bluuebunny/crossref_metadata_2025 huggingface dataset:
Fcγ-receptor-independent controlled activation of CD40 canonical signaling by novel therapeutic antibodies for cancer therapy
Authors: Reitinger Carmen , Beckmann Karsten , Carle Anna , Blümle Eva , Jurkschat Nicole , Paulmann Claudia , Prassl Sandra , Kazandijan Linda V. , Nimmerjahn Falk , Fischer Stephan
Published: January 2023

Activation of CD40-mediated signaling in antigen-presenting cells is a promising therapeutic strategy to promote immune responses against tumors. Agonistic anti-CD40 antibodies currently in development require Fcγ-receptor-mediated crosslinking of CD40 molecules for meaningful activation of CD40 signaling but have limitations due to dose-limiting toxicities. Here we describe the identification of CD40 antibodies which strongly stimulate antigen-presenting cells in an entirely Fc-independent manner. These novel Fc-silenced anti-CD40 antibodies induce upregulation of costimulatory receptors CD80 and CD86 and cytokine release by dendritic cells with an efficacy exceeding that of existing antibodies. Binding to the CD40L interaction region on CD40 appears to be a prerequisite to achieving such strong activities. Finally, the most active identified anti-CD40 antibody shows evidence of activity in terms of the expected markers of canonical CD40 signaling when injected in humanized mice. There are no signs of obvious toxicities whereas the clinical-stage anti-CD40 antibody CP-870,893 induced severe signs of toxicity in these animals despite a lower dose compared with the novel Fc-silenced canonical agonist. These studies thus demonstrate potent activation of antigen-presenting cells with anti-CD40 antibodies lacking Fcγ-receptor-binding activity and open the possibility of an efficacious and safe combination therapy for cancer patients.

One Sentence Summary

Treatment of antigen-presenting cells and humanized mice with novel Fc-silenced CD40 antibodies demonstrates an Fcγ-receptor-independent canonical agonistic mode of action for therapeutic use.
Astrocytic control of extra-cellular GABA drives circadian time-keeping in the suprachiasmatic nucleus
Authors: Patton A. P. , Morris E.L. , McManus D. , Wang H. , Li Y. , Chin J.W. , Hastings M. H.
Published: January 2023

The hypothalamic suprachiasmatic nucleus (SCN) is the master mammalian circadian clock. Its cell-autonomous timing mechanism, a transcriptional/translational feedback loop (TTFL), drives daily peaks of neuronal electrical activity. Intercellular signals synchronize and amplify TTFL and electrical rhythms across the circuit. SCN neurons are GABAergic, but the role of GABA in circuit-level time-keeping is unclear. SCN slices expressing the GABA sensor iGABASnFR demonstrate a circadian oscillation of extracellular GABA ([GABA]e) that, counter-intuitively, runs in antiphase to neuronal activity, peaking in circadian night. Resolving this paradox, we found that [GABA]eis regulated by GABA transporters (GATs), uptake peaking during circadian day. This is mediated by the circadian-regulated, astrocytically expressed GAT3 (Slc6a11). Clearance of [GABA]ein circadian day facilitates neuronal firing, neuropeptide release and TTFL rhythmicity. Moreover, genetic complementation demonstrated that the astrocytic TTFL can alone drive [GABA]erhythms. Thus, astrocytic clocks maintain SCN circadian time-keeping by temporally controlling GABAergic inhibition of SCN neurons.
The chromatin modulating NSL complex regulates genes and pathways genetically linked to Parkinson’s disease
Authors: Hicks Amy R. , Reynolds Regina , O’Callaghan Ben , Ruiz Sonia Garcia , Martinez Ana Luisa Gil , Botia Juan , Plun-Favreau Helene , Ryten Mina
Published: January 2023

Genetic variants conferring risk for Parkinson’s disease have been highlighted through genome-wide association studies, yet exploration of their specific disease mechanisms is lacking. Two Parkinson’s disease candidate genes,KAT8andKANSL1, identified through genome-wide studies and a PINK1-mitophagy screen, encode part of the histone acetylating non-specific lethal complex. This complex localises to the nucleus, where it has a role in transcriptional activation, and to mitochondria, where it has been suggested to have a role in mitochondrial transcription. In this study, we sought to identify whether the non-specific lethal complex has potential regulatory relationships with other genes associated with Parkinson’s disease in human brain.

Correlation in the expression of non-specific lethal genes and Parkinson’s disease-associated genes was investigated in primary gene co-expression networks utilising publicly available transcriptomic data from multiple brain regions (provided by the Genotype-Tissue Expression Consortium and UK Brain Expression Consortium), whilst secondary networks were used to examine cell-type specificity. Reverse engineering of gene regulatory networks generated regulons of the complex, which were tested for heritability using stratified linkage disequilibrium score regression and then validatedin vitrousing the QuantiGene multiplex assay.

Significant clustering of non-specific lethal genes was revealed alongside Parkinson’s disease-associated genes in frontal cortex primary co-expression modules. Both primary and secondary co-expression modules containing these genes were enriched for mainly neuronal cell types. Regulons of the complex contained Parkinson’s disease-associated genes and were enriched for biological pathways genetically linked to disease. When examined in a neuroblastoma cell line, 41% of prioritised gene targets showed significant changes in mRNA expression followingKANSL1orKAT8perturbation.

In conclusion, genes encoding the non-specific lethal complex are highly correlated with and regulate genes associated with Parkinson’s disease. Overall, these findings reveal a potentially wider role for this protein complex in regulating genes and pathways implicated in Parkinson’s disease.
Novel orthotopic model of neuroblastoma in RNU homozygous rats
Authors: Sever ReidAnn , Rosenblum Lauren Taylor , Schmidt Lori , Hartwick Sean , Schwab Kristina , Wu Yijen , Raphael Itay , Reyes Miguel , Edwards Wilson Barry , Malek Marcus , Kohanbash Gary
Published: January 2023

Neuroblastoma, the most common extracranial solid malignancy in children, accounts for 15% of pediatric cancer deaths despite multimodal therapy including surgical resection. Unfortunately, complete surgical resection remains challenging due to encasement of major neurovascular structures, unclear tumor margins, and remote nodal disease. While mouse models of neuroblastoma are extremely valuable for studying tumor biology and medical treatments, the small size renders the mouse model insufficient to evaluate novel surgical therapy.

Here, we have developed a novel rat model of neuroblastoma to facilitate further development of surgical treatment. Human neuroblastoma cells (SK-N-BE(2)) were injected into the adrenal gland of RNU nude rats. They developed 2 cm xenograft tumors at 5 weeks which were easily identifiable on MRI imaging and on visual inspection. The rats began losing weight and neared end stage at 7 weeks, at which point surgical resection was attempted. While surgical resection was technically feasible, the rats were too frail to survive surgery at the late stage. The pathology of the tumors was consistent with neuroblastoma: small round blue cells with strong PHOX2B staining. Thus, we present a novel rat neuroblastoma model that can be used for development of surgical techniques, such as the use of intraoperative contrast agents.
A dual MTOR/NAD+ acting gerotherapy
Authors: Li Jinmei , Kumar Sandeep , Miachin Kirill , Bean Nicholas L. , Halawi Ornella , Lee Scott , Park JiWoong , Pierre Tanya H. , Hor Jin-Hui , Ng Shi-Yan , Wallace Kelvin J. , Rindtorff Niklas , Miller Timothy M. , Niehoff Michael L. , Farr Susan A. , Kletzien Rolf F. , Colca Jerry , Tanis Steven P. , Chen Yana , Griffett Kristine , McCommis Kyle S. , Finck Brian N. , Peterson Tim R.
Published: January 2023

The geroscience hypothesis states that a therapy that prevents the underlying aging process should prevent multiple aging related diseases. The mTOR (mechanistic target of rapamycin)/insulin and NAD+ (nicotinamide adenine dinucleotide) pathways are two of the most validated aging pathways. Yet, it’s largely unclear how they might talk to each other in aging. In genome-wide CRISPRa screening with a novel class of N-O-Methyl-propanamide-containing compounds we named BIOIO-1001, we identified lipid metabolism centering on SIRT3 as a point of intersection of the mTOR/insulin and NAD+ pathways. In vivo testing indicated that BIOIO-1001 reduced high fat, high sugar diet-induced metabolic derangements, inflammation, and fibrosis, each being characteristic of non-alcoholic steatohepatitis (NASH). An unbiased screen of patient datasets suggested a potential link between the anti-inflammatory and anti-fibrotic effects of BIOIO-1001 in NASH models to those in amyotrophic lateral sclerosis (ALS). Directed experiments subsequently determined that BIOIO-1001 was protective in both sporadic and familial ALS models. Both NASH and ALS have no treatments and suffer from a lack of convenient biomarkers to monitor therapeutic efficacy. A potential strength in considering BIOIO-1001 as a therapy is that the blood biomarker that it modulates, namely plasma triglycerides, can be conveniently used to screen patients for responders. More conceptually, to our knowledge BIOIO-1001 is a first therapy that fits the geroscience hypothesis by acting on multiple core aging pathways and that can alleviate multiple conditions after they have set in.

Brief Summary

These studies characterize a novel gerotherapy, BIOIO-1001, that identifies lipid metabolism as an intersection of the mTOR and NAD+ pathways.
Fatty liver-mediated glycine restriction impairs glutathione synthesis and causes hypersensitization to acetaminophen
Authors: Ghrayeb Alia , Agranovich Bella , Peled Daniel , Finney Alexandra C. , Abramovich Ifat , Garcia Jonatan Fernandez , Traylor James , Drucker Shani , Fernandes Sara Isabelle , Weissman Natan , Chen Y. Eugene , Rom Oren , Mor Inbal , Gottlieb Eyal
Published: January 2023

Non-alcoholic fatty liver disease (NAFLD) affects nearly one third of the population worldwide. Understanding metabolic pathways involved can provide insights into disease progression. Untargeted metabolomics of livers from mice with early-stage steatosis indicated a decrease in methylated metabolites suggesting altered one carbon metabolism. The levels of glycine, a central component of one carbon metabolism, were lower in steatotic mice, in line with clinical evidence. Isotope tracing studies demonstrated that increased synthesis of serine from glycine is the underlying cause for glycine limitation in fatty livers. Consequently, the low glycine availability in steatotic livers impaired glutathione (GSH) synthesis under oxidative stress induced by acetaminophen (APAP), enhancing hepatic toxicity. Glycine supplementation mitigated acute liver damage and overall toxicity caused by APAP in fatty livers by supportingde novoGSH synthesis. Thus, early metabolic changes in NAFLD that lead to glycine depletion sensitize mice to xenobiotic toxicity even at a reversible stage of NAFLD.
The absence of a neurogenic response to a repeated concussive-like injury in mice
Authors: Weingarten A. , Madjou T. M. , Yeturu S.N. , Samudrala N. , Villasana L.E.
Published: January 2023

In response to traumatic brain injury (TBI), the brain increases its generation of new neurons (neurogenesis) within the hippocampus, a brain region critical for learning and memory. Because neurogenesis plays important roles in learning and memory, post-traumatic neurogenesis may represent an adaptive response contributing to cognitive recovery. In contrast to increases in neurogenesis acutely after injury, levels of neurogenesis become impaired long after TBI. And although chronic deficits in neurogenesis after TBI have been reported by multiple groups, it is unknown whether the hippocampus remains capable of eliciting another neurogenic response to a repeated injury. To address this lack of knowledge, we used a closed head injury model that reflects a concussive-like injury or a mild TBI (mTBI) and assessed levels of neurogenesis in male and female adult mice. Mice received one or two mTBI or sham treatments 3 weeks apart. Compared to mice with a single mTBI, proliferation and neurogenesis were blunted in mice that received a second mTBI. This impaired response was unlikely due to a short recovery time between the two mTBIs as the proliferative response to a second mTBI was also impaired when two months were allowed between injuries. We further found that proliferation was impaired in the radial-glia like cells despite an intact pool. The mice that received two mTBIs also had a blunted intensity in their GFAP staining. In contrast to reports of aberrant post-TBI neurogenesis, we found that the neurons born after mTBI had normal dendritic branches. Lastly, we found that impairments in the inability to mount a neurogenic response after a second mTBI were associated with deficits in neurogenesisstrategy flexibility in the reversal water maze task. Our data suggests that a loss in the neurogenic response could in part contribute to worse cognitive recovery after a repeated concussion. These data may expose a novel target to help improve long-term cognitive outcome following repeated brain injury.
Smart utilization of betaine lipids in giant clamTridacna crocea
Authors: Sakai Ryuichi , Goto-Inoue Naoko , Yamashita Hiroshi , Aimoto Naoya , Kitai Yuto , Maruyama Tadashi
Published: January 2023

The giant clamTridacna croceainhabits shallow tropical seas with poorly nourished water and severe sun irradiation. They harbor symbiotic algae “zooxanthellae” (dinoflagellate family Symbiodiniaceae) in the mantle tissue and are thought to thrive in this extreme environment by utilizing photosynthetic products from the algae. However, there is no measure of the detailed metabolic flow between the host and symbiont to evaluate one of the most successful symbiotic relationships in nature. Here, we employed liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based lipidomics and Fourier-transform ion cyclotron resonance MS imaging onT. croceatissues, revealing a unique lipid composition and localization with their symbiont algae. We discovered that the non-phosphorous microalgal betaine lipid diacylglycerylcarboxy-hydroxymethylcholine (DGCC) was present in all tissues and organs ofT. croceato approximately the same degree as phosphatidylcholine (PC). The fatty acid composition of DGCC was similar to that of PC, which is thought to have physiological roles similar to that of DGCC. MS imaging showed co-localization of these lipids throughout the clam tissues. Glycerylcarboxy-hydroxymethylcholine (GCC), the deacylated derivative of DGCC, was found to be a free form of DGCC in the clams and was isolated and characterized from cultured Symbiodiniaceae strains that were isolated from giant clams. These results strongly suggest that giant clams have evolved to smartly utilize DGCCs, phosphorus-free polar lipids of symbiont algae, as essential membrane components to enable them to thrive in oligotrophic coral reef milieu.
Non-glycosylated IGF2 prohormones are more mitogenic than native IGF2
Authors: Potalitsyn Pavlo , Mrázková Lucie , Selicharová Irena , Tencerová Michaela , Ferenčáková Michaela , Chrudinová Martina , Brzozowski Andrzej Marek , Marek Aleš , Kaminský Jakub , Jiráček Jiří , Žáková Lenka
Published: January 2023

Insulin-like Growth Factor-2 (IGF2) is important for the regulation of human embryonic growth and development, and for adults’ physiology. Incorrect processing of the IGF2 precursor, pro-IGF2(156), leads to the formation of two IGF2 proforms, big-IGF2(87) and big-IGF2(104). Unprocessed and mainly non-glycosylated IGF2 proforms are found at abnormally high levels in certain diseases, but their mode of action is still unclear. Here, we found that pro-IGF2(156) has the lowest ability to form its inactivating complexes with IGF-Binding Proteins and has higher proliferative properties in cells than IGF2 and other IGF prohormones. We also showed that big-IGF2(104) has a seven-fold higher binding affinity for the IGF2 receptor than IGF2, and that pro-IGF2(87) binds and activates specific receptors and stimulates cell growth similarly to the mature IGF2. The properties of these pro-IGF2 forms, especially of pro-IGF2(156) and big-IGF2(104), indicate them as hormones that may be associated with human diseases related to the accumulation of IGF-2 proforms in the circulation.
Dual Adversarial Deconfounding Autoencoder for joint batch-effects removal from multi-center and multi-scanner radiomics data
Authors: Cavinato Lara , Massi Michela Carlotta , Sollini Martina , Kirienko Margarita , Ieva Francesca
Published: January 2023

Medical imaging represents the primary tool for investigating and monitoring several diseases, including cancer. The advances in quantitative image analysis have developed towards the extraction of biomarkers able to support clinical decisions. To produce robust results, multi-center studies are often set up. However, the imaging information must be denoised from confounding factors – known as batch-effect – like scanner-specific and center-specific influences. Moreover, in non-solid cancers, like lymphomas, effective biomarkers require an imaging-based representation of the disease that accounts for its multi-site spreading over the patient’s body. In this work, we address the dual-factor deconfusion problem and we propose a deconfusion algorithm to harmonize the imaging information of patients affected by Hodgkin Lymphoma in a multi-center setting. We show that the proposed model successfully denoises data from domain-specific variability while it coherently preserves the spatial relationship between imaging descriptions of peer lesions, which is a strong prognostic biomarker for tumor heterogeneity assessment. This harmonization step allows to significantly improve the performance in prognostic models, enabling building exhaustive patient representations and delivering more accurate analyses. This work lays the groundwork for performing large-scale and reproducible analyses on multi-center data that are urgently needed to convey the translation of imaging-based biomarkers into the clinical practice as effective prognostic tools. The code is available on GitHub at thislink
Sex differences in neurotransmitter levels in different brain regions after acute and chronic morphine treatment in mice
Authors: Gabel Florian , Hovhannisyan Volodya , Berkati Abdel-Karim , Andry Virginie , Goumon Yannick
Published: January 2023

Background and Purpose

Pain management is a major health burden. Pain results from the integration of the nociceptive message and neuronal communication relying on neurotransmitters such as glutamate, γ-aminobutyric acid (GABA), dopamine, noradrenaline and serotonin in brain regions including the periaqueductal gray (PAG), the nucleus accumbens (Nac), the caudate-putamen (Cpu) and the amygdala. Morphine remains the gold standard painkiller for severe painviathe activation of the mu opioid receptors. However, among side effects, morphine chronic treatment lead to antinociceptive tolerance. As antinociceptive tolerance might be linked to neurotransmission dysregulation, we have compared various neurotransmitter concentrations in acutevschronic morphine conditions in the amygdala, PAG, Cpu, and the Nac of male and female mice.

Experimental approach

Sex differences in morphine antinociception and tolerance were assessed using the tail-immersion test. The behavioural effects of acute and chronic morphine treatments, as well as sex differences in the levels of dopamine, serotonin, noradrenaline, glutamate and GABA in the amygdala, PAG, Cpu, and the Nac were determined by an absolute quantification LC-MS/MS approach using the isotopic dilution method.

Key results

This study indicates, as previously reported, that female mice are less sensitive to morphine and develop morphine antinociceptive tolerance earlier than males (ED50 of 5.5±0.24 daysvs1.54±0.11 days, respectively). However, the rate at which the tolerance developed did not differ between both sex. We have found major differences in dopamine, serotonin, noradrenaline, glutamate and GABA levels between female and male mice in the amygdala, PAG, Cpu, and the Nac. Finally, no major effect of anti-nociceptive tolerance induced by chronic morphine was observed compared to acute administration of morphine.

Conclusion

Neurotransmitter differences are attributable mainly to sex differences in pain-related CNS regions. However, the impacts of morphine anti-nociceptive tolerance on dopamine, serotonin, noradrenaline, glutamate and GABA contents appeared to be limited.
Volumetric refractive index measurement and quantitative density analysis of mouse brain tissue with sub-micrometer spatial resolution
Authors: Lee Ariel J. , Kim Young Seo , Kim Joon-Goon , Hugonnet Herve , Lee Moosung , Ku Taeyun , Park YongKeun
Published: January 2023

High-resolution structural imaging of brain tissue is important for neuroscience research. However, conventional approaches have several limitations, such as the need for exogenous staining, limited accessibility to volumetric information, and qualitative analysis. Herein, we present high-resolution label-free volumetric imaging and analysis of mouse brain tissue using three-dimensional quantitative phase imaging. Measurement of the refractive index distribution of tissue enables direct imaging of the cellular and subcellular structures. Quantification of subcellular organelles is performed in the anatomical regions of the somatosensory cortex, corpus callosum, caudoputamen, and thalamus regions.
Mechanical models affecting beetle horn remodeling
Authors: Matsuda Keisuke , Adachi Haruhiko , Gotoh Hiroki , Inoue Yasuhiro , Kondo Shigeru
Published: January 2023

Clarifying the mechanisms of shape alteration by insect metamorphosis is important for comprehending exoskeletal morphogenesis. The large horn of the Japanese rhinoceros beetleTrypoxylus dichotomusis the result of drastic metamorphosis, wherein it appears as a rounded shape via pupation and then undergoes remodeling into an angular adult shape. However, the mechanical mechanisms of this remodeling process remain unknown. In this study, we investigated the remodeling mechanisms of the Japanese rhinoceros beetle horn by developing a physical simulation. We identified three factors contributing to remodeling by biological experiments—ventral adhesion, uneven shrinkage, and volume reduction—which were demonstrated to be crucial to the transformation by a physical simulation. We also corroborated our findings by applying the simulation to the stag beetle’s mandibular remodeling. These results indicate that the physical simulation is applicable to pupal remodeling in other beetles, and the morphogenic mechanisms could explain various exoskeletal shapes.

Significance statement

The metamorphosis in insects is a mysterious process. By metamorphosis, insects sometimes change their shape dramatically. The head horn of the Japanese rhinoceros beetle is one of the most famous examples of metamorphosis. In larva-to-pupa molting, the horn appears suddenly, caused by the “furrow formation and unfolding” mechanism. The unfolding process makes the pupal horn rounded. However, pupa-to-adult molting transforms the rounded shape into an angular shape. In this paper, we investigated the mechanisms of the transformation. We extracted factors contributing to it through observations and experiments and developed a physical simulation. It could reproduce the adult shape from the pupal shape and could be a general model for the pupa-adult transformation of beetles.
MRI-assessed locus coeruleus contrast and functional response are not associated in young and late middle-aged individuals
Authors: Berger Alexandre , Koshmanova Ekaterina , Beckers Elise , Sharifpour Roya , Paparella Ilenia , Campbell Islay , Mortazavi Nasrin , Balda Fermin , Yi Yeo-Jin , Lamalle Laurent , Dricot Laurence , Phillips Christophe , Jacobs Heidi IL , Talwar Puneet , Tahry Riëm El , Sherif Siya , Vandewalle Gilles
Published: January 2023

The brainstem locus coeruleus (LC) influences a broad range of brain processes, including cognition. The so-called LC contrast is an accepted marker of the integrity of the LC that consists of a local hyperintensity on specific Magnetic Resonance Imaging (MRI) structural images. The small size of the LC has, however, rendered its functional characterization difficult in humans, including in aging. A full characterization of the structural and functional characteristics of the LC in healthy young and late middle-aged individuals is needed to determine to potential roles of the LC in different medical conditions. Here, we wanted to determine whether the activation of the LC in a mismatch negativity task changes in aging and whether the LC functional response was associated to the LC contrast. We used Ultra-High Field (UHF) 7-Tesla functional MRI (fMRI) to record brain response during an auditory oddball task in 53 healthy volunteers, including 34 younger (age: 22.15y ± 3.27; 29 women) and 19 late middle-aged (age: 61.05y ± 5.3; 14 women) individuals. Whole-brain analyses confirmed brain responses in the typical cortical and subcortical regions previously associated with mismatch negativity. When focusing on the brainstem, we found a significant response in the rostral part of the LC probability mask generated based on individual LC images. Although bilateral, the activation was more extensive in the left LC. Individual LC activity was not significantly different between young and late middle-aged individuals. Critically, while the LC contrast was higher in older individuals, the functional response of the LC was not associated with its contrast. These findings show that the age-related alterations of the LC structural integrity may not necessarily be related to changes in its functional response. The results further indicate that LC responses could remain stable in healthy individuals aged 20 to 70.
Modulatory Effect of Levodopa on the Basal Ganglia-Cerebellum Connectivity in Parkinson’s Disease
Authors: Abulikemu Subati , Tai Yen F , Haar Shlomi
Published: January 2023

Levodopa has remained the mainstay of medical therapy for Parkinson’s disease since its development in the 1980s. However, long-term medication use is associated with declining clinical efficacy and the emergence of motor complications. Unveiling the effects of levodopa on brain functional reorganisation at a relatively early treatment phase is therefore imperative to inform the optimisation of Parkinson’s therapeutics. In this study, we comprehensively investigated levodopa’s modulation on the resting-state functional connectivity in the cortico- basal ganglia-cerebellum system at regional and network levels, with dual cross-sectional and longitudinal designs. The data was extracted from the Parkinson’s Progression Marker Initiative (PPMI) dataset. The cross-sectional patient groups comprised 17 Parkinson’s patients on stable levodopa medication and 15 drug-naïve patients, while the longitudinal set included 14 Parkinson’s patients measured at both drug-naïve and levodopa-medicated conditions. With nodes defined across cortical, basal ganglia, and cerebellar networks, we conducted univariate comparisons of the internodal connectivity strength between the medication conditions using nonparametric permutation. At the network level, we computed multivariate combinations of individual connections within and between the networks, followed by an assessment of their discriminative capabilities on patients’ medication classes using supervised machine learning. The univariate seed-based approach showed no statistically significant effect of levodopa in either dataset. However, the network connectivity pattern between basal ganglia and the cerebellum displayed a robust classification power in the longitudinal dataset and a similar trend was observed in the cross-sectional. The role of the cerebellum is often overlooked in previous functional integration investigations of Parkinson’s disease and levodopa effects. Considering the recent evidence suggesting the bidirectional communications between the cerebellum and basal ganglia networks, our study provides further insight into the importance of inter-network functional connectivity in Parkinson’s, as well as in the functional and plastic processes following levodopa medication.
G-quadruplex DNA structures mediate non-autonomous instruction of breast tumour microenvironments
Authors: Hunold Pascal , Hoehne Michaela N , Kiljan Martha , van Ray Olivia , Herter Jan , Herter-Sprie Grit S , Hänsel-Hertsch Robert
Published: January 2023

Breast cancer is characterised by genetic and epigenetic alterations, such as G-quadruplex (G4) DNA secondary structures. Here, we uncover differentially enriched G4 structure-forming regions (∆G4Rs) and interlinked transcriptomes in the tumour microenvironment (TME) of breast cancer PDX modelsin vivo. We show that well-defined breast cancer cell models non-autonomously instruct ∆G4Rs and transcriptomes in the epigenomes of primary macrophagesin vitro. Mechanistically, we uncover that TNBC secretes, amongst other factors, glucocorticoids to promote G4-linked activation ofoctamer-binding transcription factor 1(OCT-1) and thereby reprogramme macrophages into an immunosuppressed and immunosuppressive state. This epigenetic mechanism is of clinical importance since instructed macrophages selectively associate with the triple-negative breast cancer (TNBC) basal-like 2 (BL2) subtype and with the distinct TNBC molecular signature derived from 2,000 primary breast cancer samples. Altogether, our data suggest that G4 formation is not only prevalent in breast cancer genomes but relevant in their TMEs as well, which is of clinical importance for cancer stratification and the discovery of novel actionable drivers.
VAP spatially stabilizes dendritic mitochondria to locally fuel synaptic plasticity
Authors: Bapat Ojasee , Purimetla Tejas , Kruessel Sarah , Thum Christina , Rupprecht Fiona , Shah Monil , Langer Julian D. , Rangaraju Vidhya
Published: January 2023

Synapses are pivotal sites of memory formation and undergo plasticity in response to external inputs. Consequently, synapses are hotspots of energy consumption and are susceptible to dysfunction when their energy supplies are perturbed. Mitochondria are stabilized near synapses via cytoskeletal tethering and serve as local energy supplies to fuel synaptic plasticity. However, the mechanisms that tether and stabilize neuronal mitochondria for long durations and determine the spatial dendritic segment supported during synaptic plasticity are unknown. We identified a list of novel mitochondrial-cytoskeletal interactors in neurons using APEX-based proximity labeling. We narrowed down the protein candidates that exclusively tether mitochondria to actin near postsynaptic spines using high-resolution Airyscan confocal imaging. We find that VAP, the vesicle-associated membrane protein-associated protein implicated in Amyotrophic Lateral Sclerosis and interacts with the endoplasmic reticulum, stabilizes mitochondria via actin near the spines. To test if the VAP-dependent stable mitochondrial compartments can locally support synaptic plasticity, we investigated individual spines stimulated by two-photon glutamate uncaging for spine plasticity induction and their adjacent spines. We find that, along with actin, VAP functions as a spatial stabilizer of mitochondrial compartments to sustain synaptic plasticity for up to ~60 min and as a spatial ruler that determines the ~30 μm length of the dendritic segment supporting synaptic plasticity.
QC-GN2oMS2: a Graph Neural Net for High Resolution Mass Spectra Prediction
Authors: Overstreet Richard , King Ethan , Nguyen Julia , Ciesielski Danielle
Published: January 2023

Predicting the mass spectrum of a molecular ion is often accomplished via three generalized approaches: rules-based methods for bond breaking, deep learning, or quantum chemical (QC) modeling. Rules-based approaches are often limited by the conditions for different chemical subspaces and perform poorly under chemical regimes with few defined rules. Quantum chemical modeling is theoretically robust but requires significant amounts of computational time to produce a spectrum for a given target. Among deep learning techniques, graph neural networks (GNNs) have performed better than previous work with fingerprint-based neural networks in mass spectral prediction.1To explore this technique further, we investigate the effects of including quantum chemically derived features as edge features in the GNN to increase predictive accuracy. The models we investigated include categorical bond order, bond force constants derived from Extended Tight-Binding (xTB) quantum chemistry, and acyclic bond dissociation energies. We evaluated these models against a control GNN with no edge features in the input graphs. Bond dissociation enthalpies yielded the best improvement with a cosine similarity score of 0.462 relative to the baseline model (0.437). In this work we also apply dynamic graph attention which improves performance on benchmark problems and supports the inclusion of edge features. Between implementations, we investigate the nature of the molecular embedding for spectral prediction and discuss the recognition of fragment topographies in distinct chemistries for further development in tandem mass spectrometry prediction.
HuR modulation with tanshinone mimics impairs LPS response in murine macrophages
Authors: Bonomo Isabelle , Assoni Giulia , Pietra Valeria La , Canarutto Giulia , Facen Elisa , Donati Greta , Zucal Chiara , Genovese Silvia , Micaelli Mariachiara , Pérez-Ràfols Anna , Robbiati Sergio , Kontoyannis Dimitris L. , De Matteo Marilenia , Fragai Marco , Seneci Pierfausto , Marinelli Luciana , Arosio Daniela , Piazza Silvano , Provenzani Alessandro
Published: January 2023

Lipopolysaccharide exposure to macrophages induces an inflammatory response that is heavily regulated at the transcriptional and post-transcriptional levels. HuR (ELAVL1) is an RNA binding protein that binds and regulates the maturation and half-life of AU/U rich elements (ARE) containing cytokines and chemokines transcripts, mediating the LPS-induced response. Here we investigated how and to what extent small molecule tanshinone mimics (TMs) inhibiting HuR-RNA interaction counteract LPS stimulus in macrophages. We show TMs exist in solution in keto-enolic tautomerism and that, by molecular dynamic calculations, the orto quinone form is the bioactive species interacting with HuR and inhibiting its binding mode vs mRNA targets. A chemical blockage of the diphenolic, reduced form as a diacetate caused the loss of activity of TMsin vitrobut resulted to prodrug-like activityin vivo. The murine macrophage cell line RAW264.7 was treated with LPS and TMs, and the modulation of cellular LPS-induced response was monitored by RNA and Ribonucleoprotein immunoprecipitation sequencing. Correlation analyses indicated that LPS induced a strong coupling between differentially expressed genes and HuR-bound genes, and that TMs reduced such interactions. Functional annotation addressed a specific set of genes involved in chemotaxis and immune response, such asCxcl10, Il1b, Cd40, andFas, with a decreased association with HuR, a reduction of their expression and protein secretion. The same effect was observed in primary murine bone marrow-derived macrophages, andin vivoin an LPS induced peritonitis model, in which the serum level of Cxcl10 and Il1b was strongly reduced, endowing TMs such asTM7noxwith remarkable anti-inflammatory propertiesin vivo.
Apparent simplicity and emergent robustness in bacterial cell cycle control
Authors: Govers Sander K. , Campos Manuel , Tyagi Bhavyaa , Laloux Géraldine , Jacobs-Wagner Christine
Published: January 2023

To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle and growth phenotypes of a fluorescently-labeledEscherichia colistrain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often found to be nutrient-dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ-ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length). Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a systems-level understanding of the design principles by whichE. coliintegrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability.
Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids
Authors: Haloi Nandan , Huang Shan , Nichols Aaron L. , Fine Eve J. , Friesenhahn Nicholas J. , Marotta Christopher B. , Dougherty Dennis A. , Lindahl Erik , Howard Rebecca J. , Mayo Stephen L. , Lester Henry A.
Published: January 2023

We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for ΔF/F0vs [nicotine] (δ-slope, 2.7 μM-1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the “candle snuffer” mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.
A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint
Authors: Singh Vidisha , Naldi Aurelien , Soliman Sylvain , Niarakis Anna
Published: January 2023

Rheumatoid arthritis (RA) is a complex autoimmune disease with an unknown aetiology. However, rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS) play a significant role in initiating and perpetuating destructive joint inflammation by expressing immuno-modulating cytokines, adhesion molecules, and matrix remodelling enzymes. In addition, RA-FLS are primary drivers of inflammation, displaying high proliferative rates and an apoptosis-resistant phenotype. Thus, RA-FLS-directed therapies could become a complementary approach to immune-directed therapies by predicting the optimal conditions that would favour RA-FLS apoptosis, limit inflammation, slow the proliferation rate and minimise bone erosion and cartilage destruction. In this paper, we present a large-scale Boolean model for RA-FLS that consists of five submodels focusing on apoptosis, cell proliferation, matrix degradation, bone erosion and inflammation. The five phenotype-specific submodels can be simulated independently or as a global model.In-silicosimulations and perturbations reproduced the expected biological behaviour of the system under defined initial conditions and input values. The model was then used to mimic the effect of mono or combined therapeutic treatments and predict novel targets and drug candidates through drug repurposing analysis.
Non-photosynthetic bacteria produce photocurrent mediated by NADH
Authors: Shlosberg Yaniv , Limwongyut Jakkarin , Moreland Alex S. , Bazan Guillermo C.
Published: January 2023

In recent years, the concern from the global climate change has driven an urgent need to develop clean energy technologies that do not involve combustion process that emit carbon into the atmosphere. A promising concept is microbial fuel cells that utilize bacteria as electron donors in a bio-electrochemical cell performing a direct electron transfer via conductive protein complexes or by secretion of redox active metabolites such as quinone or phenazine derivatives. In the case of photosynthetic bacteria (cyanobacteria) electrons can also be extracted from the photosynthetic pathway mediated mostly by NADH and NADPH. In this work, we show for the first time that the intact non-photosynthetic bacteriaEscherichia colican produce photocurrent that is enhanced upon addition of an exogenous electron mediator. Furthermore, we apply 2D-fluorescence measurement to show that NADH is released from the bacterial cells, which may apply as a native electron mediator in microbial fuel cells.
Large-scale in-cell photocrosslinking at single residue resolution reveals the molecular basis for glucocorticoid receptor regulation by immunophilins
Authors: Baischew Asat , Engel Sarah , Geiger Thomas M. , Hausch Felix
Published: January 2023

The large immunophilins FKBP51 and FKBP52 play key roles in the Hsp90-mediated maturation of steroid hormone receptors, which is crucial for stress-related disorders and correct sexual embryonic development, respectively1–3. A prominent regulatory target is the glucocorticoid receptor (GR), whose activation is repressed by FKBP514,5and facilitated by FKBP526,7. Despite their vital roles, the molecular modes of action of FKBP51 and FKBP52 are poorly understood since the transient key states of FKBP-mediated GR-regulation have remained experimentally elusive. Here we present the architecture and functional annotation of FKBP51-, FKBP52- and p23-containing Hsp90-apoGR preactivation complexes, trapped by systematic incorporation of photoreactive amino acids8,9inside human cells. The identified crosslinking sites depended on a functional Hsp90 chaperone cycle, were disrupted by GR activation, and clustered in characteristic patterns, defining the relative orientation and contact surfaces within the FKBP/p23-apoGR complexes. Strikingly, GR binding to the FKBPFK1but not the FKBPFK2domains were modulated by FKBP ligands, explaining the lack of FKBP51-mediated GR derepression by certain classes of FKBP ligands. These findings show how FKBP51 and FKBP52 differentially interact with the apoGR ligand binding domain, they explain the differentiated pharmacology of FKBP51 ligands, and provide a structural basis for the development of FKBP ligands with higher efficacy.
Determining latent features and forecasting of COVID-19 hospitalisations in Malaysia using a national patient assessment data platform: a study of machine learning modelling against expert system
Authors: Yee Hui-Jia , Boo Ivan , Tan Ian K.T. , Tan Jih Soong , Zakariah Helmi
Published: January 2023

COVID-19 had a severe impact on Malaysia, as cases increased dramatically as the pandemic spread. In order to combat the pandemic, the Ministry of Health has established a number of standard operating procedures (SOP) and started operating COVID-19 Assessment Centers (CAC). This study compares the expert system created using the current patient evaluation standards to the capabilities of machine learning approaches in capturing the potential of being admitted directly or during home quarantine, based on the different clinical symptoms and age group. Boruta is a feature selection method that is employed to rank and extract significant characteristics.

Treatment for imbalance has been carried out by under-sampling with K-Means and over-sampling with SMOTE. It appeared that the machine learning method using Random Forest would perform better than the expert systems. There are five performance metrics used in this study, i.e. accuracy, precision, recall, F1-score, and specificity. This study focused to maximize the true positive rate while minimize the false negative rates, it is to make sure that the patient who really need to be hospitalized will not be missed out. Therefore, recall becomes the main evaluation metrics when comparing the machine learning model and the expert system. The results shown that the recall score for machine learning approach is vastly higher then of expert systems. For age group 18-59, machine learning has 32.75% recall more than the expert system to predict if a patient requires direct admission, while for age group more than 60, the recall of machine learning is 18.11% more than expert system. In addition, to predict if a patient require admission during their home quarantine due to their health deterioration, machine learning recorded 76.72% recall more than the expert system for patient aged 18 to 59, and 70.59% difference for patient more than 60 years old. This supports the potential application of machine learning for clinical decision making for COVID-19 patients.
Building resilient cervical cancer prevention through gender-neutral HPV vaccination
Authors: Man Irene , Georges Damien , Sankaranarayanan Rengaswamy , Basu Partha , Baussano Iacopo
Published: January 2023

The COVID-19 pandemic has disrupted HPV vaccination programmes worldwide. Using an agent-based model, EpiMetHeos, recently calibrated to Indian data, we illustrate how shifting from girls-only (GO) to gender-neutral (GN) vaccination strategy could improve the resilience of cervical cancer prevention against disruption of HPV vaccination. In the base case of 5-year disruption with no coverage, shifting from GO to GN strategy under 60% coverage (before disruption) would increase the resilience, in terms of cervical cancer cases still prevented in the disrupted birth cohorts per 100,000 girls born, by 2.8-fold from 107 to 302 cases, and by 2.2-fold from 209 to 464 cases under 90% coverage. Furthermore, shifting to GN vaccination helped in reaching the WHO elimination threshold. Under GO vaccination with 60% coverage, the age-standardised incidence rate (ASIR) of cervical cancer in India in the long-term with vaccination decreased from 11.0 to 4.7 cases per 100,000 woman-years (above threshold), as compared to 2.8 cases (below threshold) under GN with 60% coverage and 2.4 cases (below threshold) under GN with 90% coverage. In conclusion, GN HPV vaccination is an effective strategy to improve the resilience to disruption of cancer prevention programmes and to enhance the progress towards cervical cancer elimination.