bluuebunny/crossref_metadata_2025 huggingface dataset:
Tumor immune microenvironment permissive to metastatic progression of ING4-deficient breast cancer
Authors: Tsutsumi Emily , Macy Anne M. , LoBello Janine , Hastings Karen T. , Kim Suwon
Published: May 2024

Deficiencies in the ING4 tumor suppressor are associated with advanced stage tumors and poor patient survival in cancer. ING4 was shown to inhibit NF-κB in several cancers. As NF-κB is a key mediator of immune response, the ING4/NF-κB axis is likely to manifest in tumor-immune modulation but has not been investigated. To characterize the tumor immune microenvironment associated with ING4-deficient tumors, three approaches were employed in this study: First, tissue microarrays composed of 246 primary breast tumors including 97 ING4-deficient tumors were evaluated for the presence of selective immune markers, CD68, CD4, CD8, and PD-1, using immunohistochemical staining. Second, an immune-competent mouse model of ING4-deficient breast cancer was devised utilizing CRISPR-mediated deletion ofIng4in aTp53deletion-derived mammary tumor cell line; mammary tumors were evaluated for immune markers using flow cytometry. Lastly, the METABRIC gene expression dataset was evaluated for patient survival related to the immune markers associated withIng4-deleted tumors. The results showed that CD68, CD4, CD8, or PD-1, was not significantly associated with ING4-deficient breast tumors, indicating no enrichment of macrophages, T cells, or exhausted T cell types. In mice,Ing4-deleted mammary tumors had a growth rate comparable toIng4-intact tumors but showed increased tumor penetrance and metastasis. Immune marker analyses ofIng4-deleted tumors revealed a significant increase in tumor-associated macrophages (Gr-1loCD11b+F4/80+) and a decrease in granzyme B-positive (GzmB+) CD4+T cells, indicating a suppressive and/or less tumoricidal immune microenvironment. The METABRIC data analyses showed that low expression ofGZMBwas significantly associated with poor patient survival, as wasING4-low expression, in the basal subtype of breast cancer. Patients withGZMB-low/ING4-low tumors had the worst survival outcomes (HR=2.80, 95% CI 1.36-5.75, p=0.0004), supportive of the idea that theGZMB-low immune environment contributes to ING4-deficient tumor progression. Collectively, the study results demonstrate that ING4-deficient tumors harbor a microenvironment that contributes to immune evasion and metastasis.
Construction of a breast cancer predictive nomogram based on diverse cell death methods and reveal tumor microenvironment characterization
Authors: Wu Rihan , Wang Zirui , Dong Chunhui , Liu Yihui , Chen Ling
Published: May 2024

Objective

To develop a robust predictive model and nomogram for breast cancer (BC) linked to genes associated with diverse cell death methods.

Methods

The prognostic model was constructed using the LASSO Cox method. Model performance was assessed using K-M analysis, ROC curves, and independent prognostic analysis. Subsequently, we constructed a nomogram and analyzed differences in tumor microenvironment and drug sensitivity between different subgroups. The enrichment of differentially expressed genes between different subgroups was assessed. Additionally, we overexpressed CD24 in BC cell lines to assess its impact on cellular proliferation using CCK8 assays, migration through scratch and transwell assays, and apoptosis via flow cytometry.

Results

A prognostic model comprising twelve genes (CREB3L1, SFRP1, SHARPIN, AIFM1, IL-18, CD24, EDA2R, CRIP1, XBP1, BCL2A1, NKX3-1, and NME5) was constructed. BC patients were categorized into different subgroups, with the low-risk subgroup demonstrating superior survival. Additionally, we constructed a nomogram. The nomogram was validated as a reliable independent predictor of outcome. The enrichment analyses imply a connection between patient risk and immune response. The low-risk subgroup had a higher TME score. Patients in the high-risk group had improved responses to lapatinib, BI-2536, OSI-027, and SB505124, while those in the low-risk subgroup showed improved sensitivity to axitinib, epirubicin, fulvestrant, and olaparib. Furthermore, CD24 overexpression was found to promote proliferation and migration, while inhibiting apoptosis.

Conclusion

These findings contribute to the individualization of treatment and aid in uncovering the tumor microenvironment characterization for BC patients.
Levels of high-sensitive troponin T and mid-regional pro-adrenomedullin after COVID-19 vaccination in vulnerable groups: a prospective study on subtle and persistent cardiovascular involvement
Authors: Möckel Martin , Pudasaini Samipa , Le Ngoc Han , Huscher Dörte , Holert Fabian , Hillus David , Tober-Lau Pinkus , Kurth Florian , Sander Leif Erik
Published: May 2024

Background

This study examines potential, subtle and persistent adverse effects of COVID-19 vaccines on the cardiovascular system. Vaccine-associated myocardial injury was analysed by measuring high-sensitive troponin T (hsTnT); mid-regional pro-adrenomedullin (MR-proADM) levels were evaluated to assess endothelial dysfunction.

Methods

This was a prospective study with a vulnerable population of healthcare workers (HCWs) and elderly patients (> 70 years) who were vaccinated with either one dose of ChAdOx1 nCov-19 adenoviral vector vaccine (AZ) followed by one dose of the BNT162b2 messenger RNA vaccine (BNT), or with two doses of BNT (12thof January - 30thof November 2021). HsTnT and MR-proADM were measured in blood samples at three visits (V1: 1stimmediately before vaccination; V2, 3: 3-4 weeks after 1stand 2ndvaccination). HsTnT of HCWs was compared to a healthy reference population.

Results

N=162 volunteers were included (V1=161; V2, V3=162 each). N=74 (45.7%) received AZ/BNT and n=88 (54.3%) received BNT/BNT (elderly: n=20 (12.3%), HCWs: n=68 (42.0%)). Median hsTnT levels were 4ng/L, 5ng/L and 4ng/L (V1-V3) for AZ/BNT and at 5ng/L, 6ng/L and 6ng/L (V1-V3) for BNT/BNT. Compared to the reference population (n=300), hsTnT was significantly higher at all visits for both vaccination groups (p<0.01), without differences between the AZ/BNT and BNT/BNT cohort. MR-proADM values were 0.43nmol/L, 0.45nmol/L, 0.44nmol/L (V1-V3) in the AZ/BNT cohort and 0.49nmol/L, 0.44nmol/L, 0.47nmol/L for BNT/BNT, respectively. Change of median hsTnT and MR-proADM between visits did not show significant increases. One HCW case had a permanent and three a transient hsTnT increase ≥14ng/L.

Conclusion

With one individual exception, no overall subtle, persistent cardiovascular involvement was observed after the 2ndCOVID-19 vaccination.

Structured graphical abstract

Summary of the vaccination scheme and visiting points in the study population (of HCWs and seniors > 70 years) between the 12thof January and the 30thof November 2021. The results showed no overall subtle, chronic myocardial or vascular involvement in our COVID-19 vaccinated cohorts.

Abbreviations:AZ ChAdOx1 nCov-19 adenoviral vector vaccine from Astra Zeneca, BNT BNT162b2 messenger ribonucleic acid vaccine from BioNTech, EDTA Ethylenediaminetetraacetic acid, HCWs health care workers, hsTnT high-sensitive troponin T, mid-regional pro-adrenomedullin, V1-V3visiting times 1-3, w week(s).
LucaOne: Generalized Biological Foundation Model with Unified Nucleic Acid and Protein Language
Authors: He Yong , Fang Pan , Shan Yongtao , Pan Yuanfei , Wei Yanhong , Chen Yichang , Chen Yihao , Liu Yi , Zeng Zhenyu , Zhou Zhan , Zhu Feng , Holmes Edward C. , Ye Jieping , Li Jun , Shu Yuelong , Shi Mang , Li Zhaorong
Published: May 2024

In recent years, significant advancements have been observed in the domain of Natural Language Processing(NLP) with the introduction of pre-trained foundational models, paving the way for utilizing similar AI technologies to interpret the language of biology. In this research, we introduce “LucaOne”, a novel pre-trained foundational model designed to integratively learn from the genetic and proteomic languages, encapsulating data from 169,861 species en-compassing DNA, RNA, and proteins. This work illuminates the potential for creating a biological language model aimed at universal bioinformatics appli-cation. Remarkably, through few-shot learning, this model efficiently learns the central dogma of molecular biology and demonstrably outperforms com-peting models. Furthermore, in tasks requiring inputs of DNA, RNA, proteins, or a combination thereof, LucaOne exceeds the state-of-the-art performance using a streamlined downstream architecture, thereby providing empirical ev-idence and innovative perspectives on the potential of foundational models to comprehend complex biological systems.
Pro-inflammatory macrophage activation does not require inhibition of mitochondrial respiration
Authors: Ball Andréa B. , Jones Anthony E. , Nguyễn Kaitlyn B. , Rios Amy , Marx Nico , Hsieh Wei Yuan , Yang Krista , Desousa Brandon R. , Kim Kristen K.O. , Veliova Michaela , del Mundo Zena Marie , Shirihai Orian S. , Benincá Cristiane , Stiles Linsey , Bensinger Steven J. , Divakaruni Ajit S.
Published: May 2024

Pro-inflammatory macrophage activation is a hallmark example of how mitochondria serve as signaling organelles. Upon classical macrophage activation, oxidative phosphorylation sharply decreases and mitochondria are repurposed to accumulate signals that amplify effector function. However, evidence is conflicting as to whether this collapse in respiration is essential or largely dispensable. Here we systematically examine this question and show that reduced oxidative phosphorylation is not required for pro-inflammatory macrophage activation. Only stimuli that engage both MyD88- and TRIF-linked pathways decrease mitochondrial respiration, and different pro-inflammatory stimuli have varying effects on other bioenergetic parameters. Additionally, pharmacologic and genetic models of electron transport chain inhibition show no direct link between respiration and pro-inflammatory activation. Studies in mouse and human macrophages also reveal accumulation of the signaling metabolites succinate and itaconate can occur independently of characteristic breaks in the TCA cycle. Finally,in vivoactivation of peritoneal macrophages further demonstrates that a pro-inflammatory response can be elicited without reductions to oxidative phosphorylation. Taken together, the results suggest the conventional model of mitochondrial reprogramming upon macrophage activation is incomplete.
HYL001, a new potent TGFβ signaling inhibitor that is efficacious against microsatellite stable CRC metastasis in combination with immune checkpoint therapy in mice
Authors: Tauriello Daniele V. F. , Sancho Elena , Byrom Daniel , Sanchez-Zarzalejo Carolina , Salvany Maria , Henriques Ana , Palomo-Ponce Sergio , Sevillano Marta , Hernando-Momblona Xavier , Matarin Joan A. , Ramos Israel , Ruano Irene , Prats Neus , Batlle Eduard , Riera Antoni
Published: May 2024

Blockade of the TGFβ signalling pathway has emerged from preclinical studies as a potential treatment to enhance the efficacy of immune checkpoint inhibition in advanced colorectal cancer (CRC) and several other types of cancer. However, clinical translation of first-generation inhibitors has known little success. Here, we report the synthesis and characterization of HYL001, a potent inhibitor of TGFβ receptor 1 (ALK5), that is approximately 9 times more efficacious than the structurally related compound galunisertib, while maintaining a favourable safety profile. HYL001 in combination with immune checkpoint blockade (anti-PD1) eradicates liver metastases generated in mice by microsatellite stable, aggressive colorectal cancer tumours at doses where galunisertib is ineffective.

GRAPHICAL ABSTRACT
Cerebrovascular health mediates processing speed change through anterior white matter alterations: A UK Biobank Study
Authors: Moran KL , Smith CJ , McManus E , Allan SM , Montaldi D , Muhlert N
Published: May 2024

Cerebrovascular disease is associated with an increased likelihood of developing dementia. While cardiovascular risk factors are modifiable and may reduce the risk of later-life cognitive dysfunction, the relationship between cerebrovascular risk factors, brain integrity and cognition remains poorly characterised. Using a large UK Biobank sample of predominantly middle-aged adults, without neurological disease, our structural equation mediation models showed that poor cerebrovascular health, indicated by the presence of cerebrovascular risk factors, was associated with slowed processing speed. This effect was best explained by anterior white matter microstructure changes, rather than posterior changes. Effects were also significantly reduced when considering other forms of cognition, demonstrating both regional- and cognitive-specificity of our effects. Critically, our findings also demonstrate that including measures of risk factor duration may be particularly important for improving estimations of cerebrovascular burden. In summary, our study demonstrates the specific impact of early cerebrovascular burden on brain structure and cognitive function, highlighting the necessary next steps for improving cerebrovascular burden quantification and improving clinical predictions.
ZW sex chromosome structure in Amborella trichopoda
Authors: Carey Sarah B. , Akozbek Laramie , Lovell John T , Jenkins Jerry W , Healey Adam L. , Shu Shengqiang , Grabowsk Paul , Yocca Alan , Stewart Ada , Jones Teresa , Barry Kerrie W. , Rajasekar Shanmugam , Talag Jayson , Scutt Charlie , Lowry Porter P. , Munzinger Jerome , Knox Eric B. , Soltis Douglas E. , Soltis Pamela S. , Grimwood Jane , Schmutz Jeremy , Leebens-Mack James , Harkess Alex
Published: May 2024

Sex chromosomes have evolved hundreds of times, and their recent origins in flowering plants can shed light on the early consequences of suppressed recombination. Amborella trichopoda, the sole species on a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly-contiguous assemblies of the Z and W chromosomes. We identify a ~3-Megabase sex-determination region (SDR) captured in two strata that includes a ~300-Kilobase inversion that is enriched with repetitive sequence and contains a homolog of the Arabidopsis METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) genes, which are known to be involved in fertility. However, the remainder of the SDR does not show patterns typically found in non-recombining SDRs, like repeat accumulation and gene loss. These findings are consistent with the hypothesis that dioecy is recently derived in Amborella and the sex chromosome pair has not significantly degenerated.
Human metapneumovirus SH protein promotes JAK1 degradation to impair host IL-6 signaling
Authors: Brynes Adam , Zhang Yu , Williams John V.
Published: May 2024

Human metapneumovirus (HMPV) is a leading cause of respiratory infections in children, older adults, and those with underlying conditions1,2,3,4. HMPV must evade immune defenses to replicate successfully; however, the viral proteins used to accomplish this are poorly characterized. The HMPV small hydrophobic (SH) protein has been reported to inhibit signaling through type I and type II interferon (IFN) receptorsin vitro, in part by preventing STAT1 phosphorylation5. HMPV infection also inhibits IL-6 signaling. However, the mechanisms by which SH inhibits signaling, and its involvement in IL-6 signaling inhibition are unknown. Here, we used transfection of SH expression plasmids and SH-deleted virus (ΔSH) to show that SH is the viral factor responsible for inhibition of IL-6 signaling during HMPV infection. Transfection of SH-expression vectors or infection with wildtype, but not ΔSH virus, blocked IL-6 mediated STAT3 activation. Further, JAK1 protein (but not RNA) was significantly reduced in cells infected with wildtype but not ΔSH virus. The SH-mediated reduction of JAK1 was partially restored by addition of proteasome inhibitors, suggesting proteasomal degradation of JAK1. Confocal microscopy indicated that infection relocalized JAK1 to viral replication factories. Co-immunoprecipitation showed that SH interacts with JAK1 and ubiquitin, further linking SH to proteasomal degradation machinery. These data indicate that SH inhibits IL-6 and IFN signaling in infected cells in part by promoting proteasomal degradation of JAK1 and that SH is necessary for IL-6 and IFN signaling inhibition in infection. These findings enhance our understanding of the immune evasion mechanisms of an important respiratory pathogen.

Importance

Human metapneumovirus (HMPV) is a common cause of severe respiratory illness, especially in children and older adults, in whom it is a leading cause of hospitalization. Prior research suggests that severe HMPV infection is driven by a strong immune response to the virus, and especially by inflammatory immune signals like interferons (IFN). HMPV produces a small hydrophobic protein (SH) that is known to block IFN signaling, but the mechanism by which it functions, and its ability to inhibit other important immune signals remains unexplored. This paper demonstrates that SH can inhibit another related immune signal, IL-6, and demonstrates that SH depletes JAKs, critical proteins involved in both IL-6 and IFN signaling. A robust understanding of how HMPV and related viruses interfere with immune signals important for disease could pave the way for future treatments aimed at mitigating severe infections.
THE PHYTOPHARMACOLOGICAL EVALUATION OF THE METHANOL ROOT EXTRACT OFAZANZA GARCKEANA(MALVACEAE) ON ISOLATED WISTAR RAT UTERINE SMOOTH MUSCLES
Authors: Chanda Alfred , Gono-Bwalya Angela , prashar Lavina
Published: May 2024

Ethnopharmacological relevance

Pregnant women in Chongwe, Zambia traditionally use the root ofAzanza garckeana(F.Hffm.) Exell & Hillc (Malvalceae) to induce or accelerate labour. A previous study on the plant showed the crude root extracts to possesses uterotonic potential on isolated Wistar rat uterine smooth muscles. The methanol crude root extract was found to be the most potent.

Aim

The aim of the study was to isolated by bioactivity-guided isolation method the compound with the major uterotonic activity in the root ofAzanza garckeana.

Materials and methods

This was a laboratory-based study designed using the uterus isolated from estrogenised adult non-gravid female virgin Wistar rats. The fresh plant materials (leaves and roots) were collected from Chongwe district. The methanol crude extract was obtained by continuous maceration and it was partitioned using hexane, chloroform, ethyl acetate and n-butanol in the increasing order of polarity. The most active fraction was fractionated using column chromatography. One-way ANOVA, Bonferroni post hoc tests were used to analyze data using STATA version 13. Bar charts and dose-response curves were done using Graphpad Prism version 5.00 for Windows (San Diego California USA).

Results

The final aqueous suspension demonstrated the highest uterotonic potency (EC50= 2.49 x 10−3mg/ml; 95% CI 1.19 x 10−3to 5.23 x 10−3mg/ml, p=0.0001), while sub-fraction pool number 2 (subfractions number 41 to 61) demonstrated the highest uterotonic potency (EC50at 2.05 x 10−3mg/ml; 95% CI 2.09 x 10−3to 3.85 x 10−3mg/ml, p=0.0001). Sub-fraction pool number 2 was suggested to contain the compound with the major uterotonic activity which was suggested to be related to the family of glycosides after High Performance Liquid Chromatography (HPLC) and Fourier Transform Infrared Spectroscopy (FTIR) analysis.

Conclusions

The study suggests the presence of a major uterotonic phytochemical constituent in the methanol root crude extract ofAzanza garckeana, which was suggested to be related to the family of glycosides. The study has provided scientific evidence suggesting the root ofAzanza garckeana, a plant used traditionally for inducing or accelerating labor possess uterotonic activity. Further pharmacological and toxicological studies need to be undertaken on the plant.
Demographic, temporal, and spatial analysis of human rabid animal bite cases in Mymensingh District, Bangladesh
Authors: Chouhan Chandra Shaker , Raihan Abu , Mia Md. Manik , Banerjee Subarna , Shahriar Ishmam , Nath Proggananda , Uddin Jasim M. , Ehsan Md. Amimul , Ward Michael P. , Rahman A. K. M. Anisur
Published: May 2024

Objective

This study aimed to analyze the demographic, temporal, and spatial characteristics of rabid animal bite (RAB) cases in humans across 12 upazilas within Mymensingh district of Bangladesh.

Methods

Retrospective hospital-based data from RAB cases for 2022 and 2023 were collected from S.K Hospital. The dataset included information on victim demographics, bite details, vaccination information, and Rabies Immune Globulin (RIG) administration. Additionally, monthly case counts from 2016 to 2023 were sourced and analyzed to identify trends. Descriptive statistics and time series analysis using the seasonal decomposition technique were conducted. The risk maps for rabid animal bites in 2022 and 2023 were generated using a standardized incidence rate ratio (SIRR) approach.

Findings

An almost two-fold increase in the proportion of category 3 bites receiving Rabies Immune Globulin (RIG) from 3.6% in 2022 to 6.5% in 2023 was noted. Only 9.7% of bite cases in 2022 and 16.9% in 2023 received the vaccine promptly after the incident. However, the majority received vaccines within the first 24 hours after being bitten. Moreover, significant seasonal patterns and year-wise increasing trends in RAB cases were observed. Males and individuals <10 years old had a higher risk of being bitten. Dogs (48.2% in 2022) and cats (52.6% in 2023) were identified as the primary animals responsible for the bites. Notably, the legs were the body part most frequently bitten. The bites risk map identified four high risk upazilas.

Conclusion

There is a significant gap in ensuring timely vaccination delivery. Study results also suggest other potential improvements in healthcare practices or treatment protocols. Increasing RAB cases highlights the need to enhance surveillance and control measures. Targeted awareness campaigns and preventive measures tailored to high-risk groups − including males, children <10 years old, dogs and cats − are imperative. Coordinated efforts among healthcare professionals, policymakers, and community stakeholders are crucial to effectively mitigate the incidence of RAB cases, safeguarding public health and eradicate dog mediated rabies by 2030 in the region.
Mismatch repair gene specifications to the ACMG/AMP classification criteria: Consensus recommendations from the InSiGHT ClinGen Hereditary Colorectal Cancer / Polyposis Variant Curation Expert Panel
Authors: Plazzer John Paul , Macrae Finlay , Yin Xiaoyu , Thompson Bryony A. , Farrington Susan M , Currie Lauren , Lagerstedt-Robinson Kristina , Frederiksen Jane Hübertz , van Overeem Hansen Thomas , Graversen Lise , Frayling Ian M. , Akagi Kiwamu , Yamamoto Gou , Al-Mulla Fahd , Ferber Matthew J. , Martins Alexandra , Genuardi Maurizio , Kohonen-Corish Maija , Baert-Desurmont Stéphanie , Spurdle Amanda B. , Capellá Gabriel , Pineda Marta , Woods Michael O. , Rasmussen Lene Juel , Heinen Christopher D. , Scott Rodney J. , Tops Carli M. , Greenblatt Marc S. , Dominguez-Valentin Mev , Ognedal Elisabet , Borras Ester , Leung Suet Y. , Mahmood Khalid , Holinski-Feder Elke , Laner Andreas
Published: May 2024

Background

It is known that gene- and disease-specific evidence domains can potentially improve the capability of the ACMG/AMP classification criteria to categorize pathogenicity for variants. We aimed to include gene–disease-specific clinical, predictive, and functional domain specifications to the ACMG/AMP criteria with respect to MMR genes.

Methods

Starting with the original criteria (InSiGHT criteria) developed by the InSiGHT Variant Interpretation Committee, we systematically addressed specifications to the ACMG/AMP criteria to enable more comprehensive pathogenicity assessment within the ClinGen VCEP framework, resulting in an MMR gene-specific ACMG/AMP criteria.

Results

A total of 19 criteria were specified, 9 were considered not applicable and there were 35 variations of strength of the evidence. A pilot set of 48 variants was tested using the new MMR gene-specific ACMG/AMP criteria. Most variants remained unaltered, as compared to the previous InSiGHT criteria; however, an additional four variants of uncertain significance were reclassified to P/LP or LB by the MMR gene-specific ACMG/AMP criteria framework.

Conclusion

The MMR gene-specific ACMG/AMP criteria have proven feasible for implementation, are consistent with the original InSiGHT criteria, and enable additional combinations of evidence for variant classification. This study provides a strong foundation for implementing gene–disease-specific knowledge and experience, and could also hold immense potential in a clinical setting.
Retrospective Analysis of Neonatal Hyperbilirubinemia at Hiwot Fana Specialized Hospital, Ethiopia: Prevalence, Associated Factors, and Treatment Outcomes
Authors: Shugri Mohamed Abdirahman , Libe Temesgen Teferi , Gebru Feven Mekonnen
Published: May 2024

Background

Neonatal hyperbilirubinemia, also known as neonatal jaundice, is a condition characterized by yellowish discoloration of the skin and eyes caused by bilirubin buildup in the body. Understanding its prevalence, associated factors, and outcomes is crucial for effective management.

Objectives

This study aimed to assess the prevalence, associated factors, and treatment outcomes of neonatal hyperbilirubinemia at Hiwot Fana Specialized Hospital, Eastern Ethiopia.

Methodology

A hospital-based cross-sectional study was conducted from December 1, 2020, to December 30, 2020, involving 328 neonates admitted to the Neonatal Intensive Care Unit. Data were collected using a checklist and analyzed using SPSS version 22.

Result

Neonatal hyperbilirubinemia prevalence was 44.2%, with 1.4% progressing to bilirubin encephalopathy. Sepsis (44.8%) and prematurity (22%) were major contributing factors. Most neonates were treated with phototherapy alone (82.3%), and 93.8% showed improvement.

Conclusion

The study underscores the importance of early detection and management of neonatal hyperbilirubinemia to prevent adverse outcomes. Recommendations include integrating jaundice prevention into antenatal care and ensuring timely bilirubin level checks in neonates.
Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction
Authors: Wang Meng , Patsenker Jonathan , Li Henry , Kluger Yuval , Kleinstein Steven H.
Published: May 2024

Antibodies play a crucial role in adaptive immune responses by determining B cell specificity to antigens and focusing immune function on target pathogens. Accurate prediction of antibody-antigen specificity directly from antibody sequencing data would be a great aid in understanding immune responses, guiding vaccine design, and developing antibody-based therapeutics. In this study, we present a method of supervised fine-tuning for antibody language models, which improves on previous results in binding specificity prediction to SARS-CoV-2 spike protein and influenza hemagglutinin. We perform supervised fine-tuning on four pre-trained antibody language models to predict specificity to these antigens and demonstrate that fine-tuned language model classifiers exhibit enhanced predictive accuracy compared to classifiers trained on pretrained model embeddings. The change of model attention activations after supervised fine-tuning suggested that this performance was driven by an increased model focus on the complementarity determining regions (CDRs). Application of the supervised fine-tuned models to BCR repertoire data demonstrated that these models could recognize the specific responses elicited by influenza and SARS-CoV-2 vaccination. Overall, our study highlights the benefits of supervised fine-tuning on pre-trained antibody language models as a mechanism to improve antigen specificity prediction.

Author Summary

Antibodies are vigilant sentinels of our adaptive immune system that recognize and bind to targets on foreign pathogens, known as antigens. This interaction between antibody and antigen is highly specific, akin to a fitting lock and key mechanism, to ensure each antibody precisely targets its intended antigen. Recent advancements in language modeling have led to the development of antibody language model to decode specificity information in the sequences of antibodies. We introduce a method based on supervised fine-tuning, which enhances the accuracy of antibody language models in predicting antibody-antigen interactions. By training these models on large datasets of antibody sequences, we can better predict which antibodies will bind to important antigens such as those found on the surface of viruses like SARS-CoV-2 and influenza. Moreover, our study demonstrates the potential of the models to “read” B cell repertoire data and predict ongoing responses, offering new insights into how our bodies respond to vaccination. These findings have significant implications for vaccine design, as accurate prediction of antibody specificity can guide the development of more effective vaccines.
Enhancing affinity of neutralizing SARS-CoV-2 nanobody through facile structure-guided mutations in CDRs
Authors: Singh Vishakha , Bhutkar Mandar , Choudhary Shweta , Nehul Sanketkumar , Kumar Rajesh , Singla Jitin , Kumar Pravindra , Tomar Shailly
Published: May 2024

The optimization of antibodies to attain the desired levels of affinity and specificity holds great promise for development of the next generation therapeutics. This study delves into the refinement and engineering of CDRs throughin silicoaffinity maturation followed by binding validation using ITC and pseudovirus-based neutralization assays. Specifically, it focuses on engineering CDRs targeting the epitopes of RBD of the spike protein of SARS-CoV-2. A structure-guided virtual library of 112 single mutations in CDRs was generated and screened against RBD to select the potential affinity-enhancing mutations. Subsequent biophysical studies using ITC provided insights into binding affinity and key thermodynamic parameters. Consistent within silicofindings, seven single mutations resulted in enhanced affinity. The mutants were further tested for neutralization activity against SARS-CoV-2 pseudovirus. L106T, L106Q, S107R, and S107Q generated mutants were more effective in virus-neutralizing with IC50values of ∼0.03 µM, ∼0.13 µM, ∼0.14 µM, and ∼0.14 µM, respectively as compared to the native nanobody (IC50∼0.77 µM). Thus, in this study, the developed computational pipeline guided by structure-aided interface profiles and thermodynamic analysis holds promise for the streamlined development of antibody-based therapeutic interventions against emerging variants of SARS-CoV-2 and other infectious pathogens.
Population genomics of adaptive radiations: Exceptionally high levels of genetic diversity and recombination in an endemic spider from the Canary Islands
Authors: Escuer Paula , Guirao-Rico Sara , Arnedo Miquel A. , Sánchez-Gracia Alejandro , Rozas Julio
Published: May 2024

The spider genusDysderahas undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, ∼60 endemic species originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterized by phenotypic modifications encompassing morphological, metabolic and behavioral changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome-level genome assembly of one of the endemic species,D. silvatica,providing a high-quality reference sequence for evolutionary genomics studies. Here, we conducted a low-coverage based resequencing study of a natural population ofD. silvaticafrom La Gomera island. Taking advantage of the new high-quality genome, we characterized genome-wide levels of nucleotide polymorphism, divergence, and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome-wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. Furthermore, we identified genomic regions potentially under positive selection, shedding light on relevant biological processes, such as vision and nitrogen extraction as possible targets of adaptation and eventually, as drivers of the species diversification. This pioneering study in spiders endemic of an oceanic archipelago lays the groundwork for broader population genomics investigations aimed at understanding the genetic mechanisms driven adaptive radiations in island ecosystems.
Reconstitution of Arp2/3-Nucleated Actin Assembly with CP, V-1 and CARMIL
Authors: Mooren Olivia L. , McConnell Patrick , DeBrecht James D. , Jaysingh Anshuman , Cooper John A.
Published: May 2024

Actin polymerization is often associated with membrane proteins containing capping-protein-interacting (CPI) motifs, such as CARMIL, CD2AP, and WASHCAP/Fam21. CPI motifs bind directly to actin capping protein (CP), and this interaction weakens the binding of CP to barbed ends of actin filaments, lessening the ability of CP to functionally cap those ends. The protein V-1 / myotrophin binds to the F-actin binding site on CP and sterically blocks CP from binding barbed ends. CPI-motif proteins also weaken the binding between V-1 and CP, which decreases the inhibitory effects of V-1, thereby freeing CP to cap barbed ends. Here, we address the question of whether CPI-motif proteins on a surface analogous to a membrane lead to net activation or inhibition of actin assembly nucleated by Arp2/3 complex. Using reconstitution with purified components, we discovered that CARMIL at the surface promotes and enhances actin assembly, countering the inhibitory effects of V-1 and thus activating CP. The reconstitution involves the presence of an Arp2/3 activator on the surface, along with Arp2/3 complex, V-1, CP, profilin and actin monomers in solution, recreating key features of cell physiology.
Commensal or pathogen: computationally vectorizing microbial genomes forde novorisk assessment and virulence feature discovery inKlebsiella pneumoniae
Authors: Beck Kristen L. , Agarwal Akshay , Halpin Alison Laufer , McDonald L. Clifford , McKay Susannah L. , Kent Alyssa G. , Kaufman James H. , Mukherjee Vandana , Elkins Christopher A. , Seabolt Edward
Published: May 2024

Bacterial pathogenicity has traditionally focused on gene-level content with experimentally-confirmed functional properties. Hence, significant inferences are made based on similarity to known pathotypes and DNA-based genomic subtyping for risk. Herein, we achievedde novoprediction of human virulence inKlebsiella pneumoniaeby expanding known virulence genes with spatially proximal gene discoveries linked by functional domain architectures across all prokaryotes. This approach identified gene ontology functions not typically associated with virulencesensu stricto. By leveraging machine learning models with these expanded discoveries, public genomes were assessed for virulence prediction using categorizations derived from isolation sources captured in available metadata. Performance forde novostrain-level virulence prediction achieved 0.81 F1-Score. Virulence predictions using expanded “discovered” functional genetic content were superior to that restricted to extant virulence database content. Additionally, this approach highlighted the incongruence in relying on traditional phylogenetic subtyping for categorical inferences. Our approach represents an improved deconstruction of genome-scale datasets for functional predictions and risk assessment intended to advance public health surveillance of emerging pathogens.
Unconstrained Precision Mitochondrial Genome Editing with αDdCBEs
Authors: Castillo Santiago R. , Simone Brandon W. , Clark Karl J. , Devaux Patricia , Ekker Stephen C.
Published: May 2024

DddA-derived cytosine base editors (DdCBEs) enable the targeted introduction of C•G-to-T•A conversions in mitochondrial DNA (mtDNA). DdCBEs are often deployed as pairs, with each arm comprised of a transcription activator-like effector (TALE), a split double-stranded DNA deaminase half, and a uracil glycosylase inhibitor. This pioneering technology has helped improve our understanding of cellular processes involving mtDNA and has paved the way for the development of models and therapies for genetic disorders caused by pathogenic mtDNA variants. Nonetheless, given the intrinsic properties of TALE proteins, several target sites in human mtDNA remain out of reach to DdCBEs and other TALE-based technologies. Specifically, due to the conventional requirement for a thymine immediately upstream of the TALE target sequences (i.e., the 5’-T constraint), over 150 loci in the human mitochondrial genome are presumed to be inaccessible to DdCBEs. Previous attempts at circumventing this constraint, either by developing monomeric DdCBEs or utilizing DNA-binding domains alternative to TALEs, have resulted in suboptimal specificity profiles with reduced therapeutic potential. Here, aiming to challenge and elucidate the relevance of the 5’-T constraint in the context of DdCBE-mediated mtDNA editing, and to expand the range of motifs that are editable by this technology, we generated αDdCBEs that contain modified TALE proteins engineered to recognize all 5’ bases. Notably, 5’-T-noncompliant, canonical DdCBEs efficiently edited mtDNA at diverse loci. However, DdCBEs were frequently outperformed by αDdCBEs, which consistently displayed significant improvements in activity and specificity, regardless of the 5’-most bases of their TALE binding sites. Furthermore, we showed that αDdCBEs are compatible with DddAtoxand its derivatives DddA6, and DddA11, and we validated TALE shifting with αDdCBEs as an effective approach to optimize base editing outcomes at a single target site. Overall, αDdCBEs enable efficient, specific, and unconstrained mitochondrial base editing.
Flavin-containing siderophore-interacting protein ofShewanella putrefaciensDSM 9451 reveals substrate specificity in ferric-siderophore reduction
Authors: Trindade Inês B. , Fonseca Bruno M. , Catarino Teresa , Matias Pedro M. , Moe Elin , Louro Ricardo O.
Published: May 2024

Shewanellaare bacteria widespread in marine and brackish water environments and emergent opportunistic pathogens. Their environmental versatility is highly dependent on the ability to produce an abundance of iron-rich proteins, mainly multihemec-type cytochromes. Although iron plays a vital role in the ability ofShewanellaspecies to survive in various environments, very few studies exist regarding the strategies by which these bacteria scavenge iron from the environment. Small molecule siderophore-mediated iron transport is a strategy commonly employed for iron acquisition, and it was identified amongstShewanellaspp. over two decades ago.Shewanellaspecies produce hydroxamate-type siderophores and iron removal from these compounds can occur in the cytoplasm via Fe(III)-siderophore reduction mediated by siderophore-interacting proteins (SIPs). The genome ofShewanella putrefaciensDSM 9451 isolated from an infected child contains representatives of the two different cytosolic families of SIPs: the flavin-containing siderophore interacting protein family (SIP) and the iron−sulfur cluster-containing ferric siderophore reductase family (FSR).

Here, we report the expression and purification of the flavin-containing (SbSIP) and iron-sulfur cluster-containing (SbFSR) Fe(III)-siderophore reductases ofShewanella putrefaciensDSM 9451. The structural and functional characterization ofSbSIP shows distinct features from the highly homologous SIP fromShewanella frigidimarina(SfSIP). These include significant structural differences, different binding affinities for NADH and NADPH, and lower rates of Fe(III)-siderophore reduction, results which consolidate in the putative identification of the binding pocket for these proteins.

Overall our work highlights NADH and NADPH specificity and the different Fe(III)- siderophore reduction abilities of the SIP family suggesting a tailoring of these enzymes towards meeting different microbial iron requirements.
Structure of the lens MP20 mediated adhesive junction
Authors: Nicolas William J. , Shiriaeva Anna , Martynowycz Michael W. , Grey Angus C , Ruma Yasmeen , Donaldson Paul J , Gonen Tamir
Published: May 2024

Human lens fiber membrane intrinsic protein MP20 is the second most abundant membrane protein of the human eye lens. Despite decades of effort its structure and function remained elusive. Here, we determined the MicroED structure of full-length human MP20 in lipidic-cubic phase to a resolution of 3.5 Å. MP20 forms tetramers each of which contain 4 transmembrane α-helices that are packed against one another forming a helical bundle. Both the N- and C-termini of MP20 are cytoplasmic. We found that each MP20 tetramer formed adhesive interactions with an opposing tetramer in a head-to-head fashion. These interactions were mediated by the extracellular loops of the protein. The dimensions of the MP20 adhesive junctions are consistent with the 11 nm thin lens junctions. Investigation of MP20 localization in human lenses indicated that in young fiber cells MP20 was stored intracellularly in vesicles and upon fiber cell maturation MP20 inserted into the plasma membrane and restricted the extracellular space. Together these results suggest that MP20 forms lens thin junctions in vivo confirming its role as a structural protein in the human eye lens, essential for its optical transparency.
Prospective neuroimaging and neuropsychological evaluation in adults with newly diagnosed focal epilepsy
Authors: de Bezenac Christophe , Leek Nicola , Adan Guleed , Ali Ahmad , Mohanraj Rajiv , Biswas Shubhabrata , Mcginty Ronan , Murphy Kieran , Malone Helen , Baker Gus , Moore Perry , Marson Anthony G , Keller Simon S.
Published: May 2024

Objective

There are few prospective longitudinal studies in patients with newly diagnosed epilepsy (NDE) despite that this is a key time point to understand the underlying biology of epilepsy and to identify potential interventions and biomarkers for seizure and cognitive outcomes. Here we have performed a prospective combined neuroimaging and neuropsychological study in a cohort of patients with focal NDE and healthy controls.

Methods

We recruited 104 patients with NDE and 45 healthy controls for research-grade 3 Tesla MRI (diagnostic and structural imaging, diffusional kurtosis imaging, resting-state functional MRI, task-based functional MRI), EEG, comprehensive neuropsychological, and blood biomarker investigations. We report here on the baseline clinical, neuroradiological, MRI morphometric, and neuropsychological findings in this cohort.

Results

38% of patients had unremarkable MRI features, 12% had lesions of known significance in epilepsy, 49% with abnormalities of unknown significance in epilepsy, and 23% with incidental findings. In comparison, 56% of controls had unremarkable MRI features, 7% had lesions of known significance in epilepsy, 33% with abnormalities of unknown significance in epilepsy, and 16% had incidental findings. Patients had a higher incidence of white matter hyperintensities compared to controls. Reduced bihemispheric frontal lobe cortical thickness and thalamic volumes were observed in patients with moderate effect sizes. Patients scored significantly lower on tasks of executive function, processing speed, and visual, delayed, and immediate memory, and significantly higher on depression and anxiety assessments compared to controls. Patient neuropsychological performance was related to various brain morphometric features.

Significance

People with adult focal NDE have a greater proportion of MRI-positive findings than previously reported. Subtle white matter lesions may represent an important diagnostic criterion and have a pathophysiological basis in focal epilepsy. Morphometric and neuropsychological alterations are present at the point of diagnosis of epilepsy, which suggests that brain and cognitive changes are not exclusively due to the deleterious impact of chronic epilepsy.
Semiconservative transmission of DNAN6-adenine methylation in a unicellular eukaryote
Authors: Sheng Yalan , Wang Yuanyuan , Yang Wentao , Wang Xue Qing , Lu Jiuwei , Pan Bo , Nan Bei , Liu Yongqiang , Ye Fei , Li Chun , Song Jikui , Dou Yali , Gao Shan , Liu Yifan
Published: May 2024

Although DNAN6-adenine methylation (6mA) is best known in prokaryotes, its presence in eukaryotes has recently generated great interest. Biochemical and genetic evidence supports that AMT1, an MT-A70 family methyltransferase (MTase), is crucial for 6mA deposition in unicellular eukaryotes. Nonetheless, the 6mA transmission mechanism remains to be elucidated. Taking advantage of single-molecule real-time circular consensus sequencing (SMRT CCS), here we provide definitive evidence for semiconservative transmission of 6mA inTetrahymena thermophila. In wild-type (WT) cells, 6mA occurs at the self-complementary ApT dinucleotide, mostly in full methylation (full-6mApT); after DNA replication, hemi-methylation (hemi-6mApT) is transiently present on the parental strand, opposite to the daughter strand readily labeled by 5-bromo-2′-deoxyuridine (BrdU). In ΔAMT1cells, 6mA predominantly occurs as hemi-6mApT. Hemi-to-full conversion in WT cells is fast, robust, and processive, whereas de novo methylation in ΔAMT1cells is slow and sporadic. InTetrahymena, regularly spaced 6mA clusters coincide with the linker DNA of nucleosomes arrayed in the gene body. Importantly, in vitro methylation of human chromatin by the reconstituted AMT1 complex recapitulates preferential targeting of hemi-6mApT sites in linker DNA, supporting AMT1's intrinsic and autonomous role in maintenance methylation. We conclude that 6mA is transmitted by a semiconservative mechanism: full-6mApT is split by DNA replication into hemi-6mApT, which is restored to full-6mApT by AMT1-dependent maintenance methylation. Our study dissects AMT1-dependent maintenance methylation and AMT1-independent de novo methylation, reveals a 6mA transmission pathway with a striking similarity to 5-methylcytosine (5mC) transmission at the CpG dinucleotide, and establishes 6mA as a bona fide eukaryotic epigenetic mark.
Laser Microsurgery inDrosophilaLarvae Using the MicroPoint Ablation System
Authors: Smithson Laura J. , Waller Thomas J. , Collins Catherine A.
Published: May 2024

Laser microsurgery is a robust method to ablate specific cells in the nervous system and probe the functional consequences of their loss in the animal. By introducing focal lesions to small locations in the animal, laser microsurgery also enables disruptions of specific connections within neuronal circuits and the study of how the nervous system responds to precise forms of damage (for instance, damage to specific axons or dendrites, which have been found to evoke different kinds of responses in neurons). The MicroPoint laser is a pulsed dye laser that can be mounted onto any standard microscope, hence is an affordable alternative to two-photon lasers for providing high powered focal ablations. This protocol describes how to use a MicroPoint laser ablation system to induce focal injuries inDrosophilalarvae. This protocol guides a user who has access to a MicroPoint laser that has already been installed onto an appropriate microscope for high-resolution imaging and configured for laser ablation using Coumarin 440 dye. The protocol covers how to use the laser to carry out surgeries or ablation, how to change the laser dye and calibrate the power settings, and how to make sure the laser is properly focused. While the protocol provides an example of axotomy (axon severing) in the peripheral nervous system ofDrosophilalarvae, use of the MicroPoint system can be adapted to other focal surgeries in other organisms.