bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficacy and safety of sarilumab in patients with rheumatoid arthritis stratified by age (<65 and ≥65 years): A post hoc analysis of Japanese Phase 3 clinical trials
Authors: Tanaka Yoshiya , Takahashi Toshiya , van Hoogstraten Hubert , Kato Naoto , Kameda Hideto
Published: July 2024

Objectives

This study aimed to assess the efficacy and safety of sarilumab in older patients with active rheumatoid arthritis (RA).

Methods

This is a post hoc analysis of KAKEHASI (NCT02293902) and HARUKA (NCT02373202) trials with stratification by age (<65 and ≥65 years). Patients with moderately to severely active RA were treated with sarilumab in combination with methotrexate or with conventional synthetic disease-modifying antirheumatic drugs (csDMARDs) or as monotherapy. The primary end points in KAKEHASI and HARUKA trials were the American College of Rheumatology 20% improvement criteria (ACR20) responses at Week 24 and safety, respectively. Secondary end points were other RA disease activity measures, including Clinical Disease Activity Index (CDAI).

Results

Approximately 20% of patients were aged ≥65 years in treatment arms across both trials, except the sarilumab + csDMARD arm (40%, 12/30). ACR20 response rates were similar between age groups across sarilumab treatment arms, and similar results were obtained for the CDAI scores. Safety profiles were similar between age groups except for a higher incidence of serious adverse events in patients aged ≥65 years in the sarilumab + methotrexate arm.

Conclusions

In Japanese patients with RA enrolled in Phase 3 studies for sarilumab, no clear difference in efficacy or safety was observed between patients aged <65 and ≥65 years.
Phase 1 study of concomitant tumor treating fields and temozolomide chemoradiation for newly diagnosed glioblastoma
Authors: Goldlust Samuel A , Singer Samuel , Cappello Lori A , AlMekkawi Ahmad K , Lee Kangmin D , Ingenito Anthony C , Lewis Brett E , Nyirenda Themba , Azmi Hooman , Kaptain George J
Published: July 2024

Background

Glioblastoma (GBM) is the most common and aggressive primary brain tumor and has limited effective therapies. Tumor treating fields (TTF; Optune Gio®) is an FDA-approved device with data supporting a significant survival benefit and minimal toxicity when added to maintenance chemotherapy. Uptake in clinical practice is not universal and might improve if a shorter duration of treatment is feasible. This phase 1 trial was designed to determine the safety and preliminary efficacy of TTF concomitant to chemoradiation.

Methods

Patients with newly diagnosed, histologically confirmed GBM were eligible. Following surgery, patients were treated with TTF concomitant to standard chemoradiation. The device continued through 2 monthly cycles of maintenance temozolomide with imaging and clinical assessments at regular intervals to assess toxicity and response. The primary endpoint was the safety and tolerability of combined modality treatment based upon the incidence and severity of adverse events. Secondary endpoints were overall survival (OS) and progression-free survival (PFS).

Results

Thirteen patients were enrolled. Dermatologic adverse events were frequent but limited to grade 1/2. There was only 1 serious adverse event possibly related to TTF and no patients were unable to complete the prescribed course of multimodality treatment due to TTF-associated toxicity. Twelve patients were evaluable for median and 6-month progression-free survival which were 8.5 months (mo) and 66.7%, respectively. Median and 12 mo overall survival were 16.0 mo and 83.3%, respectively.

Conclusions

TTF can be safely delivered in conjunction with chemoradiation. The potential for a finite TTF course merits further evaluation.
HNF4α improves hepatocyte regeneration by upregulating PXR
Authors: Qiu Shantong , Pan Yangyang , Cui Yan , Li Mei , Yue Tao , Pu Sisi , Zhang Qian , Wang Meng
Published: July 2024

Hepatocyte nuclear factor 4 alpha (HNF4α) and the pregnane X receptor (PXR) are involved in hepatocyte regeneration. It is not clear whether HNF4α is involved in hepatocyte regeneration through the regulation of PXR. This study aims to explore the regulatory relationship between HNF4a and PXR, and whether it affects hepatocyte regeneration. A mouse PXR gene reporter and an HNF4α overexpression plasmid were constructed and transfected into mouse hepatoma cells (Hepa1‐6). Overexpression of HNF4α, detection of the PXR gene reporter fluorescence value, PXR gene, and protein expression analysis were conducted to explore the regulatory relationship between HNF4α and PXR. Apoptosis and cell cycle data were measured to verify whether HNF4α is involved in hepatocyte regeneration through PXR. The luciferase gene reporter assay results indicated when HNF4α was overexpressed, the fluorescence value of the PXR gene reporter was higher than that in the control at 24 h. With increasing HNF4α expression, the PXR gene and protein expression increased, indicating that HNF4α binds to the PXR promoter and upregulates PXR expression. Apoptosis and cell cycle analysis results demonstrated that when the expression of HNF4α increased, the expression of PXR increased, the apoptosis rate decreased, and the proliferation rate increased. Meanwhile, when the upward trend of PXR gene expression was inhibited by ketoconazole, the proliferation rate decreased. By inhibiting HNF4α and creating a partial hepatectomy (PHx), we demonstrated that HNF4α can upregulate PXR to promote liver regeneration in vivo. Therefore, HNF4α is shown to improve hepatocyte regeneration by upregulating PXR, which provides a reference for future research on the combined application of drugs for the treatment of liver injury.
Patellofemoral Disorders in Soccer Players
Authors: Smith Richard D.J. , Hanrahan Madalyn , Gerber Annabel , Tanaka Miho J.
Published: August 2024

Patellofemoral disorders are common in the world of soccer and impact players across all levels and ages of the sport. Patellofemoral disorders encompass a spectrum of conditions, from anterior knee pain to patellar instability, and are often influenced by complex biomechanical factors and anatomic variations that can predispose to these conditions. In recent years, there has been a growing emphasis on injury prevention strategies and data-driven approaches, championed by organizations like the Union of European Football Associations and individual professional clubs. Conservative management remains the initial approach for many players, including physical therapy and supportive devices. However, surgical intervention, particularly in cases of recurrent patellar dislocations, is often necessary. The understanding of patellofemoral biomechanics in soccer continues to evolve and offers opportunities for more effective injury prevention and tailored treatment strategies. Despite the challenges, a comprehensive approach to patellofemoral disorders in soccer is essential to preserve player health, enhance performance, and sustain the sport’s vitality.
The Cost-effectiveness of Valganciclovir Prophylaxis Versus Preemptive Therapy in CMV R+ Kidney Transplant Recipients Over the First Year Posttransplantation
Authors: Villeneuve Claire , Rerolle Jean-Phillipe , Couzi Lionel , Westeel Pierre-Francois , Etienne Isabelle , Esposito Laure , Kamar Nassim , Büchler Mathias , Thierry Antoine , Marquet Pierre , Monchaud Caroline
Published: July 2024

Background.

In kidney transplant recipients with positive serology (R+) for the cytomegalovirus (CMV), 2 strategies are used to prevent infection, whose respective advantages over the other are still debated. This study aimed to evaluate the cost-effectiveness and cost utility of antiviral prophylaxis against CMV versus preemptive therapy, considering CMV infection–free survival over the first year posttransplantation as the main clinical outcome.

Methods.

Clinical, laboratory, and economic data were collected from 186 kidney transplant patients CMV (R+) included in the cohort study (85 patients who benefited from CMV prophylaxis and 101 from preemptive therapy). Costs were calculated from the hospital perspective and quality-adjusted life years (QALYs) using the EQ5D form. Using nonparametric bootstrapping, the incremental cost-effectiveness ratio (ICER) and cost utility were estimated (euros) for each case of infection avoided and each QALY gained for 1 y, respectively.

Results.

Prophylaxis significantly decreased the risk of CMV infection over the first year posttransplantation (hazard ratio 0.22, 95% confidence interval = 0.12-0.37, P < 0.01). Compared with preemptive therapy, prophylaxis saved financial resources (€1155 per patient) and was more effective (0.42 infection avoided per patient), resulting in an ICER = €2769 per infection avoided. Prophylaxis resulted in a net gain of 0.046 in QALYs per patient and dominated over preemptive therapy with €1422 cost-saving for 1 QALY gained.

Conclusions.

This study shows that CMV prophylaxis, although considered as a more expensive strategy, is more cost-effective than preemptive therapy for the prevention of CMV infections in renal transplant patients. Prophylaxis had a positive effect on quality of life at reasonable costs and resulted in net savings for the hospital.
Expanding the Donor Pool to the Ultimate Level: Introducing the Revolutionary Hybrid Dual Graft Liver Transplant Using Domino and Living Donors
Authors: Zidan Ahmed , Momani Hammam , Sengupta Bodhisatwa , Abdullah Rehab , Bader Razan , Khan Iftikhar , Tawfeeq Mansour , Al Qahtani Mohammed
Published: July 2024

Background.

Innovative solutions are crucial as the demand for liver transplants continues to outpace available grafts. Dual graft liver transplantation offers a promising avenue to address graft volume challenges while minimizing donor risks. This report introduces a groundbreaking approach, combining a full organ domino donor graft with a living donor graft for a hybrid dual graft liver transplant.

Brief Report.

A 2-y-old child with Maple syrup urine disease and a 40-y-old adult with end-stage liver disease became the focus of this unique case. A hybrid dual graft liver transplant was executed, uniting the domino donor’s full organ graft with a living donor’s left lateral segment. Precise vascular and biliary reconstructions facilitated a successful transplant.

Conclusions.

The hybrid dual graft liver transplant, merging domino donor and living donor grafts, presents a viable strategy to combat graft shortages, particularly in regions predominantly reliant on living donor transplants. Despite challenges, this pioneering approach should be embraced by established liver transplant centers because it enables concurrent living donor liver transplantation while prioritizing donor safety and recipient outcomes.
The Cotard Delusion in a Patient With Neuropsychiatric Systemic Lupus Erythematosus: The Challenges of Autoimmune Psychosis
Authors: García-Sarreón Alexis , Escamilla-Ramírez Angel , Martínez-López Yasmin , García-Esparza Kevin A. , Kerik-Rotenberg Nora , Ramírez-Bermúdez Jesús
Published: August 2024

The clinical features of neuropsychiatric systemic lupus erythematosus (NPSLE) are heterogeneous. Furthermore, therapeutic decision-making for NPSLE depends on the recognition of clinical syndromes that have not been sufficiently studied. This report describes the case of a 36-year-old woman with NPSLE who exhibited severe cognitive dysfunction and affective psychosis with persistent nihilistic delusions such as those described in the Cotard delusion. The patient insisted for several months that she was already dead. CSF analysis showed elevated levels of anti-ribosomal P antibodies and a positive determination of oligoclonal bands. Additionally,18F-FDG PET/CT imaging revealed severe bilateral frontal hypermetabolism suggestive of brain inflammation and occipital hypometabolism. Results from the Systematic Lupus Erythematosus Disease Activity Index 2000 and the Systemic Lupus Erythematosus Disease Activity Score were consistent with an active state of the immunological disease. We then determined by an algorithm that this neuropsychiatric event could be attributed to the activity of the underlying immunological disease. Despite immunosuppressive and symptomatic treatment, only a partial improvement in cognition was achieved. The psychopathological features of the Cotard delusion remained unchanged 4 months after onset. However, we observed rapid remission of affective psychosis and significant improvement in cognition following electroconvulsive therapy. Subsequent follow-up examinations showed a sustained remission. This case describes a protracted form of the Cotard delusion, the diagnostic challenges that arise in the context of SLE, and treatment dilemmas that necessitate collaboration between neurology, psychiatry, and rheumatology.
Individualized melanoma risk prediction using machine learning with electronic health records
Authors: Wan Guihong , Khattab Sara , Roster Katie , Nguyen Nga , Yan Boshen , Rashdan Hannah , Estiri Hossein , Semenov Yevgeniy R.
Published: July 2024

Background

Melanoma is a lethal form of skin cancer with a high propensity for metastasizing, making early detection crucial. This study aims to develop a machine learning model using electronic health record data to identify patients at high risk of developing melanoma to prioritize them for dermatology screening.

Methods

This retrospective study included patients diagnosed with melanoma (cases), as well as matched patients without melanoma (controls), from Massachusetts General Hospital (MGH), Brigham and Women’s Hospital (BWH), Dana-Farber Cancer Institute (DFCI), and other hospital centers within the Research Patient Data Registry at Mass General Brigham healthcare system between 1992 and 2022. Patient demographics, family history, diagnoses, medications, procedures, laboratory tests, reasons for visits, and allergy data six months prior to the date of first melanoma diagnosis or date of censoring were extracted. A machine learning framework for health outcomes (MLHO) was utilized to build the model. Performance was evaluated using five-fold cross-validation of the MGH cohort (internal validation) and by using the MGH cohort for model training and the non-MGH cohort for independent testing (external validation). The Area Under the Receiver Operating Characteristic Curve (AUC-ROC) and the Area Under the Precision-Recall Curve (AUC-PR), along with 95% Confidence Intervals (CIs), were computed.

Results

This study identified 10,778 patients with melanoma and 10,778 matched patients without melanoma, including 8,944 from MGH and 1,834 from non-MGH hospitals in each cohort, both with an average follow-up duration of 9 years. In the internal and external validations, the model achieved AUC-ROC values of 0.826 (95% CI: 0.819–0.832) and 0.823 (95% CI: 0.809–0.837) and AUC-PR scores of 0.841 (95% CI: 0.834–0.848) and 0.822 (95% CI: 0.806–0.839), respectively. Important risk features included a family history of melanoma, a family history of skin cancer, and a prior diagnosis of benign neoplasm of skin. Conversely, medical examination without abnormal findings was identified as a protective feature.

Conclusions

Machine learning techniques and electronic health records can be effectively used to predict melanoma risk, potentially aiding in identifying high-risk patients and enabling individualized screening strategies for melanoma.
Identifying common disease trajectories of Alzheimer’s disease with electronic health records
Authors: Fu Mingzhou , Chang Timothy S.
Published: July 2024

Backgrounds

Alzheimer’s disease (AD), a leading cause of dementia, poses a growing global public health challenge. While recent studies have identified AD risk factors, they often focus on specific comorbidities, neglecting the complex interrelations and temporal dynamics. Our study addresses this by analyzing AD progression through longitudinal trajectories, utilizing clinical diagnoses over time. Using machine learning and network analysis, we created a computational framework to identify common AD progression patterns.

Methods

We analyzed patient diagnoses from UC Health Data Warehouse’s Electronic Health Records, coded with the International Classification of Diseases, version 10 (ICD-10). Using the Fine and Gray model to detect significant temporal risk factors between diagnoses, we examined associations between diagnosis pairs and refined the patients’ diagnostic trajectories, delineating all possible trajectory combinations. These refined trajectories were compared using Dynamic Time Warping and grouped into clusters with hierarchical clustering. We investigated common AD trajectories through network analysis and compared patient demographics, symptoms, and AD manifestations across clusters. The Greedy Equivalence Search algorithm was used to infer causal relationships within these trajectories. We rigorously evaluated these trajectories through association tests and comparison to controls,

Results

Our analysis included 24,473 eligible AD patients, which was filtered to include 5,762 patients with 6,794 unique AD progression trajectories. We identified four trajectory clusters: 1) a mental health cluster (e.g., anxiety disorder → depressive episode) (N_patient = 1,448); 2) an encephalopathy cluster (e.g., hypertension → other disorders of brain) (N_patient = 3,223); 3) a neurodegenerative disease cluster (e.g., transient cerebral ischemic attacks → other degenerative disease of nervous system) (N_patient = 1,502); and 4) a vascular disease cluster (e.g. hypertension → other cerebrovascular diseases) (N_patient = 1,446). Significant differences were observed in demographics, symptoms, and AD features across clusters. Causal analysis indicated that 26.2% of the identified trajectory connections were causal. We also observed patients with risk trajectories faced higher risks of AD compared to those without the trajectory or with only a single risk factor.

Conclusion

We uncovered AD diagnosis trajectories, incorporating temporal aspects and causal relationships. These insights improve our understanding of AD development and AD subtypes, and can enhance risk assessment. Our findings can significantly benefit patient care and medical research by moving toward earlier and more accurate diagnoses, along with personalized treatment, such as medical risk factors management and lifestyle modifications.
Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis
Authors: Minetti Alberto , Omrani Omid , Brenner Christiane , Allies Gabriele , Imada Shinya , Rösler Jonas , Khawaled Saleh , Cansiz Feyza , Meckelmann Sven W. , Gebert Nadja , Heinze Ivonne , Lu Jing , Spengler Katrin , Rasa Mahdi , Heller Regine , Yilmaz Omer , Tasdogan Alpaslan , Neri Francesco , Ori Alessandro
Published: July 2024

Aging hampers the regenerative potential of intestinal epithelium across species including humans, yet the underlying causes remain elusive. Here, using proteomic and metabolomic profiling of intestinal tissues together with functional assays, we characterized the temporal dynamics of regeneration following injury induced by 5-fluorouracil, a commonly used chemotherapeutic agent. Comparison of regeneration dynamics in mice of different ages revealed the emergence of a proteostasis stress signature and increased levels of polyamines following injury exclusively in old epithelia. Mechanistically, we show that delayed regeneration is an intrinsic feature of aged epithelial cells that display reduced protein synthesis and accumulation of ubiquitylated proteins. Notably, dietary restriction followed by re-feeding prior to injury increases polyamine pathway activation, enhances protein synthesis, and restores the regenerative capacity of aged intestines. Our findings highlight promising epithelial targets for interventions aimed at tackling the decline in tissue repair mechanisms associated with aging.
Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome
Authors: Metzner Eli , Southard Kaden M. , Norman Thomas M.
Published: July 2024

Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-throughput methods connecting these induced changes to their regulatory foundations are limited. Here we introduce Multiome Perturb-seq, extending single-cell CRISPR screens to simultaneously measure perturbation-induced changes in gene expression and chromatin accessibility. We apply Multiome Perturb-seq in a CRISPRi screen of 13 chromatin remodelers in human RPE-1 cells, achieving efficient assignment of sgRNA identities to single nuclei via an improved method for capturing barcode transcripts from nuclear RNA. We organize expression and accessibility measurements into coherent programs describing the integrated effects of perturbations on cell state, finding thatARID1AandSUZ12knockdowns induce programs enriched for developmental features. Pseudotime analysis of perturbations connects accessibility changes to changes in gene expression, highlighting the value of multimodal profiling. Overall, our method provides a scalable and simply implemented system to dissect the regulatory logic underpinning cell state.
The acquisition of additional control over quorum sensing regulation buffers noise in microbial growth dynamics
Authors: Fondi Marco , Riccardi Christopher , Patti Francesca Di , Coscione Francesca , Mengoni Alessio , Perrin Elena
Published: July 2024

Quorum sensing (QS) is a cell-to-cell communication system used by bacteria to act collectively. Often, bacteria possess more than one QS regulatory module that form complex regulatory networks. Presumably, these configurations have evolved through the integration of novel transcription factors into the native regulatory systems. The selective advantages provided by these alternative configurations on QS-related phenotypes is poorly predictable only based on their underlying network structure. Here we show that the acquisition of extra regulatory modules of QS has important consequences on the overall regulation of microbial growth dynamics by significantly reducing the variability in the final size of the population inBurkholderia. We mapped the distribution of horizontally transferred QS modules in extant bacterial genomes, finding that these tend to add up to already-present modules in the majority of cases, 63.32%. We then selected a strain harboring two intertwined QS modules and,using mathematical modelling, we predicted an intrinsic ability of the newly acquired module to buffer noise in growth dynamics. We experimentally validated this prediction choosing one strain possessing both systems, deleting one of the two and measuring key growth parameters and QS synthase expression. We extended such considerations on two other strains naturally implementing the two versions of the QS regulation studied herein. Finally, using transcriptomics, we show that the de-regulation of metabolism likely plays a key role in differentiating the two configurations. Our results shed light on the role of additional control over QS regulation and illuminate on the possible phenotypes that may arise after HGT events.
Characterisation of human hair follicle development
Authors: Sudderick Zoe R. , Glover James D. , Batho-Samblas Cameron , Shih Barbara Bo-Ju , Headon Denis J.
Published: July 2024

Humans have a characteristic distribution of hair across the body. Visible, relatively long and thick terminal hair fibres are present on the scalp and eyebrows in childhood, and are stimulated to grow on other parts of the body, such as the beard and armpits, by hormones during puberty. The short and fine vellus hairs, in contrast, are not readily visible and cover most of the body, including the face. Here we report quantification of the timing and characteristics of hair follicle development in human embryogenesis, from gestational weeks 8 to 19, and compare this to mouse hair follicle development. We find that human hair follicles develop first on the head, where we identify several distinct initiation sites, followed by the torso. Although terminal and vellus hair follicles have clear differences in the adult, both hair types initially develop from placodes and dermal condensates of similar size. Once their development is initiated, we find that human hair follicles grow and mature at the same rate, regardless of anatomical location, but have different density at different body sites. These findings suggest that regional hair differences in human skin, such as the distinction between scalp and forehead, are largely caused by processes acting after the initial hair follicle morphogenesis. Efforts to understand the evolution of human ‘hairlessness’ should, therefore, focus on genetic and cellular events that take place after hair follicle morphogenesis. Finally, we compared human skin appendages, including eccrine sweat glands, with those in mouse. We found that molecular markers, such as EDA, EDAR, SOX2 and WNT pathway components, are broadly similar in expression between both species, although specific differences do exist. Together with comparison of morphology and gene expression, these results support the use of embryonic mouse primary hair follicles as a model for human hair follicle development.
Cell-free expression of Nipah virus transmembrane proteins for proteoliposome vaccine design
Authors: Hu Vivian T. , Ezzatpour Shahrzad , Selivanovitch Ekaterina , Carter Jordan , Sahler Julie , Adeleke Richard Ayomide , August Avery , Aguilar Hector C. , Daniel Susan , Kamat Neha P.
Published: July 2024

Membrane proteins expressed on the surface of enveloped viruses are potent antigens in a vaccine, yet are difficult to produce and present due to their instability without a lipid scaffold. Current vaccination strategies that incorporate viral membrane proteins, such as live attenuated viruses, inactivated viruses, or extracellular vesicles, have limitations including lengthy production time, poor immunogenicity, extensive processing steps, and/or poor stability. Cell-free protein synthesis of viral membrane proteins offers a rapid, one-step method to assemble vaccine nanoparticles via cotranslational folding of membrane proteins into nanoscale liposomes. Here, we develop a vaccine candidate for the deadly Nipah virus (NiV), a highly lethal virus listed by the World Health Organization as a priority pathogen, by cell-free expressing two full-length Nipah virus membrane proteins. We demonstrate that both NiV fusion protein (NiV F) and NiV glycoprotein (NiV G) can be expressed and cotranslationally integrated into liposomes and that they fold into their native conformation. We find the removal of a signal peptide sequence and alteration of liposome lipid composition improves viral membrane protein incorporation. Furthermore, a lipid adjuvant, monophosphoryl lipid A (MPLA), can be readily added to liposomes without disrupting protein-vesicle loading or protein folding conformations. Finally, we demonstrate that our generated liposomal formulations lead to enhanced humoral responses in mice compared to empty and single-protein controls. This work establishes a platform to quickly assemble and present membrane antigens as multivalent vaccines that will enable a rapid response to the broad range of emerging pathogenic threats.
In-vitro Metabolite Identification for MEDI7219, an Oral GLP-1 Peptide, using LC-MS/MS with CID and EAD Fragmentation
Authors: Liu Kate , Huang Yue , Wang Taoqing , Mu Ruipeng , Rosenbaum Anton I.
Published: July 2024

Oral peptide therapeutics typically suffer from short half-lives as they are readily degraded by digestive enzymes. Systematic peptide engineering along with formulation optimization led to the development of a clinical candidate MEDI7219, an orally-bioavailable GLP-1 peptide, that is much more stable than wild type GLP-1 or semaglutide. In this study, we elucidated peptide biotransformation products using in vitro pancreatin assay that employed both collision-induced dissociation (CID) and electron-activated dissociation (EAD) LC-MS/MS methods. Using this approach, we have confidently identified a total of 13 metabolites. Relative quantification of these metabolites over time showed sequential cleavage pattern as peptides were further digested to smaller fragments. These 13 metabolites mapped to 8 cleavage sites on MEDI7219 structure. Most of these cleavage sites can be explained by the specificity of digestive enzymes, e.g. ,trypsin, pepsin and elastase. α-methyl-L-phenylalanine appeared to be well protected from chymotrypsin and pepsin digestion since no cleavage peptides ending with α-methyl-L-phenylalanine were observed. These study results expand upon previously published stability data and provide new insights on potential GLP1 proteolytic liabilities for future engineering. Furthermore, this study exemplifies the application of pancreatin in vitro system methodology as a valuable tool for understanding metabolism of oral peptide therapeuticsin vitro. Additionally, orthogonal MS fragmentation modes offered improved confidence in identification for peptide unknown metabolites.

Significance Statement

In vitro metabolite identification of oral GLP1 peptide that uncovers potential proteolytic hotspots that can inform future oral peptide engineering.
Comparative Genomic Analysis ofCampylobacter rectusand Closely Related Species
Authors: Hughes Lago Casey , Blackburn Dana , Kinder Pavlicek Meghan , Threadgill Deborah S.
Published: July 2024

Campylobacter rectusis a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models.C. rectusand related oralCampylobactershave been termed “emergingCampylobacterspecies” because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than singleC. rectusstrains and until recently, very fewC. rectusgenomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight newC. rectusstrains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in otherCampylobacterspecies. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome ofC. rectusconsists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present amongC. rectusisolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies onC. showaeT4SS since we have two newC. showaegenomes to report. We also demonstrate that unlikeC. rectus,C showaedoes not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequencedC. massilensishas neither T4SS or T6SS.
Multi-omics Analysis of Umbilical Cord Hematopoietic Stem Cells from a Multi-ethnic Cohort of Hawaii Reveals the Intergenerational Effect of Maternal Pre-Pregnancy Obesity and Risk Prediction for Cancers
Authors: Du Yuheng , Benny Paula A. , Shao Yuchen , Schlueter Ryan J. , Gurary Alexandra , Lum-Jones Annette , Lassiter Cameron B , AlAkwaa Fadhl M. , Tiirikainen Maarit , Towner Dena , Ward W. Steven , Garmire Lana X
Published: July 2024

Background

Maternal obesity is a health concern that may predispose newborns to a high risk of medical problems later in life. To understand the intergenerational effect of maternal obesity, we hypothesized that the maternal obesity effect is mediated by epigenetic changes in the CD34+/CD38−/Lin− hematopoietic stem cells (uHSCs) in the offspring. Towards this, we conducted a DNA methylation centric multi-omics study. We measured the DNA methylation and gene expression in the CD34+/CD38−/Lin− uHSCs and metabolomics of the cord blood, all from a multi-ethnic cohort (n=72) from Kapiolani Medical Center for Women and Children in Honolulu, Hawaii (collected between 2016 and 2018).

Results

Differential methylation (DM) analysis unveiled a global hypermethylation pattern in the maternal pre-pregnancy obese group (BH adjusted p<0.05), after adjusting for major clinical confounders. KEGG pathway enrichment, WGCNA, and PPI analyses revealed hypermethylated CpG sites were involved in critical biological processes, including cell cycle, protein synthesis, immune signaling, and lipid metabolism. Utilizing Shannon entropy on uHSCs methylation, we discerned notably higher quiescence of uHSCs impacted by maternal obesity. Additionally, the integration of multi-omics data-including methylation, gene expression, and metabolomics-provided further evidence of dysfunctions in adipogenesis, erythropoietin production, cell differentiation, and DNA repair, aligning with the findings at the epigenetic level. Furthermore, we trained a random forest classifier using the CpG sites in the genes of the top pathways associated with maternal obesity, and applied it to predict cancer vs. adjacent normal labels from samples in 14 Cancer Genome Atlas (TCGA) cancer types. Five of 14 cancers showed balanced accuracy of 0.6 or higher: LUSC (0.87), PAAD (0.83), KIRC (0.71), KIRP (0.63) and BRCA (0.60).

Conclusions

This study revealed the significant correlation between pre-pregnancy maternal obesity and multi-omics level molecular changes in the uHSCs of offspring, particularly in DNA methylation. Moreover, these maternal obesity epigenetic markers in uHSCs may predispose offspring to higher risks in certain cancers.
Conserved perception of host and non-host signals via the a-pheromone receptor Ste3 inColletotrichum graminicola
Authors: Rudolph Anina Yasmin , Schunke Carolin , Nordzieke Daniela Elisabeth
Published: July 2024

Understanding the interactions between fungal plant pathogens and host roots is crucial for developing effective disease management strategies. This study investigates the molecular mechanisms underpinning the chemotropic responses of the maize anthracnose fungusColletotrichum graminicolato maize root exudates. We identify the 7-transmembrane G-protein coupled receptor (GPCR) CgSte3 as a key player in sensing both plant-derived class III peroxidases and diterpenoids. Activation of CgSte3 initiates signaling through the Cell Wall Integrity Mitogen-Activated Protein Kinase (CWI MAPK) pathway, facilitating the pathogen’s growth towards plant defense molecules. The NADPH oxidase CgNox2 is crucial for peroxidase sensing but not for diterpenoid detection. These findings reveal that CgSte3 and CWI MAPK pathways are central toC. graminicola’sability to hijack plant defense signals, highlighting potential targets for controlling maize anthracnose.
An anomalous 3’-terminal phosphorothioated mismatch bypass activity and its application as a binary molecular switch
Authors: Kumar Shrawan , Gariya Hira Singh , Sharma Chandrika , Parveen Saba , Nair Vandana K , Sengupta Mrittika , Ghosh Souradyuti
Published: July 2024

Phosphorothioated (PST) oligonucleotides are increasingly being used in RNA silencing, antisense, and biosensing applications. However, the possibilities and consequences of their desultory interactions with other possible nucleic acids and DNA polymerases inside the cell remain inadequately characterized. In this study, we report the discovery of an unusual terminal mismatch bypass activity involving 3′-PST containing DNA primers and certain strand displacement DNA polymerases. Using rolling circle DNA amplification, we have identified that strand displacement DNA polymerases such as phi29 and BST large fragment (LF) can bypass 3′-terminal PST mismatches upto 1 – 20 nt length. Next, we explore the length and sequence dependence of this unusual attribute, incubation in near-ambient and 60 – 65°C temperatures, and measures to blockade or modulate this mismatch bypass activity to create a binary fully nucleic acid-based and non-photocontrolled molecular switch (the first of its kind). After proposing possible underlying mechanisms for this activity, we discuss its potential consequences and applications.
Development of antisense tools to studyBodo saltansand its intracellular symbiont
Authors: Ahrar Mastaneh , Glenn Lorna , Held Marie , Jackson Andrew , Kus Krzysztof , Hurst Gregory D.D. , Chrostek Ewa
Published: July 2024

Obligate symbioses are common in nature and present a particular challenge for functional genetic analysis. In many cases, the host is a non-model species with poor tools for genetic manipulation and the symbiont cannot be cultured or its gene expression manipulated to investigate function. Here we investigated the potential for using antisense inhibition to analyse host and symbiont gene function within an obligate aquatic symbiosis. We focused on the kinetoplastid hostBodo saltansand its bacterial symbiont, CandidatusBodocaedibacter vickermanii, a member ofRickettsiales. We conclude that antisense inhibition is not feasible in theB. saltansand its symbiont, as the holobiont feeds on the antisense molecules – and increases in numbers – upon treatment with the antisense construct. Although our approach has proven unsuccessful, we have developed an array of protocols which can be used to study the biology of this microeukaryote and its microbial associates.
p53 protein abundance is a therapeutic window across TP53 mutant cancers and is targetable with proximity inducing small molecules
Authors: Sadagopan Ananthan , Garaffo Nicholas , Chang Heng-Jui , Schreiber Stuart L. , Meyerson Matthew , Gibson William J.
Published: July 2024

TP53mutant cancers are associated with approximately half of cancer deaths. The most common mechanism of p53 inactivation involves missense mutations. Such mutations inTP53result in a robust upregulation of the p53 protein. Here, we demonstrate an induced proximity approach to selectively killTP53mutant cells. This approach uses the increased abundance of p53 protein inTP53mutant cancer cells to concentrate toxic molecules in these cells. We demonstrate the first generalizable strategy using a small molecule to selectively killTP53mutant cells. This molecule binds the Y220C mutant of p53 and concentrates a PLK1 inhibitor in cells harboringTP53Y220C mutations. Together, these data demonstrate that the abundance of p53 protein provides a therapeutic window forTP53missense mutant cancers that can be translated into a cell death signal using proximity-inducing small molecules.
Investigation of the threonine metabolism ofEchinococcus multilocularis: the threonine dehydrogenase as a potential drug target in alveolar echinococcosis
Authors: Kaethner Marc , Zumstein Pascal , Preza Matías , Grossenbacher Philipp , Bartetzko Anissa , Lochner Martin , Schürch Stefan , Regnault Clement , Ramírez Daniel Villalobos , Lundström-Stadelmann Britta
Published: July 2024

Alveolar echinococcosis (AE) is a severe zoonotic disease caused by the metacestode stage of the fox tapewormEchinococcus multilocularis. We recently showed thatE. multilocularismetacestode vesicles scavenge large amounts of L-threonine from the culture medium that were neither stored nor overused for protein synthesis. This motivated us to study the effect of L-threonine on the parasite and how it is metabolized. We established a novel metacestode vesicle growth assay with an automated readout, which showed that L-threonine treatment led to significantly increased parasite growth. In addition, L-threonine increased the formation of novel metacestode vesicles from primary parasite cell cultures in contrast to the non-proteinogenic threonine analog 3-hydroxynorvaline. Tracing of [U-13C]-L-threonine and metabolites in metacestode vesicles and culture medium resulted in the detection of [U-13C]-labeling in aminoacetone and glycine, indicating that L-threonine was metabolized by threonine dehydrogenase (TDH). In addition, the detection of [13C2]-glutathione, suggested thatE. multilocularismetacestode vesicles synthesize glutathione via L-threonine-derived glycine. EmTDH-mediated threonine metabolism in theE. multilocularismetacestode stage was further confirmed by quantitative real-time PCR, which demonstrated high expression ofemtdhinin vitrocultured metacestode vesicles and also in metacestode samples obtained from infected animals. EmTDH was enzymatically active in metacestode vesicle extracts. Thus, the drugs disulfiram, myricetin, quercetin, sanguinarine and seven quinazoline carboxamides were assessed for inhibition of recombinantly expressed EmTDH, and the most potent inhibitors disulfiram, myricetin and sanguinarine were further tested for activity againstE. multilocularismetacestode vesicles and primary parasite cells. Sanguinarine exhibited significantin vitroactivity and IC50-values for metacestode vesicles, primary parasite cells, as well as mammalian cells were determined. Our results suggest that sanguinarine treatment should be further assessedin vivoemploying suitable AE mouse models. Furthermore, the EmTDH assay could serve as high-throughput target-based discovery platform for novel anti-echinococcal compounds.
Gαs-specific structural elements attenuate interactions with RGS proteins
Authors: Higazy-Mreih Sabreen , Avital-Shacham Meirav , LeGouill Christian , Bouvier Michel , Kosloff Mickey
Published: July 2024

Heterotrimeric (αβγ) G proteins are molecular switches that are activated by G protein-coupled receptors (GPCRs) and regulate numerous intracellular signaling cascades. Most active Gα subunits are inactivated by Regulators of G protein Signaling (RGS) proteins, which determine the duration of G protein-mediated signaling by accelerating the catalytic turn-off of the Gα subunit. However, the G protein Gαsdoes not interact with known RGS proteins. To understand the molecular basis for this divergent phenomenon, we combined a comparative structural analysis of experimental and modelled structures with functional biochemical assays. This analysis showed that Gαscontains unique structural elements in both the helical and the GTPase domains. Modeling identified helical domain insertions, missing in experimental structures, that project towards the interface with RGS proteins, and residues in the GTPase domain that might interfere with RGS binding. Mutagenesis of Gαsand measurements of RGS GAP activity showed that three residues in the GαsGTPase domain are both necessary and sufficient to prevent Gαsinactivation by RGSs. Indeed, substitution of all three Gαsresidues with the corresponding residues from Gαi1enabled efficient inactivation by RGS proteins. These results shed new light on the mechanistic bases for G protein specificity towards RGS proteins.
Comparative Evaluation Of Machine Learning Classifiers For Brain Tumor Detection
Authors: Ali Umair
Published: August 2024

This study evaluates the effectiveness of six machine learning classifiers—Support Vector Classifier (SVC), Logistic Regression, K-Nearest Neighbors (KNN), Naive Bayes, Decision Tree, and Random Forest—in detecting brain tumors using numerical data rather than traditional imaging techniques like MRI. The results emphasize the importance of data preprocessing, particularly feature scaling, in enhancing model performance. Among the classifiers, Random Forest emerged as the top performer, achieving an accuracy of 98.27% on both original and scaled data, demonstrating its robustness and reliability. The study highlights the potential of Random Forest as a valuable tool for automated brain tumor detection in clinical settings, offering a cost-effective and accessible alternative for resource-constrained environments. The paper suggests that future research should explore advanced deep learning models, such as 3D Convolutional Neural Networks (CNNs) and Generative Adversarial Networks (GANs), to further improve diagnostic accuracy and support early intervention and personalized treatment strategies for brain tumor patients.
Genetic associations with human longevity are enriched for oncogenic genes
Authors: Park Junyoung , Peña-Tauber Andrés , Talozzi Lia , Greicius Michael D. , Guen Yann Le
Published: August 2024

Human lifespan is shaped by both genetic and environmental exposures and their interaction. To enable precision health, it is essential to understand how genetic variants contribute to earlier death or prolonged survival. In this study, we tested the association of common genetic variants and the burden of rare non-synonymous variants in a survival analysis, using age-at-death (N = 35,551, median [min, max] = 72.4 [40.9, 85.2]), and last-known-age (N = 358,282, median [min, max] = 71.9 [52.6, 88.7]), in European ancestry participants of the UK Biobank. The associations we identified seemed predominantly driven by cancer, likely due to the age range of the cohort. Common variant analysis highlighted three longevity-associated loci:APOE, ZSCAN23, andMUC5B. We identified six genes whose burden of loss-of-function variants is significantly associated with reduced lifespan:TET2,ATM,BRCA2, CKMT1B,BRCA1andASXL1. Additionally, in eight genes, the burden of pathogenic missense variants was associated with reduced lifespan:DNMT3A, SF3B1, CHL1,TET2, PTEN, SOX21, TP53andSRSF2. Most of these genes have previously been linked to oncogenic-related pathways and some are linked to and are known to harbor somatic variants that predispose to clonal hematopoiesis. A direction-agnostic (SKAT-O) approach additionally identified significant associations withC1orf52, TERT, IDH2,andRLIM, highlighting a link between telomerase function and longevity as well as identifying additional oncogenic genes.

Our results emphasize the importance of understanding genetic factors driving the most prevalent causes of mortality at a population level, highlighting the potential of early genetic testing to identify germline and somatic variants increasing one’s susceptibility to cancer and/or early death.
“Leveraging AI Tools to Bridge the Healthcare Gap in Rural Areas in India”
Authors: Kerketta Ajit , Balasundaram Sathiyaseelan
Published: August 2024

Introduction

Despite considerable progress in the healthcare sector, rural regions continue to grapple with healthcare deficiencies. However, the emergence of AI technology offers promising solutions to overcome these hurdles. Hence, the study explores the potential and efficacy of introducing artificial intelligence (AI) tools to address the healthcare disparity in rural India.

Methods

The research employed a literature review method and gathered data from various databases such as Science Direct, PubMed, and Google Scholar. The screening process was aided by the “Rayyan” electronic software. Articles published in English between January 2020 and December 2022 were selected, followed by a thematic analysis of the findings.

Results

Results indicate the potential of AI in rural healthcare settings, showing AI-driven solutions addressing healthcare access gaps and contributing to their bridging. The study also highlights hurdles related to AI tool adoption in rural healthcare and proposes collaborative efforts among policymakers, healthcare providers, and technology developers to integrate AI tools effectively. This necessitates advocating for digital infrastructure investments, capacity-building initiatives, and conducive regulatory frameworks for AI implementation.

Conclusion

The study underscores AI’s transformative role in bridging the healthcare gap in rural India. By harnessing AI technologies, healthcare providers and policymakers can surmount barriers, empower local healthcare workers, and improve health outcomes for rural communities. The insights and recommendations contribute to the evolving knowledge base on leveraging AI for adequate healthcare delivery, guiding future initiatives in similar contexts.