bluuebunny/crossref_metadata_2025_split huggingface dataset:
CDK4 and CDK6 upregulation promotes DNA replication stress, genomic instability and resistance to EGFR targeted therapy in lung cancer
Authors: Gini Beatrice , Gui Philippe , Wu Wei , Kerr D. Lucas , Tan Lisa , Barbosa Dora , Olivas Victor , Gomez Carlos , Elmes Sarah , Steri Veronica , Chakrabarti Turja , Bivona Trever G. , Blakely Collin M. 
Published: March 2024

AbstractGenetic interactions impact both normal human physiology and human diseases, such as cancer. Here, we study genetic interactions through the lens of human lung cancers driven by oncogenic forms of the epidermal growth factor receptor (EGFR), which we and others previously showed harbor a rich landscape of genetic co-alterations and potential genetic interactions. Among the most common genetic co-alterations with oncogenicEGFRare genomic amplifications of cell cycle regulatorsCDK4orCDK6, which have been implicated in EGFR inhibitor clinical resistance, although the mechanism underlying this effect is not well characterized. We show that CDK4/6 upregulation overcomes EGFR inhibitor-induced G1/S cell cycle arrest in association with increased replication stress, DNA damage and genomic instability. These biological effects arising in CDK4/6 upregulated tumors help to enable resistance to EGFR targeted therapies through established genetic resistance mechanisms. Combinatorial EGFR and CDK4/6 inhibitor treatment alleviated genomic instability and EGFR inhibitor resistance in patient-derived preclinical models. This study reveals mechanistic and clinical impacts of the genetic interaction between oncogenicEGFRandCDK4/6co-alterations in human lung cancer.
Inhibition of HDAC7 reprograms the histone H3.3 landscape to induce heterochromatin spreading and DNA replication defects in cancer cells
Authors: Hassan Ola , Pizzagalli Mattia , Leary Owen , Zepecki John P. , Corseri Adrianne , Wu Laura Jinxuan , Sasipalli Shiven , Lee Daniel , Hayward Lindsey , Tran Lily , Fajardo Eduardo , Fiser Andras , Karambizi David , Tapinos Nikos 
Published: March 2024

AbstractClass IIa histone deacetylases (HDACs) are a family of enzymes with minimal histone deacetylase activity but can function as multi-protein interaction hubs. Here we demonstrate the expression of HDAC7, a Class IIa HDAC family member, in glioblastoma tumor tissue from 84 patients, patient-derived glioma stem cells (GSCs) from six patients, and pediatric diffuse pontine glioma (DIPG) cells from three patients. HDAC7 binds to Histone H3.3 and interacts with H3.3 and HIRA on chromatin. Targeted downregulation of HDAC7 expression with a subtype-specific siRNA inhibits the interaction of H3.3 with HIRA while increasing the association of H3.3 with DAXX and H3K9me3. This results in H3.3 being deposited on H3K9me3+/DAPI+ heterochromatin nuclear foci. Inhibition of HDAC7 triggers H3K9me3+ heterochromatin spreading, increased H3K9me3 binding in the cancer genome, and significant alterations in gene expression. Using single molecule DNA fiber approach, we show that HDAC7 inhibition results in a significant increase in replication fork speed without affecting fork symmetry. This altered replication fork speed leads to replication stress, evidenced by phosphorylation of RPA2 and impact on global DNA synthesis, resulting in reduced EdU incorporation. Finally, HDAC7 depletion leads to reduced BRCA2 expression and increased sensitivity of cancer cells to DNA damaging agents. Taken together, these studies uncover the involvement of HDAC7 in the euchromatic H3.3 chaperone network and the effect of HDAC7 depletion on chromatin dynamics, inducing epigenetic restriction and DNA damage in cancer cells.
Protection againstAPOE4-associated aging phenotypes with the longevity-promoting intervention 17α-estradiol in male mice
Authors: McGill Cassandra J. , Christensen Amy , Qian Wenjie , Thorwald Max A. , Lugo Jose Godoy , Namvari Sara , White Olivia S. , Finch Caleb E. , Benayoun Bérénice A. , Pike Christian J. 
Published: March 2024

SummaryThe apolipoprotein ε4 allele (APOE4) is associated with decreased longevity, increased vulnerability to age-related declines, and disorders across multiple systems. Interventions that promote healthspan and lifespan represent a promising strategy to attenuate the development ofAPOE4-associated aging phenotypes. Here we studied the ability of the longevity-promoting intervention 17α-estradiol (17αE2) to protect against age-related impairments inAPOE4versus the predominantAPOE3genotype using early middle-aged mice with knock-in of humanAPOEalleles. Beginning at age 10 months, maleAPOE3orAPOE4mice were treated for 20 weeks with 17αE2 or vehicle then compared for indices of aging phenotypes body-wide. Across peripheral and neural measures,APOE4was associated with poorer outcomes. Notably, 17αE2 treatment improved outcomes in a genotype-dependent manner favoringAPOE4mice. These data demonstrate a positiveAPOE4bias in 17αE2-mediated healthspan actions, suggesting that longevity-promoting interventions may be useful in mitigating deleterious age-related risks associated withAPOE4genotype.
A brainstem circuit for gravity-guided vertical navigation
Authors: Zhu Yunlu , Gelnaw Hannah , Auer Franziska , Hamling Kyla R. , Ehrlich David E. , Schoppik David 
Published: March 2024

ABSTRACTThe sensation of gravity anchors our perception of the environment and is crucial for navigation. However, the neural circuits that transform gravity into commands for navigation are undefined. We first determined that larval zebrafish (Danio rerio) navigate vertically by maintaining a consistent heading across a series of upward climb or downward dive bouts. Gravity-blind mutant fish swim with more variable heading and excessive veering, leading to inefficient vertical navigation. After targeted photoablation of ascending vestibular neurons and spinal projecting midbrain neurons, but not vestibulospinal neurons, vertical navigation was impaired. These data define a sensorimotor circuit that uses evolutionarily-conserved brainstem architecture to transform gravitational signals into persistent heading for vertical navigation. The work lays a foundation to understand how vestibular inputs allow animals to move efficiently through their environment.
PURIFICATION METHOD FOR ADENO-ASSOCIATED VIRAL VECTOR SEROTYPE 9 USING CERAMIC HYDROXYAPATITE CHROMATOGRAPHY AND ITS QUALIFICATION
Authors: Kurosawa Yae , Tsunekawa Yuji , Wada Mikako , Aizen Yuko , Nitahara-Kasahara Yuko , Okada Takashi 
Published: March 2024

ABSTRACTAdeno-associated virus (AAV) vectors can efficiently transduce exogenous genes into various tissuesin vivo. Owing to their convenience, high efficiency, long-term stable gene expression, and minimal side effects, AAV vectors have become one of the gold standards for investigating gene functionsin vivo, especially in non-clinical studies. However, challenges persist in efficiently preparing a substantial quantity of high-quality AAV vectors that comprise only genome-packaged full particles. Commercial AAV vectors are typically associated with high costs. Further, in-laboratory production is hindered by the lack of specific laboratory equipment, such as ultracentrifuges. Therefore, a simple, quick, and scalable preparation method for AAV vectors is needed for proof-of-concept experiments. Herein, we present an optimized method for producing and purifying high-quality AAV serotype 9 (AAV9) vectors using standard laboratory equipment and chromatography. Using ceramic hydroxyapatite as a mixed-mode chromatography medium can markedly increase the quality of purified AAV vectors. Basic protocols and optional methods for evaluating purified AAV vectors are also described.
Diverse origins of near-identical antifreeze proteins in unrelated fish lineages provide insights into evolutionary mechanisms of new gene birth and protein sequence convergence
Authors: Rives Nathan , Lamba Vinita , Cheng C.-H. Christina , Zhuang Xuan 
Published: March 2024

AbstractDetermining the origins of novel genes and the genetic mechanisms underlying the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. The convergently evolved fish antifreeze proteins provide excellent opportunities to investigate evolutionary origins and pathways of new genes. Particularly notable is the near-identical type I antifreeze proteins (AFPI) in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages, revealing different paths by which a similar protein arose from diverse genomic resources. Comprehensive comparative analyses ofde novosequenced genome of the winter flounder and grubby sculpin, available high-quality genome of the cunner and 14 other relevant species found that the near-identical AFPI originated from a distinct genetic precursor in each lineage. Each independently evolved a coding region for the novel ice-binding protein while retaining sequence identity in the regulatory regions with their respective ancestor. The deduced evolutionary processes and molecular mechanisms are consistent with the Innovation-Amplification-Divergence (IAD) model applicable to AFPI formation in all three lineages, a new Duplication-Degeneration-Divergence (DDD) model we propose for the sculpin lineage, and a DDD model with gene fission for the cunner lineage. This investigation illustrates the multiple ways by which a novel functional gene with sequence convergence at the protein level could evolve across divergent species, advancing our understanding of the mechanistic intricacies in new gene formation.
Tracking inflammation resolution signatures in lungs after SARS-CoV-2 omicron BA.1 infection of K18-hACE2 mice
Authors: Carolin Agnes , Yan Kexin , Bishop Cameron R. , Tang Bing , Nguyen Wilson , Rawle Daniel J. , Suhrbier Andreas 
Published: March 2024

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which can result in severe disease, often characterised by a ‘cytokine storm’ and the associated acute respiratory distress syndrome. However, many infections with SARS-CoV-2 are mild or asymptomatic throughout the course of infection. Although blood biomarkers of severe disease are well studied, less well understood are the inflammatory signatures in lung tissues associated with mild disease or silent infections, wherein infection and inflammation are rapidly resolved leading to sequelae-free recovery. Herein we described RNA-Seq and histological analyses of lungs over time in an omicron BA.1/K18-hACE2 mouse infection model, which displays these latter features. Although robust infection was evident at 2 days post infection (dpi), viral RNA was largely cleared by 10 dpi. Acute inflammatory signatures showed a slightly different pattern of cytokine signatures compared with severe infection models, and where much diminished 30 dpi and absent by 66 dpi. Cellular deconvolution identified significantly increased abundance scores for a number of anti-inflammatory pro-resolution cell types at 5/10 dpi. These included type II innate lymphoid cells, T regulatory cells, and interstitial macrophages. Genes whose expression trended downwards over 2 – 66 dpi included biomarkers of severe disease and were associated with ‘cytokine storm’ pathways. Genes whose expression trended upward during this period were associated with recovery of ciliated cells, AT2 to AT1 transition, reticular fibroblasts and innate lymphoid cells, indicating a return to homeostasis. Very few differentially expressed host genes were identified at 66 dpi, suggesting near complete recovery. The parallels between mild or subclinical infections in humans and those observed in this BA.1/K18-hACE2 mouse model are discussed with reference to the concept of “protective inflammation”.
Host evolution improves genetic circuit function in complex growth environments
Authors: Zhang Joanna T. , Lezia Andrew , Emmanuele Philip , Wu Muyao , Olson Connor A. , Feist Adam M. , Hasty Jeff 
Published: March 2024

AbstractGenetically engineered bacteria have become an attractive platform for numerous biomedical and industrial applications. Despite genetic circuitry functioning predictably under favorable growth conditions in the lab, the same cannot be said when placed in more complex environments for eventual deployment. Here, we used a combination of evolutionary and rational engineering approaches to enhanceE. colifor robust genetic circuit behavior in non-traditional growth environments. We utilized adaptive laboratory evolution (ALE) onE. coliMG1655 in a minimal media with a sole carbon source and saw improved dynamics of a population-lysis-based circuit after host evolution. Additionally, we improved lysis circuit tolerance of a more clinically relevant strain, the probioticE. coliNissle, using ALE of the host strain in a more complex media environment with added reactive oxygen species (ROS) stress. We observed improved recovery from circuit-induced lysis in the evolved Nissle strain, and in combination with directed mutagenesis, recovered circuit function in the complex media. These findings serve as a proof-of-concept that relevant strains of bacteria can be optimized for improved growth and performance in complex environments using ALE and that these changes can modify and improve synthetic gene circuit function for real-world applications.
Assessing Long-Term Stored Tissues for Multi-Omics Data Quality and Proteogenomics Suitability
Authors: Song Kyu Jin , Kim Minsuh , Heo Yong Jin , Cho Kyung-Cho , Oh Jae-Won , Kim Dae Ho , Hwa Chanwoong , Do Yeji , Choi Seunghyuk , Hwang Hee Sang , Kim Kwoneel , Kim Kyunggon , Na Seungjin , Paek Eunok , An Joon-Yong , Jang Se Jin , Kim Min-Sik , Kim Kwang Pyo 
Published: March 2024

AbstractAs research into the complexities of cancer biology deepens, the integration of multi-omics analyses has emerged as a powerful approach to unravel the complex molecular basis of cancers. However, challenges related to sample availability, including size, collection procedures, and storage duration, hinder the broad application of this methodology. Despite these limitations, there is a growing interest in exploring the potential of archived samples to expand the scope of multi-omics research. Our study aims to investigate the impact of storage duration on the measurment in genomic, transcriptomic, and proteomic profiles of archived samples, demonstrating their viability for advancing our understanding of cancer biology. To comprehensively address these trends and limitations, we systematically examined archived samples collected over a decade, focusing on their transcriptomic, proteomic, and phosphoproteomic attributes. Analysis revealed intricate patterns and dynamic shifts, especially in long-term transcriptomic data, with observed declines in read counts related to protein coding and gene coverage. However, these changes did not compromise the fundamental gene expression landscape. Proteomic result also demonstrated that storage period did not significantly influence proteomic measurement. Comparisons of housekeeping gene (HKG) and housekeeping protein (HKP) expressions unveiled consistent transcriptomic levels across samples, while distinctive proteomic disparities between tumor and normal tissues. In conclusion, the challenges posed by limited sample availability in multi-omics studies can be partially overcome through the strategic integration of archived samples. While technical shifts were evident in certain aspects of transcriptomic data, core gene expression patterns remained robust, and the functionality of essential transcription factors (TFs) and kinases remained unaffected. These findings underscore the potential of archived samples as valuable resources for multi-omics research, providing a broader landscape for investigating cancer biology and paving the way for more comprehensive insights into this intricate field.
Single Cell MALDI-MSI Analysis of Lipids and Proteins within a Replicative Senescence Fibroblast Model
Authors: Sekera Emily R. , Rosas Lorena , Holbrook Joseph H. , Angeles-Lopez Quetzalli D. , Khaliullin Timur , Rojas Mauricio , Mora Ana L. , Hummon Amanda B. 
Published: March 2024

ABSTRACTIn this study, we evaluate lipids and select proteins in human lung fibroblasts (hLFs) to interrogate changes occurring due to aging and senescence. To study single cell populations, a comparison of cells adhered onto slides using poly-D-lysine versus centrifugal force deposition was first analyzed to determine whether specific alterations were observed between preparations. The poly-D-lysine approach was than utilized to interrogate the lipidome of the cell populations and further evaluate potential applications of the MALDI-immunohistochemistry (IHC) platform for single-cell level analyses. Two protein markers of senescence, vimentin and p21, were both observed within the fibroblast populations and quantified. Lipidomic analysis of the fibroblasts found twelve lipids significantly altered because of replicative senescence, including fatty acids, such as stearic acid, and ceramide phosphoethanolamine species (CerPE). Similar to previous reports, alterations were detected in putative fatty acid building blocks, ceramides, among other lipid species. Altogether, our results reveal the ability to detect lipids implicated in senescence and show alterations to protein expression between normal and senescent fibroblast populations, including differences between young and aged cells. This report is the first time that the MALDI-IHC system has been utilized at a single-cell level to analyze both protein expression and lipid profiles in cultured cells, with a particular focus on changes associated with aging and senescence.
Comprehensive analysis of RNA-chromatin, RNA- and DNA-protein interactions
Authors: Khlebnikov Daniil A. , Nikolskaya Arina A. , Zharikova Anastasia A. , Mironov Andrey A. 
Published: March 2024

AbstractRNA-chromatin interactome data is considered to be one of the noisiest types of data in biology. This is due to protein-coding RNA contacts and non-specific interactions between RNA and chromatin caused by protocol specifics. Therefore, finding regulatory interactions between certain transcripts and genome loci requires a wide range of filtering techniques to obtain significant results. Using data on pairwise interactions between these molecules, we propose a concept of triad interaction involving RNA, protein and a DNA locus. The constructed triads show significantly less noise contacts and are more significant when compared to a background model for generating pairwise interactions. RNA-chromatin contacts data can be used to validate the proposed triad object as positive (Red-ChIP experiment) or negative (RADICL-Seq NPM) controls. Our approach also filters RNA-chromatin contacts in chromatin regions associated with protein functions based on ChromHMM annotation.
Bacterial RNA promotes proteostasis through inter-tissue communication inC. elegans
Authors: Kyriakakis Emmanouil , Medde Chiara , Ritz Danilo , Fucile Geoffrey , Schmidt Alexander , Spang Anne 
Published: March 2024

AbstractLife expectancy has been increasing over the last decades, which is not matched by an increase in healthspan. Besides genetic composition, environmental and nutritional factors influence both health- and lifespan. Diet is thought to be a major factor for healthy ageing. Here, we show that dietary RNA species extend healthspan inC. elegans. Inherent bacterial-derived double stranded RNA reduces protein aggregation in aC. elegansmuscle proteostasis model. This beneficial effect depends on low levels of systemic selective autophagy, the RNAi machinery in the germline, even when the RNA is delivered through ingestion in the intestine and the integrity of muscle cells. Our data suggest a requirement of inter-organ communication between the intestine, the germline and muscles. Our results demonstrate that bacterial-derived RNAs elicit a systemic response inC. elegans, which protects the animal from protein aggregation during ageing. We provide evidence that low stress levels are beneficial for healthspan.One-Sentence SummaryBacteria-derived dietary cues and inter-tissue communication promote proteostasis and fitness inC. elegans
Mutability and hypermutation antagonize immunoglobulin codon optimality
Authors: McGrath Joshua J.C. , Park Juyeon , Troxell Chloe A. , Chervin Jordan C. , Li Lei , Kent Johnathan R. , Changrob Siriruk , Fu Yanbin , Huang Min , Zheng Nai-Ying , Wilbanks G. Dewey , Nelson Sean A. , Sun Jiayi , Inghirami Giorgio , Madariaga Maria Lucia L. , Georgiou George , Wilson Patrick C. 
Published: March 2024

AbstractThe efficacy of polyclonal antibody responses is inherently linked to paratope diversity, as generated through V(D)J recombination and somatic hypermutation (SHM). These processes arose in early jawed vertebrates; however, little is known about how immunoglobulin diversity, mutability, and hypermutation have evolved in tandem with another more ubiquitous feature of protein-coding DNA – codon optimality. Here, we explore these relationships through analysis of germlineIGgenes, natural V(D)J repertoires, serum VH usage, and monoclonal antibody (mAb) expression, each through the lens of multiple optimality metrics. Strikingly, proteomic serum IgG sequencing showed that germlineIGHVcodon optimality positively correlated with VH representation after influenza vaccination, andin vitro, codon deoptimization of mAbs with synonymous amino acid sequences caused consistent expression loss. Germline V genes exhibit a range of codon optimality that is maintained by functionality, and inversely related to mutability. SHM caused a load-dependent deoptimization ofIGHVDJ repertoires within human tonsils, bone marrow, and lymph nodes (including SARS-CoV-2-specific clones from mRNA vaccinees), influenza-infected mice, and zebrafish. Comparison of natural mutation profiles to true random suggests the presence of selective pressures that constrain deoptimization. These findings shed light on immunoglobulin evolution, providing unanticipated insights into the antagonistic relationship between variable region diversification, codon optimality, and antibody secretion; ultimately, the need for diversity takes precedence over that for the most efficient expression of the antibody repertoire.