bluuebunny/crossref_metadata_2025 huggingface dataset:
Impaired DNA damage response and inflammatory signalling underpins hematopoietic stem cell defects inGata2haploinsufficiency
Authors: Abdelfattah Ali , Habib Ahmad , Thomas Leigh-anne , Menendez-Gonzalez Juan Bautista , Almotiri Alhomidi , Alqahtani Hind , Lawson Hannah , Taha Sarab , Steadman Millie , Athalye Radhika , Gibbs Alex , Alzahrani Hamed , Cato Alice , Giles Peter , Tonks Alex , Boyd Ashleigh S. , Kranc Kamil R. , Rodrigues Neil P.
Published: August 2024

ClinicalGATA2deficiency syndromes arise from germline haploinsufficiency inducing mutations inGATA2, resulting in immunodeficiency that evolves to myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML). HowGATA2haploinsufficiency disrupts the function and transcriptional network of hematopoietic stem/progenitors (HSCs/HSPCs) to facilitate the shift from immunodeficiency to pre-leukemia is poorly characterised. Using a conditional mouse model harboring a single allele deletion ofGata2from the start of HSC developmentin utero, we identified pervasive defects in HSPC differentiation from young adultGata2haploinsufficient mice during B-cell development, early erythroid specification, megakaryocyte maturation to platelets and inflammatory cell generation.Gata2haploinsufficiency abolished HSC self-renewal and multi-lineage differentiation capacity. These functional alterations closely associated with deregulated DNA damage responses and inflammatory signalling conveyed fromGata2haploinsufficient HSCs. We identified genetic interplay betweenGata2andAsxl1, a driver of DNA damage and inflammation and, notably, a recurrent secondary mutation found inGATA2haploinsufficiency disease progression to MDS/AML. shRNA mediated knockdown ofAsxl1inGata2haploinsufficient HSPCs led to an enhanced differentiation blockin vitro. By analysis of HSCs from young adult compoundGata2/Asxl1haploinsufficient mice, we discovered hyperproliferation of double haploinsufficient HSCs, which were also functionally compromised in transplantation compared to their singleGata2 or Asxl1haploinsufficient counterparts. Through bothGata2/Asxl1dependent and unique transcriptional programs, HSCs from compoundGata2/Asxl1haploinsufficient fortified deregulated DNA damage responses and inflammatory signalling initiated inGata2haploinsufficient HSCs and established a broad pre-leukemic program. Our data reveal howGata2haploinsufficiency initially drives deregulation of HSC genome integrity and suggest the mechanisms of how secondary mutations likeASXL1take advantage of HSC genomic instability to nurture a pre-leukemic state inGATA2haploinsufficiency syndromes.
Dev-Atlas: A reference atlas of functional brain networks for typically developing adolescents
Authors: Doucet Gaelle E. , Goldsmith Callum , Myers Katrina , Rice Danielle L. , Ende Grace , Pavilka Derek J. , Joliot Marc , Calhoun Vince , Wilson Tony W. , Uddin Lucina Q.
Published: August 2024

Adolescence is a critical period for neural changes, including maturation of the brain’s cognitive networks, but also a period of increased vulnerability to psychopathology. It is well accepted that the brain is functionally organized into multiple interacting networks and extensive literature has demonstrated that the spatial and functional organization of these networks shows major age-related changes across the lifespan, but particularly during adolescence. Yet, there is limited option for a reference functional brain atlas derived from typically developing adolescents, which is especially problematic as the reliable and reproducible identification of functional brain networks crucially depends on the use of such reference functional atlases. In this context, we utilized resting-state functional MRI data from a total of 1,391 typically developing youth between the ages of 8 and 17 years to create a new adolescent-specific reference atlas of functional brain networks. We further investigated the impact of age and sex on these networks. Using a multiscale individual component clustering algorithm (MICCA), we identified 24 reliable functional brain networks, classified within six domains: Default-Mode (5 networks), Control (4 networks), Salience (3 networks), Attention (4 networks), Somatomotor (5 networks), and Visual (3 networks). We identified reliable and large effects of age on the spatial topography of these majority of networks, as well as on the functional network connectivity (FNC) between networks. The DMN showed reduced FNC with the other networks with older age. Sex effects were not as widespread. No significant sex-by-age interactions were detected. Overall, we created a novel brain atlas, named Dev-Atlas, focused on a typically developing sample, with the hope that this atlas can be used in future independent developmental network neuroscience studies. Dev-Atlas is freely available to the research community.
Endoplasmic reticulum patterns insect cuticle nanostructure
Authors: Inagaki Sachi , Wada Housei , Itabashi Takeshi , Itakura Yuki , Nakagawa Reiko , Chen Lin , Murata Kazuyoshi , Iwane Atsuko H. , Hayashi Shigeo
Published: August 2024

Insect cuticles with nano-level structures exhibit functional surface properties such as structural color and superhydrophobicity. Despite the enormous influence the cuticle has had on biomimetic industrial applications, molecular and cellular mechanisms of cuticular extracellular matrix (ECM) assembly into nanoscale structures remain poorly understood in insects and other taxa. Ghiradella (1989) described how a crystallin-like lattice of endoplasmic reticulum (ER) prefigures the patterning of the porous cuticle of the butterfly wing scale with structural color1. Building on that insight, we show that the nanopore structure of the olfactory (olf) organs, which serve as molecular filters inDrosophila,is built through a novel process in which ER material is trafficked to the plasma membrane mediated by the autophagy pathway. The process is controlled by the insect-specific protein Gore-tex/Osiris23 (Gox)2, which is localized to the tubular ER of olf hair cells. Gox recruits Ref(2)P, the fly counterpart of mammalian p62/SQSTM13, to initiate ER scission. The excised ER fragments are processed by autophagy to gain access to the plasma membrane and trigger membrane invagination, which plays a role in remodeling the cuticular envelope layer to the nanopore formation. This repurposing of the ER phagy for machinery to support the fabrication of nanoscale ECM by the Gox protein sheds light on the nanopatterning of insect cuticles and their genetic control.
Evidencing the role of a conserved polar signaling channel in the activation mechanism of the μ-opioid receptor
Authors: Sarkar Arijit , Dvorácskó Szabolcs , Lipinszki Zoltán , Mitra Argha , Harmati Mária , Buzás Krisztina , Borics Attila
Published: August 2024

The activity of G protein-coupled receptors has been generally linked to dynamically interconverting structural and functional states and the process of activation was proposed to be controlled by an interconnecting network of conformational switches in the transmembrane domain. However, it is yet to be uncovered how ligands with different extent of functional effect exert their actions. According to our recent hypothesis, the transmission of the external stimulus is accompanied by the shift of macroscopic polarization in the transmembrane domain, furnished by concerted movements of conserved polar amino acids and the rearrangement of polar species. Previously, we have examined the μ-opioid, β2-adrenergic and type 1 cannabinoid receptors by performing molecular dynamics simulations. Results revealed correlated dynamics of a polar signaling channel connecting the orthosteric binding pocket and the intracellular G protein-binding surface in all three class A receptors. In the present study, the interplay of this polar signaling channel in the activation mechanism was evidenced by systematic mutation of the channel residues of the μ-opioid receptor. Mutant receptors were analyzed utilizing molecular dynamics simulations and characterizedin vitroby means of radioligand receptor binding and G protein stimulation assays. Apart from one exception, all mutants failed to bind the endogenous agonist endomorphin-2 and to stimulate the Giprotein complex. Furthermore, mutation results confirmed strong allosteric coupling between the binding pocket and the intracellular surface. The strong association and optimal bioactive orientation of the bound agonist was found to be crucial for the initiation of correlated motions and consequent signaling.
Herpes Simplex Virus 1 Envelope Glycoprotein C Shields Glycoprotein D to Protect Virions from Entry-Blocking Antibodies
Authors: Hull McKenna A. , Pritchard Suzanne M. , Nicola Anthony V.
Published: August 2024

Herpes simplex virus 1 (HSV-1) gD interaction with the host cell receptor nectin-1 triggers the membrane fusion cascade during viral entry. Potent neutralizing antibodies to gD prevent receptor-binding or prevent gD interaction with gH/gL critical for fusion. HSV has many strategies to evade host immune responses. We investigated the ability of virion envelope gC to protect envelope gD from antibody neutralization. HSV-1 lacking gC was more sensitive to neutralization by anti-gD monoclonal antibodies than a wild type rescuant virus. gD in the HSV-1 gC-null viral envelope had enhanced reactivity to anti-gD antibodies compared to wild type. HSV-1 ΔgC binding to the nectin-1 receptor was more readily inhibited by a neutralizing anti-gD monoclonal antibody. HSV-1 ΔgC was also more sensitive to inhibition by soluble nectin-1 receptor. The viral membrane protein composition of HSV-1 ΔgC was equivalent to that of wild type, suggesting that the lack of gC is responsible for the increased reactivity of gD-specific antibodies and the consequent increased susceptibility to neutralization by those antibodies. Together, the results suggest that gC in the HSV-1 envelope shields both receptor-binding domains and gH/gL-interacting domains of gD from neutralizing antibodies, facilitating HSV cell entry.

Importance

HSV-1 causes lifelong infections. There is no vaccine and no cure. Understanding HSV immune evasion strategies is an important goal. HSV-1 gC is a multi-functional envelope glycoprotein. This study suggests that virion gC physically shields neighboring gD from antibodies, including neutralizing monoclonal antibodies. This mechanism may allow HSV to escape immune detection, promoting HSV infection in the host.
The molecular mechanism of temperature-dependent phase separation of Heat shock factor 1
Authors: Ren Qiunan , Li Linge , Li Juan , Shi Chaowei , Sun Yujie , Yao Xuebiao , Hou Zhonghuai , Xiang ShengQi
Published: August 2024

Heat shock factor 1 (HSF1) is the critical orchestrator for a cell responding to heat shock, and its dysfunction is linked to cancers and neurodegenerative diseases. HSF1 undergoes phase separation upon heat shock, and its activity is regulated by various post-translational modifications (PTMs). Despite its importance, the molecular details underlying HSF1 phase separation, temperature sensing, and post-translational modifications (PTMs) regulation remain poorly understood. Here, we discovered that HSF1 exhibits temperature-dependent phase separation with a lower critical solution temperature (LCST) behavior due to entropy contribution from solvent molecules, providing a new conceptual mechanism accounting for HSF1 activation. We employed a synergistic approach combining coarse-grain simulation and nuclear magnetic resonance spectroscopy to reveal the residue-level molecular details of the interactions driving the phase separation of wild-type HSF1 and its distinct PTM patterns at various temperatures. The identified interaction sites were further validated with biochemistry assays and mapped interface accounts for HSF1 functions reported. Importantly, the amino acid substitution experiment reveals the molecular grammar for temperature-dependent HSF1 phase separation is species-specific and physiologically relevant. These findings delineate chemical code that integrates protein PTM patterns with accurate phase separation for body physiological temperature control in animals.
Multivalent administration of dengue E dimers on liposomes elicits type-specific neutralizing responses without immune interference
Authors: Phan Thanh T. N. , Hvasta Matthew G. , Thiono Devina J. , Shah Ruby P. , Ajo Gisselle Prida , Huang Wei-chiao , Lovell Jonathan , Tian Shaomin , de Silva Aravinda M. , Kuhlman Brian
Published: August 2024

The four serotypes of dengue virus (DENV1-4) are a major health concern putting 50% of the global population at risk of infection. Crucially, DENV vaccines must be tetravalent to provide protection against all four serotypes because immunity to only one serotype can enhance infections caused by heterologous serotypes. Uneven replication of live-attenuated viruses in tetravalent vaccines can lead to disease enhancement instead of protection. Subunit vaccines are a promising alternative as the vaccine components are not dependent on viral replication and antigen doses can be controlled to achieve a balanced response. Here, we show that a tetravalent subunit vaccine of dengue envelope (E) proteins computationally stabilized to form native-like dimers elicits type-specific neutralizing antibodies in mice against all four serotypes. The immune response was enhanced by displaying the E dimers on liposomes embedded with adjuvant, and no interference was detected between the four components.
Evolutionary and Functional Analysis of Monoamine Oxidase C (MAO C): A Novel Member of the MAO Gene Family
Authors: Merello Gianluca , Olivares-Costa Montserrat , Basile Lorenzo , Pastor Tammy P. , Mendoza-Soto Pablo , Padilla-Santiago Luis , Mardones Gonzalo , Binda Claudia , Opazo Juan C.
Published: August 2024

The monoamine oxidase (MAO) gene family encodes for enzymes that perform the oxidative deamination of monoamines, a process required to degrade norepinephrine, serotonin, dopamine, and other amines. While mammalian MAO enzymes, MAO A and MAO B, have been extensively studied, the molecular properties of the other family members are only partly uncovered. This study aims to explore the evolution of monoamine oxidases, emphasizing understanding the MAO gene repertoire among vertebrates. Our analyses show that the duplication that gave rise to MAO A and MAO B occurred in the ancestor of tetrapods, between 408 and 352 million years ago. Non-tetrapod jawed vertebrates possess the ancestral preduplicative condition of MAO A/B. Our results also identified a new family member, MAO C, in non-tetrapod jawed vertebrates. Thus, most jawed vertebrates possess a repertoire of two MAO genes, MAO A and MAO B in tetrapods and MAO A/B and MAO C in non-tetrapod jawed vertebrates, representing different MAO gene lineages. Jawless vertebrates possess the ancestral condition of a single copy gene, MAO A/B/C. Enzymatic assays conducted on the MAO recombinant enzymes of the Indo-Pacific tarpon show that both proteins, MAO A/B and MAO C, have enzymatic and molecular properties more similar to human MAO A, with the former featuring a strikingly higher activity rate when compared to all other MAO enzymes. Our analyses underscore the importance of scanning the tree of life for new gene lineages to understand phenotypic diversity and gain detailed insights into their function.
Quantifying microbial fitness in high-throughput experiments
Authors: Fink Justus Wilhelm , Manhart Michael
Published: August 2024

Few concepts are as central to evolution as is fitness, and yet the quantification of fitness is often ambiguous. In particular, high-throughput experiments to measure mutant fitness in microbes are increasingly common but vary widely in their definitions of fitness, which makes their results difficult to compare. What are the consequences of these different fitness statistics, and is there a best way to quantify fitness in a given context? Here we systematize the set of possible fitness statistics according to the following three choices: 1) the encoding of relative abundance (e.g., transforming by a log or logit function), 2) the time scale over which to measure the change in relative abundance, and 3) the choice of a reference subpopulation for calculating fitness in bulk competition experiments, such as those using DNA-barcoded mutants. We show that these different choices can lead to significantly different interpretations of mutant fitness, affecting the magnitude of fitness effects, the presence of epistasis, and even the fitness ranking across mutants. This can confound predictions for evolutionary dynamics and gene functions. Altogether our results demonstrate the importance of consistent fitness definitions for reproducible results across experiments.
A framework for chronic care quality: results of a scoping review and Delphi survey
Authors: Ku Grace Marie V. , Van De Put Willem , Katsuva Deogratias , Ag Ahmed Mohamad Ali , Rosenberg Megumi , Meessen Bruno
Published: August 2024

Frameworks conceptualising quality of care abound and vary; some concentrate on specific aspects (e.g., safety, access, effectiveness), others all-encompassing. However, to our knowledge, tailoring to systematically arrive at a comprehensive care for chronic conditions quality (CCCQ) framework has never been done. We conducted scoping review and Delphi survey to produce a CCCQ framework, comprehensively delineating aims, determinants and measurable attributes.

With the assumption that specific groups (people with chronic conditions, care providers, financiers, policy-makers, etc) view quality of care differently, we analysed 48 scientific and 26 grey literature deductively and inductively using the Institute of Medicine’s quality of care framework as the foundation. We produced a zero-version of the quality of chronic care framework, detailing aims, healthcare system determinants, and measurement mechanisms. This was presented in a Delphi survey to 49 experts with diverse chronic care expertise/experience around the world. Consensus was obtained after the first round, with the panel providing suggestions and justifications to expand the agreed-upon components. Through this exercise, a comprehensive CCCQ framework encompassing the journey through healthcare of people with chronic conditions was developed. The framework specifies seven CCCQ ‘aims’ and identifies health system determinants which can be acted upon with ‘organising principles’ and measured through chronic care quality ‘attributes’ related to structures, processes and outcomes. Tailoring quality of care based on the nature of the diseases/conditions and considering different views can be done to ensure a comprehensive offer of healthcare services, and towards better outcomes that are acceptable to both the health system and PwCCs.
Hospital based Multi-centric Diabetes Registry
Authors: KALRA PRAMILA , Mohan Gurinder , Bhattacharya Prasanta Kumar , Tiewsoh Iada , K.R Raveendra , M Ravi Kiran , Kumar Sreejith N , Ghosh Sujoy , S Chitra , Pandit Kaushik , Chandey Manish , Lyngdoh Monaliza , Mukhopadhyay Pradip , Thaman Richa G , Jain Smitha , R Sundararaman , Jagadeesan Vedantha S , Sreejith Veena , Singh Reetu , Sekhar Theertha , Elizabeth R Mercy , PR Sreelakshmi
Published: August 2024

Non-communicable chronic diseases, particularly Diabetes mellitus, a silent epidemic of this era, are rapidly on the rise in India. It is critical to devise strategies to ensure effective diagnosis, prevention, and treatment of the increasing disease burden. Given the lack of large-scale information on Type 1 and Type 2 Diabetes mellitus, the pan-India diabetes registry is hugely pertinent to the Indian situation. The registry would be able to continuously provide data on real-world practices and standard of care for Diabetes mellitus in India. To ensure the correct blend in site selection, the centers have been chosen from different geographical regions across India with a combination of government and private sectors. All the sites will harmonize in terms of protocol, training, SOPs, and data management. This hospital-based observational cross-sectional registry will be carried out without any intervention. Patients who are known cases of Type 1 and Type 2 Diabetes mellitus visiting the outpatient departments (OPD) of all the seven Hospitals will be evaluated for eligibility and willingness to participate in future clinical trials after acquiring their informed consent or assent form (for minors). A common IT platform for entering and preserving registry data will be developed, which will enable us to establish a central database that could be utilized for future clinical trials. This will minimize the time and expense of setting up a Diabetes mellitus repository.
Unraveling the impact of COVID-19 on urban mobility: A Causal Machine Learning Analysis of Beijing's Subway System
Authors: Zou Linmu , Chen Yanhua , Guo Rui , Wang Peicheng , He Yanrong , Chen Shiyu , Wang Zijia , Zhu Jiming
Published: August 2024

The COVID-19 pandemic has drastically altered urban travel patterns, particularly in public transportation systems like subways. This study examines the effects of the pandemic on subway ridership in Beijing by analyzing the influence of 19 factors, including demographics, land use, network metrics, and weather conditions, before and during the pandemic. Data was collected from June 2019 and June 2020, covering 335 subway stations and over 258 million trips. Using a three-stage analytical framework - comprising Light Gradient Boosting Machine (LightGBM) for fitting, Meta-Learners for causal analysis, and SHapley Additive exPlanations (SHAP) for interpretation - we observed a substantial decline in ridership, with approximately 10,000 fewer passengers per station daily, especially in densely populated areas. Our findings reveal significant shifts in influential factors such as centrality, housing prices, and restaurant density. The spatiotemporal analysis highlights the dynamic nature of these changes. This study underscores the need for adaptive urban planning and provides insights for public health strategies to enhance urban resilience in future pandemics.
Knowledge, attitude and perception regarding HIV/AIDS among Khartoum University medical campus students – a cross-sectional study 2018
Authors: Mohamed Elamir Ahmed Alasaad Kamel , Dafalla Rana Ibrahim Abdalla , Ali Raghda , Elhussain Mohamed O. , Abdelsalam Ahmed Abdelaziz Abugrain , Sharif Abraa Awad , Halali Sayed
Published: August 2024

Background

Clinical training is a part of curriculum for medical campus students, where there is a chance of exposure to HIV infection. Hence, this study was conducted to assess their knowledge, attitude and perception towards HIV/AIDS.

Method

This is a descriptive, non-interventional, cross-sectional study. Data collection took place December 2017 and January 2018. The study population included medical students at the University of Khartoum during the study period. Data were collected through a structured adapted questionnaire covering socio demographic details, General knowledge about HIV/AIDS, medical campus students perception towards the possible causes of HIV infection, medical campus students attitude towards HIV/AIDS patients used to collect data from medical students.

Results

This study investigated the knowledge, attitude and perception regarding HIV/AIDS among 288 medical students at University of Khartoum. It was found that the means and standard deviation of the total knowledge, attitude and perception score towards HIV/AIDS in general were 15.45±2.93. which was categorized fair (reference ranging from 13 to 18). the total knowledge, attitude and perception was significantly associated with the academic year (p=0.000), but no association was found between the attitude score and the academic year (p = 0.620).

Conclusion

The overall rate of knowledge and attitude about HIV/AIDS among medical campus students of Khartoum University was acceptable. However, appreciated number of the students have had a negative attitude towards HIV/AIDS patient.
Recognizing the Evolution of Clinical Syndrome Spectrum Progression in Individuals with Single Large-Scale mitochondrial DNA deletion syndromes (SLSMDS)
Authors: Ganetzky Rebecca D , Stanley Katelynn D , MacMullen Laura E , George-sankoh Ibrahim , Wang Jing , Goldstein Amy , Falk Marni J.
Published: August 2024

Introduction Single large-scale mtDNA deletions (SLSMD) result in Single Large Scale Deletion Syndromes (SLSMDS). SLSMDS presentations have classically been recognized to encompass at least three distinct clinical phenotypes, Pearson Syndrome (PS), Kearns-Sayre Syndrome (KSS), and Chronic Progressive Ophthalmoplegia (CPEO). Methods Facilitated review of electronic medical records, manual charts, and REDCap research databases was performed to complete a retrospective natural history study of 32 SLSMDS participants in a single health system seen between 2002 and 2020. Characteristics evaluated included genetic and clinical laboratory test values, growth parameters, signs and symptoms, demographics, and patient reported outcome measures of fatigue, quality of life, and overall function. Results Detailed cohort characterization highlighted that a recurrent deleted region involving MT-ND5 occurs in 96% of SLSMD subjects regardless of clinical phenotype, which tended to evolve over time. Higher blood heteroplasmy correlated with earlier age of onset. GDF-15 was elevated in all SLSMD subjects. A PS history yielded negative survival prognosis. Furthermore, increased fatigue and decreased quality of life were reported in SLSMD subjects with advancing age. Conclusion Retrospective natural history study of SLSMDS subjects demonstrated the evolution of classically considered PS, KSS, and CPEO clinical presentations within affected individuals, which may inform future clinical trial development.
Altered neurobehavioral reward response predicts psychotic-like experiences in youth exposed to cannabis prenatally
Authors: Amir Carolyn M. , Ghahremani Dara G. , Chang Sarah E. , Cooper Ziva D. , Bearden Carrie E.
Published: August 2024

Importance

Rates of prenatal cannabis exposure (PCE) are rising with increasingly permissive legislation regarding cannabis use, which may be a risk factor for psychosis. Disrupted reward-related neural circuitry may underlie this relationship.

Objective

To elucidate neural mechanisms involved in the association between PCE and youth-onset psychotic-like experiences by probing correlates of reward anticipation, a neurobehavioral marker of endocannabinoid-mediated dopaminergic function.

Design, setting, and participants

This longitudinal, prospective study analyzed task-related functional neuroimaging data from baseline (n=11,368), 2-year follow-up (n=7,928), and 4-year follow-up (n=2,982) of the ongoing Adolescent Brain and Cognitive Development (ABCD) Study, which recruited children aged 9 to 10 years old at baseline from 22 sites across the United States.

Results

PCE (n=652 exposed youth) is longitudinally associated with psychotic-like experiences. Blunted neural response to reward anticipation is associated with psychotic-like experiences, with stronger effects observed in PCE youth (all |β| > 0.5; false discovery rate [FDR]–correctedP< .05). This hypoactivation at baseline predicts psychosis symptomatology in middle adolescence (4-year follow-up visit; β=-.004; FDR-correctedP< .05). Dampened behavioral reward sensitivity is associated with psychotic-like experiences across baseline, 2-year follow-up visit, and 4-year follow-up visit (|β| = .21; FDR-correctedP< .001). Psychotic-like experiences are positively associated with trait-level measures of reward motivation and impulsivity, with stronger effects for PCE youth (all |β| > 0.1; all FDR-correctedP< .05).

Conclusions and Relevance

Blunted activation in reward-related brain regions may serve as a biomarker for disrupted reward processing and increased psychosis risk during development. PCE may affect childhood behaviors and traits related to altered reward sensitivity.
Prior antiretroviral therapy exposure among clients presenting for HIV treatment initiation in South Africa: an exploratory mixed-methods study using multiple indicators of exposure
Authors: Benade Mariet , Maskew Mhairi , Ntjikelane Vinolia , Scott Nancy , Ngcobo Nkosinathi , Nichols Brooke , Malala Lufuno , Manganye Musa , Rosen Sydney
Published: August 2024

Background The era of universal treatment for HIV has seen high rates of disengagement from antiretroviral therapy (ART) programs and re-engagement after interruptions, with modeled estimates of non-naive initiators >50% in many places. Most re-engagers are reluctant to admit prior antiretroviral exposure, and non-self-reported data on proportions of re-initiators are scarce. We synthesized data from multiple sources to explore the proportion of people who present for initiation with evidence of prior ART use in South Africa. Methods We enrolled a sequential sample of adults presenting to initiate ART or to re-initiate ART after an interruption >3 months and collected 1) self-reported previous treatment experience; 2) electronic medical record (EMR) evidence of prior ART clinic visits; 3) baseline blood tests for metabolites of tenofovir diphosphate; and 4) laboratory records indicating prior ART-related tests. Interviews were conducted with a sub-sample of clients who self-reported no prior ART use but had evidence of metabolites. Results Among 89 enrolled participants (median age 32.5, 62% female), 16 (18%) self-reported previously taking ART >3 months prior to enrolment. An additional 33 (45%) who did not self-report prior exposure had EMR or laboratory evidence of prior ART use, for a total of 49 (55%) clients with known prior treatment exposure at initiation. Sensitivity of self-report was 40%, EMR 43%, metabolite testing 45%, and laboratory records 73%. Interviewees (n=11) reported opting to present as naive because they perceived that disclosure of prior disengagement would cause delays accessing treatment, require additional documentation, and elicit negative responses from healthcare workers. Study limitations included short duration of metabolite detectability (90 days), inability to link individuals within the EMR to discern ART experience at other facilities, and lack of baseline viral load testing. Conclusions At least 55% of clients initiating ART in South Africa have prior treatment experience, but only a third of re-initiators voluntarily reveal this. Laboratory records, which reflect long-term experience, yielded the most accurate results for ascertaining prior treatment exposure. As numbers re-engaging in HIV care after a treatment interruption increase, understanding reluctance to self-report ART experience and exploring opportunities to overcome barriers are critical for preventing repeated interruptions.
Evidence for causal links between known modifiable risk factors and dementia: A systematic review of Mendelian randomization studies
Authors: Desai Roopal , John Amber , Anderson Emma , Stafford Jean , Marchant Natalie L. , Charlesworth Georgina , Zuber Verena , Stott Joshua
Published: August 2024

Background: We aimed to systematically review the evidence for causal associations between the known modifiable risk factors and dementia based on Mendelian randomization (MR) studies. Method: Five databases were searched from inception to April 2024 investigating the association between the twelve risk factors identified in the Lancet Commission and dementia. Evaluable analyses were categorised into one of four levels (robust, probable, suggestive, insufficient) based on estimate significance level and concordance of direction of effect between main and sensitivity analyses. Results: 47 articles were included representing 160 separate analyses (136 unique; 104 evaluable) for ten risk factors and six dementia outcomes. There were no valid analyses for air pollution and traumatic brain injury. Of the unique and evaluable analyses over half (59.3%) were evaluated as providing insufficient evidence of causal links. There was no evidence that genetically predicted liability to hearing loss was associated with dementia and limited genetic evidence for social contact. Evidence for education, obesity, depression, alcohol consumption and physical activity was inconclusive. There was probable evidence that smoking was protective against dementia risk however this may be an artefact of survivor bias. The two risk factors with the strongest genetic evidence for links with dementia were diabetes (probable evidence) and blood pressure (probable and suggestive evidence). Conclusion: Genetic evidence for eight of the risk factors examined was insufficient or inconclusive. However, the null findings should be interpreted in the light of the biases inherent to MR studies. The strongest genetic evidence supported a causal link between diabetes and dementia.
Randomized Phase 2 Trial of Lirilumab as maintenance Treatment in Acute Myeloid Leukemia: Results of the EFFIKIR Trial
Authors: Vey N. , Chretien AS. , Dumas PY. , Recher C. , Gastaud L. , Lioure B. , Bulabois CE. , Pautas C. , Marolleau JP. , Lepretre S. , Raffoux E. , Thomas X. , Hichri Y. , Bonmati C. , Quesnel B. , Rousselot P. , Jourdan E. , Malfuson JV. , Guillerm G. , Bourhis JH. , Ojeda-Uribe M. , Hunault M. , Ben Amara A. , Rouvière MS. , Boucherit N. , André P. , Preudhomme C. , Dulphy N. , Toubert A. , Ifrah N. , Olive D. , Dombret H.
Published: August 2024

Lirilumab is a fully human monoclonal antibody designed to block killer inhibitory receptors (KIR), which are major immune checkpoints involved in the regulation of NK cell-mediated killing of HLA-I-expressing tumors. EFFIKIR is a multicenter randomized double-blind 3-arm placebo-controlled phase II trial with lirilumab as single-agent as maintenance therapy of elderly patients with AML in first complete remission (NCT01687387). Two dose schedules led to either continuous or intermittent KIR occupancy. 153 patients were randomized and 152 patients were treated after 3+7 induction therapy. The median follow-up was 36.6 months. Lirilumab was well tolerated, with no significant hematological toxicity. The median LFS were 17.6, 6.7 and 13.9 months in the 0.1mg/kg arm, 1mg/kg arm and placebo arm, respectively. An excess in early relapse led to early termination of treatment in the 1mg/kg arm. Extensive analysis of immune cell fate following KIR blockade evidenced a decrease of KIR+NK cell absolute counts following KIR blockade, associated with a decrease of Bcl-2. Lirilumab also bound antigen-experienced CD8+T cells, and induced a transient decrease of CD69 expression. Besides, lirilumab bound vδ2+γδT cells with a high cytotoxic potential, and induced a decrease of DNAM-1 and Bcl-2, the latter being associated with a decrease of KIR+γδT cell, and with a drastic reduction of time to relapse. Overall, the potentially deleterious effects on immune effectors may have resulted in the impairment of immune surveillance associated with an unexpected high rate of early relapse in the group of patients exposed to prolonged full KIR blockade.

KEY POINTS

Prolonged full KIR blockade leads to potentially deleterious effects on NK cells, CD8+T cells and vδ2+γδT cells

Combined inhibitory effects of KIR blockade may have resulted in the impairment of immunosurveillance associated with high rate of relapse
De novo designed inhibitor confers protection against lethal toxic shock
Authors: Ragotte Robert J. , Liang Huazhu , Berman Jacob M. , Glögl Matthias , Schramek Daniel , Melnyk Roman A. , Baker David
Published: August 2024

Paeniclostridium sordelliicauses a toxic shock syndrome with a mortality rate of nearly 70%, primarily affecting postpartum and post-abortive women. This disease is driven by the production of theP. sordelliilethal toxin, TcsL, for which there are currently no effective treatments. We used a protein diffusion model, RFdiffusion, to design high affinity TcsL inhibitors. From a very small set of 48 starting designs and 48 additional sequence optimized designs, we developed a potent inhibitor with <100 pM affinity that protects mice prophylactically and therapeutically (post exposure) from lung edema and death in a stringent lethal challenge model. This inhibitor, which can be lyophilized without any loss of activity, is a promising therapeutic candidate for this rare but deadly disease, and our results highlight the ability of deep learning-based protein design to rapidly generate biologics with potential clinical utility.
Accurate antibody loop structure prediction enables zero-shot design of target-specific antibodies
Authors: Bang Yewon , Choi Yoon-Aa , Gu Jeonghyeon , Kwon Sohee , Lee Dohoon , Lee Eun Seo , Lee Myeong Sup , Lee Sangchoon , Lee Soyul , Lee Su Jung , Lim Jungsub , Maeng Jin Young , Nam Juno , Noh Jinsung , Oh Hyunjeong , Park Sun-Young , Park Taeyong , Seo Sumin , Seok Chaok , Song Moo Young , Won Jonghun , Woo Hyeonuk , Yang Jinsol , Yoon Min Ji , Bae Woong , Kim Jaehoon , Lee Dongjin , Lee Jaemyung , Lee Youhan , Yu Hasun
Published: August 2024

Protein loops, characterized by their versatile structures with varying sizes and shapes, can recognize a wide range of targets with high specificity and affinity. The variable loops of the antibody complementarity-determining region (CDR) are particularly crucial for immune responses and therapeutic applications due to their effective target recognition capabilities. Accurate structure prediction of these antibody loops is essential for the efficientin silicodesign of target-binding antibodies for therapeutic or industrial use. However, predicting antibody loop structures is challenging due to the lack of evolutionary information from related proteins. Thus, a successfulab initiostructure prediction method, which operates without structural templates or related sequences, is crucial for the effective design of antibody loop-mediated interactions. This study demonstrates that highly accurate antibody loop structure prediction enables the effective zero-shot design of target-binding antibody loops. The performance of loop design has been shown to depend on the accuracy ofab initioloop structure prediction, as tested with two versions of our design model. The high affinity, diversity, novelty, and specificity of the antibody loops designed with these new methods were validated experimentally on four target proteins.
The SWI/SNF PBAF complex facilitates REST occupancy at repressive chromatin
Authors: Grossi Elena , Nguyen Christie B. , Carcamo Saul , Moran Shannon , Callaú Valentina Kirigin , Filipescu Dan , Hasson Dan , Bernstein Emily
Published: August 2024

Multimeric SWI/SNF chromatin remodelers assemble into discrete conformations with unique complex functionalities difficult to dissect. Distinct cancers harbor mutations in specific subunits, altering the chromatin landscape, such as the PBAF-specific component ARID2 in melanoma. Here, we performed comprehensive epigenomic profiling of SWI/SNF complexes and their associated chromatin states in melanoma and melanocytes and uncovered a subset of PBAF-exclusive regions that coexist with PRC2 and repressive chromatin. Time-resolved approaches revealed that PBAF regions are generally less sensitive to ATPase-mediated remodeling than BAF sites. Moreover, PBAF/PRC2-bound loci are enriched for REST, a transcription factor that represses neuronal genes. In turn, absence of ARID2 and consequent PBAF complex disruption hinders the ability of REST to bind and inactivate its targets, leading to upregulation of synaptic transcripts. Remarkably, this gene signature is conserved in melanoma patients with ARID2 mutations. In sum, we demonstrate a unique role for PBAF in generating accessibility for a silencing transcription factor at repressed chromatin, with important implications for disease.
A structural perspective on the temperature-dependent activity of enzymes
Authors: McLeod Matthew J. , Barwell Sarah A. E. , Holyoak Todd , Thorne Robert Edward
Published: August 2024

Enzymes are biomolecular catalysts whose activity varies with temperature. Unlike for small-molecule catalysts, the structural ensembles of enzymes can vary substantially with temperature, and it is in general unclear how this modulates the temperature dependence of activity. Here multi-temperature X-ray crystallography was used to record structural changes from −20°C to 40°C for a mesophilic enzyme in complex with inhibitors mimicking substrate-, intermediate-, and product-bound states, representative of major complexes underlying the kinetic constantkcat. Both inhibitors, substrates and catalytically relevant loop motifs increasingly populate catalytically competent conformations as temperature increases. These changes occur even in temperature ranges where kinetic measurements show roughly linear Arrhenius/Eyring behavior where parameters characterizing the system are assumed to be temperature independent. Simple analysis shows that linear Arrhenius/Eyring behavior can still be observed when the underlying activation energy / enthalpy values vary with temperature, e.g., due to structural changes, and that the underlying thermodynamic parameters can be far from values derived from Arrhenius/Eyring model fits. Our results indicate a critical role for temperature-dependent atomic-resolution structural data in interpreting temperature-dependent kinetic data from enzymatic systems.

One-Sentence Summary

Structural data spanning a 60°C temperature range for enzyme complexes mimicking the substrate-, intermediate-, and product-bound states illuminate how small temperature-dependent structural changes may modulate activity and render parameters deduced from Arrhenius/Eyring plots unreliable.
HMGB1 restores a dynamic chromatin environment in the presence of linker histone by deforming nucleosomal DNA
Authors: Saunders Hayden S. , Chio Un Seng , Moore Camille M. , Ramani Vijay , Cheng Yifan , Narlikar Geeta J
Published: August 2024

The essential architectural protein HMGB1 increases accessibility of nucleosomal DNA and counteracts the effects of linker histone H1. However, HMGB1 is less abundant than H1 and binds nucleosomes more weakly raising the question of how HMGB1 effectively competes with H1. Here, we show that HMGB1 rescues H1’s inhibition of nucleosomal DNA accessibility without displacing H1. HMGB1 also increases the dynamics of condensed, H1-bound chromatin. Cryo-EM shows that HMGB1 binds at internal locations on a nucleosome and locally distorts the DNA. These sites, which are away from the binding site of H1, explain how HMGB1 and H1 co-occupy a nucleosome. Our findings lead to a model where HMGB1 counteracts the activity of H1 by distorting nucleosomal DNA and by contacting the H1 C-terminal tail. Compared to direct competition, nucleosome co-occupancy by HMGB1 and H1 allows a greater diversity of dynamic chromatin states and may be generalizable to other chromatin regulators.
The Transcription Factor Binding Landscape of Mouse Development
Authors: Nordin Anna , Zambanini Gianluca , Jonasson Mattias , Weiss Tamina , van de Grift Yorick , Pagella Pierfrancesco , Cantù Claudio
Published: August 2024

Gene regulators physically associate to the genome, in a combinatorial fashion, to drive tissue-specific gene expression programs. Uncovering the genome-wide activity of all gene regulators across tissues is therefore needed to understand how the genome is regulated during development. Here, we take a first step forward towards achieving this goal. Using CUT&RUN, we systematically measured the genome-wide binding profiles of key transcription factors and cofactors that mediate the activity of ontogenetically relevant signaling pathways in select mouse tissues at two developmental stages. Computation of the numerous genome-wide binding datasets unveiled a large degree of tissue and time-specific activity for each gene regulator, and several factor-specific idiosyncrasies. Moreover, we identified “popular” regulatory regions that are bound by a multitude of pathway regulators. Popular regions tend to be more evolutionarily conserved, implying their essentiality. Consistently, they lie in the proximity of genes whose dysregulation causes early embryonic lethality in the mouse. Moreover, the human homologs of these regions are also bound by many gene regulators and are highly conserved in human populations, indicating that they retain functional relevance for human development. This work constitutes a decisive step towards understanding how the genome is simultaneously read and used by gene regulators in a holistic fashion and unveils multiple genomic mechanisms that drive embryonic development.
ARTIC RSV amplicon sequencing reveals global RSV genotype dynamics
Authors: Maloney Daniel M , Fernandes Goncalo , Jasim Seema , Williams Tom , Namugenyi Sarah , Carr Michael , Meyer Jennifer R , Sharma Aryan , Marshal Louise , Nunley B Ethan , Xie Hong , Carvajal Mateo , Kunerth Henry D. , Tanmoy Arif , O’Toole Áine , Weixler Amelia , Lanter Kelsey R , Gonzalez Gabrial , Sereewit Jaydee , Guevara Rommel , Loose Matt , Fanning Padraic M. , Benítez Denisse , Fernandez Juan Carlos , Cárdenas Paúl , Hare Daniel , Greninger Alex , Williams Thomas , Nebbia Gaia , Fries Anthony C. , McClure Patrick , Roychoudhury Pavitra , Wang Xiong , Saha Senjuti , Dewar Rebecca , Templeton Kate , Rambaut Andrew
Published: August 2024

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections (LTRIs) in young children and adults over 65, contributing significantly to global healthcare burdens. With the recent approval of multiple pharmacological interventions for RSV, there is an increased demand for efficient, high-throughput sequencing methods to monitor RSV genetic diversity and any potential impact these interventions may have. Here we introduce two novel amplicon-based sequencing schemes designed for RSV A and B, optimised for integration with widespread existing ARTIC sequencing workflows. We demonstrate that these primer schemes can produce high quality genomes from RSV samples across the globe, with eight laboratories in five countries generating complete genomes on both Nanopore and Illumina sequencing platforms. The ability to effectively multiplex these RSV A and B primer schemes, enables streamlined, high-throughput sequencing without prior subtyping. Furthermore, these results provide a snapshot of the circulating diversity of RSV. Phylogenetic analysis of the 882 samples sequenced for this study suggests only minimal geographic clustering of RSV sequences, underscoring the global nature of RSV spread. It also highlights the distinct lineage dynamics seen between RSV A and B. This study represents an advancement in RSV genomics, providing robust tools for global sequencing efforts aimed at tracking RSV evolution and assessing the efficacy of new therapeutic interventions both rapidly and at scale.
Gaps in the global protection of terrestrial genetic diversity
Authors: Schultz Jana Tabea , Geldmann Jonas , Theodoridis Spyros , Nogues-Bravo David
Published: August 2024

In recent decades, increased anthropogenic impact has led to a global decline in genetic diversity. Before the Kunming-Montreal Global Biodiversity Framework (2022), the absence of international consensus on how to directly assess and monitor genetic diversity, hampered large-scale conservation efforts. Scarcity of assessable genetic data has hindered the evaluation of conservation policies in safeguarding genetic diversity. This study presents the first global approach for evaluating the protection of genetic diversity. By examining the global distribution of mammalian intraspecific mitochondrial DNA and protected area coverage, we identify regions with high genetic diversity and insufficient protection coverage, e.g. regions of critical importance for biodiversity in the Brazilian Atlantic Forest. Additionally, we estimate the impact of global change scenarios on genetically diverse regions with a low degree of protection, revealing high vulnerability of areas in Central Africa. Nonetheless, integrating robust analysis into conservation planning remains challenging. Incorporating Macrogenetics into conservation planning holds the potential to reverse biodiversity decline.