bluuebunny/crossref_metadata_2025 huggingface dataset:
Reshaped functional connectivity gradients in acute ischemic stroke
Authors: Koba Cemal , Falcó-Roget Joan , Crimi Alessandro
Published: April 2024

Ischemic brain stroke disrupts blood flow, leading to functional and structural changes associated with behavioral deficits. Importantly, despite this disruption occurring in localized regions, the resulting changes in the functional organization are both high-dimensional and widespread across the human cortex. However, the mechanisms with which these global patterns emerge and the subsequent behavioral deficits they entail, remain largely unexplored. Functional connectivity gradients provide consistent, reproducible, and robust low-dimensional representations of brain function that can be explored to reduce brain heterogeneity to a handful of axes along which brain function is organized. Here, we investigated how stroke disrupts this canonical gradient space by aligning each patient to a control-averaged gradient embedding and computing the distances to the “correct” positions to quantify functional deviations and their contribution to behavioral deficits. Importantly, we explicitly corrected these gradients for stroke-induced hemodynamic lags to further study their contribution. We found that lag correction enhanced the functional connectivity gradients most prominently in the second gradient, on which visual and somatomotor function is concentrated. Additionally, we identified significant functional deviations primarily within somatomotor, visual, and ventral attention networks, correlating with behavioral impairments. We studied the hemispheric asymmetries of these deviations finding that intact hemispheres preserve comparable patterns of asymmetry while damaged ones presented important changes. Lastly, right-sided lesions displayed more localized functional deviations than their contralateral lesions. Overall, we provide evidence that 1) correcting for hemodynamic lags improves gradient accuracy, as indicated by increased percentages of explained variance, and 2) behavioral impairments and hemispheric asymmetries result from a repositioning of region-based connectivity profiles in a low-dimensional, interpretable space. This suggests that large-scale brain function alterations manifest in slight, predictable movements largely confined to the visual-somatomotor axis.
In situcell condensation-based cartilage tissue engineering via immediately implantable high-density stem cell core and rapidly degradable shell microgels
Authors: Lee Sang Jin , Jeon Oju , Lee Yu Bin , Alt Daniel S. , Ding Aixiang , Tang Rui , Alsberg Eben
Published: April 2024

Formation of chondromimetic human mesenchymal stem cells (hMSCs) condensations typically requiredin vitroculture in defined environments. In addition, extendedin vitroculture in differentiation media over several weeks is usually necessary prior to implantation, which is costly, time consuming and delays clinical treatment. Here, this study reports on immediately implantable core/shell microgels with a high-density hMSC-laden core and rapidly degradable hydrogel shell. The hMSCs in the core formed cell condensates within 12 hours and the oxidized and methacrylated alginate (OMA) hydrogel shells were completely degraded within 3 days, enabling spontaneous and precipitous fusion of adjacent condensed aggregates. By delivering transforming growth factor-β1 (TGF-β1) within the core, the fused condensates were chondrogenically differentiated and formed cartilage microtissues. Importantly, these hMSC-laden core/shell microgels, fabricated without anyin vitroculture, were subcutaneously implanted into mice and shown to form cartilage tissue via cellular condensations in the core after 3 weeks. This innovative approach to form cell condensationsin situwithoutin vitroculture that can fuse together with each other and with host tissue and be matured into new tissue with incorporated bioactive signals, allows for immediate implantation and may be a platform strategy for cartilage regeneration and other tissue engineering applications.
Different molecular recognition by three domains of the full-length GRB2 to SOS1 proline-rich motifs and EGFR phosphorylated sites
Authors: Tateno Keita , Ando Takami , Tabata Maako , Sugasawa Haruka , Hayashi Toshifumi , Sayeesh PM , Inomata Kohsuke , Mikawa Tsutomu , Ito Yutaka , Ikeya Teppei
Published: April 2024

The adaptor protein human GRB2 plays crucial roles in mediating signal transduction from cell membrane receptors to RAS and its downstream proteins by recruiting SOS1. Recent studies have revealed that GRB2 also serves as a scaffold for liquid-liquid phase separation (LLPS) with SOS1 and transmembrane receptors, which is thought to regulate the magnitude of cell signalling pathways. In this study, we employed solution NMR spectroscopy to investigate the interactions of the full-length GRB2 with proline-rich motifs (PRMs) derived from ten potential GRB2-binding sites in SOS1, as well as a peptide from a phosphorylation site of EGFR. Our findings indicate that the binding affinity of the two SH3 domains of GRB2 for PRMs differs by a factor of ten to twenty, with the N-terminal SH3 domain (NSH3) exhibiting a markedly higher affinity. The interactions of PRMs with the SH3 domains affected not only the regions surrounding the PRM binding sites on the SH3 domains but also the linker area connecting the three domains and parts of the SH2 domain. Analysis of the interaction between the phosphorylated EGFR binding site and the SH2 domain revealed chemical shift perturbations in regions distal from the known binding site of SH2. Moreover, we observed that the inter-domain interactions of the two SH3 domains with the SH2 domain of GRB2 are asymmetric. These findings suggest that the local binding of PRMs and phosphorylated EGFR to GRB2 impacts the overall structure of the GRB2 molecule, including domain orientation and dimerisation, which may contribute to LLPS formation.
Antithrombotic Efficacy and Bleeding Risks of Vaccine-Induced Immune Thrombotic Thrombocytopenia Treatments
Authors: Leung H.H.L. , Ahmadi Z. , Casey J. , Ratnasingam S. , McKenzie S.E. , Perdomo J.S. , Chong B.H.
Published: April 2024

Current guidelines for treating vaccine-induced immune thrombotic thrombocytopenia (VITT) recommend non-heparin anticoagulants and intravenous immunoglobulin (IVIg). However, the efficacy of these treatments remains uncertain due to a lack of comparative clinical trials or animal studies. A recent study proposed danaparoid and heparin as potential VITT therapies due to their ability to disrupt VITT IgG-PF4 binding. Here, we examined the effects of various anticoagulants (including unfractionated (UF) heparin, danaparoid, bivalirudin, fondaparinux, and argatroban), IVIg, and the FcγRIIa receptor-blocking antibody, IV.3, in relation to VITT pathophysiology. Our investigation focused on VITT IgG-PF4 binding, platelet activation, thrombocytopenia, and thrombosis. Danaparoid, at therapeutic doses, was the sole anticoagulant that reduced VITT IgG-PF4 binding, verified by purified anti-PF4 specific VITT IgG. Low-dose UF heparin (< 2U/mL) augmented VITT IgG binding to PF4 on platelets. While danaparoid and high-dose UF heparin (10 U/mL) inhibited platelet activation, none of the anticoagulants significantly affected thrombocytopenia in our VITT animal model, and all prolonged bleeding time. IVIg and all anticoagulants, except UF heparin, protected VITT mice from thrombosis. Direct FcγRIIa receptor inhibition with IV.3 antibody proved the most effective approach for managing both thrombosis and thrombocytopenia in VITT. Our results underscore the necessity of animal model investigations to inform patient treatment strategies. This study provides compelling evidence for developing FcγRIIa receptor blockers to treat VITT and other FcγRIIa-related thrombotic inflammatory disorders.

Key points

Non-heparin anticoagulants and IVIg reduce thrombosisin vivoby varying degrees whereas heparin exacerbates thrombosis.

Direct blocking of FcγRIIa receptor is the most effective strategy to treating both thrombosis and thrombocytopenia in VITT.
Organ specificity and commonality of epigenetic aging in low- and high-running capacity rats
Authors: Kawamura Takuji , Kerepesi Csaba , Torma Ferenc , Bori Zoltan , Zhou Lei , Bakonyi Peter , Kolonics Attila , Balogh Laszlo , Higuchi Mitsuru , Koch Lauren Gerard , Britton Steven Loyal , Koltai Erika , Radak Zsolt
Published: April 2024

Background

Epigenetic drift, which are gradual age-related changes in DNA methylation patterns, plays a significant role in aging and age-related diseases. However, the relationship between exercise, epigenetics, and aging and the molecular mechanisms underlying their interactions are poorly understood. The aim of this study was to investigate the relationship between cardiorespiratory fitness (CRF), epigenetic aging, and promoter methylation of individual genes across multiple organs in selectively bred low- and high-capacity runner (LCR and HCR) aged rats.

Methods

In this study, we performed reduced representation bisulfite sequencing (RRBS) on LCR and HCR aged rats, focusing on the hippocampus, heart, soleus muscle, and large intestine samples. We calculated various epigenetic indicators, including rat epigenetic clocks, global mean DNA methylation (GMM), mean methylation entropy (MME), and gene-specific promoter methylation.

Results

Epigenetic clocks, trained on available rat blood-derived RRBS data did not reflect differences in CRF between LCR and HCR rats across all four organs. However, we observed organ specific differences in GMM and MME between LCR and HCR rats. The direction of these differences was the opposite compared to the age-related changes in the rat blood suggesting that a high CRF may mitigate age-related epigenetic changes in an organ-specific manner. Notably the soleus muscle, exhibited the most pronounced differences in promoter methylation due to CRF. We also identified seven genes whose promoter methylation was consistently influenced by CRF in all four organs. Moreover, we found that age acceleration of the soleus muscle was significantly higher compared to the heart and the hippocampus, and significantly lower compared to the large intestine. Finally, we found that the age acceleration was not consistent across organs.

Conclusions

Our data suggest that CRF associates with epigenetic aging in an organ-specific manner and regulates the promoter methylation of individual genes in an organ-specific and organ-common manner. Our findings provide important insights into the biology of aging and emphasize the need to validate rejuvenation strategies in the context of the organ-specific nature of epigenetic aging.
More the merrier? Influence of Mango Orchards on the Composition of the Reptile Communities of the Lateritic Plateaus, Maharashtra, India
Authors: Amberkar Prathamesh , Mungikar Rahul
Published: April 2024

Change in land use patterns affects a landscape by changing the composition of local flora and fauna. The lateritic plateaus in Konkan are one such example of this rapid land use change. The area between the West coast and the Northern-Western Ghats of India, the Konkan region is characterized by these plateaus. Although these plateaus are rich in endemic flora and fauna, they are considered as wastelands due to lack of woody vegetation and thus, are subjected to various land uses. Mango cultivation in this region has become a major source of income since it’s known for its Alphonso variety of mangoes. Hence, over the last few decades, many plateaus have been converted into mango orchards. However, how the conversion of plateaus to mango orchards have effected species composition of different groups of organisms remains unclear. In the present study, we sampled the lateritic plateaus and plateaus converted into mango orchards in Ratnagiri, Maharashtra, to investigate the response of the reptile communities. We observed more species heterogeneity in the orchards compared to the plateaus. Since, the orchards offered more diverse microhabitats for species to occupy. Moreover, it appeared that there was a species turnover when the plateaus were converted into orchards. The generalist and widespread species such as agamids and skinks and very few specialist species were comparatively more abundant in the orchards. On a contrary, the plateaus without orchards harboured more specialist species likeHemidactylus albofasciatus,Echis carinatusandOphisops jerdoniicompared to the generalist species.
Metabolic Reprogramming Driven by Ant2 -Targeting Augments T-Cell Function and Anti-Tumor Immunity
Authors: Yosef Omri , Cohen-Daniel Leonor , Shamriz Oded , Bar-On Zahala , Saragovi Amijai , Abramovich Ifat , Agranovich Bella , Lutz Veronika , Tam Joseph , Permyakova Anna , Gottlieb Eyal , Huber Magdalena , Berger Michael
Published: April 2024

T-cell activation requires a substantial increase in NAD+production, often exceeding the capacity of oxidative phosphorylation (OXPHOS). To investigate how T cells adapt to this metabolic challenge, we generated T cell-specific ADP/ATP translocase-2 knockout (Ant2−/−) mice. Loss of Ant2, a crucial protein mediating ADP/ATP exchange between mitochondria and cytoplasm, induces OXPHOS restriction by limiting ATP synthase activity, impeding NAD+regeneration. Interestingly, Ant2−/−naïve T cells exhibited enhanced activation, proliferation, and effector functions compared to wild-type controls. Metabolic profiling revealed that these cells adopt an activated-like metabolic program with increased mitobiogenesis and anabolism. Pharmacological inhibition of ANT in wild-type T cells recapitulated the Ant2−/−phenotype, and improved adoptive cell therapy of cancer. Our findings suggest that Ant2-deficient T cells bypass the typical metabolic reprogramming required for activation, leading to enhanced T-cell function. These results highlight the critical role of mitochondrial metabolism in regulating T-cell fate and underscore the therapeutic potential of targeting ANT for immune modulation.
Bilateral cellular flows display asymmetry prior to left-right organizer formation in amniote gastrulation
Authors: Asai Rieko , Sinha Shubham , Prakash Vivek N. , Mikawa Takashi
Published: April 2024

A bilateral body plan is predominant throughout the animal kingdom. Bilaterality of amniote embryos becomes recognizable as midline morphogenesis begins at gastrulation, bisecting an embryonic field into the left and right sides, and left-right asymmetry patterning follows. While a series of laterality genes expressed after the left-right compartmentalization has been extensively studied, the laterality patterning prior to and at the initiation of midline morphogenesis has remained unclear. Here, through a biophysical quantification in a high spatial and temporal resolution, applied to a chick model system, we show that a large-scale bilateral counter-rotating cellular flow, termed as ‘polonaise movements’, display left-right asymmetries in early gastrulation. This cell movement starts prior to the formation of the primitive streak (the earliest midline structure) and the subsequent appearance of Hensen’s node (the left-right organizer). The cellular flow speed and vorticity unravel the location and timing of the left-right asymmetries. The bilateral flows displayed a Right dominance after six hours since the start of cell movements. Mitotic arrest that diminishes primitive streak formation resulted in changes in the bilateral flow pattern, but the Right dominance persisted. Our data indicate that the left-right asymmetry in amniote gastrula becomes detectable earlier than suggested by current models, which assume that the asymmetric regulation of the laterality signals at the node leads to the left-right patterning. More broadly, our results suggest that physical processes can play an unexpected but significant role in influencing left-right laterality during embryonic development.

Significance Statement

Bilaterians are defined by a bilaterally symmetrical body plan. Vertebrates exhibit external bilateral symmetry but display left-right (LR) asymmetry in their internal organs. Amniote embryos switch the patterning of internal organs from bilateral symmetry to LR-asymmetry. Using chick embryos as a model system, here we examined the initiation of LR symmetry breaking. Our biophysical approaches to quantify cellular flows inferred that LR symmetry breaking occurs before the formation of Hensen’s node, a LR organizer, which serves as a signaling center for LR patterning-gene programs. Our work demonstrates that quantitative biophysical parameters can help unravel the initiation of LR symmetry breaking, suggesting an involvement of physical mechanisms in this critical biological patterning process.
Parallel genetic adaptation amidst a background of changing effective population sizes in divergent yellow perch (Perca flavescens) populations
Authors: Yin Xiaoshen , Schraidt Claire E. , Sparks Morgan M. , Euclide Peter T. , Hoyt Tyler J. , Ruetz Carl R. , Höök Tomas O. , Christie Mark R.
Published: April 2024

Aquatic ecosystems are highly dynamic environments vulnerable to natural and anthropogenic disturbances. High-economic value fisheries are one of many ecosystem services affected by these disturbances and it is critical to accurately characterize the genetic diversity and effective population sizes of valuable fish stocks through time. We used genome-wide data to reconstruct the demographic histories of economically important yellow perch (Perca flavescens) populations. In two isolated and genetically divergent populations, we provide independent evidence for simultaneous increases in effective population sizes over both historic and contemporary time scales including negative genome-wide estimates of Tajima’s D, 3.1 times more SNPs than adjacent populations, and contemporary effective population sizes that have increased 10- and 47-fold from their minimum, respectively. The excess of segregating sites and negative Tajima’s D values likely arose from mutations accompanying historic population expansions with insufficient time for purifying selection, whereas linkage disequilibrium-based estimates ofNealso suggest contemporary increases that may have been driven by reduced fishing pressure or environmental remediation. We also identified parallel, genetic adaptation to reduced visual clarity in the same two habitats. These results suggest that the synchrony of key ecological and evolutionary processes can drive parallel demographic and evolutionary trajectories across independent populations.
Neutrophils secrete exosome-associated DNA to resolve sterile acute inflammation
Authors: Arya Subhash B. , Collie Samuel P. , Xu Yang , Fernandez Martin , Sexton Jonathan Z. , Mosalaganti Shyamal , Coulombe Pierre A. , Parent Carole A.
Published: April 2024

Acute inflammation, characterized by a rapid influx of neutrophils, is a protective response that can lead to chronic inflammatory diseases when left unresolved. Secretion of LTB4-containing exosomes is required for effective neutrophil infiltration during inflammation. In this study, we show that neutrophils release nuclear DNA in a non-lytic, rapid, and repetitive manner, via a mechanism distinct from suicidal NET release and cell death. The packaging of nuclear DNA occurs in the lumen of nuclear envelope (NE)-derived multivesicular bodies (MVBs) that harbor the LTB4synthesizing machinery and is mediated by the lamin B receptor (LBR) and chromatin decondensation. Disruption of secreted exosome-associated DNA (SEAD) in a model of sterile inflammation in mouse skin amplifies and prolongs the presence of neutrophils, impeding the onset of resolution. Together, these findings advance our understanding of neutrophil functions during inflammation and the physiological significance of NETs, with implications for novel treatments for inflammatory disorders.
Tumor suppressor p73 transcriptionally regulatesc-FLIPto impede its priming of extrinsic apoptosis while a “switcher compound” degrades c-FLIP protein
Authors: Zhang Shengliang , Zhou Lanlan , El-Deiry Wafik S.
Published: April 2024

The tumor suppressor p73 is a member of the p53 family, and transcriptionally activates multiple p53-targets involved in cell cycle regulation and apoptosis. In addition to pro-apoptotic signaling, outcomes of p73 activation include cell survival signals. Thus, p73 activity and targets may provide insight in cell fate outcomes between cell survival and apoptosis following cellular stress. We report thatcellular FLICE inhibitory protein(c-FLIP), a master antiapoptotic factor, is a transcriptional target of p73. The activation of p73 (α and β isoforms) transcriptionally upregulatesc-FLIP-L/Sexpression in cancer cells. The cell fate decision following p73 activation is determined by the adjustment of the balance of outcomes of p73 activation between p73-induced pro-apoptotic signaling andc-FLIP-L/Sexpression in cancer cells. p73 primes extrinsic apoptosis via an autocrine death ligand-DR5 axis, and the priming appears to be titrated at the level of c-FLIP-L/S. The p73-upregulation ofc-FLIP-L/Sincreases the threshold of extrinsic apoptosis. Cells with poor priming levels convert to cell cycle arrest and survival. Depletion ofc-FLIP-L/Sincreases the p73-priming levels towards extrinsic apoptosis and sensitizes cancer cells to p73-primed extrinsic apoptosis. We further identified a small-molecule CB-7587351 (“switcher compound”) that alters p73 activation outcomes through c-FLIP-L/S protein degradation. Therapeutic activation of p73 can restore p53-signaling in mutant p53-expressing cancer cells effectively bypassing the p53 deficiency in cancer cells. Our discovery of p73 transcriptional upregulation of c-FLIP provides a promising strategy for depleting c-FLIP to improve antitumor efficacy of p73-targeting cancer therapy for p53-mutant tumors.
Theta oscillons in behaving rats
Authors: Zobaer M. S. , Lotfi N. , Domenico C. M. , Hoffman C. , Perotti L. , Ji D. , Dabaghian Y.
Published: April 2024

Recently discovered constituents of the brain waves—theoscillons—provide high-resolution representation of the extracellular field dynamics. Here we study the most robust, highest-amplitude oscillons that manifest in actively behaving rats and generally correspond to the traditionalθ-waves. We show that the resemblances betweenθ-oscillons and the conventionalθ-waves apply to the ballpark characteristics—mean frequencies, amplitudes, and bandwidths. In addition, both hippocampal and cortical oscillons exhibit a number of intricate, behavior-attuned, transient properties that suggest a new vantage point for understanding theθ-rhythms’ structure, origins and functions. We demonstrate that oscillons are frequency-modulated waves, with speed-controlled parameters, embedded into a noise background. We also use a basic model of neuronal synchronization to contextualize and to interpret the observed phenomena. In particular, we argue that the synchronicity level in physiological networks is fairly weak and modulated by the animal’s locomotion.
Anemonefish use sialic acid metabolism as Trojan horse to avoid giant sea anemone stinging
Authors: Roux Natacha , Delannoy Clément , Yu Shin-Yi , Miura Saori , Carlu Lilian , Besseau Laurence , Nakagawa Takahiro , Sato Chihiro , Kitajima Ken , Guerardel Yann , Laudet Vincent
Published: April 2024

Anemonefish association with giant sea anemone is an iconic example of mutualistic symbiosis. Living inside the sea anemone without triggering the firing of highly toxic nematocysts present at the surface of sea anemone tentacles provides a unique shelter to the fish, which in return, by its territorial aggressiveness, protects the sea anemone from predators. The mechanisms by which the fish avoids triggering nematocysts discharge remain elusive. One hypothesis proposes that absence of sialic acids might disable nematocysts discharge. Here, we verified four predictions about the role of sialic acids in anemonefish protection: (i) sialic acid levels are lower in anemonefish mucus than in non-symbiotic and sensitive damselfish mucus; (ii) this decrease is specific to mucus and not observed in other organs; (iii) during post-embryonic development the levels of sialic acids are inversely correlated with the level of protection; (iv) the levels of sialic acids are minimal in sea anemone mucus. Taken together, our results allow us to propose a general model, in which anemonefish specifically regulates the level of sialic acids in their mucus to avoid nematocysts discharge. Our analysis also highlights several genes implicated in sialic acid removal as potential targets for allowing protection. Interestingly, our results also suggest that unrelated juveniles of damselfish (Dascyllus trimaculatus) capable to live in proximity with giant sea anemone may use the same mechanisms. Altogether, our data suggest that clownfish use sialic acids as a Trojan horse system to downplay the defenses of the sea anemones and illustrate the convergent tinkering used by fish to allow a mutualistic association with their hosts.

Significance statement

The mutualistic relationship between anemonefish and giant sea anemones, where the fish shelter among the anemone’s tentacles while defending it from predators, is a classic example of symbiosis. However, how the fish avoids triggering the anemone’s venomous nematocysts has remained a mystery. This study reveals that the fish decrease the levels of sialic acids in their mucus, potentially preventing nematocyst discharge. This finding shed light on the mechanisms underlying this symbiotic relationship. Moreover, the discovery that unrelated damselfish may employ similar strategies underscores the broader significance of convergent adaptations in facilitating similar mutualistic associations in marine fishes.
Molecular and physiological characterization of brassinosteroid receptor BRI1 mutants inSorghum bicolor
Authors: Rico-Medina Andrés , Blasco-Escámez David , Fontanet-Manzaneque Juan B. , Laibach Natalie , Lozano-Elena Fidel , Martignago Damiano , Caño-Delgado Ana I.
Published: April 2024

The high sequence and structural similarities between BRI1 brassinosteroid receptors of Arabidopsis (AtBRI1) and sorghum (SbBRI1) prompted us to study the functionally conserved roles of BRI in both organisms.

Introducing sorghum SbBRI1 in Arabidopsisbri1mutants restores defective growth and developmental phenotypes to WT levels.

Sorghum mutants for SbBRI1 receptors show defective BR sensitivity and impaired growth and development throughout the entire sorghum life cycle. Embryonic analysis of sorghum primary roots permit to trace back root growth and development to early stages, revealing the functionally conserved roles of SbBRI1 receptor in BR perception during meristem development. RNA-seq analysis uncovers the downstream regulation of the SbBRI1 pathway in cell wall biogenesis during cell growth.

Together, these results uncover that sorghum SbBRI1 receptor protein play functionally conserved roles in plant growth and development, while encourage the study of BR pathways in sorghum and its implications for improving resilience in cereal crops.
Specific oncogene activation of the cell of origin in mucosal melanoma
Authors: Babu Swathy , Chen Jiajia , Robitschek Emily , Baron Chloé S. , McConnell Alicia , Wu Constance , Dedeilia Aikaterini , Sade-Feldman Moshe , Modhurima Rodsy , Manos Michael P. , Chen Kevin Y. , Cox Anna M. , Ludwig Calvin G. , Yang Jiekun , Kellis Manolis , Buchbinder Elizabeth I. , Hacohen Nir , Boland Genevieve M. , Abraham Brian J. , Liu David , Zon Leonard I. , Insco Megan L.
Published: April 2024

Mucosal melanoma (MM) is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics, we developed a zebrafish model in which all melanocytes experienced CCND1 expression and loss of PTEN and TP53. Surprisingly, melanoma only developed from melanocytes lining internal organs, analogous to the location of patient MM. We found that zebrafish MMs had a unique chromatin landscape from cutaneous melanoma. Internal melanocytes could be labeled using a MM-specific transcriptional enhancer. Normal zebrafish internal melanocytes shared a gene expression signature with MMs. Patient and zebrafish MMs have increased migratory neural crest gene and decreased antigen presentation gene expression, consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors, allowing this model to be used for MM therapeutic discovery.
Effects of diet particle size on growth performance of the edible cricket,Teleogryllus occipitalis(Orthoptera: Gryllidae)
Authors: Murata Kohyoh , Suzuki Takeshi
Published: April 2024

Farming edible crickets has environmental and nutritional benefits, as well as social benefits such as livelihood diversification. Commercial feeds for poultry and fish farming are often used to feed crickets, and in recent years, crop and food-processing by-products have also been used to improve sustainability. However, the design of feed for crickets has not been standardized. Here, we investigated growth and development of the Asian field cricket,Teleogryllus occipitalis(Audinet-Serville) (Orthoptera: Gryllidae), fed on different forms of the same diet. Body weights and the rate of development were significantly greater in crickets fed on millimetre-order granules than in crickets fed on micrometre-order powder. The result suggests that the granular form is easier forT. occipitalisto grasp and ingest than the powdery form, or that greater hydrophobicity of the powdery form inhibits digestion. Simply feeding millimetre-order granules may contribute to the development of feed design for farming edible crickets.
PACS-1 variant protein is aberrantly localized inC. elegansmodel of PACS1/PACS2 syndromes
Authors: Byrd Dana T. , Han Ziyuan Christina , Piggott Christopher A. , Jin Yishi
Published: April 2024

PACS (Phosphofurin Acidic Cluster Sorting Protein) proteins are known for their roles in sorting cargo proteins to organelles and can physically interact with WD40 repeat-containing protein WDR37. PACS1, PACS2, and WDR37 variants are associated with multisystemic syndromes and neurodevelopmental disorders characterized by intellectual disability, seizures, developmental delays, craniofacial abnormalities, and autism spectrum disorder. However, the effects of syndromic variants on functionin vivoremains unknown. Here, we report the expression pattern ofC. elegansorthologs of PACS and WDR37 and their interaction. We show that cePACS-1 and ceWDR-37 co-localize to somatic cytoplasm of many types of cells, and are mutually required for expression, supporting a conclusion that the intermolecular dependence of PACS1/PACS2/PACS-1 and WDR37/WDR-37 is evolutionarily conserved. We further show that editing in PACS1 and PACS2 variants in cePACS-1 changes protein localization in multiple cell types, including neurons. Moreover, expression of human PACS1 can functionally complementC. elegansPACS-1 in neurons, demonstrating conserved functions of the PACS-WDR37 axis in an invertebrate model system. Our findings reveal effects of human variants and suggest potential strategies to identify regulatory network components that may contribute to understanding molecular underpinnings of PACS/WDR37 syndromes.
Octopus Hypnosis: Non-Chemical Sedation in Studying Arm-Sucker Coordination
Authors: Gribkova Ekaterina D. , Cui Jilai , Gillette Rhanor
Published: April 2024

Effective methods of anesthesia for octopuses are important for physiological studies as well as for their welfare in scientific research. Neurophysiological studies of octopus usually use general anesthesia for invasive procedures like electrode implantation. However, commonly used forms of general anesthesia using ethanol, magnesium chloride, and similar agents have certain drawbacks in levels of stress, recovery, and tissue viability in octopuses much as in humans. We explore an old, rarely used method of octopus “hypnosis”, in which a still reaction is induced where communication between central and peripheral nervous systems is seemingly decreased. We modify the procedure for better handling, continuous respiration, and isolation of peripheral nervous system of the arm cords from the central nervous system (CNS), providing alternative to general anesthesia. Illustrative small studies of arm-sucker coordination and electrode placements are presented. The modified procedure limits negative side-effects, markedly reduces animals’ stress levels, and offers new avenues for octopus neurobehavioral research.
Association of Genetically Predicted Levels of Circulating Blood Lipids with Coronary Artery Disease Incidence
Authors: Manikpurage Hasanga D. , Ricard Jasmin , Houessou Ursula , Bourgault Jérôme , Gagnon Eloi , Gobeil Emilie , Girard Arnaud , Li Zhonglin , Eslami Aida , Mathieu Patrick , Bossé Yohan , Arsenault Benoit J. , Thériault Sébastien
Published: April 2024

Background

Estimating the genetic risk of coronary artery disease (CAD) is now possible by aggregating data from genome-wide association studies (GWAS) into polygenic risk scores (PRS). Combining multiple PRS for specific circulating blood lipids could improve risk prediction. Here, we sought to evaluate the performance of PRS derived from CAD and blood lipids GWAS to predict the incidence of CAD.

Methods

This study included individuals aged between 40 and 69 recruited in UK Biobank (UKB). We conducted GWAS for blood lipids measured by nuclear magnetic resonance in individuals without lipid-lowering treatments (n=73,915). Summary statistics were used to derive and calculate PRS in the remaining participants (n=318,051). A PRSCADwas also derived using the CARDIoGRAMplusC4D GWAS. Hazard ratios (HR) for CAD (9,017 / 301,576; median follow-up time: 12.6 years) were calculated per standard deviation increase in each PRS. Discrimination capacity and goodness of fit of the models were evaluated.

Results

Out of 30 PRS, 28 were significantly associated with the incidence of CAD (P<0.05). The optimal combination of PRS included PRS for CAD, VLDL-C, total cholesterol and triglycerides. Discriminative capacities were significantly increased in the model including PRSCADand clinical risk factors (CRF) (C-statistic=0.778 [0.773-0.782]) compared to the model with CRF only (C-statistic=0.755 [0.751-0.760]). Although the C-statistic remained similar when independent lipids PRS were added to the model with PRSCADand CRF (C-statistic=0.778 [0.773-0.783]), the goodness of fit was significantly increased (chi-square test statistic=20.18,P=1.56e-04).

Conclusions

Although independently associated with CAD incidence, blood lipids PRS provide modest improvement in the predictive performance when added to PRSCAD.

Highlights

Genome-wide association studies were conducted on 29 selected lipid traits measured by nuclear magnetic resonance spectroscopy in 73,915 participants from UK Biobank who were not taking lipid-lowering treatment.

Polygenic risk scores for 27 out of 29 of these traits were associated with the incidence of coronary artery disease (CAD) in 9,017 cases out of 301,576 individuals followed for a median of 12.6 years.

When combined to a PRS for coronary artery disease, there was a significant but modest improvement in the discrimination capacity for incident CAD.

PRS for certain lipid traits might help to stratify the risk of CAD.

Graphical Abstract
Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity
Authors: Schwartz Irene , Budroni Valentina , Meyenberg Mathilde , Hornegger Harald , Hacker Kathrin , Schwartz Siegfried , Hodakova Zuzana , Grabarczyk Daniel B. , Ehrmann Julian F. , Scinicariello Sara , Haselbach David , Menche Jörg , Clausen Tim , Karagöz G. Elif , Versteeg Gijs A.
Published: April 2024

Highlights

RNA-free APOBEC3 (A3) can enter the nucleus, leading to genomic mutations.

Three E3 ligases specifically bind the RNA-binding domain of nuclear A3s.

Cancer-associated A3B and A3H-I are thereby targeted for proteasomal degradation.

These E3 ligases thus act as genome guardians by limiting A3-mediated mutagenesis.

APOBEC family members play crucial roles in antiviral restriction. However, certain APOBEC3 (A3) proteins drive harmful hypermutation in humans, contributing to cancer. The cancer-associated A3 proteins are capable of transiting from the cytosol to the nucleus, where they can cause genome mutations. Here, we uncover a specific set of cellular pathways that protect genomic DNA from the major cancer-associated A3 proteins. Through genetic and proteomic screening we identify UBR4, UBR5, and HUWE1 as key ubiquitin E3 ligases marking cancer-associated A3B and A3H-I for degradation, thereby limiting A3-driven hypermutation. Mechanistically, UBR5 and HUWE1 recognize unoccupied A3 RNA-binding domains, thus promoting proteasomal degradation of APOBEC3 protein that is not engaged in its antiviral cellular function. Depletion or mutation of the E3 ligases in cells and human cancer samples increases A3-driven genome mutagenesis. Our findings reveal that UBR4, UBR5, and HUWE1 are crucial factors in a ubiquitination cascade that maintains human genome stability.
Interpreting mammalian evolutionary constraint at synonymous sites in light of the unwanted transcript hypothesis
Authors: Christmas Matthew J. , Dong Michael , Meadows Jennifer R. S. , Kozyrev Sergey V. , Lindblad-Toh Kerstin
Published: April 2024

The unwanted transcript hypothesis presents a potential explanation for cryptic evolutionary constraint at synonymous sites in species with low effective population sizes, such as humans and other mammals. Selection for higher GC content and against mutations that alter splicing in native transcripts is predicted to shape synonymous site content and protect against unwanted transcripts. Here, we interpret mammalian synonymous site constraint in this context. Utilising the largest alignment of 240 placental mammal genomes and single-base resolution constraint scores, we show that 20.8% of four-fold degenerate sites are under significant constraint across mammals. There is a strong bias for guanine (G) and cytosine (C) at constrained sites, marked constraint near splice sites, and variation in human populations shows a bias against mutations that reduce synonymous site GC content. We find evidence for higher constraint on four-fold degenerate sites in species with small historic effective population sizes and high young transposable element genome content. Genes enriched for synonymous site constraint, including those forming CpG sites, are tightly regulated and integral to organismal viability through their involvement in embryo development and transcriptional regulation.
Synaptic architecture of a memory engram in the mouse hippocampus
Authors: Uytiepo Marco , Zhu Yongchuan , Bushong Eric , Polli Filip , Chou Katherine , Zhao Elise , Kim Christine , Luu Danielle , Chang Lyanne , Quach Tom , Haberl Matthias , Patapoutian Luca , Beutter Elizabeth , Zhang Weiheng , Dong Brian , McCue Elle , Ellisman Mark , Maximov Anton
Published: April 2024

Memory engrams are formed through experience-dependent remodeling of neural circuits, but their detailed architectures have remained unresolved. Using 3D electron microscopy, we performed nanoscale reconstructions of the hippocampal CA3-CA1 pathway following chemogenetic labeling of cellular ensembles with a remote history of correlated excitation during associative learning. Projection neurons involved in memory acquisition expanded their connectomes via multi-synaptic boutons without altering the numbers and spatial arrangements of individual axonal terminals and dendritic spines. This expansion was driven by presynaptic activity elicited by specific negative valence stimuli, regardless of the co-activation state of postsynaptic partners. The rewiring of initial ensembles representing an engram coincided with local, input-specific changes in the shapes and organelle composition of glutamatergic synapses, reflecting their weights and potential for further modifications. Our findings challenge the view that the connectivity among neuronal substrates of memory traces is governed by Hebbian mechanisms, and offer a structural basis for representational drifts.
The attenuation of activity-based anorexia by obese adipose tissue transplant is AgRP neuron-dependent
Authors: Yoon Dongmin J. , Zhang Jie , Zapata Rizaldy C. , Ulivieri Martina , Libster Avraham M. , McMurray Matthew S. , Osborn Olivia , Dulawa Stephanie C.
Published: April 2024

Anorexia nervosa (AN) is an eating disorder observed primarily in girls and women, and is characterized by a low body mass index, hypophagia, and hyperactivity. The activity-based anorexia (ABA) paradigm models aspects of AN, and refers to the progressive weight loss, hypophagia, and hyperactivity developed by rodents exposed to time-restricted feeding and running wheel access. Recent studies identified white adipose tissue (WAT) as a primary location of the ‘metabolic memory’ of prior obesity, and implicated WAT-derived signals as drivers of recidivism to obesity following weight loss. Here, we tested whether an obese WAT transplant could attenuate ABA-induced weight loss in normal female mice. Recipient mice received a WAT transplant harvested from normal chow-fed, or HFD-fed obese mice; obese fat recipient (OFR) and control fat recipient (CFR) mice were then tested for ABA. During ABA, OFR mice survived longer than CFR mice, defined as maintaining 75% of their initial body weight. Next, we tested whether agouti-related peptide (AgRP) neurons, which regulate feeding behavior and metabolic sensing, mediate this effect of obese WAT transplant. CFR and OFR mice received either control or neonatal AgRP ablation, and were assessed for ABA. OFR intact mice maintained higher body weights longer than CFR intact mice, and this effect was abolished by neonatal AgRP ablation; further, ablation reduced survival in OFR, but not CFR mice. In summary, obese WAT transplant communicates with AgRP neurons to increase body weight maintenance during ABA. These findings encourage the examination of obese WAT-derived factors as potential treatments for AN.
A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors
Authors: Schmidt Henri , Raphael Benjamin J.
Published: April 2024

Motivation

DNA sequencing of multiple bulk samples from a tumor provides the opportunity to investigate tumor heterogeneity and reconstruct a phylogeny of a patient’s cancer. However, since bulk DNA sequencing of tumor tissue measures thousands of cells from a heterogeneous mixture of distinct sub-populations, accurate reconstruction of the tumor phylogeny requires simultaneous deconvolution of cancer clones and inference of ancestral relationships, leading to a challenging computational problem. Many existing methods for phylogenetic reconstruction from bulk sequencing data do not scale to large datasets, such as recent datasets containing upwards of ninety samples with dozens of distinct sub-populations.

Results

We develop an approach to reconstruct phylogenetic trees from multi-sample bulk DNA sequencing data by separating the reconstruction problem into two parts: a structured regression problem for a fixed tree 𝒯, and an optimization over tree space. We derive an algorithm for the regression sub-problem by exploiting the unique, combinatorial structure of the matrices appearing within the problem. This algorithm has both asymptotic and empirical improvements over linear programming (LP) approaches to the problem. Using our algorithm for this regression sub-problem, we developfastBE, a simple method for phylogenetic inference from multi-sample bulk DNA sequencing data. We demonstrate on simulated data with hundreds of samples and upwards of a thousand distinct sub-populations thatfastBEoutperforms existing approaches in terms of reconstruction accuracy, sample efficiency, and runtime. Owing to its scalability,fastBEalso enables phylogenetic reconstruction directly from indvidual mutations without requiring the clustering of mutations into clones. On real data from fourteen B-progenitor acute lymphoblastic leukemia patients,fastBEinfers similar phylogenies to the existing, state-of-the-art method, but with fewer violations of a widely used evolutionary constraint and better agreement to the observed mutational frequencies. Finally, we show that on two patient-derived colorectal cancer models,fastBEalso infers phylogenies with less violation of a widely used evolutionary constraint compared to existing methods, and leads to distinct interpretations of the intra-tumor heterogeneity.

Availability

fastBEis implemented in C++and is available at: github.com/raphael-group/fastBE.
Twin study provides heritability estimates for 2,321 plasma proteins and assesses missing SNP heritability
Authors: Drouard Gabin , Hagenbeek Fiona A. , Ollikainen Miina , Zheng Zhili , Wang Xiaoling ,   FinnGen, Ripatti Samuli , Pirinen Matti , Kaprio Jaakko
Published: April 2024

Assessing how much of the variability in blood plasma proteins is due to genetic or environmental factors is essential for advancing personalized medicine. While large-scale studies have established SNP-based heritability (SNP-h2) estimates for plasma proteins, less is known about the proportion of total genetic effects on protein variability. We applied quantitative genetic twin models to estimate the heritability of 2,321 plasma proteins and to assess the proportion of heritability accounted for by SNP-h2estimates. Olink proteomics data were generated for 401 twins aged 56-70, including 196 complete same-sex twin pairs. On average, 40% of protein variability was attributable to genetic effects. Twin-based heritability estimates were highly correlated with published SNP-h2estimates from the UK Biobank (Spearman coefficient: r=0.80). However, on average, only half of the total heritability was covered by SNP-h2, and the other half, representing one-fifth of total protein phenotypic variability, remains missing.
No-code machine learning in radiology: implementation and validation of a platform that allows clinicians to train their own models
Authors: Elton Daniel C. , Dasegowda Giridhar , Sato James Y. , Frias Emiliano G. , Bridge Christopher P. , Mamonov Artem B. , Walters Mark , Ziemelis Martynas , Schultz Thomas J. , Bizzo Bernardo C. , Dreyer Keith J. , Kalra Mannudeep K.
Published: April 2024

Machine learning models can assist clinicians and researchers in many tasks within radiology such as diagnosis, triage, segmentation/measurement, and quality assurance. To better leverage machine learning we have developed a platform that allows users to label data and train models without requiring any programming knowledge. The technology stack consists of a TypeScript web application running on .NET for user interaction, Python, PyTorch, and MONAI for machine learning, DICOM WADO-RS to retrieve data from clinical systems, and Docker for model management. As a first trial of the system, researchers used it to train a model for clavicle fracture detection as part of an IRB-approved retrospective study. The researchers labeled 4,135 clavicle radiographs from 2,039 patients across 13 sites. The platform automatically split the data into training, validation, and test sets and trained a model until the validation loss plateaued. The system then returned a receiver operating characteristic curve, AUC, F1, and other metrics. The resulting model identifies clavicle fractures with 90% sensitivity, 87% specificity, and 88% accuracy with an AUC of 0.95. This model performance is equivalent to or better than similar models reported in the literature. More recently, our system was used to train a model to identify if ultrasound frames that contain personally identifiable information (PII). After validation, the model was used to help de-identify a large dataset that was to be used for research. This first-of-its-kind system streamlines model development and deployment and opens up an exciting new pathway for the use of AI within healthcare.