bluuebunny/crossref_metadata_2025 huggingface dataset:
Introduction of the topic of snake bite and envenomation in medical curriculum using a problem-based learning approach
Authors: Thantry Anita Devi Krishnan , Lin Wai Marr , Zahadi Raja Norazura Raja
Published: September 2024

Introduction

Snake bite is a neglected tropical disease of Asia and African countries. The risk factors, disease burden, pathology, clinical management aspects of the condition deserve to be emphasized in the medical curriculum especially in the tropical countries. In Malaysia, there are at least 18 different species of venomous land snakes among which cobra bites and Malayan pit viper bites predominate. The coverage of snake bite envenomation in medical school curriculum is inadequate judging from the poor knowledge among health care providers. PBL is an instructional mode where “triggers” from a problem case is used to define learning objectives. PBL enables students to understand the relevance of underlying scientific knowledge and principles in clinical practice.

Methods

We attempted the delivery of topic of snake bite to 100 students in Year 1 module “Body reactions to Various Agents” using a problem-based learning (PBL) approach. The PBL case was designed; conducted according to standard format. The students were evaluated during the first and second session according to standard format. A questionnaire on the various aspects of the case, group work and facilitator was circulated and survey was based on the Likert scale. Problem based question on the same topic was used in end of block examination to assess knowledge assimilation.

Results and conclusion

The study showed a positive response in the students’ attitude, perception and gain of knowledge on the topic of snake bite envenomation. Problem based learning was considered an enjoyable and well-suited model for the delivery of the topic. The paucity of student friendly and medically relevant literature in textbooks and E-resources was highlighted by the students. The student score for the PBL sessions was high while the marks scored for the problem –based question showed a significant positive association between the top-scorers of the year group and the PBQ marks (p > 0.05). The PBL method is proven to improve the affective skills in the students while the cognitive skills improvement is not enhanced.
Real-time detection of spoken speech from unlabeled ECoG signals: A pilot study with an ALS participant
Authors: Angrick Miguel , Luo Shiyu , Rabbani Qinwan , Joshi Shreya , Candrea Daniel N. , Milsap Griffin W. , Gordon Chad R. , Rosenblatt Kathryn , Clawson Lora , Maragakis Nicholas , Tenore Francesco V. , Fifer Matthew S. , Ramsey Nick F. , Crone Nathan E.
Published: September 2024

Objective. Brain-Computer Interfaces (BCIs) hold significant promise for restoring communication in individuals with partial or complete loss of the ability to speak due to paralysis from amyotrophic lateral sclerosis (ALS), brainstem stroke, and other neurological disorders. Many of the approaches to speech decoding reported in the BCI literature have required time-aligned target representations to allow successful training – a major challenge when translating such approaches to people who have already lost their voice.Approach. In this pilot study, we made a first step toward scenarios in which no ground truth is available. We utilized a graph-based clustering approach to identify temporal segments of speech production from electrocorticographic (ECoG) signals alone. We then used the estimated speech segments to train a voice activity detection (VAD) model using only ECoG signals. We evaluated our approach using held-out open-loop recordings of a single dysarthric clinical trial participant living with ALS, and we compared the resulting performance to previous solutions trained with ground truth acoustic voice recordings.Main results. Our approach achieves a median error rate of around 0.5 seconds with respect to the actual spoken speech. Embedded into a real-time BCI, our approach is capable of providing VAD results with a latency of only 10 ms.Significance. To the best of our knowledge, our results show for the first time that speech activity can be predicted purely from unlabeled ECoG signals, a crucial step toward individuals who cannot provide this information anymore due to their neurological condition, such as patients with locked-in syndrome.Clinical Trial Information. ClinicalTrials.gov, registration numberNCT03567213.
Autologous P63+ lung progenitor cell transplantation in idiopathic pulmonary fibrosis: a phase 1 clinical trial
Authors: Zhang Shiyu , Zhou Min , Shao Chi , Zhao Yu , Liu Mingzhe , Ni Lei , Bao Zhiyao , Zhang Qiurui , Zhang Ting , Luo Qun , Qu Jieming , Xu Zuojun , Zuo Wei
Published: September 2024

In idiopathic pulmonary fibrosis (IPF) patients, alveolar epithelium architectures are persistently lost and lung gas transfer function would decline over time, which cannot be rescued by conventional anti-fibrotic therapy. P63+ airway basal progenitor cells are previously reported to have great potential to repair damaged lung epithelium. Here, we successfully cloned and expanded the autologous P63+ progenitor cells from IPF patients to manufacture the cell therapeutic product REGEND001, which were further characterized by cell morphology and single-cell transcriptomic analysis. Subsequently, an open-label, dose-escalation autologous progenitor cell transplantation clinical trial (CTR20210349) was conducted. The primary outcome was the incidence and severity of the cell therapy-related adverse events (AEs); secondary outcome included other safety and efficacy evaluation in each dose groups. We treated 12 patients with ascending doses of cells: 0.6x, 1x, 2x and 3.3× 106cells/kg bodyweight. The data revealed that P63+ basal progenitor cell was safe and well tolerated at all doses, with no dose-limiting toxicity or cell therapy-related severe adverse events observed. Patients in the three higher dose groups showed statistically significant improvement of lung gas transfer function as well as exercise ability after REGEND001 therapy. Resolution of honeycomb lesion was also observed in patients of higher dose groups. Altogether these results indicated that REGEND001 has high safety profile and meanwhile encourages further efficacy exploration in IPF patients.
Allium Vegetables Intake and Digestive System Cancer Risk: A Study Based on Mendelian Randomization, Network Pharmacology and Molecular Docking
Authors: Li Shuhao , Lou Jingwen , Mulatihan Yelina , Xiong Yuhang , Li Yao , Xu Qi
Published: September 2024

Background

Allium vegetables (garlic and onion) are one of the flavorings in people’s daily diets. Observational studies suggest that intake of allium vegetables may be correlated with a lower incidence of digestive system cancers. However, the existence of a causal relationship is still controversial due to confounding factors and reverse causation. Therefore, we explored the causal relationship between intake of allium vegetables and digestive system cancers using Mendelian randomization approach.

Methods

First, we performed Mendelian randomization analyses using inverse variance weighting (IVW), weighted median, and MR-Egger approaches, and demonstrated the reliability of the results in the sensitivity step. Second, Multivariable Mendelian randomization was applied to adjust for smoking and alcohol consumption. Third, we explored the molecular mechanisms behind the positive results through network pharmacology and molecular docking methods.

Results

The study suggests that increased intake of garlic reduced gastric cancer risk. However, onion intake was not statistically associated with digestive system cancer.

Conclusion

Garlic may have a protective effect against gastric cancer.
Efficacy and Safety of Beta Blockers for Patients with Myocardial Infarction in the Percutaneous Coronary Intervention Era: A Systematic Review and Meta-Analysis
Authors: Irtaza Ahmed , Junaid Muhammad , Saqlain Muhammad , Akram Ayesha , Khan Ayesha , Sarwari Areeba Shams , Ali Hussain , Ahsan Salman , Ahmed Tayyab , Talib Tuba , Ebad Ur Rehman Mohammad , Ahmad Cheema Huzaifa , Ahmad Adeel , Ur Rehman Wajeeh , Wahab Arif Abdul , Dani Sourbha S.
Published: September 2024

Background

Beta-blockers are commonly prescribed to patients after MI. However, the evidence is based on studies conducted before the widespread use of PCI for treating MI. We conducted this meta-analysis to evaluate beta-blockers’ efficacy post-MI in the modern day and age.

Methods

We conducted our search using and one clinical trial registry to get RCTs and propensity-matched observational studies comparing the use of beta-blockers after MI to control in post-MI patients. The primary outcome of our analysis was the likelihood of all-cause mortality.

Results

Our analysis included 3 RCTs and 12 propensity-matched observational studies with a total study population of 102,794. Our results showed a statistically significant decrease in all-cause mortality in the beta-blocker group compared to the non-beta-blocker group (RR 0.63, 95% CI 0.47-0.83; p= 0.001). However, this decrease was not observed when only RCTs were considered (RR 0.91). Beta-blockers were also found to reduce the risk of MI and heart failure with RR of 0.86 (95% CI 0.75-1.00; p=0.05) and 0.84 (95% CI 0.73-0.97; p=0.02), respectively.

Conclusion

Beta-blockers effectively reduce mortality and decrease the risk of MI and heart failure without a significant increase in adverse effects. Thus, our findings support the contemporary use of beta blockers in post-MI patients. However, more long-term studies need to be done to determine the sustained benefits of beta blockers in the context of evolving cardiac care.
Family income is associated with regional brain glucose metabolism in middle-aged adults
Authors: Pak Kyoungjune , Shin Seunghyeon , Nam Hyun-Yeol , Kim Keunyoung , Kim Jihyun , Lee Myung Jun
Published: September 2024

Socioeconomic status is a multifaceted construct that plays a prominent role in shaping our environment by defining our access to healthcare, nutrition, and enrichment, as well as represents social standing. Therefore, to address the effects of family income, and education level on brain glucose metabolism, we analyzed a large cohort of healthy middle-aged adults who underwent brain18F-FDG PET, and survey of family income and education level. We retrospectively analyzed data of healthy males who underwent health check-up program. Health check-up program included 1) Brain18F-FDG PET, 2) anthropometric measurements, 3) survey of family income and education level, and 4) measures of stress, anxiety, and depression. The effects of family income and education level on regional SUVR were investigated using Bayesian hierarchical modelling. A total of 233 healthy males were included in this study. Family income was positively correlated with education level. There was no significant indirect effect of family income or education level via stress, anxiety, or depression on regional brain glucose metabolism. Family income is positively associated with brain glucose metabolism in caudate, putamen, anterior cingulate, hippocampus, and amygdala, while education level does not show any significant association with brain glucose metabolism in middle-aged adults. In conclusion, family income is positively associated with brain glucose metabolism in caudate, putamen, anterior cingulate, hippocampus, and amygdala, while education level does not show any significant association with brain glucose metabolism. This finding might reflect the link between family income, and reward sensitivity, stress in middle-aged adults.
Tracing SARS-CoV-2 Clusters Across Local Scales Using Genomic Data
Authors: Lyu Leke , Gill Mandev , Stott Guppy , Subedi Sachin , Dailey Cody , Veytsel Gabriella , Alabady Magdy , Fujimoto Kayo , Penn Ryker , Brown Pamela , Sealy Roger , Bahl Justin
Published: September 2024

Quantitatively understanding local transmission dynamics is essential for designing effective prevention strategies. In this study, we developed a novel algorithm to identify introductions and trace locally circulating clusters. We analyzed over 26,000 SARS-CoV-2 genomes and their associated metadata, collected between January and October 2021, to explore introduction and dispersal patterns in Greater Houston, a major metropolitan area known for its demographic diversity. Our analysis identified more than 1,000 independent introduction events, resulting in clusters of varying sizes. Earlier clusters were generally larger and posed greater challenges for control efforts. Characterization of introduction sources revealed that domestic origins were more significant than international ones. Additionally, analysis of locally circulating clusters highlighted age-structured transmission dynamics. Geographic reconstruction of cluster spread identified Harris County as the primary viral source for surrounding counties. Harris county sustained the local epidemic with a smaller proportion of new cases driven by external importations and longer persistence times of circulating lineages. Overall, our high-resolution spatiotemporal reconstruction of the epidemic in Greater Houston provides critical insights into the heterogeneous transmission landscape, supporting regional response strategies and public health planning.

Significance Statement

The growing recognition of genome sequencing as a critical tool for outbreak response has driven a rapid increase in the availability of sequence data. Here, we present an analytical workflow to trace imported SARS-CoV-2 clusters using large-scale genome datasets. Our approach pinpoints when, where, and how many introductions occurred, while also tracking the circulation of resulting clusters. By incorporating metrics such as the Source Sink Score, Local Import Score, and Persistence Time, our analysis reveals transmission heterogeneity between subregions of the focal area. These insights are essential for monitoring viral introductions and guiding targeted control measures, enhancing the ability of local responders to address the challenges of current and future pandemics as new variants emerge.
Role of Forkhead box F1 in the Pathobiology of Pulmonary Arterial Hypertension
Authors: Gomez-Arroyo Jose , Houweling Arjan C. , Bogaard Harm Jan , Aman Jurjan , Kitzmiller Joseph A. , Porollo Aleksey , Dooijes Dennis , Meijboom Lilian J. , Hale Phillip , Pauciulo Michael W. , Hong Jason , Zhu Na , Welch Carrie , Shen Yufeng , Zacharias William J. , McCormack Francis X. , Aldred Micheala A. , Weirauch Matthew T. , Graf Stefan , Rhodes Christopher , Chung Wendy K. , Whitsett Jeffrey A. , Martin Lisa J. , Kalinichenko Vladimir V. , Nichols William C.
Published: September 2024

Rationale

Approximately 80% of patients with non-familial pulmonary arterial hypertension (PAH) lack identifiable pathogenic genetic variants. While most genetic studies of PAH have focused on predicted loss-of-function variants, recent approaches have identified ultra-rare missense variants associated with the disease.FOXF1encodes a highly conserved transcription factor, essential for angiogenesis and vasculogenesis in human and mouse lungs.

Objectives

We identified a rareFOXF1missense coding variant in two unrelated probands with PAH.FOXF1is an evolutionarily conserved transcription factor required for lung vascular development and vascular integrity. Our aims were to determine the frequency ofFOXF1variants in larger PAH cohorts compared to the general population, studyFOXF1expression in explanted lung tissue from PAH patients versus control (failed-donor) lungs, and define potential downstream targets linked to PAH development.

Methods

Three independent, international, multicenter cohorts were analyzed to evaluate the frequency ofFOXF1rare variants. Various composite prediction models assessed the deleteriousness of individual variants. Bulk RNA sequencing datasets from human explanted lung tissues were compared to failed-donor controls to determineFOXF1expression. Bioinformatic tools identified putativeFOXF1binding targets, which were orthogonally validated using mouse ChIP-seq datasets.

Measurements and Main Results

Seven novel or ultra-rare missense coding variants were identified across three patient cohorts in different regions of theFOXF1gene, including the DNA binding domain.FOXF1expression was dysregulated in PAH lungs, correlating with disease severity. Histological analysis showed heterogeneousFOXF1expression, with the lowest levels in phenotypically abnormal endothelial cells within complex vascular lesions in PAH samples. A hybrid bioinformatic approach identified FOXF1 downstream targets potentially involved in PAH pathogenesis, includingBMPR2.

Conclusions

Large genomic and transcriptomic datasets suggest that decreasedFOXF1expression or predicted dysfunction is associated with PAH.
Increased cGMP improves microvascular exercise training adaptations independent of endothelial nitric oxide synthase
Authors: Winn Nathan C. , Cappel David A. , Pollock Ethan D. , Lantier Louise , Riveros Jillian K. , Debrow Payton , Bracy Deanna P. , Beckman Joshua A. , Wasserman David H.
Published: September 2024

Impaired microvascular function is a hallmark of pre-diabetes. With development of atherosclerosis this impaired microvascular function can result in diminished capacity for ambulation and is a risk factor for Type 2 Diabetes. Dynamic changes in vascular tone are determined, in large part, by the eNOS/NO/cGMP axis. We used gain of function of the eNOS/NO/cGMP axis in diet-induced obese (DIO) mice and reduced function in lean mice to test the hypothesis that functionality of this vascular control mechanism parallels the benefits of an exercise training regimen. DIO mice have lower exercise capacity than lean mice and were used for pharmacological gain of function. The PDE-5a inhibitor – sildenafil – increases cGMP and was administered to DIO mice daily. In sedentary mice, we find that sildenafil does not improve exercise capacity. In contrast, it amplifies the microcirculatory effects of exercise training. Sildenafil synergizes with exercise training to improve performance during an incremental exercise test. Improved exercise performance was accompanied by increased skeletal muscle capillary flow velocity and capillary density measured via intravital microscopy. Loss of function was tested in lean mice hemizygous for endothelial cell (EC) specific eNOS creating an EC-eNOS knockdown (KD). EC-eNOS KD decreases capillary density and exercise tolerance in sedentary mice; however, it did not prevent exercise-training induced improvements in endurance capacity. These data show that 1) increasing cGMP with sildenafil enhances microcirculatory function and exercise work tolerance that results from training; 2) eNOS KD does not prevent the microcirculatory or improvements in exercise tolerance with training. PDE-5a inhibitors combined with physical exercise are a potential mechanism for improving ambulation in patients with circulatory limitations.
Monocyte-derived cells but not Microglia cause Oxidative Tissue Damage in Neuroinflammation
Authors: Villar-Vesga Juan , De Feo Donatella , Clément Pauline , Ingelfinger Florian , Ulutekin Can , Kim Jeanne , Pena-Francesch Maria , Schmidt Katarina Wendy , Meuffels Elèni , Bugada Viola , Greis Deborah , Costa-Pereira Sara , Oberbichler Laura , Seehusen Frauke , Prisco Francesco , Dalvi Urvashi , Münz Christian , Saab Aiman S. , Becher Burkhard , Mundt Sarah
Published: September 2024

Multiple sclerosis (MS) is characterized by neuroinflammation, oxidative stress, iron toxicity and mitochondrial dysfunction. Reactive oxygen species (ROS) produced by mononuclear phagocytes (MPs) are widely held to drive tissue damage, yet the specific roles of central nervous system (CNS)- resident versus CNS-invading MPs remain unclear. Here, by combining single-cell profiling with conditional gene targeting, we systematically dissected and interfered with ROS production across CNS MPs in a preclinical model for neuroinflammation. We show that CNS-invading monocyte derived cells (MdCs) exhibit a higher oxidative stress gene signature and produce more ROS compared to CNS-resident microglia. While NADPH oxidase 2 (NOX2), a phagocytic source of ROS, proved redundant, our findings underscore the critical role of mitochondrial ROS (mtROS) in driving oxidative tissue damage. Quenching mtROS through mitocatalase overexpression in MdCs, but not microglia, significantly alleviated neuroinflammation in mice. Thus, our study resolves a longstanding controversy, identifying MdCs as the primary driver of ROS-mediated neuropathology.
Overcoming immune evasion from post-translational modification of a mutant KRAS epitope to achieve TCR-T cell-mediated antitumor activity
Authors: Lee Jihoon William , Chen Emily Y. , Hu Taylor , Perret Rachel , Chaffee Mary E. , Martinov Tijana , Mureli Shwetha , McCurdy Clara L. , Jones Lisa A. , Gafken Philip R. , Chanana Pritha , Su Yapeng , Chapuis Aude G. , Bradley Philip , Schmitt Thomas M. , Greenberg Philip D.
Published: September 2024

T cell receptor (TCR)-T cell immunotherapy, in which T cells are engineered to express a TCR targeting a tumor epitope, is a form of adoptive cell therapy (ACT) that has exhibited promise against various tumor types. Mutants of oncoprotein KRAS, particularly at glycine-12 (G12), are frequent drivers of tumorigenicity, making them attractive targets for TCR-T cell therapy. However, class I-restricted TCRs specifically targeting G12-mutant KRAS epitopes in the context of tumors expressing HLA-A2, the most common human HLA-A allele, have remained elusive despite evidence an epitope encompassing such mutations can bind HLA-A2 and induce T cell responses. We report post-translational modifications (PTMs) on this epitope may allow tumor cells to evade immunologic pressure from TCR-T cells. A lysine side chain-methylated KRASG12Vpeptide, rather than the unmodified epitope, may be presented in HLA-A2 by tumor cells and impact TCR recognition. Using a novel computationally guided approach, we developed by mutagenesis TCRs that recognize this methylated peptide, enhancing tumor recognition and destruction. Additionally, we identified TCRs with similar functional activity in normal repertoires from primary T cells by stimulation with modified peptide, clonal expansion, and selection. Mechanistically, a gene knockout screen to identify mechanism(s) by which tumor cells methylate/demethylate this epitope unveiled SPT6 as a demethylating protein that could be targeted to improve effectiveness of these new TCRs. Our findings highlight the role of PTMs in immune evasion and suggest identifying and targeting such modifications should make effective ACTs available for a substantially greater range of tumors than the current therapeutic landscape.

One-sentence summary

Tumor cell methylation of KRASG12Vepitope in HLA-A2 permits immune evasion, and new TCRs were generated to overcome this with engineered cell therapy.
Development of a small-molecule epigenetic regenerative therapy. Subcutaneous administration of alginate formulations with high loads of zebularine and retinoic acid promotes tissue growth, vascularization and innervation and induces extensive epigenetic repatterning
Authors: Słonimska Paulina , Baczyński-Keller Jakub , Płatek Rafał , Deptuła Milena , Dzierżyńska Maria , Sawicka Justyna , Król Oliwia , Sosnowski Paweł , Koczkowska Magdalena , Kostecka Anna , Crossman David K. , Crowley Michael R. , Sass Piotr , Smoleński Ryszard Tomasz , Skowron Piotr M. , Piotrowski Arkadiusz , Pikuła Michał , Rodziewicz-Motowidło Sylwia , Sachadyn Paweł
Published: September 2024

Recently, zebularine, a small-molecule epigenetic inhibitor and retinoic acid, acting as a transcriptional activator, have been found to induce tissue regeneration. In this study, the pro-regenerative properties of zebularine and retinoic acid were combined with the potential of the alginate carrier to expand its therapeutic possibilities.

Alginate formulations of zebularine and retinoic acid were developed for subcutaneous administration to mice. Hydrophilic zebularine formed a homogenous formulation with extreme drug loadings reaching 240 mg of zebularine per 1 ml of 2% sodium alginate, while hydrophobic retinoic acid, 0.8 mg/ml, dispersed as fine crystals. Cell culture tests exhibited no significant cytotoxicity of the alginate formulations.

Subcutaneous administration of zebularine and retinoic acid in 2% sodium alginate promoted regenerative responses in a mouse model of ear pinna punch wound mice involving the restoration of tissue architecture, nerve and vessel growth, and extensive epigenetic and transcriptional repatterning with no adverse effects observed in the animals. Significant trancriptomic responses to the epigenetic treatment included the induction of epithelium development genes contrasted with the downregulation of muscle development genes on day 7 post-injury. Among the remarkable changes in global gene methylation are those in neurodevelopmental genes.In vitrostudies showed rapid zebularine but no retinoic acid discharge from the alginate formulations. Live ultrasound imaging demonstrated gradual absorption of the subcutaneously injected alginate formulations, which may explain thein vivoactivity of retinoic acid following subcutaneous administration.

Effective induction of tissue regeneration together with a high safety profile and of the subcutaneously administered pro-regenerative alginate formulations opens the way to testing further regenerative therapies for hard-to-reach lesions.
Influence of stereochemistry in a local approach for calculating protein conformations
Authors: da Rocha Wagner , Liberti Leo , Mucherino Antonio , Malliavin Therese E
Published: September 2024

Protein structure prediction is usually based on the use of local conformational information coupled with long-range distance restraints. Such restraints can be derived from the knowledge of a template structure or the analysis of protein sequence alignment in the framework of models arising from the physics of disordered systems. The accuracy of approaches based on sequence alignment, however, is limited in the case where the number of aligned sequences is small. Here we derive protein conformations using only local conformations knowledge by means of the interval Branch-and-Prune algorithm. The computation efficiency is directly related to the knowledge of stereochemistry (bond angle and ω values) along the protein sequence, and in particular to the variations of the torsion angle ω. The impact of stereochemistry variations is particularly strong in the case of protein topologies defined from numerous long-range restraints, as in the case of protein of β secondary structures. The systematic enumeration of the conformations improves the efficiency of the calculations. The analysis of DNA codons permits to connect the variations of torsion angle ω to the positions of rare DNA codons.
The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics
Authors: Matentzoglu Nicolas , Bello Susan M , Stefancsik Ray , Alghamdi Sarah M. , Anagnostopoulos Anna V. , Balhoff James P. , Balk Meghan A. , Bradford Yvonne M. , Bridges Yasemin , Callahan Tiffany J. , Caufield Harry , Cuzick Alayne , Carmody Leigh C , Caron Anita R. , de Souza Vinicius , Engel Stacia R. , Fey Petra , Fisher Malcolm , Gehrke Sarah , Grove Christian , Hansen Peter , Harris Nomi L. , Harris Midori A. , Harris Laura , Ibrahim Arwa , Jacobsen Julius O.B. , Köhler Sebastian , McMurry Julie A. , Munoz-Fuentes Violeta , Munoz-Torres Monica C. , Parkinson Helen , Pendlington Zoë M , Pilgrim Clare , Robb Sofia MC , Robinson Peter N. , Seager James , Segerdell Erik , Smedley Damian , Sollis Elliot , Toro Sabrina , Vasilevsky Nicole , Wood Valerie , Haendel Melissa A. , Mungall Christopher J. , McLaughlin James A. , Osumi-Sutherland David
Published: September 2024

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses.

A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed.

We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.
Widespread selection relaxation in aquatic mammals
Authors: Farina B.M. , Latrille T. , Salamin N. , Silvestro D. , Faurby S.
Published: September 2024

While mammals are predominantly terrestrial, several lineages within them have independently transitioned to aquatic environments and exhibit a great variety of evolutionary changes, which ultimately lead to irreversible transitions to aquatic lifestyle. Such changes should also be detectable at the molecular level and, for instance, olfactory genes have been found to evolve under reduced selection and functionality in whales. However, the presence of a molecular signature related to aquatic transitions across other genes remains unknown as is the degree to which this affects only fully aquatic groups or also semiaquatic ones. Here, we use a Bayesian framework to investigate differences in the strength of purifying selection among terrestrial, semiaquatic and fully aquatic mammals using a set of 1000 orthologous genes, while accounting for shared ancestry, and controlling for body mass and effective population size. We found that selection relaxation linked to aquatic transitions is not only occurring in olfactory genes, but also detected across 20% of the other genes analysed here. This consistent trend of genes under weaker selection is inferred in both semi- and fully aquatic mammals although the pattern is stronger in the latter. While most of the genes analysed here likely remain functional in all mammals, their evolution is inferred to be neutral in a substantial number of aquatic species, consistently with genes that might be losing their functionality. The inferred widespread relaxation of selection among genes is consistent with a macroevolutionary scenario where secondary transitions to aquatic environment eventually become irreversible.
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair
Authors: McDaniel Jennifer H. , Patel Vaidehi , Olson Nathan D. , He Hua-Jun , He Zhiyong , Cole Kenneth D. , Schmitt Anthony , Sikkink Kristin , Sedlazeck Fritz J , Doddapaneni Harsha , Jhangiani Shalini N. , Muzny Donna M. , Gingras Marie-Claude , Mehta Heer , Paulin Luis F , Hastie Alex R , Yu Hung-Chun , Weigman Victor , Rojas Alison , Kennedy Katie , Remington Jamie , Gonzalez Isai , Sudkamp Mitch , Wiseman Kelly , Lajoie Bryan R. , Levy Shawn , Jain Miten , Akeson Stuart , Narzisi Giuseppe , Steinsnyder Zoe , Reeves Catherine , Shelton Jennifer , Kingan Sarah B. , Lambert Christine , Bayabyan Primo , Wenger Aaron M. , McLaughlin Ian J. , Adamson Aaron , Kingsley Christopher , Wescott Melanie , Kim Young , Paten Benedict , Park Jimin , Violich Ivo , Miga Karen H , Gardner Joshua , McNulty Brandy , Rosen Gail , McCoy Rajiv , Brundu Francesco , Sayyari Erfan , Scheffler Konrad , Truong Sean , Catreux Severine , Hannah Lesley Chapman , Lipson Doron , Benjamin Hila , Iremadze Nika , Soifer Ilya , Eacker Stephen , Wood Mary , Cross Erin , Husar Greg , Gross Stephen , Vernich Michael , Kolmogorov Mikhail , Ahmad Tanveer , Keskus Ayse , Bryant Asher , Thibaud-Nissen Francoise , Trow Jonathan , Proszynski Jacqueline , Hirschberg Jeremy W. , Ryon Krista , Mason Christopher E. , Wagner Justin , Xiao Chunlin , Liss Andrew S. , Zook Justin M.
Published: September 2024

The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from thirteen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies,de novoassembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.
Broadly Reactive Anti-VHH Antibodies for Characterizing, Blocking, or Activating Nanobody-Based CAR-T Cells
Authors: McComb Scott , Dupont Bianca , Shepherd Alex , Bennychen Bigitha , Marcil Anne , Arbabi-Ghahroudi Mehdi , Tamblyn Laura , Raphael Shalini , Sheff Joey , Hussack Greg , Moraitis Anna N. , Wu Cunle , Aubry Annie , Gadoury Christine , Lippens Julie , Pagé Martine , Fortin Annie , Joubert Simon , Lamoureux Linda , Parat Marie , Plante Pierre , Malenfant Félix , Acchione Mauro , Pohankova Petra , Schrag Joe , Acel Andrea , Coutu Mathieu , Smith Emma , Bakkouri Majida El , Hill Jennifer J. , Tremblay Tammy-Lynn , Aziza Manceur , Faulkes Sharlene , Webb John , Zafer Ahmed , Zhu Qin , Nguyen Tina , Pon Robert A. , Weeratna Risini D.
Published: September 2024

Production of chimeric antigen receptor T cell (CAR-T) therapies is dependent on the use of antibody reagents to label, isolate, and/or expand T cell products. We sought to create antibody-based tools that directly target the variable domain of heavy-chain only antibodies (VHH or nanobody) used in some CAR molecules. Two murine antibodies were identified which bind to distinct epitopes in the conserved framework regions of llama-derived VHHs, and not to human VH domains. We produced a high-quality dual-clonal anti-VHH antibody product which reacts with over 98% of VHH proteins, regardless of their antigenic specificity. Anti-VHH binding did not disrupt VHH/antigen interaction, and thus could be used for secondary labeling to assess cellular or tissue reactivity of VHH molecules. Despite not interfering with antigen binding, anti-VHH antibodies potently inhibited VHH-CAR function, blocking CAR-T activation and cytolytic killing of target cells. When immobilized, anti-VHH antibodies could also be applied for activation and expansion of VHH CAR-T cells, inducing 730-fold mean expansion, >94% CAR purity, with retained CD8/CD4 heterogeneity. Functionally, anti-VHH antibody-expanded CAR-T cells maintained strong antigen specific activity without functional exhaustion. Overall, these data identify a useful new tool for understanding and manipulating VHH-based CAR-T cells.

Funding Source

This work was funded by the National Research Council Canada Disruptive Technology Solutions Cell and Gene Therapy challenge program, and BioCanRx

Declaration of interests

The anti-VHH antibodies reported here are the subject of a provisional patent application by the National Research Council of Canada
Accessible chromatin regions and DNA methylation regulate gene expression leading to changes in agronomic traits inBrassicaallotriploid hybrids
Authors: Quan Chengtao , Zhang Qin , Zhang Xiaoni , Chai Kexin , Cheng Guoting , Ma Chaozhi , Dai Cheng
Published: September 2024

Introduction

Interspecific hybridization is a common method in plant breeding to combine traits from different species, resulting in allopolyploidization and significant genetic and epigenetic changes. However, our understanding of genome-wide chromatin and gene expression dynamics during allopolyploidization remains limited.

Objectives

We aimed to explore the relationship and underlying mechanisms between accessible chromatin regions and DNA methylation and gene transcription in genome-wide reorganization after interspecific hybridization.

Methods

This study generated twoBrassicaallotriploid hybrids via interspecific hybridization, combining transcriptomics, whole-genome bisulfite sequencing (WGBS) and assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq), revealing that accessible chromatin regions (ACRs) and DNA methylation regulate gene expression after interspecific hybridization, ultimately influencing the agronomic traits of the hybrids.

Results

A total of 234,649 ACRs were identified in the parental lines and hybrids, the hybridization process induces changes in the distribution and abundance of there accessible chromatin regions, particularly in gene regions and their proximity. On average, genes associated with Proximal ACRs were more highly expressed than the genes associated with Distal and Genic ACRs. More than half of novel ACRs drove transgressive gene expression in the hybrids, and the transgressive up-regulated genes showed significant enrichment in metal ion binding, especially magnesium ion, calcium ion, and potassium ion binding. We also identified theBna.bZIP11in the single-parent activation ACR (SPA-ACR), which binds toBnaA06.UF3GTto promote anthocyanin accumulation in F1hybrids. Additionally, in F1hybrids, the level of DNA methylation in ACRs was higher compared to gene bodies, and the A-subgenome ACRs were associated with genome dosage rather than DNA methylation.

Conclusions

The interplay among DNA methylation, TEs, and sRNA contributes to the dynamic landscape of ACRs during interspecific hybridization, resulting in distinct gene expression patterns on the genome.

HIGHLIGHTS

The study utilized the accessible chromatin regions (ACR) and DNA methylation to elucidate the mechanism behind gene expression changes following interspecific hybridization.

Whole-genome recombination after interspecific hybridization leads to the rearrangement of ACR, and novel ACR and single-parent activation ACR regulate the expression of genes.

DNA methylation plays a role in repressing gene expression within ACRs, and unmethylated ACRs have more transcriptionally active.

A-subgenome ACRs were associated with genome dosage rather than DNA methylation.

GRAPHICAL ABSTRACT
Family-Wide Photoproximity Profiling of Integrin Protein Social Networks in Cancer
Authors: Carlos Anthony J. , Yang Dongbo , Thomas Deborah M. , Huang Shuyuan , Harter Keira I. , Moellering Raymond E.
Published: September 2024

Integrin family transmembrane receptors mediate dynamic interactions between cells and their extracellular microenvironment. The heterogeneous interaction partners of integrins directly regulate cell adhesion, motility, proliferation, and intracellular signaling. Despite the recognized importance of protein-protein interactions and the formation of signaling hubs around integrins, the ability to detect and quantify these dynamic binding partners with high spatial and temporal resolution remains challenging. Here, we developed an integrin-family-directed quantitative photoproximity protein interaction (PhotoPPI) profiling method to detect and quantify native integrin-centered protein social networks on live cells and tissues without the need for genetic manipulation, antibodies, or non-physiologic cell culture conditions. We drafted quantitative maps of integrin-centered protein social networks, highlighting conserved and unique binding partners between different cell types and cellular microenvironments. Comparison of integrin social networks in cancer cell lines of diverse tissue of origin and disease state identified specific AND-gate binding partners involved cell migration, microenvironmental interactions and proliferation that serve as markers of tumor cell metastatic state. Finally, we identified unique combinations – or barcodes - of integrin-proximal proteins on the surface of pre- and post-metastatic triple negative breast cancer (TNBC) cells whose expression strongly correlate with both positive and negative disease progression and outcomes in TNBC patients. Taken together, these data provide the first family-wide high-resolution maps of native protein interactors on live cells and identify dynamic integrin-centered social networks as potential AND-gate markers of cell identity, microenvironmental context and disease state.
Peptide-MHC-targeted retroviruses enablein vivoexpansion and gene delivery to tumor-specific T cells
Authors: Xu Ellen J.K. , Smith Blake E. , Conce Alberto Winiffer D. , Walsh Michael J. , Lim Birkley , Hoffman Megan T. , Qiang Li , Dong Jiayi , Garmilla Andrea , Zhao Qingyang Henry , Perez Caleb R. , Gaglione Stephanie A. , Dobson Connor S. , Dougan Michael , Dougan Stephanie K. , Birnbaum Michael E.
Published: September 2024

Tumor-infiltrating-lymphocyte (TIL) therapy has demonstrated that endogenous T cells can be harnessed to initiate an effective anti-tumor response. Despite clinical promise, current TIL production protocols involve weeks-longex vivoexpansions which can affect treatment efficacy. Therefore, additional tools are needed to engineer endogenous tumor-specific T cells to have increased potency while mitigating challenges of manufacturing. Here, we present a strategy for pseudotyping retroviral vectors with peptide-major histocompatibility complexes (pMHC) for antigen-specific gene delivery to CD8 T cells and examine the efficacy of these transduced cells in immunocompetent mouse models. We demonstrate that pMHC-targeted viruses are able to specifically deliver function-enhancing cargoes while simultaneously activating and expanding anti-tumor T cells. The specificity of these viral vectors enablesin vivoengineering of tumor-specific T cells, circumventingex vivomanufacturing processes and improving overall survival in B16F10-bearing mice. Altogether, we have established that pMHC-targeted viruses are efficient vectors for reprogramming and expanding tumor-specific populations of T cells directlyin vivo, with the potential to substantially streamline engineered cell therapy production for a variety of applications.
Dramatic evolutionary changes of conserved noncoding elements accompanied by extraordinary features ofCaenorhabditis inopinata
Authors: Tamagawa Katsunori , Oomura Shun , Sugimoto Asako , Makino Takashi
Published: September 2024

Phenotypic evolution is caused by mutations in noncoding and protein-coding regions. Conserved noncoding elements (CNEs) have—at least partially—gene regulatory functions and contribute to the evolution of organisms by modifying their gene expression. While evolutionary changes of CNEs—such as loss and accelerated evolution—have been intensively studied in vertebrates, only a few studies have focused on invertebrates. The availability of detailed functional genomic information of the model nematodeCaenorhabditis elegansand recent accumulation of genome sequences within the same genus facilitate the use of these nematodes in comparative genomics focusing on CNEs. The recently discovered speciesCaenorhabditis inopinatahas several peculiar traits characterized by a larger body size than that of its close relatives and are regarded as an appropriate species that links phenotypic evolution with genomic changes. Herein, using comparative genomics and transcriptomics inC. inopinata, we analyzed the evolution of CNEs and their functions during phenotypic evolution. We detected substantial evolutionary changes in CNEs inC. inopinatacompared to other relatives—changes frequently associated with body morphology and behavior corresponding to extraordinary body size and unique life cycles. Our study revealed an association between noncoding elements and substantial phenotypic evolution in invertebrates.
Motif distribution in genomes gives insights into gene clustering and co-regulation
Authors: Chakraborty Atreyi , Chopde Sumant , Madhusudhan M.S
Published: September 2024

We read the genome as proteins in the cell would - by studying the distributions of 5-6 base motifs of DNA in the whole genome or smaller stretches such as parts of, or whole chromosomes. This led us to some interesting findings about motif clustering and chromosome organisation. It is quite clear that the motif distribution in genomes is not random at the length scales we examined: 1kbps to entire chromosomes. The observed to expected (OE) ratios of motif distributions show strong correlations in pairs of chromosomes that are susceptible to translocations. With the aid of examples, we suggest that similarity in motif distributions in promoter regions of genes could imply co-regulation. A simple extension of this idea empowers us with the ability to construct gene regulatory networks. Further, we could make inferences about the spatial proximity of genomic fragments using these motif distributions. Spatially proximal regions, as deduced by Hi-C or pcHi-C, were ∼3.5 times more likely to have their motif distributions correlated than non-proximal regions. These correlations had strong contributions from the CTCF protein recognizing motifs which are known markers of TADs. In general, correlating genomic regions by motif distribution comparisons alone is rife with functional information.

GRAPHICAL ABSTRACT