bluuebunny/crossref_metadata_2025 huggingface dataset:
Arid5a uses disordered extensions of its core ARID domain for distinct DNA- and RNA-recognition and gene regulation
Authors: von Ehr Julian , Oberstrass Lasse , Yazgan Ege , Schnaubelt Lara Ina , Blümel Nicole , McNicoll Francois , Weigand Julia E. , Zarnack Kathi , Müller-McNicoll Michaela , Korn Sophie Marianne , Schlundt Andreas
Published: March 2024

AT-rich interacting domain (ARID)-containing proteins, Arids, are a heterogeneous DNA-binding protein family involved in transcription regulation and chromatin processing. For the member Arid5a, no exact DNA-binding preference has been experimentally defined so far. Additionally, the protein binds to mRNA motifs for transcript stabilization, supposedly through the DNA-binding ARID domain. To date, however, no unbiased RNA motif definition and clear dissection of nucleic acid-binding through the ARID domain have been undertaken. Using NMR-centered biochemistry, we here define the Arid5a DNA preference. Further, high-throughput in vitro binding (RBNS) reveals a consensus RNA-binding motif engaged by the core ARID domain. Finally, transcriptome-wide binding (iCLIP2) reveals that Arid5a has a weak preference for (A)U-rich regions in pre-mRNA transcripts of factors related to RNA processing. We find that the intrinsically disordered regions (IDR) flanking the ARID domain modulate the specificity and affinity of DNA-binding, while they appear crucial for RNA interactions. Ultimately, our data suggest that Arid5a uses its extended ARID domain for bi-functional gene regulation and that the involvement of IDR extensions is a more general feature of Arids in interacting with different nucleic acids at the chromatin-mRNA interface.
Development of an orally bioavailable mSWI/SNF ATPase degrader and acquired mechanisms of resistance in prostate cancer
Authors: He Tongchen , Cheng Caleb , Qiao Yuanyuan , Cho Hanbyul , Young Eleanor , Mannan Rahul , Mahapatra Somnath , Miner Stephanie J. , Zheng Yang , Kim NamHoon , Zeng Victoria Z. , Wisniewski Jasmine P. , Hou Siyu , Jackson Bailey , Cao Xuhong , Su Fengyun , Wang Rui , Chang Yu , Kuila Bilash , Mukherjee Subhendu , Dukare Sandeep , Aithal Kiran B. , D.S. Samiulla , Abbineni Chandrasekhar , Lyssiotis Costas A. , Parolia Abhijit , Xiao Lanbo , Chinnaiyan Arul M.
Published: March 2024

Mammalian switch/sucrose non-fermentable (mSWI/SNF) ATPase degraders have been shown to be effective in enhancer-driven cancers by functioning to impede oncogenic transcription factor chromatin accessibility. Here, we developed AU-24118, a first-in-class, orally bioavailable proteolysis targeting chimera (PROTAC) degrader of mSWI/SNF ATPases (SMARCA2 and SMARCA4) and PBRM1. AU-24118 demonstrated tumor regression in a model of castration-resistant prostate cancer (CRPC) which was further enhanced with combination enzalutamide treatment, a standard of care androgen receptor (AR) antagonist used in CRPC patients. Importantly, AU-24118 exhibited favorable pharmacokinetic profiles in preclinical analyses in mice and rats, and further toxicity testing in mice showed a favorable safety profile. As acquired resistance is common with targeted cancer therapeutics, experiments were designed to explore potential mechanisms of resistance that may arise with long-term mSWI/SNF ATPase PROTAC treatment. Prostate cancer cell lines exposed to long-term treatment with high doses of a mSWI/SNF ATPase degrader developed SMARCA4 bromodomain mutations and ABCB1 overexpression as acquired mechanisms of resistance. Intriguingly, while SMARCA4 mutations provided specific resistance to mSWI/SNF degraders, ABCB1 overexpression provided broader resistance to other potent PROTAC degraders targeting bromodomain-containing protein 4 (BRD4) and AR. The ABCB1 inhibitor, zosuquidar, reversed resistance to all three PROTAC degraders tested. Combined, these findings position mSWI/SNF degraders for clinical translation for patients with enhancer-driven cancers and define strategies to overcome resistance mechanisms that may arise.

Significance Statement

The mSWI/SNF complex is a promising therapeutic target for enhancer-driven cancers. PROTACs, which enable the targeting of “undruggable” proteins, often face the challenge of achieving oral bioavailability. Here, we present AU-24118, a first-in-class, orally bioavailable mSWI/SNF ATPase dual degrader with remarkable efficacy inin vitroandin vivomodels. Additionally, our study describes two distinct mechanisms of resistance to PROTAC degraders, providing crucial insights into potential challenges facing their clinical application. These findings are critical for advancing PROTAC-based therapies to clinical settings as targeted therapies for cancers.
The transcriptional regulator Lrp activates the expression of genes involved in tilivalline enterotoxin biosynthesis inKlebsiella oxytoca
Authors: De la Cruz Miguel A. , Valdez-Salazar Hilda A. , Robles-Leyva Nayely , Siqueiros-Cendón Tania , Rascón-Cruz Quintín , Rodríguez-Valverde Diana , León-Montes Nancy , Soria-Bustos Jorge , Rosales-Reyes Roberto , Cedillo María L. , Yañez-Santos Jorge A. , Ibarra J. Antonio , Torres Javier , Girón Jorge A. , Fox James G. , Ares Miguel A.
Published: March 2024

The toxigenicKlebsiella oxytocastrains secret the tilivalline enterotoxin, which causes antibiotic-associated hemorrhagic colitis. The tilivalline is a non-ribosomal peptide synthesized by enzymes encoded in two divergent operons clustered in a pathogenicity island. The transcriptional regulator Lrp (leucine-responsiveregulatoryprotein) controls the expression of several bacterial genes involved in virulence. In this work, we determined the transcriptional expression ofaroXandnpsA, the first genes of each tilivalline biosynthetic operon inK. oxytocaMIT 09-7231 wild-type and its derivatives Δlrpmutant and complemented strains. The results show that Lrp directly activates the transcription of botharoXandnpsAgenes by binding to the intergenic regulatory region in a leucine-dependent manner. Furthermore, the lack of Lrp significantly diminished the cytotoxicity ofK. oxytocaon HeLa cells due to tilivalline reduced production. Altogether, our data highlight Lrp as a new regulator by which cytotoxin-producingK. oxytocastrains control the expression of genes involved in the biosynthesis of their main virulence factor.

IMPORTANCE

Tilivalline is an enterotoxin that is a hallmark for the cytotoxin-producingK. oxytocastrains, which cause antibiotic-associated hemorrhagic colitis. The biosynthesis of tilivalline is driven by enzymes encoded by thearoX- and NRPS-operons. In this study, we discovered that the transcriptional regulator Lrp directly activates expression of thearoX- and NRPS-operons and, in turn, tilivalline biosynthesis. Our results underscore a molecular mechanism by which tilivalline production by toxigenicK. oxytocastrains is regulated and shed further light on developing strategies to prevent the intestinal illness caused by this enteric pathogen.
Hypertrophic cardiomyopathy mutations Y115H and E497D disrupt the folded-back state of human beta-cardiac myosin allosterically
Authors: Nandwani Neha , Bhowmik Debanjan , Childers Matthew C , Goluguri Rama Reddy , Dawood Aminah , Regnier Michael , Spudich James A , Ruppel Kathleen M
Published: March 2024

At the molecular level, clinical hypercontractility associated with many hypertrophic cardiomyopathy (HCM)-causing mutations in beta-cardiac myosin appears to be driven by their disruptive effect on the energy-conserving, folded-back, super relaxed (SRX) OFF-state of myosin. A pathological increase in force production results from release of heads from this OFF-state, which results in an increase in the number of heads free to interact with actin and produce force. Pathogenic mutations in myosin can conceivably disrupt the OFF-state by (1) directly affecting the intramolecular interfaces stabilizing the folded-back state, or (2) allosterically destabilizing the folded-back state via disruption of diverse conformational states of the myosin motor along its chemomechanical cycle. However, very little is understood about the mutations that fall in the latter group. Here, using recombinant human beta-cardiac myosin, we analysed the biomechanical properties of two such HCM-causing mutations, Y115H (in the transducer) and E497D (in the relay helix), neither of which falls in the regions that interact to stabilize the myosin folded-back state. We find these mutations have diverse effects on the contractility parameters of myosin, yet the primary hypercontractile change in both cases is the destabilization of the OFF-state of myosin and increased availability of active myosin heads for actin-binding. Experimental data and molecular dynamics simulations indicate that these mutations likely destabilize the pre-powerstroke state of myosin, the conformation the motor adopts in the inactive folded-back state. We propose that destabilization of the folded-back state of myosin, directly and/or allosterically, is the molecular basis of hypercontractility in HCM in a far greater number of pathogenic mutations than currently thought.
RIPK3 coordinates RHIM domain-dependent inflammatory transcription in neurons
Authors: Kofman Sigal B. , Chu Lan H. , Ames Joshua M. , Chavarria Suny Dayane , Lichauco Katrina , Daniels Brian P. , Oberst Andrew
Published: March 2024

Neurons are post-mitotic, non-regenerative cells that have evolved fine-tuned immunological responses to maintain life-long cellular integrity; this includes resistance to common programmed cell death (PCD) pathways, including apoptosis and necroptosis. We have previously demonstrated a necroptosis-independent role for the key necroptotic kinase RIPK3 in host defense against neurotropic flavivirus infection. While this work showed that neuronal RIPK3 expression is essential for chemokine production and recruitment of peripheral immune cells to the infected CNS, the full RIPK3-dependent transcriptional signature, and the molecular mechanism underlying RIPK3-dependent transcription in neurons are incompletely understood. It also remains unclear what factors govern differential RIPK3 effector functions in different cell types. Here, we show that RIPK3 activation has distinct outcomes in primary cortical neurons when compared to mouse embryonic fibroblasts (MEFs) during Zika virus (ZIKV) infection or following sterile activation. We found that RIPK3 activation does not induce death in neurons; in these cells, RIPK3 is the dominant driver of antiviral gene transcription following ZIKV infection. While RIPK3 activation in MEF cells induces cell death, ablation of downstream cell death effectors unveils a RIPK3-dependent transcriptional program which largely overlaps with that observed in ZIKV-infected neurons. Using death resistant MEFs as a model to study RIPK3 signaling revealed that RIPK3 transcription relied on interactions with the RHIM domain-containing proteins RIPK1 and TRIF, effects mirrored in the RIPK3-dependent antiviral transcriptional signature observed in ZIKV-infected neurons. These findings suggest the pleotropic functions of RIPK3 are largely context dependent and that in cells that are resistant to cell death, RIPK3 acts as a mediator of inflammatory transcription.

One Sentence Summary

RHIM-domain containing proteins form a conserved signaling network capable of mediating inflammatory transcription and cell death.
Personalized Brain-Computer Interface-based Intervention for Mindful Anxiety Regulation in Young Adults: A Randomized Clinical Trial
Authors: Tan Wan Jie , Ding Yi , Lin Xiangting Bernice , Robinson Neethu , Zeng Qiuhao , Zhang Su , Wai Aung Aung Phyo , Lee Tih-Shih , Guan Cuntai
Published: March 2024

Importance

Brain-computer interface-(BCI-) based interventions are promising means for self-administered anxiety treatment due to their non-invasiveness and portability. However, few studies have explored their viability in the home setting.

Objective

To evaluate the feasibility and preliminary efficacy of a novel, personalized, BCI-based intervention integrating mindfulness principles for anxiety regulation in the home setting.

Design

An open-label, two-arm randomized clinical trial was conducted from January 2021 to December 2021.

Setting

The study was conducted at Duke-NUS Medical School, Singapore.

Participants

Thirty young adults from the community aged 21-35 with at least moderate anxiety were randomized 1:1 to either the intervention or waitlist-control group.

Intervention

The intervention was self-administered by the participants and involved eight 30-minute sessions held at home over 2 weeks.

Main Outcomes and Measures

The primary outcomes were safety, acceptability, and anxiety (Beck Anxiety Inventory II, State-Trait Anxiety Inventory [Form Y], and electroencephalography [EEG] data). Secondary outcomes were quality of sleep (Insomnia Severity Index), emotion regulation (Difficulties in Emotion Regulation Scale), mindful awareness (Mindfulness Awareness Attention Scale), and depression and stress subscales in the Depression Anxiety Stress Scale-21.

Results

The intervention was safe and acceptable. No severe adverse events were reported. The attrition rate was 40%, predominantly due to technical issues. Pooled analyses indicated a significant reduction in anxiety, depression, stress, and insomnia from pre- to post-intervention. Improvements in anxiety were supported by physiological changes. Participants also reported significantly greater mindful awareness, access to emotion regulation strategies, and control over impulses.

Conclusion and Relevance

These findings suggest that our BCI-based intervention is feasible and potentially efficacious for participants to entrain anxiety regulation independently at home. A larger trial is warranted.

Trial Registration

ClinicalTrials.govNCT04626713;https://tinyurl.com/27hn2m76
The impact of localization and registration accuracy on estimates of deep brain stimulation electrode position in stereotactic space
Authors: Abbass Mohamad , Gilmore Greydon , Santyr Brendan , Chalil Alan , Taha Alaa , Jog Mandar , MacDougall Keith , Parrent Andrew G. , Peters Terry M. , Lau Jonathan C.
Published: March 2024

Effects of deep brain stimulation (DBS) depend on millimetric accuracy and are commonly studied across populations by registering patient scans to a stereotactic space. Multiple factors contribute to estimates of electrode position, but the millimetric contributions of these factors remains poorly quantified. We previously validated 32 anatomical fiducials (AFIDs) to measure AFID registration error (AFRE), which can capture focal misregistration not observed using volume-based methods. To this end, we used the AFIDs framework to examine the effects of misregistration on electrode position in stereotactic space, leveraging a retrospective series of patients who underwent subthalamic nucleus DBS. Raters independently localized DBS electrodes and AFIDs on patient scans, which were non-linearly registered to a common stereotactic (MNI) space. AFIDs provided intuitive measures of registration accuracy, with AFREs ranging from 1.49 mm to 6.85 mm across brain regions. Subcortical AFIDs in proximity to the DBS target had AFREs that spatially covaried, suggesting consistent spatial patterns of misregistration to stereotactic space. These identified spatial patterns explained 28% of the variance in electrode position along the axis of maximum variance, corresponding to a median of 0.64 mm (range of 0.05 to 2.05 mm). To our knowledge, these represent the first millimetric estimates of registration accuracy in DBS, allowing uncoupling of registration-related factors from other sources of variance in electrode position. Furthermore, they can be employed for estimating registration-related variance in population studies, for quality control, and to provide a basis for comparison as well as optimization of registration parameters and software.
Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis
Authors: Sreenivasan Akshai Parakkal , Vaivade Aina , Noui Yassine , Khoonsari Payam Emami , Burman Joachim , Spjuth Ola , Kultima Kim
Published: March 2024

Accurate assessment of progression and disease course in multiple sclerosis (MS) is vital for timely and appropriate clinical intervention. The transition from relapsing-remitting MS (RRMS) to secondary progressive MS (SPMS) is gradual and diagnosed retrospectively with a typical delay of three years. To address this diagnostic delay, we developed a predictive model that is able to distinguish between RRMS and SPMS with high accuracy, trained on data from electronic health records collected at routine hospital visits obtained from the Swedish MS Registry containing 22,748 patients with 197,227 hospital visits. To be useful within a clinical setting, we applied conformal prediction to deliver valid measures of uncertainty in predictions at the level of the individual patient. We showed that the model was theoretically and empirically valid, having the highest efficiency at a 92% confidence level, and demonstrated on an external test set that it enables effective prediction of the clinical course of a patient with individual confidence measures. We applied the model to a set of patients who transitioned from RRMS to SPMS during the cohort timeframe and showed that we can accurately predict when patients transition from RRMS to SPMS. We also identified new patients who, with high probability, are in the transition phase from RRMS to SPMS but have not yet received a clinical diagnosis. We conclude that our methodology can assist in monitoring MS disease progression and proactively identify patients undergoing transition to SPMS. An anonymized, publically accessible version of the model is available athttps://msp-tracker.serve.scilifelab.se/.
Protocol For Human Evaluation of Artificial Intelligence Chatbots in Clinical Consultations
Authors: Chiu Edwin Kwan-Yeung , Chung Tom Wai-Hin
Published: March 2024

Background

Generative artificial intelligence (AI) technology has the revolutionary potentials to augment clinical practice and telemedicine. The nuances of real-life patient scenarios and complex clinical environments demand a rigorous, evidence-based approach to ensure safe and effective application.

Methods

We present a protocol for the systematic evaluation of generative AI large language models (LLMs) as chatbots within the context of clinical microbiology and infectious disease consultations. We aim to critically assess the clinical accuracy, comprehensiveness, coherence, and safety of recommendations produced by leading generative AI models, including Claude 2, Gemini Pro, GPT-4.0, and a GPT-4.0-based custom AI chatbot.

Discussion

A standardised healthcare-specific prompt template is employed to elicit clinically impactful AI responses. Generated responses will be graded by a panel of human evaluators, encompassing a wide spectrum of domain expertise in clinical microbiology and virology and clinical infectious diseases. Evaluations are performed using a 5-point Likert scale across four clinical domains: factual consistency, comprehensiveness, coherence, and medical harmfulness. Our study will offer insights into the feasibility, limitations, and boundaries of generative AI in healthcare, providing guidance for future research and clinical implementation. Ethical guidelines and safety guardrails should be developed to uphold patient safety and clinical standards.
Pattern and mechanisms of atrophy progression in individuals with a family history of Alzheimer’s disease: a comparative study
Authors: Tremblay Christina , Rahayel Shady , Pastor-Bernier Alexandre , St-Onge Frédéric , Vo Andrew , Rheault François , Daneault Véronique , Morys Filip , Rajah Natasha , Villeneuve Sylvia , Dagher Alain ,   the PREVENT-AD Research Group,   Alzheimer’s Disease Neuroimaging Initiative (ADNI)
Published: March 2024

Alzheimer’s disease (AD) includes a long period of presymptomatic brain changes. Different risk factors are associated with AD development, including having a family history of AD (FHAD). The Braak scheme suggests that tau pathology, in synergy with amyloid-beta (Aβ), spreads along structural connections in AD, eventually leading to atrophy. Studying the pathways in which atrophy spreads early on, as well as the factors underpinning this pathway, is crucial for improving diagnostic accuracy and early interventions. However, the pattern of atrophy progression in people with a FHAD and the biological factors associated with this progression remain unclear. Here we used structural MRI from three databases (ADNI, PREVENT-AD and Montreal Adult Lifespan Study) to map the atrophy progression in FHAD and AD and assess the constraining effects of structural connectivity on atrophy progression. Cross-sectional and longitudinal data up to 4 years were used to perform atrophy progression analysis in FHAD and AD compared to controls. Positron emission tomography (PET) radiotracers were also used to quantify the distribution of tau and Aβ proteins at baseline. We first derived cortical atrophy progression maps using deformation-based morphometry from 153 FHAD, 156 AD, and 116 controls with similar age, education, and sex at baseline. We next examined the spatial relationship between atrophy progression and spatial patterns of tau and Aβ deposition, structural connectivity, and neurotransmitter receptor and transporter distributions. Our results show that there were similar patterns of atrophy progression in FHAD and AD, notably in the cingulate, temporal and parietal cortices, with more widespread and severe atrophy in AD. Both tau and Aβ pathology tended to accumulate in regions that were structurally connected in FHAD and AD. The pattern of atrophy and its progression also aligned with existing structural connectivity in FHAD. In AD, our findings suggest that atrophy progression results from propagating pathology that occurred much earlier, on an intact connectome. Moreover, a relationship was found between the serotonin 5-HT6 receptors spatial distribution and atrophy progression in AD, supporting an important role of these receptors in neurodegeneration. The current study demonstrates that regions showing atrophy progression in FHAD and AD present with specific connectivity and cellular characteristics, uncovering certain of the mechanisms involved in preclinical and clinical neurodegeneration.
Body composition and checkpoint inhibitor treatment outcomes in advanced melanoma: a multicenter cohort study
Authors: Maat L.S. Ter , Van Duin I.A.J. , Verheijden R.J. , Moeskops P. , Verhoeff J.J.C. , Elias S.G. , van Amsterdam W.A.C. , Burgers F.H. , Van den Berkmortel F.W.P.J. , Boers-Sonderen M.J. , Boomsma M.F. , De Groot J.W. , Haanen J.B.A.G. , Hospers G.A.P. , Piersma D. , Vreugdenhil G. , Westgeest H.M. , Kapiteijn E. , Labots M. , Veldhuis W.B. , Van Diest P.J. , De Jong P.A. , Pluim J.P.W. , Leiner T. , Veta M. , Suijkerbuijk K.P.M.
Published: March 2024

Introduction

The association of body composition with checkpoint inhibitor outcomes in melanoma is a matter of ongoing debate. In this study, we aim to add to previous evidence by investigating body mass index (BMI) alongside CT derived body composition metrics in the largest cohort to date.

Method

Patients treated with first-line anti-PD1 ± anti-CTLA4 for advanced melanoma were retrospectively identified from 11 melanoma reference centers in The Netherlands. Age, sex, Eastern Cooperative Oncology Group performance status, serum lactate dehydrogenase, presence of brain and liver metastases, number of affected organs and BMI at baseline were extracted from electronic patient files. From baseline CT scans, five body composition metrics were automatically extracted: skeletal muscle index, skeletal muscle density, skeletal muscle gauge, subcutaneous adipose tissue index and visceral adipose tissue index. All predictors were correlated in uni- and multivariable analysis to progression-free, overall and melanoma-specific survival (PFS, OS and MSS) using Cox proportional hazards models.

Results

A total of 1471 eligible patients were included. Median PFS and OS were 8.8 and 34.8 months, respectively. A significantly worse PFS was observed in underweight patients (multivariable HR=1.87, 95% CI 1.14–3.07). Furthermore, better OS was observed in patients with higher skeletal muscle density (multivariable HR=0.91, 95% CI 0.83-0.99) and gauge (multivariable HR=0.88, 95% CI 0.84-0.996), and a worse OS with higher visceral adipose tissue index (multivariable HR=1.13, 95% CI 1.04-1.22). No association with survival outcomes was found for overweightness or obesity and survival outcomes, or for subcutaneous adipose tissue.

Discussion

Our findings suggest that underweight BMI is associated with worse PFS, whereas higher skeletal muscle density and lower visceral adipose tissue index were associated with better OS. These associations were independent of previously identified predictors, including sex, age, performance status and extent of disease. No significant association between higher BMI and survival outcomes was observed.
Lifestyle interventions for dementia prevention in Low- and Middle-Income Countries: A systematic review
Authors: Espinoza Jeraldo Rosario Isabel , Zabihi Sedigheh , Miranda-Castillo Claudia , Marshall Charles R , Cooper Claudia
Published: March 2024

By 2050, two-thirds of people with dementia will live in Low- and Middle-Income Countries (LMICs). Efforts to adapt and test multi-modal prevention interventions focusing on lifestyle changes for people at risk of dementia are being developed predominantly in higher income countries, for people with and without cognitive symptoms. However, there is evidence that needs may differ between these groups. We systematically reviewed Randomized Controlled Trials (RCTs) evaluating non-pharmacological interventions in individuals with Mild Cognitive Impairment (MCI) and Subjective Cognitive Decline (SCC) in LMICs. We analysed study quality using the Mixed Methods Assessment Tool (MMAT), meta-analysed and synthesized evidence. We included 25 RCTs, from six countries (most in China, n=17), involving 1304 participants. Across the 15 studies for which there was sufficient data to meta-analyse, we found significant positive effects on cognitive outcomes favouring interventions [1.49 (standardised mean difference, 95% Confidence Interval= 1.06-1.93)]. There was significant publication bias. Using an a priori standard framework, we classified interventions into exercise, multidomain, and arts/creative expression. Group exercise [1.67, 1.24-2.11, n=8]. and multidomain [1.22, 0.22-2.21, n=5] had replicated evidence of effectiveness. There was insufficient data to meta-analyse the creative arts category. We identified one high quality, multi-modal intervention, which combined Chinese mind-body exercises and health education, reporting a positive outcome. The first robust dementia prevention trials are underway in LMICs, evaluating effectiveness of models developed in higher income countries. We propose greater consideration and investment in development of interventions that account for specific LMIC contexts from the outset, so they are acceptable and used by local services.

Highlights

There was evidence that group exercise and multimodal interventions were effective for people with memory concerns in LMICs.

We identified publication bias in meta-analyses; the open science agenda is critical to improving care in LMICs and reducing global inequalities.

Most included studies were conducted in China, reflecting a need for high-quality evidence from underrepresented regions, including Africa and Latin America.

We propose greater investment in developing interventions that account for specific LMIC contexts from the outset, so they are acceptable and used by local services.
The role of dopaminergic medication, lipid, and endocannabinoid pathway alterations in idiopathic andPRKN/PINK1-mediated Parkinson’s disease – a large-scale targeted metabolomics study
Authors: Balck Alexander , Borsche Max , Campbell Philip , Luo Xi , Harvey John , Brückmann Theresa , Ludwig Charlotte , Harms Amy , Lohmann Katja , Morris Huw R , Schapira Anthony H , Hankemeier Thomas , Fleming Ronan , Szymczak Silke , Klein Christine
Published: March 2024

Alterations in many metabolites and biochemical pathways have been described in Parkinson’s Disease (PD). However, only a small fraction of these have been replicated in independent studies. As almost every PD patient is treated with dopaminergic medication, it is challenging to discriminate between disease- and drug-related effects, especially in relation to dopamine metabolism. We conducted a large-scale metabolomic study in plasma from 140 idiopathic (IPD), 19PRKN/PINK1-linked PD patients, and 64 healthy controls to disentangle disease-related metabolite alterations from drug-related effects. We distinguished between L-Dopa and non-L-Dopa treated PD patients to uncover nuanced metabolic changes associated with different therapies. We demonstrate that L-Dopa treatment uniquely influences the metabolome, with methyldopa and methoxytyramine, both L-Dopa breakdown products, elevated in L-Dopa-treated IPD andPRKN/PINK-linked PD patients. These alterations were not seen in untreated IPD patients and those on agonist treatment only. Polyamine metabolism alterations, notably elevation of putrescine and ornithine, were partly caused by L-Dopa treatment but also found in non-L-Dopa treated PD patients. In non-L-Dopa-treated patients, endocannabinoid metabolites were lowered and associated with disease duration. We observed lipid metabolism alterations, highlighting potential crosslinks with alpha-synuclein and providing insights into pathophysiological mechanisms. AllPRKN/PINK1-linked PD patients received L-Dopa treatment. However, our data potentially support the well-established role of oxidative damage in these subtypes of PD. In conclusion, our study emphasizes the significant impact of L-Dopa treatment on the metabolome, which might be of relevance not only for metabolomics studies but also for PD biomarker research in general. Finally, our study highlights potential biomarkers and pathways crucial for the understanding disease mechanisms of PD.
Continuous Associations Between Remote Self-Administered Cognitive Measures and Imaging Biomarkers of Alzheimer’s Disease
Authors: Boots Elizabeth A. , Frank Ryan D. , Fan Winnie Z. , Christianson Teresa J. , Kremers Walter K. , Stricker John L. , Machulda Mary M. , Fields Julie A. , Hassenstab Jason , Graff-Radford Jonathan , Vemuri Prashanthi , Jack Clifford R. , Knopman David S. , Petersen Ronald C. , Stricker Nikki H.
Published: March 2024

Background

Easily accessible and self-administered cognitive assessments that can aid early detection for Alzheimer’s disease (AD) dementia risk are critical for timely intervention.

Objectives/Design

This cross-sectional study investigated continuous associations between Mayo Test Drive (MTD) – a remote, self-administered, multi-device compatible, web-based cognitive assessment – and AD-related imaging biomarkers.

Participants/Setting

684 adults from the Mayo Clinic Study of Aging and Mayo Clinic Alzheimer’s Disease Research Center participated (age=70.4±11.2, 49.7% female). Participants were predominantly cognitively unimpaired (CU; 94.0%).

Measurements

Participants completed (1) brain amyloid and tau PET scans and MRI scans for hippocampal volume (HV) and white matter hyperintensities (WMH); (2) MTD remotely, consisting of the Stricker Learning Span and Symbols Test which combine into an MTD composite; and (3) in-person neuropsychological assessment including measures to obtain Mayo Preclinical Alzheimer’s disease Cognitive Composite (Mayo-PACC) and Global-z. Multiple regressions adjusted for age, sex, and education queried associations between imaging biomarkers and scores from remote and in-person cognitive measures.

Results

Lower performances on MTD were associated with greater amyloid, entorhinal tau, and global tau PET burden, lower HV, and higher WMH. Mayo-PACC and Global-z were associated with all imaging biomarkers except global tau PET burden. MCI/Dementia participants showed lower performance on all MTD measures compared to CU with large effect sizes (Hedge’s g’s=1.65-2.02), with similar findings for CU versus MCI only (Hedge’s g’s=1.46-1.83).

Conclusions

MTD is associated with continuous measures of AD-related imaging biomarkers, demonstrating ability to detect subtle cognitive change using a brief, remote assessment in predominantly CU individuals and criterion validity for MTD.
Osteoarthritis across Joint Sites in the Million Veteran Program: Insights from Electronic Health Records and Military Service History
Authors: Lavin Kaleen M , Richman Joshua S , McDonald Merry-Lynn N , Singh Jasvinder A.
Published: March 2024

Objective

To characterize the relationship between OA frequency and a host of demographic characteristics, comorbidities, military service history, and physical health variables in a veteran population.

Methods

We investigated the Million Veteran Program (MVP) cohort to outline frequency of OA across six joint sites (knee, spine, hip, hand, finger, thumb) in veterans with respect to demographics (age, sex, race/ethnicity, etc.), military service data, and detailed electronic health records profiling OA and other comorbidities. The large veteran contingent provided the unique opportunity to investigate the association of OA with prior service across military branches and war eras.

Results

We validated previous reports of sex- and age-dependent differences in OA frequency, and we identified that generalized OA was associated with a higher frequency of sixteen Deyo-Charlson comorbidities. These associations generally persisted within each isolated joint site-specific OA. Depending on military branch, prior military engagement was differentially associated with frequency of OA. Prior Army and Navy service were associated with higher and lower risk, respectively of OA across all joint sites. However, multivariable-adjusted models adjusting for a range of covariates (including age, sex, and ancestry) reversed the apparent protective effect of prior Navy service

Conclusion

These findings highlight the breadth of factors associated with OA in the MVP veteran population and suggest that physical status may be a modifiable risk factor for OA. This work may contribute to designing strategies to optimize appropriate detection, intervention, treatment, and even rehabilitation strategies for OA in veterans and the general population.
Digital Nanofluidic Chip for Simple and Highly Quantitative Detection of HPV Target
Authors: Liu Li , Dollery Stephen J. , Tobin Gregory J. , Lu Guoyu , Du Ke
Published: March 2024

Quantitative analysis of human papillomavirus (HPV)-infected cervical cancer is essential for early diagnosis and timely treatment of cervical cancer. Here, we introduce a novel energy transfer-labeled oligonucleotide probe to enhance the loop-mediated isothermal amplification (LAMP) assay for highly sensitive and specific detection of HPV 16. Conducted as a single-step assay within a digital nanofluidic chip featuring numerous reaction reservoirs, our method facilitates target amplification under isothermal conditions. Targeting an HPV 16 gene, our chip demonstrates the capability to detect HPV DNA at concentrations as low as 1 fM, spanning a dynamic range of five orders of magnitude. Importantly, our digital chip allows for highly quantitative detection of target genes at low concentrations, with the correlation between target concentration and the number of microwells exhibiting fluorescence signals. Furthermore, we have developed a computer vision method for automated and 100% accurate quantification of target concentrations. This research holds promising applications in clinical diagnosis and is poised for seamless integration into both hospital and point-of-care settings.
Evaluation of Molecular-based Methods for the Detection and Quantification ofCryptosporidiumspp. in Wastewater
Authors: Hachimi Oumaima , Falender Rebecca , Davis Gabriel , Vranka Wafula Rispa , Sutton Melissa , Bancroft June , Cieslak Paul , Lininger Noah , Kelly Christine , Kaya Devrim , Radniecki Tyler S.
Published: March 2024

Cryptosporidium, a eukaryotic protozoan parasite, poses a significant public health risk as a cause of waterborne disease worldwide. Clinical surveillance of cryptosporidiosis is estimated to be largely underreported due to the asymptomatic and mildly symptomatic infections, clinical misdiagnoses, and barriers to access testing. Unlike clinical surveillance, wastewater surveillance overcomes these limitations and could serve as an effective tool for identifying cryptosporidiosis at the population level. Despite its potential, the lack of standardized methods forCryptosporidiumspp. detection in wastewater challenges the comparability of studies. Additionally, the use of standard methods for the detection and quantification ofCryptosporidiumspp. in surface waters may not be appropriate for wastewater samples due to the more complex composition of the wastewater matrix. Thus, in this study, we evaluated methods for concentratingCryptosporidiumoocysts from wastewater, extracting DNA, and detecting its genetic markers, using wastewater seeded withC. parvumoocysts. The evaluated concentration methods included electronegative membrane filtration, Envirocheck HV capsule filtration, centrifugation, and Nanotrap Microbiome particles. All methods except the Nanotrap Microbiome particles were conducted with or without additional purification via immunomagnetic separation. For DNA extractions, we tested the DNeasy Powersoil Pro kit and the QIAamp DNA Mini kit, while assessing the impact of bead beating and freeze-thaw cycles on DNA yield. Genetic detection was performed using qPCR targeting theCryptosporidium18S rRNA gene. Our results indicated that centrifugation yielded the highest oocyst recoveries (39-77%), followed by the Nanotrap Microbiome particles (24%), electronegative filtration with a phosphate buffered saline with 20% Tween 80 elution (22%), and Envirocheck HV capsule filtration (13%). IMS was found to be unsuitable due to interference from the wastewater matrix, significantly reducing recovery rates to 0.03 to 4%. DNA yields were highest with bead-beating pretreatment with either the DNeasy Powersoil Pro kit (314 gc/μL DNA) or the QIAamp DNA Mini kit (238 gc/μL DNA). In contrast, freeze-thaw pretreatment reduced DNA yields to under 92 gc/μL DNA, likely through DNA degradation. This study is amongst the first to compare different concentration methods, including Nanotrap Microbiome particles, and DNA extraction methods that can be utilized forCryptosporidiumspp. wastewater surveillance, highlighting the importance of method selection for accurate detection and quantification.
Structural Requirements for Activity of Mind bomb1 in Notch Signaling
Authors: Cao Ruili , Gozlan Oren , Tveriakhina Lena , Zhou Haixia , Jiang Hanjie , Cole Philip A. , Aster Jon C. , Sprinzak David , Blacklow Stephen C.
Published: March 2024

Mind bomb 1 (MIB1) is a RING E3 ligase that ubiquitinates Notch ligands, a necessary step for induction of Notch signaling. The structural basis for binding of the JAG1 ligand by the N-terminal region of MIB1 is known, yet how the ankyrin (ANK) and RING domains of MIB1 cooperate to catalyze ubiquitin transfer from E2∼Ub to Notch ligands remains unclear. Here, we show that the third RING domain and adjacent coiled coil region of MIB1 (ccRING3) drives MIB1 dimerization and that ubiquitin transfer activity of MIB1 relies solely on RING3. We report x-ray crystal structures of a UbcH5B-ccRING3 complex as a fusion protein and of the ANK region. Directly tethering the N-terminal region to ccRING3 forms a minimal MIB1 protein, which is sufficient to induce a Notch response in receiver cells. Together, these studies define the functional elements of an E3 ligase needed for ligands to induce a Notch signaling response.
O-GlcNAcylation of FOXK1 orchestrates the E2F pathway and promotes oncogenesis
Authors: Masclef Louis , Ahmed Oumaima , Iannantuono Nicholas , Gagnon Jessica , Gushul-Leclaire Mila , Boulay Karine , Estavoyer Benjamin , Echbicheb Mohamed , Poy Marty , Ali Boubacar Kalidou , Boubekeur Amina , Menggad Saad , Schcolnik-Cabrera Alejandro , Balsalobre Aurelio , Bonneil Eric , Thibault Pierre , Hulea Laura , Tanaka Yoshiaki , Antoine-Mallette Frédérick , Drouin Jacques , Affar El Bachir
Published: March 2024

Gene transcription is a highly regulated process, and deregulation of transcription factors activity underlies numerous pathologies including cancer. Albeit near four decades of studies have established that the E2F pathway is a core transcriptional network that govern cell division in multi-cellular organisms1,2, the molecular mechanisms that underlie the functions of E2F transcription factors remain incompletely understood. FOXK1 and FOXK2 transcription factors have recently emerged as important regulators of cell metabolism, autophagy and cell differentiation3–6. While both FOXK1 and FOXK2 interact with the histone H2AK119ub deubiquitinase BAP1 and possess many overlapping functions in normal biology, their specific functions as well as deregulation of their transcriptional activity in cancer is less clear and sometimes contradictory7–13. Here, we show that elevated expression of FOXK1, but not FOXK2, in primary normal cells promotes transcription of E2F target genes associated with increased proliferation and delayed entry into cellular senescence. FOXK1 expressing cells are highly prone to cellular transformation revealing important oncogenic properties of FOXK1 in tumor initiation. High expression of FOXK1 in patient tumors is also highly correlated with E2F gene expression. Mechanistically, we demonstrate that FOXK1, but not FOXK2, is specifically modified by O-GlcNAcylation. FOXK1 O-GlcNAcylation is modulated during the cell cycle with the highest levels occurring during the time of E2F pathway activation at G1/S. Moreover, loss of FOXK1 O-GlcNAcylation impairs FOXK1 ability to promote cell proliferation, cellular transformation and tumor growth. Mechanistically, expression of FOXK1 O-GlcNAcylation-defective mutants results in reduced recruitment of BAP1 to gene regulatory regions. This event is associated with a concomitant increase in the levels of histone H2AK119ub and a decrease in the levels of H3K4me1, resulting in a transcriptional repressive chromatin environment. Our results define an essential role of O-GlcNAcylation in modulating the functions of FOXK1 in controlling the cell cycle of normal and cancer cells through orchestration of the E2F pathway.
Structural architecture of amyloid-β oligomers, curvilinear protofibrils and annular assemblies, imaged by cryo-EM and cryo-ET
Authors: Liang Ruina , Torres-Flores Andrea P. , Qi Shang , Khursheed Anum , Tian Yao , Szwedziak Piotr , Baker Mark D. , Volkov Vladimir A. , Darbari Vidya C. , Viles John H.
Published: March 2024

Small prefibrillar structures of the amyloid-β peptide (Aβ) are believed to be central to cytotoxicity in Alzheimer’s disease, the most common form of dementia. A snapshot of these prefibrillar assemblies has therefore been characterized using a combination of cryo-ET and cryo-EM single particle analysis. This has facilitated an understanding of the relationship between, oligomers, curvilinear protofibrils and annular assemblies. A highly consistent diameter for all curvilinear protofibrils and oligomers of 28 Å, indicates that these assemblies are simply structural extensions from the smaller oligomers. Furthermore, their basic crosssection suggests mature amyloid fibrils might be initiated by the lateral binding of two curvilinear protofibrils.Ab-initio3D reconstruction also reveals ring-shaped annular assemblies. These possess a central internal channel,ca. 14 Å in diameter and 54 Å long, which is capable of traversing lipid membranes. Large conductance recorded using patch-clamp electrophysiology, match the internal diameter of the Aβ annular architecture.
Structure and RNA-binding of the helically extended Roquin CCCH-type zinc finger
Authors: Tants Jan-Niklas , Oberstrass Lasse , Weigand Julia E. , Schlundt Andreas
Published: March 2024

Zinc finger (ZnF) domains appear in a pool of structural contexts and despite their small size achieve varying target specificities, covering single-stranded and double-stranded DNA and RNA as well as proteins. Combined with other RNA-binding domains, ZnFs enhance affinity and specificity of RNA-binding proteins (RBPs). The ZnF-containing immunoregulatory RBP Roquin initiates mRNA decay, thereby controlling the adaptive immune system. Its unique ROQ domain shape-specifically recognizes stem-looped cis-elements in mRNA 3’-untranslated regions (UTR). The N-terminus of Roquin contains a RING domain for protein-protein interactions and a ZnF, which was suggested to play an essential role in RNA decay by Roquin. The ZnF domain boundaries, its RNA motif preference and its interplay with the ROQ domain have remained elusive, also driven by the lack of high-resolution data of the challenging protein. We provide the solution structure of the Roquin-1 ZnF and use an RBNS-NMR pipeline to show that the ZnF recognizes AU-rich elements (ARE). We systematically refine the contributions of adenines in a poly(U)-background to specific complex formation. With the simultaneous binding of ROQ and ZnF to a natural target transcript of Roquin, our study for the first time suggests how Roquin integrates RNA shape and sequence specificity through the ROQ-ZnF tandem.
EXCRETE enables deep proteomics of the microbial extracellular environment
Authors: Russo David A. , Oliinyk Denys , Pohnert Georg , Meier Florian , Zedler Julie A. Z.
Published: March 2024

Extracellular proteins play a significant role in shaping microbial communities which, in turn, can impact ecosystem function, human health, and biotechnological processes. Yet, for many ubiquitous microbes, there is limited knowledge regarding the identity and function of secreted proteins. Here, we introduce EXCRETE (enhanced exoproteome characterization by mass spectrometry), a workflow that enables comprehensive description of microbial exoproteomes from minimal starting material. Using cyanobacteria as a case study, we benchmark EXCRETE and show a significant increase over current methods in the identification of extracellular proteins. Subsequently, we show that EXCRETE can be miniaturized and adapted to a 96-well high-throughput format. Application of EXCRETE to cyanobacteria from different habitats (Synechocystissp. PCC 6803,Synechococcussp. PCC 11901, andNostoc punctiformePCC 73102), and in different cultivation conditions, identified up to 85% of all predicted secreted proteins. Finally, functional analysis reveals that cell envelope maintenance and nutrient acquisition are central functions of the cyanobacterial secretome. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and point to a functional conservation of the secretome across freshwater, marine, and terrestrial species.
Evaluation ofPeregrinus maidis transformer-2as a target for CRISPR-based control
Authors: Wang Yu-Hui , Rivera Dina Espinoza , Klobasa William , Lorenzen Marcé D.
Published: March 2024

The corn planthopper,Peregrinus maidis, is an economically important pest of corn and sorghum. Here we report the initial steps towards developing a CRISPR-based control method, precision guided sterile insect technique (pgSIT), for this hemipteran pest. Specifically, we evaluated the potential oftransformer-2(tra-2) as a target for sterilizing insects. First, we identifiedtra-2transcripts within ourP. maidistranscriptome database and performed RNA interference (RNAi) to confirm functional conservation. RNAi-mediated knockdown ofPmtra-2in nymphs transformed females into pseudomales with deformed ovipositors resembling male claspers. While males showed no overt difference in appearance, they were indeed sterile. Importantly, the results were similar to those observed in another planthopper,Nilaparvata lugens. We also used CRISPR/Cas9 genome editing to assess the impact oftra-2knockout in injectees. CRISPR-mediated knockout ofPmtra-2had lethal effects on embryos, and hence not many injectees reached adulthood. However, mosaic knockout ofPmtra-2did impact female and male fertility, which supports the use oftra-2as a target for pgSIT in this hemipteran species.