bluuebunny/crossref_metadata_2025 huggingface dataset:
Breast Cancer Risk Factors in the Abu Dhabi Population: A Retrospective Cohort Study
Authors: AlKetbi Latifa Baynouna , AlAzeezi Maha , Ashoor Rawan , Nagelkerke Nico , AlAlawi Noura , AlKetbi Rudina , Aleissaee Hamda , AlShamsi Noura , Humaid Ahmed , Abdulbaqi Hanan , Fahmawee Toqa , AlHashaikeh Basil , AlDobaee Muna , AlAhbabi Nayla , AlAzeezi AlYazia , Shuaib Fatima , Alnuaimi Jawaher , Mahmoud Esraa , AlMansoori Mohammed , AlKalbani Sanaa , AlDerie Wesayef , Saeed Ekram , AlAhmadi Amira , Sahyouni Mohammad , AlShamsi Reem
Published: February 2025

Background

Breast cancer is the most common cancer in the United Arab Emirates (UAE), with the majority of cases characteristically occurring in women younger than 50 years. Studies on breast cancer risk factors in the UAE are few.

Methods

This retrospective study, from 2011 to 2013 until 2023, aimed to estimate the prevalence of a history of cancer and lifetime risk. A nested case-control study was designed from the cohort to study breast cancer risk with four controls for each case matched by the date of diagnosis.

Results

Breast cancer incidence was 0.85 %, 37 cases out of the 4338 females in the cohort. No males were diagnosed with the condition. Out of the 129 females with cancer, breast cancer was the most common type, 28% of all kinds of cancers.

Three risk factors for breast cancer were identified using conditional Cox regression analysis of the matched nested case-control study. The strongest was being a patient with diabetes Mellitus, HR=13.1 (3.2-52.8) P<0.001. Another metabolic abnormality that is associated with the occurrence of breast cancer in this population was a higher level of total cholesterol, HR=1.59 (1.03-2.44), P-value=0.035. Vitamin D showed a protective association with 58% reduced risk with levels above 75, HR=0.042 (0.002-0.73) P=0.042. The area under the ROC Curve for predicting breast cancer using this model was 0.753 (0.666-0.839). The area under the ROC Curve for predicting breast cancer using this model was 0.753 (0.666-0.839).

Conclusion

This study highlights the importance of understanding the various risk factors associated with breast cancer development and stresses the pivotal role of advancing diagnostic methods to improve early detection. By synthesizing current knowledge, this study aims to enhance our understanding of breast cancer’s complex nature and guide future research directions, screening practices, and preventive measurements.
T cell responses in repeated controlled human schistosome infection compared to natural exposure
Authors: Driciru Emmanuella , Koopman Jan Pieter R. , Steenbergen Sanne , Sonnet Friederike , Stam Koen A. , de Bes-Roeleveld Helena , Iliopoulou Eva , Janse Jacqueline J. , Sijtsma Jeroen , Nambuya Irene , Hilt Stan T. , König Marion , Kruize Yvonne , Casacuberta-Partal Miriam , Egesa Moses , van Dam Govert J. , Corstjens Paul L.A.M. , van Lieshout Lisette , Mpairwe Harriet , MacDonald Andrew S. , Yazdanbakhsh Maria , Elliott Alison M. , Roestenberg Meta , Houlder Emma L.
Published: February 2025

Schistosomiasis affects over 250 million people, predominantly in Sub-Saharan Africa. InSchistosoma-endemic regions a lack of natural sterilizing immunity means individuals are repeatedly infected, treated and reinfected. Due to difficulties in tracking infection in endemic areas, the kinetics of the host immune response during these reinfections have not been elucidated. Here, we use repeated (3x) controlled humanSchistosoma mansoni(Sm) infection (repeated CHI) to directly study how antigen-specific T cells develop during reinfection. We compared these responses to naturalSm-infected endemic Ugandan individuals. We report that a mixed Th1/Th2/regulatory CD4+T cell response develops in repeated CHI, primarily against adult worm antigens. Adult worm-specific responses after repeated CHI were similar to those observed in naturally infected endemic participants. However, endemic participants showed differential responses to antigens from the egg and cercariae life-cycle stages. Repeated CHI (3x) with sequential exposure toSmcercariae of different sexes (male-female-male) revealed an elevated CD4+T cell cytokine response to adult worm and egg antigens. Our findings demonstrate that reinfection with single-sex schistosomes elicits adult worm-specific T cell cytokine responses that reflect endemic-natural infection, highlighting the translatability of the CHI model to natural infection in endemic settings. Overall, this study advances our understanding of how schistosome immune responses develop over reinfection cycles in the human host, thereby increasing our understanding of the immunology of natural schistosome (re)infection.
Serum Troponin T levels as a therapy response marker in SOD1-mediated ALS
Authors: Bernsen Sarah , Fabian Rachel , Koc Yasemin , Schumann Peggy , Körtvélyessy Peter , Castro-Gomez Sergio , Meyer Thomas , Weydt Patrick
Published: February 2025

Introduction

Serum cardiac troponin T (cTnT) levels are elevated in the majority of amyotrophic lateral sclerosis (ALS) patients and increase over time. Neurofilament light chain (NfL) is an established therapy response biomarker in ALS as superoxide dismutase 1 (SOD1)-ALS patients treated with the antisense oligonucleotide tofersen show a decrease in NfL. In this study we assess the course of cTnT levels in SOD1-ALS at baseline and during tofersen treatment.

Methods

Serum cTnT was analyzed at baseline and during tofersen treatment in 23 SOD1-ALS patients at two specialized ALS centers in Germany and compared to a control cohort of 74 ALS patients without SOD1-mutations and not treated with tofersen.

Results

cTnT levels increased in the control ALS-cohort over time (p<0.0001) but not in the tofersen group (p=0.36). CK, and CK-MB levels did not show relevant changes over time. The median monthly increase of cTnT was 0.045 points (IQR 0.02-0.08) in the control ALS cohort and 0.01 points (IQR −0.01-0.03) in the tofersen group (p=0.0013). The fold change in cTnT levels of the tofersen-treated cohort (median 1.2; IQR 0.77-1.59) was significantly less and even showed a reduction in some patients compared to the control group (median 1.89; IQR 1.35-2.75) (p=0.0003).

Discussion

In this study, we find a response signal of cTnT to tofersen treatment, which supports the value of cTnT as an independent biomarker in ALS. These results contribute to the notion that cTnT may provide additional value as a progression and treatment response biomarker in ALS complementary to NfL and warrant further investigations.

Graphical Abstract
Association of Cut-point Free Metrics and Common Clinical Tests among Older Adults after Proximal Femoral Fracture
Authors: Younesian Hananeh , Singleton David , Vereijken Beatrix , Garcia-Aymerich Judith , Rochester Lynn , Berge Martin Aursand , Engdal Monika , Buekers Joren , Koch Sarah , Helbostad Jorunn L. , Alvarez Paula , Jansen Carl-Philipp , Aminian Kamiar , Ionescu Anisoara , Becker Clemens , Caulfield Brian
Published: February 2025

Wearable and lightweight devices facilitate real-world physical activity (PA) assessments. MX metrics, as a cut-point-free parameter, evaluate acceleration above which the most active X minutes are accumulated. It provides insights into the intensity of PA over specific durations. This study evaluated the association of MX metrics and clinical tests in older adults recovering from proximal femoral fracture (PFF). Analyses were conducted on the PFF cohort from the baseline assessment of the Mobilise-D project using an accelerometer-based device. Participants (N=396) were categorized into four recovery groups: acute, post-acute, extended recovery, and long-term recovery. Mobility capacity was assessed through the 6-min walking test (6MinWT), Short Physical Performance Battery (SPPB), 4-meter walking test (4MWT), and hand grip (HG) strength. Mobility perception was evaluated using the Late-Life Function and Disability Instrument (LLFDI). Eight MX metrics (M1-M90) were calculated using the GGIR package in R. Results showed moderate to strong positive correlation between M1-M30 and lower limb mobility capacity tests, and mobility perception (Lower Extremity domains) particularly in the extended and long-term recovery groups. MX metrics can be used for measuring PA intensity among older adults recovering from PFF. Shorter duration of MX metrics had higher association with lower limb mobility capacity and perception outcomes.

Highlights

What are the main findings?

Clinical lower limb assessments (both subjective and objective) were more discriminative in differentiating between the four PFF recovery groups in older adults.

Older adults in the acute proximal femoral fracture recovery group demonstrated lower physical activity intensity compared to those in later recovery groups, with the differences being more pronounced for shorter-duration MX metrics (M1-M5)

What is the implication of the main finding?

The cut-point free method (e.g., MX metrics) is useful for measuring physical activity magnitude of older adult recovering from proximal femoral fracture.

Higher lower limb capacity and perception outcomes were strongly correlated with greater daily activity intensity, particularly in older adults at later stages of proximal femoral fracture recovery.
Targeting Pre-existing Club-Like Cells in Prostate Cancer Potentiates Androgen Deprivation Therapy
Authors: Baurès Manon , Aleixo Anne-Sophie Vieira , Pacreau Emeline , Koshy Aysis , Diedisheim Marc , Raigel Martin , Hua Yichao , Dariane Charles , Boutillon Florence , Kenner Lukas , Marine Jean-Christophe , Laverny Gilles , Metzger Daniel , Rambow Florian , Guidotti Jacques-Emmanuel , Goffin Vincent
Published: February 2025

A critical knowledge gap in prostate cancer research is understanding whether castration-tolerant progenitor-like cells that reside in treatment-naïve tumors play a direct role in therapy resistance and tumor progression. Herein, we reveal that the castration tolerance of LSCmed(Lin-, Sca-1+, CD49fmed) progenitor cells, the mouse equivalent of human prostatic Club cells, arises not from intrinsic properties but from significant transcriptional reprogramming. Utilizing single-cell RNA sequencing of LSCmedcells isolated from prostate-specific Pten-deficient (Ptenpc-/-) mice, we identify the emergence of castration-resistant LSCmedcells enriched in stem-like features, driven by the transcription factor Fosl1/AP-1. We demonstrate that cells exhibiting Ptenpc-/-LSCmedcharacteristics are prevalent in the aggressive mesenchymal stem-like prostate cancer (MSPC) subtype recently identified in human castration-resistant prostate cancer (CRPC). Furthermore, our findings show that the dual-targeting agents JQ-1 and CX-6258—focused on Fosl1/AP-1 and PIM kinases, respectively—effectively suppress both the progenitor properties and the growth of mouse and human MSPC surrogatesin vitroandin vivo. Thus, early eradication of castration-tolerant Club-like cells presents a promising therapeutic strategy to mitigate prostate cancer progression toward CRPC.
Transgenerational effects of heat shock on gene regulation and fitness-related traits are stronger in arid than temperate Drosophila populations
Authors: Harney Ewan , González Josefa
Published: February 2025

Heat stress will increasingly affect populations as climate change leads to higher temperatures and more extreme events such as heat waves. Adaptation is predicted to occur over long evolutionary timescales, but recent work suggests that interactions between the epigenome and transposable elements (TEs) could link environmental acclimation with rapid adaptation. Yet combining all these factors in a tractable model system remains challenging; consequently little is known about how these processes interact in natural genetic backgrounds or shape evolutionarily relevant phenotypes. To investigate these interactions, we carried out laboratory experiments measuring gene expression and chromatin accessibility responses to heat shock in female D. melanogaster from arid and temperate climates and their associations with population variation in TEs. The consequences for fitness-related phenotypes were characterised in the offspring, and we also measured expression, chromatin accessibility and phenotypic traits three generations later to explore transgenerational inheritance. Expression and accessibility responses to heat shock varied between populations and were influenced by the presence of TEs, with more upregulated responses in the arid population. Effects of heat shock on transcription were detected three generations later, especially in the arid population, with many epigenetic genes transgenerationally expressed, although this was not driven by chromatin accessibility. Heat shock negatively affected phenotypes in the initial offspring cohort, but later arid population cohorts developed quicker than controls, indicating hormesis, an effect still present in the great-great-grandoffspring. These results demonstrate the transgenerational inheritance of a potentially beneficial hormetic phenotype and associated patterns of gene expression in a natural insect population.
RUNX1::RUNX1T1 Depletion Eliminates Stemness and Induces Bidirectional Differentiation of Acute Myeloid Leukemia
Authors: Derevyanko Polina K , Swart Laura E. , Casimiro L. Daniel Mata , van den Brink Luca , van Oort Anita T. , Ashtiani Minoo , Zwaan C. Michel , Krippner-Heidenreich Anja , Bonifer Constanze , Schiffelers Raymond , Vormoor H. Josef , Kellaway Sophie G. , Heidenreich Olaf
Published: February 2025

Chromosomal rearrangements that generate novel fusion genes are a hallmark of acute myeloid leukemia (AML). Depletion experiments in cell line models have suggested that continued expression is required for maintaining their leukemic phenotype and they therefore represent ideal cancer-specific therapeutic targets. However, to which extent this result holds true for the different stages of hematopoietic development in primary cells and whether therapeutic agents can be efficiently delivered to those cells is still unclear. In this study, we demonstrate that primary AML cells harboring the chromosomal translocation t(8;21) are critically dependent on the corresponding fusion gene,RUNX1::RUNX1T1, to suppress differentiation and maintain stemness. SilencingRUNX1::RUNX1T1expression using siRNA-loaded lipid nanoparticles induces substantial changes in chromatin accessibility, thereby redirecting the leukemia-associated transcriptional network towards a myeloid differentiation program. Single-cell analyses reveal that this transcriptional reprogramming is associated with the depletion of immature stem and progenitor-like cell populations, accompanied by an expansion of granulocytic and eosinophilic/mast cell-like populations with impaired self-renewal capacity. These findings underscore the essential role ofRUNX1::RUNX1T1in sustaining AML and highlight the therapeutic potential of targeting fusion gene expression in primary AML cells.

Abstract Figure
Clonal memory of colitis accumulates and promotes tumor growth
Authors: Nagaraja Surya , Ojeda-Miron Lety , Zhang Ruochi , Oreskovic Ena , Hu Yan , Zeve Daniel , Sharma Karina , Hyman Roni R. , Zhang Qiming , Castillo Andrew , Breault David T. , Yilmaz Ömer H. , Buenrostro Jason D.
Published: February 2025

Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution, characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerate tumor growth. This includes a subpopulation of tumors that have exceptionally high AP-1 activity and the additional upregulation of pro-oncogenic programs. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions.
Robust analytical methods for bis(monoacylglycero)phosphate profiling in health and disease
Authors: Dong Wentao , Nyame Kwamina , Rawat Eshaan S. , Medoh Uche N. , Xiong Jian , Bonin Caio C. , Alsohybe Hisham N. , Liu Hunter Y. , Gomes Sara , Hsieh Tammy , Arnold Marianna , Hsieh Frank , Sammler Esther , Abu-Remaileh Monther
Published: February 2025

Bis(monoacylglycero)phosphate (BMP), a distinct anionic phospholipid predominantly found in late endosomes and lysosomes, plays a pivotal role in supporting lysosomal functions and maintaining metabolic homeostasis. Its impaired function is associated with an array of disorders, notably neurodegenerative diseases. However, the identification and quantitation of BMP remains difficult due to its structural similarity to isomer phosphatidylglycerol (PG), thus necessitating robust analytical methods for accurate and reliable BMP profiling. In this study, we present comprehensive liquid chromatography – tandem mass spectrometry (MS2) methodologies for the precise and systematic analysis of BMP species in biological samples. We detail LC/MS methods for both an untargeted Orbitrap mass spectrometer and a targeted triple quadrupole (QQQ) mass spectrometer. We utilize differences in polarity and structure to annotate BMPs and PGs based on retention time and positive mode MS2 fragmentation patterns, respectively. Further, we propose a new approach for overcoming common challenges in BMP profiling by leveraging the newly discovered biochemical function of CLN5 as the BMP synthase. Since genetic ablation of CLN5 leads to specific depletion of BMPs but not PGs, we use lipid extracts fromCLN5knockout (KO) and wild-type (WT) cells as biological standards to confidently annotate BMPs as targets with significantly low BMP Identification Index (BMPII), defined as BMPII =CLN5KO / WT. We additionally propose the BMP enrichment score (BMPES) as a secondary validation metric, defined as lysosomal abundance of BMP / whole-cell abundance. Altogether, this approach constitutes a robust method for BMP profiling and annotation, furthering research into health and disease.
A flexible Bayesian method for estimating stratigraphic intervals and their co-occurrence in time
Authors: Ballen Gustavo A.
Published: February 2025

1

The fossil record is both incomplete and full of biases, which hinders making inferences about the past of life on earth. Stratigraphic intervals help us estimate two important quantities from the fossil record of a given lineage, its origination and extinction times.

Many models are available in the literature. This toolset is complemented here by proposing a flexible method which allows to estimate origination and extinction times, as well as model preservation potential in flexible ways.

A method is presented for representing the stratigraphic interval as a continuous distribution by integrating over parameter uncertainty throughthe use of the posterior predictive distribution. It is possible then to combine these distributions using conflation, to build a time probabilistic model for the co-occurrence of these intervals.

Empirical examples using Palynomorphs and the origination time of the marine Barracudas are used for illustrating the potential of the method. The methods are implemented in theStratIntervals.jlJulia package, which allows a big amount of possible prior distributions, and MCMC samplers.
Identifying clusters of people with Multiple Long-Term Conditions using Large Language Models: a population-based study
Authors: Smith Alexander , Beaney Thomas , Hockham Carinna , Su Bowen , Elliott Paul , Downey Laura , Denaxas Spiros , Barnaghi Payam , Dehghan Abbas , Tzoulaki Ioanna
Published: February 2025

Background

Identifying clusters of people with similar patterns of Multiple Long-Term Conditions (MLTC) could help healthcare services to tailor management for each group. Large Language Models (LLMs) can utilise complex longitudinal electronic health records (EHRs) which may enable deeper insights into patterns of disease. Here, we develop a pipeline, incorporating an LLM, to generate gender-specific clusters using clinical codes recorded in EHRs.

Methods

In this population-based study, we used EHRs from individuals aged ≥50 years from Clinical Practice Research Datalink in the UK. Longitudinal sequences of medical histories including diagnoses, diagnostic tests and medications were used to pre-train an LLM based on DeBERTa. The LLM, called EHR-DeBERTa, includes embedding layers for age of diagnosis, calendar year of diagnosis, gender, and visit number with a diagnosis vocabulary of 3776 tokens, covering the entire ICD-10 hierarchy. We fine-tuned EHR-DeBERTa using contrastive learning and generated patient embeddings for all individuals. A bootstrapping clustering pipeline was applied separately for females and males and gender-specific patient clusters were characterised by disease prevalence, ethnicity and deprivation.

Findings

A total of 5,846,480 patients were included. We identified fifteen clusters in females and seventeen clusters in males, grouped into five categories: i) low disease burden; ii) mental health; iii) cardiometabolic diseases; iv) respiratory diseases, and v) mixed diseases. Cardiometabolic and mental health conditions showed the strongest separation across clusters. People in low disease burden and mental health clusters were younger, whereas those in cardiometabolic clusters were older, with females in cardiometabolic clusters older than their male counterparts.

Interpretation

Using an LLM applied to longitudinal EHRs, we generated interpretable and gender-specific clusters of diseases, providing insights into patterns of diseases. Extending these methods in future to incorporate clinical outcomes could enable identification of high-risk patients and support precision-medicine approaches for managing MLTC.
Infections in the Atlantic Blue CrabCallinectes sapidus(Rathbun, 1896) in coastal Adriatic, Aegean sea, and Atlantic Iberian coast
Authors: Schott Eric , Šćepanović Marina Brailo , Lučić Jasna Maršić , Pares Olivia , Zhao Mingli , Hrabar Jerko , Glamuzina Luka , Pećarević Marijana , Grđan Sanja , da Silva Encarnação João Pedro , Ana Pešić Pedro Morais , Ćetković Ilija , Glamuzina Branko
Published: February 2025

In the Mediterranean Sea, the abundance of the invasive portunid crab,Callinectes sapidus, has dramatically increased in recent years. This raises concerns about damage to ecosystems, but also offers opportunities for exploitation of a new fishery. Newly invasive species may escape from pathogens in their endemic range, may introduce new pathogens, or can become host to endemic pathogens. Understanding these factors is important for predicting or managing natural resources in the invaded range. This study investigated the prevalence of two pathogens common inC. sapidusin its home range of North America: the reovirus CsRV1 and the protozoan parasiteHematodiniumsp. In crabs collected from Aegean, Adriatic, and Atlantic waters, the CsRV1 virus was not detected. In contrast, the parasiteHematodiniumsp. was found in all areas except the Aegean Sea. Sequence analysis of theHematodiniumsp. ITS1 gene indicated that the strains observed are most related toHematodiniumsp. strains already described in Europe and the Mediterranean, and not to strains from the Americas. The arrival of new species and new potential pathogens is ongoing through transfer of ballast water to the Atlantic and Mediterranean. Although systems are in place to exchange or inactivate ballast water, it is advisable to continue and expand surveillance for pathogens in introduced species, to inform management of movement of these species between regions.
Evolution of the conformational ensemble and allosteric networks of apoptotic caspases in chordates
Authors: Joglekar Isha , Karadi Giridhar Mithun Nag , Diaz David A. , Deo Ankit , Clay Clark A.
Published: February 2025

Caspases, known for their role in apoptosis and inflammation, have recently emerged as potential regulators of cell differentiation and proliferation. The regulation of caspase conformations to affect these specific pathways is not well understood. Understanding the conformational landscapes, intermediate states, and mechanisms for fine-tuning these ensembles is critical for unraveling their diverse regulatory functions. We combined experimental and computational techniques to characterize the evolution of conformational ensemble in caspases. Using ancestral protein reconstruction, molecular dynamics simulations, and network analysis, we identify a network of residues that serve as a scaffold for conformational variation, and the network has been faithfully passed down over 500 million years of apoptotic caspase evolution. In addition, investigations of free energy landscapes provide thermodynamic insights into how initiator and effector caspase subfamilies stabilize monomeric and dimeric conformations while undergoing conformational dynamics. We find, through mutational in-vitro folding analysis, that the small subunit and amino acid networks at the base of the structure are essential for conformational dynamics beyond a ubiquitous intermediate present in the conformational ensemble of all apoptotic chordate caspases. We identify key allosteric hub residues that regulate the equilibrium in the conformational ensembles of all apoptotic caspases in chordates. Lastly, by combining our new data set with previous folding studies we provide a comprehensive model for folding of all apoptotic caspases in chordates.
Biochemical and structural basis of Dicer helicase function unveiled by resurrecting ancient proteins
Authors: Aderounmu Adedeji M. , Maus-Conn Josephine , Consalvo Claudia D. , Shen Peter S. , Bass Brenda L.
Published: February 2025

A fully functional Dicer helicase, present in the modern arthropod, uses energy generated during ATP hydrolysis to power translocation on bound dsRNA, enabling the processive dsRNA cleavage required for efficient antiviral defense. However, modern Dicer orthologs exhibit divergent helicase functions that affect their ability to contribute to antiviral defense, and moreover, mechanisms that couple ATP hydrolysis to Dicer helicase movement on dsRNA remain enigmatic. Here, we used biochemical and structural analyses of ancestrally reconstructed Dicer helicases to map evolution of dsRNA binding affinity, ATP hydrolysis and translocation. We found that loss of affinity for dsRNA occurred early in Dicer evolution, coinciding with a decline in translocation activity, despite preservation of ATP hydrolysis activity, exemplified by the ancient deuterostome Dicer. Ancestral nematode Dicer also exhibited significant decline in ATP hydrolysis and translocation, but studies of antiviral activities in the modern nematodeC. elegansindicate Dicer retained a role in antiviral defense by recruiting a second helicase. Cryo-EM analyses of an ancient metazoan Dicer allowed capture of multiple helicase states revealing the mechanism that connects each step of ATP hydrolysis to unidirectional movement along dsRNA. Overall, our study rationalizes the diversity in modern Dicer helicases by connecting ancestral functions to observations in extant enzymes.

Significance Statement

Among invertebrates, the contribution of Dicer’s helicase to recognition and elimination of viral double-stranded RNA varies from phylum to phylum. At the extreme end of the spectrum, vertebrate Dicers show no helicase activity. On the other end, an arthropod ortholog uses helicase translocation to efficiently move double-stranded RNA into Dicer’s cleavage site. The biochemical and structural basis of Dicer’s helicase function, as well as the evolutionary events that contribute to a divergence in function, have remained unknown. This study shows how ancient Dicer helicase tightly binds double-stranded RNA and couples ATP hydrolysis to movement along this substrate. In addition, the data reveal how components of this intricate system declined along different clades of animal evolution.
Structural patterns and transcriptional effects of integrated Epstein-Barr virus revealed by long-read sequencing and RNA-sequencing in Nasopharyngeal Carcinoma
Authors: Kardan Zahra , Kadam Adway , Chai Annie Wai Yeeng , Cheong Sok Ching , Loganathan Sampath Kumar
Published: February 2025

Integration of Epstein–Barr virus (EBV) DNA into the human genome is a critical event in nasopharyngeal carcinogenesis. Here, we comprehensively characterize large-scale virus-human integration events in four EBV-positive nasopharyngeal carcinoma (NPC) cell lines and tumors using Nanopore long-read sequencing technology. We identified four distinct integration types, with Type I being particularly notable, characterized by continuous long reads covering nearly the entire EBV genome. Our findings reveal the involvement of multiple integration events in inducing inter-chromosomal translocations, leading to significant genomic disruption through chromosomal rearrangements. Additionally, we explore the relationship between EBV integration sites and structural variations, further supporting the role of EBV integration in driving genomic instability. By integrating RNA-seq data, we demonstrate the potential for EBV integration to disrupt gene expression, highlighting several integration sites within cancer-associated genes such as CD96, ARHGAP27, ASH1L, KDM3B, ZMYM2, and PIK3C2A. Notably, EBV-human fusion events were prevalent in EBV-associated NPCs, including intriguing fusion transcripts such as LRRC8C-RPMS1 and LINC00486-RPMS1, which provide further evidence of the oncogenic potential of EBV integration. Taken together, this study uncovers EBV integration patterns in Nasopharyngeal carcinogenesis using long-read sequencing technology.
CITEgeist: Cellular Indexing of Transcriptomes and Epitopes for Guided Exploration of Intrinsic Spatial Trends
Authors: Chang Alexander Chih-Chieh , Schlegel Brent T. , Carleton Neil , McAuliffe Priscilla F. , Oesterreich Steffi , Schwartz Russell , Lee Adrian V.
Published: February 2025

Spatial transcriptomics provides insights into tissue architecture by linking gene expression with spatial localization. Current deconvolution methods rely heavily on single-cell RNA sequencing (scRNA-seq) references, which are costly and often unavailable, mainly if the tissue under evaluation is limited, such as in a core biopsy specimen. We present a novel tool, CITEgeist, that deconvolutes spatial transcriptomics data using antibody capture from the same slide as the reference, directly leveraging cell surface protein measurements from the same tissue section. This approach circumvents the limitations of scRNA-seq as a reference, offering a cost-effective and biologically grounded alternative. Our method employs mathematical optimization to estimate cell type proportions and gene expression profiles, incorporating sparsity constraints for robustness and interpretability. Benchmarks against state-of-the-art deconvolution methods show improved accuracy in cell type resolution, particularly in dense tumor microenvironments, while maintaining computational efficiency. This antibody-based tool advances spatial transcriptomics by providing a scalable, accurate, and reference-independent solution for deconvolution in complex tissues. We validate this tool by using a combined approach of simulated data and clinical samples by applying CITEgeist to translational pre-treatment and post-treatment ER+ breast tumors from an ongoing clinical trial, emphasizing the applicability and robustness of CITEgeist.
A dual mechanism of sensitivity to PLK4 inhibition by RP-1664 in neuroblastoma
Authors: Soria-Bretones Isabel , Casás-Selves Matias , Goodfellow Elliot , Li Li , Caron Cathy , Shiwram Ariya , Kim Hyeyeon , Henry Danielle , Laterreur Nancy , Bowlan Julian , Álvarez-Quilón Alejandro , Vallée Frédéric , Veloso Artur , Young Jordan T.F. , Hyer Marc L. , Morris Stephen J. , Marshall C. Gary , Zimmermann Michal
Published: February 2025

A novel therapeutic strategy was recently proposed for high-risk neuroblastoma carrying copy number gain of theTRIM37gene: centriole loss upon inhibition of polo-like kinase 4 (PLK4), while tolerated by normal cells, induces aberrant mitotic spindle formation and p53-dependent cell death inTRIM37-overexpressing cells. Interestingly, while full PLK4 inhibition causes centriole loss, partial inhibition is known to elevate centriole numbers. Here we show using a novel selective PLK4 inhibitor RP-1664 that both centriole loss and amplification contribute to hypersensitivity of neuroblastoma cells. Whereas inactivation ofTRIM37andTP53rescues neuroblastoma cell death at higher concentrations of RP-1664, at lower doses cell death isTRIM37/TP53-independent. With CRISPR screens and live cell imaging we demonstrate that upon centriole amplification, neuroblastoma cells succumb to multipolar mitoses due to inability to cluster or inactivate supernumerary centrosomes.In vivo, RP-1664 shows robust efficacy in neuroblastoma xenografts at doses consistent with centriole amplification.

STATEMENT OF SIGNIFICANCE

High-risk neuroblastoma is associated with poor outcomes in pediatric patients and novel therapies need to be developed. We show that neuroblastoma cells are remarkably sensitive to PLK4 inhibitors due to a combination of two complementary mechanisms, supporting the evaluation of PLK4 inhibitors in clinical trials of high-risk neuroblastoma.
Conserved metabolic adaptation mechanisms in cancer cells and yeast against mitochondrial dysfunction indicate an additional role of aerobic glycolysis for cell survival
Authors: Sawai Akane , Taniguchi Takeo , Noguchi Kohsuke , Seike Taisuke , Okahashi Nobuyuki , Takaine Masak , Matsuda Fumio
Published: February 2025

Eukaryotic cells primarily generate ATP through oxidative phosphorylation and substrate-level phosphorylation. Despite the superior efficiency of oxidative phosphorylation, eukaryotic cells often utilize both pathways as aerobic glycolysis even in the presence of oxygen. However, its role in cell survival remains poorly understood. In this study, aerobic glycolysis of the Warburg effect in breast cancer cells (MCF7) and the Crabtree effect in a laboratory strain ofSaccharomyces cerevisiae(S288C) were compared following treatment with electron transport chain inhibitors, including FCCP, antimycin A, and oligomycin. MCF7 and S288C exhibited strikingly similar metabolic rewiring toward substrate-level phosphorylation against the inhibitor treatment, suggesting that mitochondrial oxidative phosphorylation and cytosolic substrate-level phosphorylation communicate through a common mechanism. Measurements of mitochondrial membrane potential (MMP) and ATP concentration further indicated that cytosolic ATP was transported into the mitochondria under conditions of reduced electron transport chain activity. This ATP was likely utilized by the reverse mode of H+/ATPase to maintain the MMP which contributed to avoiding programmed cell death. These results suggest that the ATP supply to mitochondria plays a conserved role in aerobic glycolysis across yeast and mammalian cancer cells. This mechanism likely contributes to cell survival under conditions of fluctuating oxygen availability.
A uniform stress response of stream microbiomes in the hyporheic zone across North America
Authors: Stach Tom L. , Starke Jörn , Bouderka Feriel , Bornemann Till L.V. , Soares André R. , Wilkins Michael J. , Goldman Amy E. , Stegen James C. , Borton Mikayla A. , Probst Alexander J.
Published: February 2025

Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental stressors. Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies. The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems.
MCAK/Kif2C centromeric activity level tunes K-fiber stability
Authors: Wordeman Linda , Wagenbach Mike , Vicente Juan Jesus
Published: February 2025

MCAK/Kif2C is a microtubule-depolymerizing kinesin that is implicated in the correction of chromosome attachment errors. When this protein is eliminated from kinetochores, cells exhibit delayed congression and a modest increase in chromosome mis-segregation. Curiously, MCAK/Kif2C overexpression (OE) promotes these same defects. These mitotic delays are restricted to prometaphase and can be rescued by modulating MCAK/Kif2C activity solely at the centromere. Both excessive depletion and surplus levels of centromeric MCAK/Kif2C increased inter-kinetochore distances (IKDs) commensurate with an increase in acetylated tubulin in the spindle, a readout for k-fiber stability. Because both high and low levels of centromere-associated MCAK/Kif2C increased k-fiber stability, we conclude that this is the likely mechanism for the increased chromosome segregation errors observed in both these antagonistic conditions. Loss of centromeric MCAK/Kif2C delayed the conversion from lateral to end-on motility was delayed in MCAK/Kif2C-depleted cells. This likely represents the key activity that MCAK/Kif2C imparts to the centromere which, when present at consistently incorrect levels, slows k-fiber turnover and congression.
Decoding RNA-RNA Interactions: The Role of Low-Complexity Repeats and a Deep Learning Framework for Sequence-Based Prediction
Authors: Setti Adriano , Bini Giorgio , Maiorca Valentino , Pellegrini Flaminia , Proietti Gabriele , Miltiadis-Vrachnos Dimitrios , Armaos Alexandros , Martone Julie , Monti Michele , Ruocco Giancarlo , Rodolà Emanuele , Bozzoni Irene , Colantoni Alessio , Tartaglia Gian Gaetano
Published: February 2025

RNA-RNA interactions (RRIs) are fundamental to gene regulation and RNA processing, yet their molecular determinants remain unclear. In this work, we analyzed several large-scale RRI datasets and identified low-complexity repeats (LCRs), including simple tandem repeats, as key drivers of RRIs. Our findings reveal that LCRs enable thermodynamically stable interactions with multiple partners, positioning them as key hubs in RNA-RNA interaction networks. RNA-sequencing of the interactors of the Lhx1os lncRNA allowed to validate the importance of LCRs in shaping interactions potentially involved in neuronal development.Recognizing the pivotal role of sequence determinants, we developed RIME, a deep learning model that predicts RRIs by leveraging embeddings from a nucleic acid language model. RIME outperforms traditional thermodynamics-based tools, successfully captures the role of LCRs and prioritizes high-confidence interactions, including those established by lncRNAs. RIME is freely available athttps://tools.tartaglialab.com/rna_rna.
Tiling of large-scaled environments by grid cells requires experience
Authors: Gutiérrez-Guzmán Blanca E. , Hernández-Pérez J Jesús , Dannenberg Holger
Published: February 2025

Grid cells in the medial entorhinal cortex are widely believed to provide a universal spatial metric supporting vector-based navigation irrespective of the spatial scale of an environment. However, using single unit recordings in freely behaving mice, we demonstrate that spatial periodicity in grid cell firing is substantially disrupted when transitioning from a small to a large-scale arena when the scale ratio is larger than the scale ratio of successive grid modules. Remarkably, grid patterns reemerge with experience in the large-scale arena, suggesting that grid cells can learn to represent large-scale spaces with experience.

Scaling of grid maps is limited by the scale ratio of successive grid modules.

Grid maps cannot be sustained in novel large-scaled environments.

The recovery of the grid map requires multi-day experience.
Application and mechanism of anticancer peptides in organoid models of intrahepatic cholangiocarcinoma
Authors: Hu Xuekai , Zhang Yue , Li Yanchen , Zheng Qiuxia , Zhao Haixia , Zhang Yun , Ni Jingman , Yao Jia
Published: February 2025

Background

The clinical manifestations of intrahepatic cholangiocarcinoma (ICC) are non-specific, and only a small number of patients are eligible for surgical resection at the time of diagnosis, limiting treatment options. Anticancer peptides (ACPs) exhibit strong inhibitory activity against tumour cell lines, exhibit minimal side effects, are easily modified and optimised, and have low production costs. These attributes make ACPs a prospect for clinical applications. Simultaneously, the development of patient-derived three-dimensional organoids as a novel disease model has enabled the replication of the structure and heterogeneity of solid tumours. These organoids provide valuable tools for understanding disease mechanisms, conducting drug sensitivity tests, and developing targeted therapies.

However, the effect of ACPs at the organoid level in ICC remains unknown. Therefore, this study aims to explore the potential of ACPs in treating ICC using patient-derived organoids as a model system to evaluate their efficacy and optimize therapeutic strategies.

Methods

We designed and synthesised a novel ACP sequence and applied it to a patient-derived organoids (PDOs) model. Organoids were evaluated using histochemistry analysis and whole-exome sequencing. ACPs were compared with representative chemotherapeutic drugs, including sorafenib and gemcitabine, to assess treatment differences. Additionally, scanning electron microscopy and flow cytometry were performed for further mechanistic analyses.

Results

Organoid models exhibited histological characteristics similar to those of maternal tumours, especially showing strong positivity for EpCAM and KRT19 expression. Furthermore, whole-exome sequencing of the primary tumour and derived organoids revealed that PDOs closely recapitulated the genomic similarities of the primary tumour across multiple levels. Drug response analyses revealed that ACPs exhibited highly efficient anti-tumour effects, with specific differences observed between patients. ACPs affected the growth of tumour cells and exerted anticancer effects through direct membrane disruption and indirect induction of apoptosis.

Conclusion

In this study, organoids derived from patients with ICC were established. Thisin vitromodel provides valuable tools for evaluating the therapeutic response of ACPs and offers novel insight for the study of ICC.
Heterogenous mitochondrial ultrastructure and metabolism of human glioblastoma cells: differences between stem-like and differentiated cancer cells in response to chemotherapy
Authors: Bogataj Urban , Novak Metka , Galun Simona Katrin , Fon Tacer Klementina , Vittori Miloš , Van Noorden Cornelis J.F. , Breznik Barbara
Published: February 2025

Background

Glioblastoma stem-like cells (GSCs) contribute to the resistance of glioblastoma (GBM) tumors to standard therapies. The cellular and molecular background of the resistance of GSCs to the chemotherapeutic agent temozolomide is not yet fully understood, in particular in the context of cellular metabolism and the role of mitochondria. The aim of this study was to perform a detailed ultrastructural characterization of the mitochondria of GSCs prior and post temozolomide exposure and to compare it to differentiated GBM cells.

Methods

Patient-derived and established GSC and GBM differentiated cell lines were used for the study. The ultrastructure of the mitochondria of the examined cell lines was assessed by transmission electron microscopy. The microscopic analysis was complemented and compared by an analysis of cell metabolism using cell viability assay and extracellular flux analysis using Seahorse assay.

Results

We found that the metabolic profile of GSCs is quiescent and aerobic. Their elongated mitochondria with highly organized cristae is indicating increased biogenesis and mitochondrial fusion and corresponds to a more OXPHOS-dependent metabolism. The metabolism of GSCs is dependent on OXPHOS and there are no changes in defective mitochondria fraction after the treatment with temozolomide. In contrast, differentiated GBM cells with fragmented mitochondria, which have less organized cristae, are more energetic and glycolytic. Temozolomide treatment induced significant ultrastructural mitochondrial damage in differentiated GBM cells and had less effect on mitochondria in GSCs, suggesting that mitochondria play an important role in the resistance of GSCs to temozolomide treatment.

Conclusions

We demonstrated differences in mitochondrial ultrastructure and cellular metabolism between GSCs and differentiated GBM cells in response to temozolomide. This study provides a basis for further studies addressing the chemotherapy resistance of GSCs and the effects of different treatment regimens on the mitochondrial structure and function of GSCs.

Graphical Abstract