bluuebunny/crossref_metadata_2025 huggingface dataset:
Critical anatomical variants in preoperative computed tomography of paranasal sinuses in a tertiary care center: a cross-section study
Authors: Dahal Prajwal , Parajuli Sabina , Maharjan Santosh , Adhikari Govinda , Upadhyaya Rudra Prasad , Ghimire Samjhana , Dhakal Natasha
Published: February 2025

Background:

Certain anatomical variants of the paranasal sinuses (PNS) predispose to injury of surrounding critical structures during functional endoscopic sinus surgery (FESS) and occurrence of common pathologies like sinusitis. However, they are often not reported in pre-operative computed Tomography (CT).

Methods:

The CT scan of paranasal sinuses and head of 360 adults (age > 13 years) were retrospectively evaluated for variants of cribriform plate, olfactory fossa, lamina papyracea, uncinate process, sphenoid pneumatization and anterior ethmoid artery by 4 radiologists with experience of 3 to 6 years. Prevalence of each variant was obtained. Chi-squared and independent sample t-tests were used to analyze relationships between variables, with significance set at p < 0.05.

Results:

The prevalence of Keros type 1, type 2 and type 3 olfactory fossa was 24.4 %, 66.9 % and 8.6 % respectively in right side and 20.6 %, 69.2 % and 10.3% respectively in left side. Mean depth of right and left olfactory fossa was 4.9 mm (±1.9) and 5.2 mm (± 1.8) respectively. Dehiscence/ remote fracture of anterior skull base was seen in 1.9% cases. Dehiscence/ remote fracture of lamina papyracea was present in 2.8 % cases. Haller cells were seen in 13.9%. Conchal, presellar, incomplete sellar and complete sellar pattern of pneumatization of sphenoid sinus had prevalences of 2.5%, 6.4%, 26.7% and 64.4% respectively. The prevalence of dehiscence of carotid canal in sphenoid sinus was 7.2 %. The prevalence of bony septa inserting onto carotid canal was 37.8 %. The prevalence of supra-orbital pneumatization was 51.4 %. Prevalence of agger nasi cell and pneumatization of crista galli was 82.2% and 16.7% respectively.

Conclusion:

Preoperative CT provides opportunity to look for critical structures in relation to the PNS. Radiologists should report these findings to prevent potential complications during FESS.
Improving Postpartum Depression Screening Rates Using a Quality Improvement Framework in a Community-based Academic Primary Care Clinic
Authors: Epee-Bounya Alexandra , Mari Elizabeth , Seals Jahmakah-Lynn , Regan Shannon , Rea Corinna J.
Published: February 2025

Introduction:

Maternal postpartum depression (PPD) is the most common diagnosis during the postpartum period, with a higher incidence in underserved populations. Though PPD often goes undiagnosed, prompt diagnosis has a positive impact on several measures of children’s health and development, as well as maternal health. To increase routine screening per American Academy of Pediatrics recommendations, we implemented a multipronged quality improvement (QI) initiative centered around a newborn coordinator embedded in our primary care clinic.

Methods:

A multidisciplinary team implemented a QI initiative in a community-based academic primary care clinic. We used the plan-do-study-act method and other QI tools to improve our processes and p-type control charts to monitor improvements. The interventions centered on workflow changes and staff education with aims to increase our PPD screening rates to 75%, maintain appropriate referral rates for parents with positive PPD screeners above 90%, and ensure no disparity in rates of screening regardless of race/ethnicity, language, and insurance status.

Results:

PPD screening rates for all well child care visits from birth to age 6 months increased from a mean of 16 % at baseline to 72%. Additionally, we maintained a referral rate for positive PPD screens above 90%. Our health equity analysis did not demonstrate any disparity in our screening rates.

Conclusions:

Applying a combination of education and process workflow changes can successfully increase screening rates for PPD in a community-based academic primary care clinic.
Judicial Opinion 131
Authors: Arahal David R. , Bull Carolee T. , Christensen Henrik , Dunlap Christopher , Montero-Calasanz Maria del Carmen , Parker Charles T. , Vandamme Peter , Ventosa Antonio , Ventura Stefano , Young Peter , Göker Markus
Published: February 2025

Opinion 131 addresses a Request for an Opinion asking the Judicial Commission to conserve the genus name Proteus Hauser 1885 (Approved Lists 1980) over its earlier homonym, the protozoan genus name Proteus Müller 1786. The Judicial Commission agrees that the later homonym is illegitimate and that the replacement of the prokaryotic name Proteus would be undesirable. It is also concluded that Proteus Müller 1786 is an objectively invalid name under the International Code of Zoological Nomenclature. Judicial Opinions 9, 12 and 130 serve as precedents for the conservation of Proteus Hauser 1885 (Approved Lists 1980) over Proteus Müller 1786. This action is taken here and makes the prokaryotic name Proteus legitimate.
Promoter-centric gene regulation in drug-resistant cancer
Authors: Kameswaran Vasumathi , Paul Sayantanee , Le Daniel , Hoover Jonathan , Zhao Luke Y. , Guarnaccia Alissa D. , Hagenbeek Thijs J. , Lund Jessica M. , Xavier-Magalhaes Ana , Shi Minyi , Lau Julia , De Simone Marco , Liang Yuxin , Dey Anwesha , Modrusan Zora , Daniel Bence
Published: February 2025

In eukaryotic cells, gene-distal regulatory elements (REs) facilitate long-range gene regulation, ensuring cell type-specific transcriptional programs. This mechanism is frequently disrupted in cancer, often driven by transcription factors (TFs) that serve as targets for cancer therapy. However, targeting these TFs can lead to acquired resistance mechanisms that are not fully understood. We show that mesothelioma cancer cells, dependent on the oncogenic driver TF TEAD, develop resistance to a pan-TEAD inhibitor and revert to an evolutionarily ancient, promoter-centric gene regulatory mechanism to recover gene expression following TEAD inhibition. Base-pair-resolution 3D chromatin conformation mapping reveals that RE-promoter interactions are disrupted in resistant cells, despite epigenetic and transcriptomic recovery. Mechanistically, in resistant cells, TF complexes, including resistance-specific FOSL1 and KLF4, preferentially bind and enhance promoter activity to recover gene expression, rendering distal REs dispensable. Our findings highlight promoter elements and promoter-specific TFs as potential therapeutic targets using a model of drug-resistant cancer.
The Pro- vs. Anti-Angiogenic Capacity of Short Chain Fatty Acids is Dependent on the Bioavailability of FFAR3 in Peripheral Artery Disease.
Authors: Kuppuswamy Sivaraman , Patel Kripa , Zhi Wenbo , Ganta Vijay C
Published: February 2025

Background. Our current study builds on our recent report that showed Palmitate aggravates ischemic endothelial (EC) dysfunction in vitro and aims to determine whether Palmitate is a critical determinant of PAD severity. In contrast to Palmitate, we studied the role of short-chain fatty acids (SCFAs) in regulating ischemic revascularization in PAD. Methods: Femoral artery ligation and resection was used as preclinical-PAD model. Hypoxia serum starvation was used as in vitro PAD model. Results: Palmitate dramatically decreased ischemic-EC survival and angiogenic capacity in vitro, whereas SCFAs significantly induced their angiogenic capacity. LC-MRM MS analysis showed decreased SCFA content in ischemic-muscle. Laser Speckle perfusion imaging showed that intramuscular SCFA treatment significantly induced perfusion recovery, whereas Palmitate showed a modest but significant impairment in perfusion recovery. Immunoblot analysis showed that SCFAs preferentially induce Free fatty acid receptor (FFAR)-3, but not FFAR2. Accordingly, silencing FFAR3 decreased ischemic-EC angiogenic capacity, whereas inhibiting FFAR2 induced ischemic angiogenesis. Pharmacological inhibition of FFAR3 by beta-hydroxybutyrate (BHB) significantly decreased perfusion recovery. SCFA treatment further decreased perfusion recovery in BHB-treated ischemic-muscle. Mechanistically, inhibiting FFAR3-induced FFAR2-levels that inhibited ischemic-EC angiogenic capacity by decreasing NO and inducing ROS levels in SCFA-treated ischemic-ECs. Conclusions: Our data shows that Palmitate alone is not sufficient to drive the PAD severity. Increased FFAR3 levels in ischemic-muscle allow SCFAs to activate the AKT-NO axis to induce ischemic angiogenesis and perfusion recovery. However, loss of FFAR3 in ischemic-muscle promotes FFAR2 activation that blocks SCFA-induced NO-production and redox balance thereby inhibiting perfusion recovery in preclinical-PAD.
Atypical endo-β-1,4-mannannases are necessary for normal glucomannan synthesis in Arabidopsis
Authors: Kikuchi Aina , Sato Eriko , Yoshimi Yoshihisa , Takasaki Hironori , Nishigaki Naho , Atsuzawa Kimie , Kaneko Yasuko , Yamaguchi Masatoshi , Takahashi Daisuke , Dupree Paul , Kotake Toshihisa
Published: February 2025

The molecular mechanisms underlying the synthesis and secretion of large cell wall polysaccharides in plant cells are not fully understood. In this study, we report that two atypical endo-β-1,4-mannanases (MANs), which are not secreted and do not degrade glucomannan in the cell wall, play a novel role in glucomannan synthesis. Among the six MANs in Arabidopsis, AtMAN2 and AtMAN5 contain a transmembrane (TM) domain at their N-terminal region instead of a signal peptide. Subcellular localization using MAN protein fused with fluorescent protein demonstrated that AtMAN2 localizes to the Golgi apparatus in vascular and interfascicular fiber cells. We found that an Arabidopsisman2 man5double mutant lost 65% of glucomannan in the cell walls of the inflorescence stem. Immunostaining revealed that the double mutant retained a small amount of glucomannan in the vacuole instead of secreting it to the cell walls. Arabidopsis possesses another atypical MAN, AtMAN6, with an HDEL retention signal at its C-terminus. However, mutation of AtMAN6 did not affect glucomannan content in the cell walls, suggesting distinct functions for these MANs. This study revealed that the function of AtMAN2 and AtMAN5 is necessary for normal glucomannan synthesis. We suggest that thesemanmutants point to an uncharacterized transport pathway in plant cells, through which glucomannan is trafficked to the vacuole instead of the cell walls.

SIGNIFICANCE STATEMENT

Cell wall polysaccharides are synthesized from building block nucleotide sugars by the action of glucosyltransferases, but other factors facilitating the synthesis and secretion of large polysaccharides without aggregation remain to be identified. Here, we focused on the importance and functions of two atypical Arabidopsis endo-β-1,4-mannanases that have a transmembrane domain instead of a secretion signal, and which are widely distributed in angiosperms but have not been well characterized. Arabidopsis mutants impaired in these endo-β-1,4-mannanases lost 65% cell wall glucomannan, indicating that the hydrolysis by these enzymes is necessary for normal synthesis. Enhanced retention of glucomannan inside cells in the mutant hints at a transport route to deliver glucomannan to the vacuole.
Conditional Diffusion with Locality-Aware Modal Alignment for Generating Diverse Protein Conformational Ensembles
Authors: Wang Baoli , Wang Chenglin , Chen Jingyang , Liu Danlin , Sun Changzhi , Zhang Jie , Zhang Kai , Li Honglin
Published: February 2025

Recent advances in AI have enabled the accurate prediction of a single stable protein structure solely based on its amino acid sequence. However, capturing the complete conformational landscape of a protein and its dynamic flexibility remains challenging. In this work, we developed Modal-aligned conditional Diffusion (Mac-Diff), a score based diffusion model for generating the conformational ensembles for unseen proteins. Central to Mac-Diff is an innovative attention module that enforces a delicate, locality-aware alignment between the conditional view (protein sequence) and the target view (residue pair geometry) to compute highly contextualized features for effective structural denoising. Furthermore, Mac-Diff leverages semantically rich sequence embedding from Protein Language Models like ESM-2 in enforcing the protein sequence condition that captures evolutionary, structural and functional information. This compensates for protein structural heterogeneity more effectively than embeddings from structure prediction models that are possibly biased to the dominant conformation. Mac-Diff showed promising results in generating realistic and diverse protein structures. It successfully recovered conformational distributions of fast folding proteins, captured multiple meta-stable conformations that were only observed in long MD simulation trajectories and efficiently predicted alternative conformations for allosteric proteins. We believe that Mac-Diff offers a useful tool to improve understanding of protein dynamics and structural variability, with broad implications for structural biology, drug discovery, and protein engineering.
Retroelement co-option disrupts the cancer transcriptional programme
Authors: Loong Jane , Thompson Rachael , Hall Callum , Doglio Laura , Pape Judith , Kassiotis George
Published: February 2025

Background: Transcriptional activation of otherwise repressed endogenous retroelements (RTEs) is a hallmark of cancer, shaping tumour progression and immunogenicity by multifaceted, yet incompletely understood mechanisms. Methods: We used an extended pan-cancer transcriptome assembly to identify potential effects of RTEs on the genes near or within which they have integrated. These were subsequently verified in test cases by further analysis of transcriptional profiles in cancer patient data, and by in vitro studies involving restoration of gene activity, and proliferation and migration assays in cancer cell lines. Results: We report that cancer-specific transcriptional activation of RTEs causes frequent reduction or loss of gene function. Exonisation and alternative splicing of RTEs creates non-functional RNA and protein isoforms and derepressed RTE promoter activity initiates antisense transcription, both at the expense of the canonical isoforms. Contrary to theoretical expectation, transcriptionally activated RTEs affect genes with established tumour-promoting function, including the common essential RNGTT and the lung cancer-promoting CHRNA5 genes. Furthermore, the disruptive effect of RTE activation on adjacent tumour-promoting genes is associated with slower disease progression in clinical data, whereas experimental restoration of gene activity enhances tumour cell in vitro growth and invasiveness Conclusions: These findings underscore the gene-disruptive potential of seemingly innocuous germline RTE integrations, unleashed only by their transcriptional utilisation in cancer. They further suggest that such metastable RTE integrations are co-opted as sensors of the epigenetic and transcriptional changes occurring during cellular transformation and as executors that disrupt the function of tumour-promoting genes.
Optimized upstream analytical workflow for single-nucleus transcriptomics in main metabolic tissues
Authors: Dong Pengwei , Ding Shitong , Wang Guanlin
Published: February 2025

Single-nucleus RNA sequencing (snRNA-seq) has emerged as a powerful approach for studying cellular heterogeneity in metabolic tissues. However, snRNA-seq analysis remains challenging due to low gene expression and data complexity. Here, we introduce an optimized upstream analytical workflow for snRNA-seq data from 67 samples across white adipose tissue, muscle, liver and the hypothalamus. We emphasized the importance of key steps including ambient RNA removal, doublet identification and data integration to ensure accurate downstream analysis. This workflow offers a valuable resource for researchers in metabolism, facilitating deeper insights into cellular diversity and metabolic function through rigorous snRNA-seq analysis.
Systemic MIF facilitates chronic lymphocytic leukemia development independent of its cellular source
Authors: Kohlhas Viktoria , Reinart Nina , Rosen Natascha , Reinartz Sebastian , Nguyen Phuong-Hien , Hallek Michael
Published: February 2025

Macrophage migration inhibitory factor (MIF) is broadly produced by various cell types, particularly immune cells, and functions as a key modulator of innate and adaptive immunity. Increasing evidence has linked MIF to the pathogenesis of both solid tumors and hematologic malignancies, including chronic lymphocytic leukemia (CLL). We previously showed that the global deletion of Mif in the TCL1 transgenic mouse model for CLL significantly delayed disease development leading to longer overall survival of the knockout mice. In this study, we demonstrated that adaptive transfer of murine CLL cells failed to establish disease in Mif-deficient recipients due to impaired homing of leukemic cells into the spleens, indicating that host-derived Mif is essential for leukemic infiltration and expansion. To identify the most relevant source of Mif in CLL, we generated two CLL mouse strains with B-lymphoid- or myeloid-lineage-specific Mif deletion. In contrast to the global Mif knockout, neither conditional Mif knockout significantly altered CLL progression, illustrating that the cellular source of Mif is less critical than its systemic presence in the tissue environment. Taken together, these in vivo findings indicate that MIF plays a relevant role in CLL pathogenesis, acting independently of its specific cellular origin.
Lowering CD40L expression in Murine Lupus Results in an Increase in Disease Indicators in Female but not Male B6 mice
Authors: Prado De Maio Diego J. , Tetteh Sandra , Ayers Christopher J. , Brown Michelle , Covey Lori R
Published: February 2025

Our lab has previously described a mouse model (CD40LΔ5) that produces only 60% of WT CD40L due to a targeted deletion in an RNA binding site within the CD40L message. The CD40LΔ5 mutation, which destabilizes CD40L mRNA during T cell activation, causes disrupted germinal center (GC) formation leading to reduced levels of memory B cells and switched antibodies. In this study, we used our model of limited CD40L expression to investigate its effect on Systemic Lupus Erythematosus (SLE or lupus). Two mouse models of SLE were assessed: The first, termed PIL, used pristane to induce disease over a six-month period and the second utilized a chronic graft-versus-host disease (bm12-cGVHD) that resembles lupus based on multiple parameters and allowed us to monitor the early events in disease development. Importantly, we found that in both model systems female mice expressing the CD40LΔ5 mutation showed a consistent increase in elevated antibody secreting cells and autoantibody titers. Also, PIL female CD40LΔ5 mice had higher levels of immunocomplex deposition in the kidney compared to all other cohorts. In the bm12-cGVHD model, cellular increases in GC cells along with an altered cytokine profile of donor CD4+ T cells and host dendritic cells (DCs) reflected a significant skewing of CD40LΔ5 female CD4 T cells towards a Th2 phenotype. Overall, our results support a more nuanced role for CD40L in lupus than previously described and suggest a sex-determined threshold of CD40L-CD40 signaling that demarcates an interface between protection and exacerbation at the very early steps of disease progression.
Integrating gene expression, mutation and copy number data to identify driver genes of recurrent chromosome-arm losses
Authors: Shamir Ron , Ben-David Uri , Saad Ron
Published: February 2025

Aneuploidy is a hallmark of cancer, yet the specific genes driving recurrent chromosome-arm losses remain largely unknown. Here, we present a systematic framework integrating gene expression, mutation, and copy number data to identify candidate driver genes of cancer type-specific recurrent chromosome-arm losses across 20 cancer types, using ~7,500 tumors from The Cancer Genome Atlas. By analyzing focal deletions and point mutations that co-occur with, or are mutually exclusive with, chromosome-arm losses, we pinpoint 311 candidate drivers associated with 160 cancer type-specific recurrent events. Our approach identifies known aneuploidy drivers such as TP53 and PTEN, while revealing multiple novel candidates, including established tumor suppressor genes not previously linked to aneuploidy. Furthermore, we leverage gene expression changes associated with these chromosome-arm losses to propose pathway-level alterations that may drive cancer progression. Integrating these findings highlights key candidate drivers underlying the observed gene expression alterations, thereby reinforcing their biological relevance. This work provides the first comprehensive catalogue of candidate driver genes for recurrently lost chromosome-arms in human cancer.
Cigarette Smoke and Decreased DNA Repair by Xeroderma Pigmentosum Group C Use a Double Hit Mechanism for Epithelial Cell Lung Carcinogenesis
Authors: Al Nasrallah Nawar , Lee Bowa , Wiese Benjamin M. , Karam Marie N. , Mickler Elizabeth A. , Zhou Huaxin , Paolelli Nicki , Stearman Robert , Geraci Mark W , Sears Catherine Rufatto
Published: February 2025

Emerging evidence suggests a complex interplay of environmental and genetic factors in non-small cell lung cancer (NSCLC) development. Among these factors, compromised DNA repair plays a critical but incompletely understood role in lung tumorigenesis and concurrent lung diseases, such as chronic obstructive lung disease (COPD). In this study, we investigated the interplay between cigarette smoke, DNA damage and repair, focusing on the Nucleotide Excision Repair (NER) protein Xeroderma Pigmentosum Group C (XPC). We found decreased XPC mRNA expression in most NSCLCs compared to subject-matched, non-cancerous lung. In non-cancerous bronchial epithelial cells, cigarette smoke decreased NER, increased total DNA damage and resultant apoptosis, each exacerbated by XPC deficiency. In contrast, lung cancer cells exhibit greater resilience to cigarette smoke, requiring higher doses to induce comparable DNA damage and apoptosis, and are less reliant on XPC expression for survival. Importantly, XPC protects against chromosomal instability in benign bronchial epithelial cells, but not in lung cancer cells. Our findings support a "double hit" mechanism wherein early decreased XPC expression and resultant aberrant DNA repair, when combined with cigarette smoke exposure, may lead to loss of non-malignant epithelial cells (as observed in COPD), and contributes to early NSCLC transition through altered DNA damage response.
Multi-platform evaluation and optimization of single-cell RNA isoform sequencing
Authors: Webber James T. , Bartlett Daniel A. , Al-Eryani Ghamdan , Khorgade Akanksha , Shin Asa , Georgescu Christophe , Yu Houlin , Haas Brian J. , Popic Victoria , Al'Khafaji Aziz M.
Published: February 2025

Long-read transcriptomics enables isoform identification and quantification at single-cell resolution, but analysis is complicated by artifacts introduced during library preparation. We characterize the distinct artifact profiles of three popular single-cell platforms and demonstrate their impact on isoform identification. We introduce a new method for the identification of a wide range of artifacts in cDNA libraries and novel biochemical and bioinformatic strategies to significantly reduce their impact on downstream applications. Finally, we provide a comprehensive framework for RNA isoform sequencing analysis and interpretation as the field continues to develop.
Computational investigation unveils pathogenic LIG3 non-synonymous mutations and therapeutic targets in acute myeloid leukemia
Authors: Hossen Md. Arif , Jahan Umme Mim Sad , Hossain Md. Arju , Asif Khalid Hossain , Rahmana Ahona , Ahmed Sabbir , Uddin Md. Moin , Amin Md Faisal , Barik Muhammad Abdul , Islam Mohammod Johirul , Kamruzzaman Mohammad , Hasnat Soharth , Uddin Mohammad Nasir , Islam Tofazzal , Hoque M. Nazmul
Published: February 2025

Single nucleotide polymorphisms (SNPs) in DNA repair genes can impair protein structure and function, contributing to disease development, including cancer. Non-synonymous SNPs (nsSNPs) in the LIG3 gene are linked to genomic instability and increased cancer risk, particularly acute myeloid leukemia (AML). This study aims to identify the most deleterious nsSNPs in the LIG3 gene and potential therapeutic targets for DNA repair restoration in AML. We employed in-silico computational methods to analyze LIG3 nsSNPs, using PredictSNP and Mutation3D to assess pathogenicity. Subsequently, molecular docking and dynamics simulations were conducted to evaluate ligand-binding affinities and protein stability. Out of the 12,191 mapped SNPs, 132 were nsSNPs located in the coding region. Among these, 18 nsSNPs were identified as detrimental including 12 destabilizing and 6 stabilizing nsSNPs. Nine cancer-associated nsSNPs, including L381R and R528C, were predicted due to their structural and functional impacts. Further analysis revealed key phosphorylation and methylation sites, such as 529S and 224R. Molecular dynamics simulations highlighted stable interactions of compounds AHP-MPC and DM-BFC with wild-type and R528C mutant LIG3 proteins, while R671G and V781M mutants showed instability. Protein-protein interaction networks and functional enrichment linked LIG3 to DNA repair pathways. Kaplan-Meier analysis associated high LIG3 expression with improved survival in breast cancer and AML, suggesting its role as a prognostic biomarker. This study emphasizes the mutation-specific effects of LIG3 nsSNPs on protein stability and ligand interactions. We recommend identifying DM-BFC to advance personalized medicine approaches for targeting deleterious variants, following in vitro and in vivo validation for AML treatment.
Cell surface proteomics of patient-derived malignant rhabdoid tumor organoids identifies ROBO1 as potential CAR T cell target for pediatric solid tumors.
Authors: Buhl Juliane L. , Koelewijn Jannet , De Munter Stijn , Cruz Victoria M. , Chin Daryl Jun Kai , Zhang Baojie , van Hoesel Marliek , van Herk Nienke , Paassen Irene , Nachataya Katie , Hofman Laura , de Boed Ella , Nierkens Stefan , Kemmeren Patrick , Cornel Annelisa M. , Wu Wei , Vandekerckhove Bart , Drost Jarno , Janda Claudia Yvonne
Published: February 2025

Malignant rhabdoid tumors are highly aggressive pediatric malignancies with limited treatment options and poor outcomes. To expand therapeutic options, we employed mass spectrometry-based cell surface proteomics on malignant rhabdoid tumor and patient-matched normal kidney organoids to identify potential CAR T cell targets. Integrating these findings with transcriptomics and protein expression data, we revealed ROBO1 as a promising target, showing strong and uniform expression across malignant rhabdoid and other pediatric tumors. ROBO1-targeted CAR T cells displayed potent anti-tumor activity in vitro, effectively eliminating tumor cells in co-cultures with organoids from malignant rhabdoid tumors, rhabdomyosarcoma, and neuroblastoma. In vivo, ROBO1 CAR T cells infiltrated tumors, induced potent tumor regression and significantly increased survival in malignant rhabdoid tumor-bearing mice. These findings establish ROBO1 as a compelling therapeutic target for CAR T cell therapy and offer a promising approach to address the critical need for effective treatments in high-risk pediatric solid tumors.
Incongruent end structures of leading and lagging telomeres dictate the nature of end replication problem
Authors: Ye Tiantian , Yuan Qingqing , Wu Shuheng , Zhao Jing-Tong , Wu Zhi-Jing , Liu Jia-Cheng , Wu Wei , Zhou Jin-Qiu
Published: February 2025

The end replication problem refers to the incomplete replication of parental DNA at telomeres, a process whose molecular depiction is hampered by the complex nature of telomere ends. Here we recapitulate this process using a synthetic de novo telomere in yeast and delineate distinct molecular fates of telomere ends in vivo. We show that the lagging strand telomere carries a ~10 nt 3-overhang, while the leading strand telomere has a Yku-protected blunt end, which is prevalent on native telomeres. In addition, RNase H2 but not RNase H1 is mainly responsible for the removal of the last RNA primer. Consistently, in the absence of RNase H2 activity, RNA primer is retained on the lagging strand telomere, attenuating telomere erosion and delaying senescence in telomerase-null cells. These findings highlight incongruent end structures on telomeres and clarify that the primary culprit behind end replication problem is the incompletely replicated lagging strand telomere.
A Theory of Heterosis
Authors: Zeng Zhao-Bang , Gesteira Gabriel De Siqueira , Mo Lujia , Xiao Yingjie , Yan Jianbing
Published: February 2025

Heterosis refers to the superior performance of a hybrid over its parents. Biologically, it is the opposite of inbreeding depression. It is the basis for hybrid breeding particularly for maize and rice. Genetically it is due to interactions between alleles of quantitative trait loci (QTL) (dominance and epistasis). Despite enormous interest and efforts to study the genetic basis of heterosis, the relative contribution of dominance vs. epistasis to heterosis is still not clear. This is because most published studies estimate QTL effects in pieces, not able to put them together to assess the overall pattern adequately. We propose a theoretical framework that focuses on the inference of the relationship between genome and traits that includes the identification of multiple QTL and estimation of the whole set of QTL (additive, dominant, and epistatic) effects. Used for heterosis, it gives a clear genetic definition and interpretation of heterosis. We applied the theory and methods to a large maize dataset with a factorial design of many male and female inbred lines and their hybrid crosses. Heterosis of ear weight in maize is primarily due to QTL dominant effects, many are over-dominant. The contribution to heterosis due to epistasis is small and diffused. For comparison, we also analyzed a rice dataset that is an F2-type population derived from a cross between two inbred lines. The result indicates that dominance is still the main contributor to heterosis, and epistasis contribution is small, although the model fitting is somewhat unstable for the rice data due to the relatively small sample size.
Inferring active mutational processes in cancer using single cell sequencing and evolutionary constraints
Authors: Satas Gryte , Myers Matthew A. , McPherson Andrew , Shah Sohrab P.
Published: February 2025

Ongoing mutagenesis in cancer drives genetic diversity throughout the natural history of cancers. As the activities of mutational processes are dynamic throughout evolution, distinguishing the mutational signatures of 'active' and 'historical' processes has important implications for studying how tumors evolve. This can aid in understanding mutagenic states at the time of presentation, and in associating active mutational process with therapeutic resistance. As bulk sequencing primarily captures historical mutational processes, we studied whether ultra-low-coverage single-cell whole-genome sequencing (scWGS), which measures the distribution of mutations across hundreds or thousands of individual cells, could enable the distinction between historical and active mutational processes. While technical challenges and data sparsity have limited mutation analysis in scWGS, we show that these data contain valuable information about dynamic mutational processes. To robustly interpret single nucleotide variants (SNVs) in scWGS, we introduce ArtiCull, a method to identify and remove SNV artifacts by leveraging evolutionary constraints, enabling reliable detection of mutations for signature analysis. Applying this approach to scWGS data from pancreatic ductal adenocarcinoma (PDAC), triple-negative breast cancer (TNBC), and high-grade serous ovarian cancer (HGSOC), we uncover temporal and spatial patterns in mutational processes. In PDAC, we observe a temporal increase in mismatch repair deficiency (MMRd). In cisplatin-treated TNBC patient-derived xenografts, we identify therapy-induced mutagenesis and inactivation of APOBEC3 activity. In HGSOC, we show distinct patterns of APOBEC3 mutagenesis, including late tumor-wide activation in one case and clade-specific enrichment in another. Additionally, we detect a clone-specific increase in SBS17 activity, in a clone previously linked to recurrence. Our findings establish ultra-low-coverage scWGS as a powerful approach for studying active mutational processes that may influence ongoing clonal evolution and therapeutic resistance.
Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity
Authors: Cediel-Becerra José D D , Cumsille Andrés , Guerra Sebastian , Ding Yousong , de Crécy-Lagard Valérie , Chevrette Marc G
Published: February 2025

Gene clusters, groups of physically adjacent genes that work collectively, are pivotal to bacterial fitness and valuable in biotechnology and medicine. While various genome mining tools can identify and characterize gene clusters, they often overlook their evolutionary diversity, a crucial factor in revealing novel cluster functions and applications. To address this gap, we developed GATOR-GC, a targeted genome mining tool that enables comprehensive and flexible exploration of gene clusters in a single execution. We show that GATOR-GC identified a diversity of over 4 million gene clusters similar to experimentally validated biosynthetic gene clusters (BGCs) that other tools fail to detect. To highlight the utility of GATOR-GC, we identified previously uncharacterized co-occurring conserved genes potentially involved in mycosporine-like amino acid biosynthesis and mapped the taxonomic and evolutionary patterns of genomic islands that modify DNA with 7-deazapurines. Additionally, with its proximity-weighted similarity scoring, GATOR-GC successfully differentiated BGCs of the FK-family of metabolites (e.g., rapamycin, FK506/520) according to their chemistries. We anticipate GATOR-GC will be a valuable tool to assess gene cluster diversity for targeted, exploratory, and flexible genome mining. GATOR-GC is available at https://github.com/chevrettelab/gator-gc.
Regulation of Steady State Ribosomal Transcription inMycobacterium tuberculosis: Intersection of Sigma Subunits, Superhelicity, and Transcription Factors.
Authors: Ruiz Manzano Ana , Jensen Drake , Galburt Eric A
Published: February 2025

The regulation of ribosomal RNA (rRNA) is closely tied to nutrient availability, growth phase, and global gene expression, serving as a key factor in bacterial adaptability and pathogenicity.Mycobacterium tuberculosis(Mtb) stands out from other species with a single ribosomal operon controlled by two promoters:rrnAP3 andrrnAP1 and a high ratio of sigma (σ) factors to genome size. While the primary σ factor σAis known to drive ribosomal transcription, the alternative σ factor σBhas been proposed to contribute to the transcription of housekeeping genes, including rRNA under a range of conditions. However, σB's precise role remains unclear. Here, we quantify steady-state rates in reconstituted transcription reactions and establish that σA-mediated transcription fromrrnAP3 dominates rRNA production by almost two orders of magnitude with minimal contributions from σBholoenzymes and/orrrnAP1 under all conditions tested. We measure and compare the kinetics of individual initiation steps for both holoenzymes which, taken together with the steady-state rate measurements, lead us to a model where σBholoenzymes exhibit slower DNA unwinding and slower holoenzyme recycling. Our data further demonstrate that the transcription factors CarD and RbpA reverse or buffer the stimulatory effect of negative superhelicity on σAand σBholoenzymes respectively. Lastly, we show that a major determinant of σA's increased activity is due to its N-terminal 205 amino acids. Taken together, our data reveal the intricate interplay of promoter sequence, σ factor identity, DNA superhelicity, and transcription factors in shaping transcription initiation kinetics and, by extension, the steady-state rates of rRNA production in Mtb.
Electrokinetic detection of single-molecule phosphorylation
Authors: Wang Quan
Published: February 2025

Current single-molecule fluorescence experiments lack direct sensitivity to molecular phosphorylation state. We show that electrokinetic properties measured with an anti-Brownian trap resolve the number of phosphorylated sites on individual biomolecules and can monitor phosphorylation cycles with single kinase turn overs. As an application, we directly visualize the rate limiting step in the kinase catalytic cycle.
Mental Health Literacy questionnaire short-version: psychometric properties in young adults from Brazil, Germany, Greece, Lithuania, Malaysia, Nepal, Nigeria, Pakistan, Poland, Serbia and Turkey.
Authors: Costa Diogo , Costa Marisa , Moreira Wanderson Carneiro , Nobrega Maria do Perpetuo SS , Fritz Birthe , Wessa Michele , Kalaitzaki Argyroula , Meintani Flora , Aturu Olamide , Yong Teresa Sui Mien , Johari Mohammad Zabri , Dhakal Sandesh , Poudel Dev Bandhu , Ashraf Mujeeba , Soroko Emilia , Lepojevic Marina Kovacevic , Radanovic Ana , Gunaydin Nevin , Ozpulat Funda , Campos Luisa , Dias Pedro
Published: February 2025

Objectives: The prevalence of mental health disorders has increased in recent years, representing a major public health concern. Increasing the literacy about mental health signs and symptoms is paramount for effective prevention. Having previously studied the psychometric properties of the Mental Health Literacy Questionnaire for young adults-short version (MHLq-SVa) in six countries, we now extend the validity study of this 16-item scale to eleven countries, namely Brazil, Germany, Greece, Lithuania, Malaysia, Nepal, Nigeria, Pakistan, Poland, Serbia and Turkey. Study Design: Multicentre cross-sectional study Methods: Translated and adapted versions of the MHLq-SVa were administered to young adults aged 17-25 years in all countries, totalling 5054 (72% women) with full information for all scale items. Confirmatory factor analysis and internal consistency (Cronbach alphas) were computed to test the scales four-dimensional structure (Knowledge of mental health problems; Erroneous beliefs/stereotypes; First-aid skills and help-seeking behaviour; Self-help strategies) and reliability. Results: Goodness-of-fit indices for the four-factor solution model suggested good fit in all countries. Exceptions were Pakistan with higher Root mean squared error of approximation and Standardized root mean squared residual, and Brazil with a higher chi-square value and lower Comparative fit index. Conclusions: The construct validity of the MHLq-SVa was supported by data from eleven countries, adding to previous research on the MHLq-SVa psychometrics, suggesting cross-cultural reliability as a Mental Health Literacy assessment tool.
RNA Modifications and Prp24 Coordinate Lsm2-8 Binding Dynamics duringS. cerevisiaeU6 snRNP Assembly
Authors: Liu Ye , Nomura Yuichiro , BUTCHER SAMUEL , Hoskins Aaron
Published: February 2025

In eukaryotes, the process of intron removal from nuclear pre-mRNA is performed by the spliceosome, a dynamic molecular machine composed of small nuclear ribonucleoproteins (snRNPs; U1, U2, U4, U5, and U6) and dozens of other protein splicing factors. The U6 snRNP contains the U6 snRNA and the proteins Prp24 and Lsm2-8 heteroheptamer. A key feature of the snRNP is a modified U6 snRNA 3' end, which in S. cerevisiae (yeast) contains a 3' phosphate. U6 plays an essential role in splicing, and the U6 snRNP must be completely disassembled for splicing to occur. Once splicing is finished, the snRNP must then be reassembled to participate in a subsequent splicing reaction. While splicing efficiency depends on rapid U6 snRNP assembly, this process has not yet been kinetically characterized. Here, we use colocalization single molecule spectroscopy (CoSMoS) to dissect the kinetic pathways of yeast U6 snRNA association with the Lsm2-8 complex and their dependence on the Prp24 protein and post-transcriptional snRNA modification. In the absence of 3' end processing, Lsm2-8 association with the RNA is highly dependent on Prp24. However, processed RNAs can rapidly recruit Lsm2-8 in Prp24's absence. Post-transcriptional processing facilitates Lsm2-8 association while the presence of Prp24 promotes both recruitment and retention of the complex. This suggests that efficient U6 snRNP assembly could depend on kinetic selection of Lsm2-8 binding to 3'-end modified or Prp24 bound U6 snRNAs in order to discriminate against association with other RNAs.
Intraguild parasitism promotes the persistence of facultative hyperparasitoids by extending temporal host availability
Authors: Wang Hua , Xu Nuo , Xu Chi , Liao Jinbao , Wang Shaopeng , Sun Shucun , Xi Xinqiang
Published: February 2025

Intraguild predation (IGP) is pervasive in natural food webs, although theoretical models predict restricted parameter space for the coexistence of IG-prey and IG-predators. One potential mechanism is that IGP persistence might be increased when IG-prey extend resource availability for IG-predators. Here we test this hypothesis using manipulative experiments in combination with mathematical modeling. Our experiment system includes Drosophila flies (Drosophila melanogaster, basal resources), primary larval parasitoids (Asobara leveri, IG-prey) and facultative pupal hyperparasitoid (Pachycrepoideus vindemiae, IG-predator). We measured the performance of facultative pupal parasitoids with and without the primary larval parasitoid. Our study revealed that larval parasitoids significantly increased the number of pupal parasitoids emerged from limited host resources, due to the extended resource availability to facultative hyperparasitoid. Specifically, immature primary parasitoids within Drosophila pupae can be explored by facultative hyperparasitoids for up to 14 days, while the healthy fly pupae are available to hyperparasitoids for only 5 days. Despite a significant reduction in offspring fitness of the facultative hyperparasitoids when reared on larval parasitoids versus healthy Drosophila pupae, adult female facultative hyperparasitoids showed no significant preference for healthy fly pupae over immature primary parasitoids. Our theoretical models demonstrated that an extended development period of the primary parasitoid can promote the persistence of the facultative hyperparasitoids and allow their coexistence with the primary parasitoid, although too prolonged development could drive the extinction of the primary parasitoid. As IG-prey often take longer time to develop after consuming the shared resources, extension of temporal resource availability could be a general mechanism contribute to the persistence of intraguild predators.
Evolutionary History of Treponema pallidum subsp. pertenue: Insights into Host Ancestry and Cross-Species Transmission
Authors: Lima Sabrina Karolaine , Sakamoto Tetsu
Published: February 2025

Treponema pallidum, a bacterium from the Spirochaetota phylum, is responsible for treponematoses, such as syphilis, yaws, bejel, and pinta. Different subspecies of this bacterium cause each of these diseases. This study focuses on Treponema pallidum subsp. pertenue (TPE), which causes yaws in humans and is primarily transmitted through direct contact with skin lesions, mainly affecting children and preadolescents. If untreated, it can progress to severe deformities in bones and cartilage. During the 20th century, significant progress was made in the eradication and control of this disease. However, in recent decades, there has been an increase in the number of reported cases. Until recently, it was believed that this subspecies affected only humans, but recent studies have identified that non-human primates (NHPs) have also been naturally infected with TPE. Considering the impacts of this disease on both humans and other species, TPE has become a focus of surveillance and scientific investigation. This study aims to clarify the relationship between infection in humans and other primate species, contributing to a better understanding of transmission dynamics and potential control and prevention strategies. To achieve this, we used genome sequences from 58 TPE strains (24 from humans and 19 from NHPs) available in public repositories and applied phylogenetic analyses and computational tools for recombinant region detection. The phylonetic analysis demonstrated a rapid expansion of the subspecies at the base of the tree and clustered the samples into nine groups. No groups contained both human and NHP samples, indicating that interactions between the two sample groups are rare or nonexistent. Recombination analyses detected only one region where an NHP sample may have recombined with a human sample. The application of the molecular clock in phylogenetic inference indicated a recent origin of TPE in 1885. The study of trait evolution further suggests that the host of the most recent common ancestor of TPE was humans. The analyses conducted in this study provided deeper insights into the spread of the disease and its interaction across different species.
Evaluation of parasitic contamination and effects on estimates of mitochondrial enzymatic activities in infected fish livers
Authors: Pepin Tommy , Melancon Vincent , Binning Sandra A , Breton Sophie
Published: February 2025

Parasites can impair host performance through various physiological processes, including alterations to host metabolism. Since mitochondria are responsible for cellular energy production, it is likely that disruptions in host cellular metabolism contribute to changes in metabolism at the organismal level. However, some studies investigating parasite-induced alteration in cellular metabolism have not taken the presence of parasites in the target tissues into account, potentially biasing results. It is therefore critical to confirm that the measured enzyme activities reflect those of the hosts rather than the parasites themselves. Here, we tested a parasite extraction protocol to evaluate the extent to which parasite contamination impacts estimates of cellular enzyme activities in hepatic tissues of wild pumpkinseed sunfish (Lepomis gibbosus) infected with bass tapeworm cestodes (Proteocephalus ambloplitis). We tested four treatments: uninfected livers, cleaned infected livers, infected livers (repopulated) and parasites alone. We then compared the activity of key metabolic enzymes among groups. PCR tests were used to assess parasitic contamination of samples after applying the parasite extraction protocol on hepatic tissue. Enzyme activities of cleaned livers and contaminated livers were similar despite PCR tests revealing contamination. The intensity of cestode infection also did not influence enzyme activity, which suggests that parasite presence in liver tissues does not impact the accuracy of the enzyme activity estimates. These results suggest that studying the organs of heavily parasitized individuals is possible. Nevertheless, we recommend that our cleaning protocol is applied to infected organs to avoid any perception of biases in highly infected individuals.