential use of NMD inhibition as a therapeutic approach.
Widespread PRC barrel proteins play critical roles in archaeal cell division
Authors: Zhao Shan , Makarova Kira S , Zheng Wenchao , Liu Yafei , Zhan Le , Wan Qianqian , Gong Han , Krupovic Mart , Lutkenhaus Joe , Chen Xiangdong , Koonin Eugene V , Du Shishen
Published: March 2023

Cell division is fundamental to all cellular life. Most of the archaea employ one of two alternative division machineries, one centered around the prokaryotic tubulin homolog FtsZ and the other around the endosomal sorting complex required for transport (ESCRT). However, neither of these mechanisms has been thoroughly characterized in archaea. Here, we show that three of the four PRC (Photosynthetic Reaction Center) barrel domain proteins ofHaloferax volcanii(renamedCelldivisionproteins B1/2/3 (CdpB1/2/3)), play important roles in division. CdpB1 interacts directly with the FtsZ membrane anchor SepF and is essential for division, whereas deletion ofcdpB2andcdpB3causes a major and a minor division defect, respectively. Orthologs of CdpB proteins are also involved in cell division in other haloarchaea. Phylogenetic analysis shows that PRC barrel proteins are widely distributed among archaea, including the highly conserved CdvA protein of the crenarchaeal ESCRT-based division system. Thus, diverse PRC barrel proteins appear to be central to cell division in most if not all archaea. Further study of these proteins is expected to elucidate the division mechanisms in archaea and their evolution.
Deep Active Learning for Robust Biomedical Segmentation
Authors: Arikan Mustafa , Sallo Ferenc , Montesel Andrea , Ahmed Hend , Hagag Ahmed , Book Marius , Faatz Henrik , Cicinelli Maria , Meshkinfamfard Sepehr , Ongun Sevim , Dubis Adam , Lilaonitkul Watjana
Published: March 2023

Deep learning for medical applications faces many unique challenges. A major challenge is the large amount of labelled data for training, while working in a relatively data scarce environment. Active learning can be used to overcome the vast data need challenge. A second challenged faced is poor performance outside of a experimental setting, contrary to the high requirement for safety and robustness. In this paper, we present a novel framework for estimating uncertainty metrics and incorporating a similarity measure to improve active learning strategies. To showcase effectiveness, a medical image segmentation task was used as an exemplar. In addition to faster learning, robustness was also addressed through adversarial perturbations. Using epistemic uncertainty and our framework, we can cut number of annotations needed by 39% and by 54% using epistemic uncertainty and a similarity metric.