Biological Similarities Research Articles

Disentangled similarity graph attention heterogeneous biological memory network for predicting disease-associated miRNAs

BackgroundThe association between MicroRNAs (miRNAs) and diseases is crucial in treating and exploring many diseases or cancers. Although wet-lab methods for predicting miRNA-disease associations (MDAs) are effective, they are often expensive and time-consuming. Significant advancements have been made using Graph Neural Network-based methods (GNN-MDAs) to address these challenges. However, these methods still face limitations, such as not considering nodes’ deep-level similarity associations and hierarchical learning patterns. Additionally, current models do not retain the memory of previously learned heterogeneous historical information about miRNAs or diseases, only focusing on parameter learning without the capability to remember heterogeneous associations.ResultsThis study introduces the K-means disentangled high-level biological similarity to utilize potential hierarchical relationships fully and proposes a Graph Attention Heterogeneous Biological Memory Network architecture (DiGAMN) with memory capabilities. Extensive experiments were conducted across four datasets, comparing the DiGAMN model and its disentangling method against ten state-of-the-art non-disentangled methods and six traditional GNNs. DiGAMN excelled, achieving AUC scores of 96.35%, 96.10%, 96.01%, and 95.89% on the Data1 to Data4 datasets, respectively, surpassing all other models. These results confirm the superior performance of DiGAMN and its disentangling method. Additionally, various ablation studies were conducted to validate the contributions of different modules within the framework, and’s encoding statuses and memory units of DiGAMN were visualized to explore the utility and functionality of its modules. Case studies confirmed the effectiveness of DiGAMN’s predictions, identifying several new disease-associated miRNAs.ConclusionsDiGAMN introduces the use of a disentangled biological similarity approach for the first time and successfully constructs a Disentangled Graph Attention Heterogeneous Biological Memory Network model. This network can learn disentangled representations of similarity information and effectively store the potential biological entanglement information of miRNAs and diseases. By integrating disentangled similarity information with a heterogeneous attention memory network, DiGAMN enhances the model’s ability to capture and utilize complex underlying biological data, significantly outperforming many existing models. The concepts used in this method also provide new perspectives for predicting miRNAs associated with diseases.

The Rhesus Macaque as an Animal Model for Human Nutrition: An Ecological-Evolutionary Perspective.

Nutrition is a complex and contested area in biomedicine, which requires diverse evidence sources. Nonhuman primate models are considered an important biomedical research tool because of their biological similarities to humans, but they are typically used with little explicit consideration of their ecology and evolution. Using the rhesus macaque (RM), we consider the potential of nutritional ecology for enriching the use of primates as models for human nutrition. We introduce some relevant aspects of RM evolutionary and social ecology and discuss two examples where they have been used in biomedical research: obesity and aging. We next consider how insights from nutritional ecology can help inform and direct the use of RM as a biomedical model. We conclude by illustrating how conceptual tools might inform the use of RM as a model for human nutrition and extracting insights from RM that might be relevant to broader theoretical considerations around animal model systems.

PD-1 blockade plus cisplatin-based chemotherapy in patients with small cell/neuroendocrine bladder and prostate cancers

Small cell neuroendocrine cancers share biologic similarities across tissue types, including transient response to platinum-based chemotherapy with rapid progression of disease. We report a phase 1b study of pembrolizumab in combination with platinum-based chemotherapy in 15 patients with stage III-IV small cell bladder (cohort 1) or small cell/neuroendocrine prostate cancers (cohort 2). Overall response rate (ORR) is 43% with two-year overall survival (OS) rate of 86% (95% confidence interval [CI]: 0.63, 1.00) for cohort 1 and 57% (95% CI: 0.30, 1.00) for cohort 2. Treatment is tolerated well with grade 3 or higher adverse events occurring in 40% of patients with no deaths or treatment cessation secondary to toxicity. Single-cell and Tcell receptor sequencing of serial peripheral blood samples reveals clonal expansion of diverse Tcell repertoire correlating with progression-free survival. Our results demonstrate promising efficacy and safety of this treatment combination and support future investigation of this biomarker. This study was registered at ClinicalTrials.gov (NCT03582475).

GBNSS: A Method Based on Graph Neural Networks (GNNs) for Global Biological Network Similarity Search

Biological network similarity search plays a crucial role in the analysis of biological networks for human disease research and drug discovery. A biological network similarity search aims to efficiently identify novel networks biologically homologous to the query networks. Great progress has been achieved in biological network similarity searches. However, it remains a challenge to mine the biological network information fully to improve the accuracy of query results without increasing time overheads. In this study, we propose a biological network similarity search method based on graph neural networks named GBNSS, which combines topological and biological information (GO annotations) of biological networks into graph neural networks to find topologically and biologically similar biological networks in the database. Additionally, GBNSS is a topology-free biological network similarity search method with an arbitrary network structure. The experimental results on four benchmark datasets show that GBNSS outperforms the existing methods in terms of computational efficiency and search accuracy. Case studies further demonstrate that GBNSS is capable of searching similar networks in real-world biological networks.

Detection of PIK3CA hotspot mutations in canine mammary tumors using droplet digital PCR: tissue validation and liquid biopsy feasibility

Domestic dogs (Canis lupus familiaris) serve as valuable translational models for human cancer research due to their biological similarities. Canine mammary tumors (CMTs), frequently diagnosed in female dogs, share various characteristics with human breast cancers. This study investigates the PIK3CA (H1047R) mutation in CMTs using droplet digital PCR (ddPCR) and explores the potential of liquid biopsy for non-invasive detection. We analyzed 80 formalin-fixed, paraffin-embedded (FFPE) CMT tissue samples and compared ddPCR results with next-generation sequencing (NGS) data, achieving high concordance. Plasma and serum samples were also assessed for mutation concordance with tissue results. Our findings indicate a higher frequency of the PIK3CA (H1047R) mutations in benign and grade I malignant CMTs compared to more aggressive malignancies. The ddPCR assay demonstrated high sensitivity and specificity, with plasma testing showing 78.6% sensitivity and 87.5% specificity, and serum testing showing 66.7% sensitivity and 90.0% specificity. These results highlight the viability of liquid biopsy as a minimally invasive method for monitoring PIK3CA mutations in canine patients. The study suggests that liquid biopsy techniques hold significant promise for improving the early detection and monitoring of canine cancers, warranting further research to refine these methods and explore their applications in canine cancer diagnostics and treatment.

RECAPITULATING THE POST-SURGICAL BRAIN MICROENVIRONMENT OF ATYPICAL TERATOID RHABDOID TUMOURS TO IDENTIFY MEMBRANE PROTEINS FOR TARGETED THERAPY

Abstract AIMS Atypical Teratoid Rhabdoid Tumours (AT/RT) are rare aggressive tumours primarily arising in the hind brain of children under three, conferring median survival of <12 months. Surgery remains the only standard treatment; however tumours recur from post-surgical residual disease. Decellularised human brain cerebellum aim to recapitulate AT/RT post-surgical brain microenvironments which retain extracellular matrix (ECM) ligands, and where AT/RT plasma membrane proteins are hypothesised to represent viable molecular therapy targets. METHOD AT/RT, astrocyte and human brain cerebellum (decellularised and non-decellularised) membrane protein fractions were extracted and analysed using liquid chromatography-mass spectrometry. Proteomic analysis tools were integrated to identify differential expressed proteins and identify shared correlations. RESULTS Decellularised cerebellar ECM exhibited an enriched membrane proteome relative to total proteome, evidence of complete removal of intracellular components. Furthermore, decellularised and non-decellularised cerebellar tissue expressed comparable levels of membrane proteins and protein networks, indicative of ECM ligand retention. AT/RT and astrocyte KEGG Pathway analysis revealed specific oncology-based pathway expression in membrane protein compared to total protein, reinforcing membrane proteins as more visible therapeutic targets. Between the top 20 expressed proteins, ATP1A1 was the only membrane protein shared exclusively between all AT/RT cells and astrocytes, suggesting a critical functional role. Membrane proteins showing shared expression when normalised against each AT/RT cell line included ATP1A1, HSPD1, GNA13 and SLC3A2, indicating biological similarities between AT/RT molecular subtypes, which may offer candidate ubiquitous therapy targets. Membrane proteins expressed similarly in AT/RT-MYC molecular subtypes include ATP1A1, SLC7A5 and EEF1A1. STRING membrane pathway analysis also identified shared proteins between AT/RT and astrocyte cell populations. CONCLUSION AT/RT membrane protein pathways provide ideal therapeutic targets directly amenable for drug repurposing. Future work prioritises proteomic analysis utilising 3D AT/RT spheroids and cerebellum brain tissue to maximise accurately recapitulating the AT/RT post-surgical microenvironment. Cerebellum decellularisation still permits retention of essential proteins and ligands.

P19-61 Combining chemical, biological similarity and metabolite data in read-across approach

P19-61 Combining chemical, biological similarity and metabolite data in read-across approach

Carvacrol-loaded premixed calcium phosphate bone cements with exceptional osteogenic and antibacterial properties to heal infected bone defects

The healing of infected bone fractures represents a significant clinical challenge in orthopedic surgery. Calcium phosphate cements (CPCs) are attractive materials, highly applicable in bone healing due to their satisfactory biological properties and chemical similarity to bone minerals. However, manual mixing is often required before localized application of conventional CPCs, increasing the risk of infection. Moreover, their antibacterial properties are often insufficient for treating infected fractures. In this study, antimicrobial two-paste premixed CPCs loaded with carvacrol were developed. The influence of the carvacrol on the setting properties and mechanical strength of the cement was studied. In vitro studies demonstrated the biocompatibility, osteogenic potential, and broad-spectrum antimicrobial efficacy of the premixed bone cements, including effectiveness against gram-positive, gram-negative, and drug-resistant bacteria. Notably, in vivo studies revealed exceptional antimicrobial and osteogenic properties of the carvacrol-loaded cements, confirming the promising potential of the premixed cements for the healing of infected bone defects.

Beyond the petri dish: Model organisms in non-clinical exploration

Animal models have been integral to scientific research for decades, offering invaluable insights into complex biological processes, advancing medical knowledge, and aiding the development of new treatments. This review explores the significance of animal models in various research fields, emphasizing their biological similarity to humans as a key factor. Animals, ranging from mice and rats to primates, fruit flies, and worms, share fundamental physiological, anatomical, and genetic characteristics with humans, making them crucial proxies for studying diseases and biological pathways. This review underscores the essential role of animal models in preclinical research, particularly in evaluating drug candidates for safety, efficacy, and potential side effects before human trials. The controlled experimental environment provided by animal models allows researchers to manipulate variables, isolate factors, and establish cause-and-effect relationships, enhancing the understanding of complex genetic disorders.

The EphA2 Receptor Regulates Invasiveness and Drug Sensitivity in Canine and Human Osteosarcoma Cells.

Osteosarcoma is an aggressive bone cancer affecting both humans and dogs, often leading to pulmonary metastasis. Despite surgery and chemotherapy being the primary treatment modalities, survival rates remain low in both species, underscoring the urgent need for more efficacious therapeutic options. Accumulating evidence indicates numerous biological and clinical similarities between human and canine osteosarcoma, making it an ideal choice for comparative oncological research that should benefit both species. The EphA2 receptor has been implicated in controlling invasive responses across different human malignancies, and its expression is associated with poor prognosis. In this study, we utilized a comparative approach to match EphA2 functions in human and canine osteosarcoma models. Our objectives were to assess EphA2 levels and its pro-malignant action in osteosarcoma cells of both species. We found that EphA2 is overexpressed in most of both canine and human osteosarcoma cell lines, while its silencing significantly reduced cell viability, migration, and invasion. Moreover, EphA2 silencing enhanced the sensitivity of osteosarcoma cells to cisplatin, a drug commonly used for treating this cancer. Furthermore, inhibition of EphA2 expression led to a significant reduction in tumor development capability of canine osteosarcoma cells. Our data suggest that these EphA2 effects are likely mediated through various signaling mechanisms, including the SRC, AKT, and ERK-MAPK pathways. Collectively, our findings indicate that EphA2 promotes malignant behaviors in both human and canine osteosarcoma and that targeting EphA2, either alone or in combination with chemotherapy, could offer potential benefits to osteosarcoma patients.

Promoting biological similarity by collagen microfibers in 3D colorectal cancer-stromal tissue: Replicating mechanical properties and cancer stem cell markers

The extracellular matrix (ECM) of cancer tissues is rich in dense collagen, contributing to the stiffening of these tissues. Increased stiffness has been reported to promote cancer cell proliferation, invasion, metastasis, and prevent drug delivery. Replicating the structure and mechanical properties of cancer tissue in vitro is essential for developing cancer treatment drugs that target these properties. In this study, we recreated specific characteristics of cancer tissue, such as collagen density and high elastic modulus, using a colorectal cancer cell line as a model. Using our original material, collagen microfibers (CMFs), and a constructed three-dimensional (3D) cancer-stromal tissue model, we successfully reproduced an ECM highly similar to in vivo conditions. Furthermore, our research demonstrated that cancer stem cell markers expressed in the 3D cancer-stromal tissue model more closely mimic in vivo conditions than traditional two-dimensional cell cultures. We also found that CMFs might affect an impact on how cancer cells express these markers. Our 3D CMF-based model holds promise for enhancing our understanding of colorectal cancer and advancing therapeutic approaches. Statement of significanceReproducing the collagen content and stiffness of cancer tissue is crucial in comprehending the properties of cancer and advancing anticancer drug development. Nonetheless, the use of collagen as a scaffold material has posed challenges due to its poor solubility, hindering the replication of a cancer microenvironment. In this study, we have successfully recreated cancer tissue-specific characteristics such as collagen density, stiffness, and the expression of cancer stem cell markers in three-dimensional (3D) colorectal cancer stromal tissue, utilizing a proprietary material known as collagen microfiber (CMF). CMF proves to be an ideal scaffold material for replicating cancer stromal tissue, and these 3D tissues constructed with CMFs hold promise in contributing to our understanding of cancer and the development of therapeutic drugs.

Establishment of Primary Cell Cultures from Canine Oral Melanomas via Fine-Needle Aspiration: A Novel Tool for Tumorigenesis and Cancer Progression Studies.

Oral melanomas are the most common oral malignancies in dogs and are characterized by an aggressive nature, invasiveness, and poor prognosis. With biological and genetic similarities to human oral melanomas, they serve as a valuable spontaneous comparative model. Primary cell cultures are widely used in human medicine and, more recently, in veterinary medicine to study tumorigenesis, cancer progression, and innovative therapeutic approaches. This study aims to establish two- and three-dimensional primary cell lines from oral canine melanomas using fine-needle aspiration as a minimally invasive sampling method. For this study, samples were collected from six dogs, represented by four primary oral melanomas and five lymph nodal metastases. The cells were digested to obtain single-cell suspensions, seeded in flasks, or processed with Matrigel® to form organoids. The cell cultures were characterized through flow cytometry using antibodies against Melan-A, PNL2, and Sox-10. This technique offers a minimally invasive means to obtain cell samples, particularly beneficial for patients that are ineligible for surgical procedures, and enables the establishment of in vitro models crucial for comparative studies in mucosal melanoma oncology. To the best of our knowledge, this is the first work establishing neoplastic primary cell cultures via fine-needle aspiration in dogs.

ATRT-02. RECAPITULATING THE POST-SURGICAL BRAIN MICROENVIRONMENT OF ATYPICAL TERATOID RHABDOID TUMOURS TO IDENTIFY MEMBRANE PROTEIN CANDIDATES FOR TARGETED THERAPY

Abstract BACKGROUND Atypical Teratoid Rhabdoid Tumours – (AT/RT) are rare and aggressive tumours primarily arising in the hind brain of children under three, conferring median survival of <12 months. Surgery remains the only standard treatment; however tumours recur from post-surgical residual disease. The utilisation of PolyEthylene Glycol Diacrylate – (PEGDA) hydrogel and decellularised human brain cerebellum extracellular matrix aim to recapitulate AT/RT post-surgery brain microenvironments, where we hypothesise AT/RT plasma membrane proteins represent viable molecular therapy targets. METHODS AT/RT and astrocyte membrane protein cellular fractions were extracted and analysed using liquid chromatography-mass spectrometry. Proteomic analyses was integrated to identify differentially expressed AT/RT and astrocyte membrane proteins. RESULTS PEGDA and decellularised brain tissue were biocompatible for AT/RT-astrocyte co-cultured spheroid growth. AT/RT and astrocyte KEGG Pathway analysis revealed more specific oncology-based pathway expression in membrane protein than total protein, thus reinforcing membrane proteins as suitable therapeutic targets. Between the top 20 expressed membrane proteins, only ATP1A1 was shared exclusively between all AT/RT cells and astrocytes, suggesting a potential functional role. Membrane proteins showing shared expression when normalised against each AT/RT cell line included ATP1A1, HSPD1, GNA13 and SLC3A2, indicating biological similarities between AT/RT subtypes. Membrane proteins expressed similarly in AT/RT-MYC subtypes include ATP1A1, SLC7A5 and EEF1A1. ATP1A1 network analyses of AT/RT and astrocyte membrane protein pathways displayed strong interactions with ATP1B1, SLC7A5 and SLC3A2, therefore likely to map common expressed shared pathways. CONCLUSIONS AT/RT membrane protein pathways offer novel therapeutic targets directly amenable for drug repurposing. Future work prioritises proteomic analysis utilising 3D AT/RT spheroids and cerebellum brain tissue to maximise accurately recapitulating AT/RT post-surgical microenvironments.

Bacterial Pangenome: A Review on the Current Strategies, Tools and Applications

The genomic research has grown by the advancement of sequencing technologies, which aim to capture the "totality" of life diversity by progressing from single strain to species or even higher taxa. Out of this scientific progress and inquisitiveness, the term "pangenome" was created. The goal of a pangenome is to represent all of a species genetic variation. It divides the genome into core, accessory and unique genes. Since the introduction of pangenomics, many software programs have been actively used for pangenome analysis. This review focuses on providing a snapshot of useful tools with their use, execution and computational details. In addition to tools for pangenome, the components, approaches, mechanism of variation, applications and challenges associated with pangenome analysis are also discussed in this article. Here, we have also discussed the increasing trend of bacterial pangenome studies with few studies and their significant findings. It has been proved that pangenomics is useful for understanding the clade of bacteria that helps in developing strategies for various application based on biological similarities and differences.

Perspectives on animal experimentation in herbal medicine research: ethical dilemmas and scientific progress

Animal experimentation has long been an integral part of biomedical and cosmetics research, with historical roots dating back to ancient Greece. During that period, physicians constrained by cultural taboos that forbade the use of human cadavers, turned to the dissection of animals for their anatomical studies. The use of specific animal models in research has often been justified by the remarkable biological similarities between animals and humans. However, there are instances where animal models, such as fish and frogs, are used, despite significant disparities in their anatomy and physiology compared to humans. In herbal medicine research, animal experimentation has found various applications. Numerous plant species from diverse global regions, including the United Kingdom, United States, China, India, and Africa, have been studied to identify their pharmacological properties and therapeutic indications. Nevertheless, the use of animals in these studies, while offering undeniable advantages, remains a subject of intense debate and contention, mainly arising from the ethical challenges it presents, as well as the substantial financial burden it imposes, and its inability to reliably predict human responses. This paper, therefore, proposes a comprehensive list of research methodologies that are ethical, practical, cost-effective, and consistent with the real ethos of herbal medicine. These alternative methods, which include in vitro studies, human cell cultures, computational modelling, culturally sensitive clinical trials, and ethnobotanical surveys, have the potential to provide cost-effective healthcare solutions, without subjecting animals to unnecessary suffering.

Correlation of hormone receptor positive HER2-negative/MammaPrint high-2 breast cancer with triple negative breast cancer: Results from gene expression data from the ISPY2 trial.

573 Background: A subset of Hormone Receptor positive (HR+), HER2 negative (HER2-) breast cancers (BCs) classified by the MammaPrint (MP) assay as High-2 (MP-H2) show clinical behavior similar to triple-negative (TN) BC. The aim of this analysis was to assess molecular similarities between the HR+/HER2-/MP-H2 (HR+/MP-H2), HR+/HER2-/MP-High-1 (HR+/MP-H1), and TN/MP-H2 (TN/MP-H2) BCs. Methods: Gene expression data used for this analysis [GEO GSE194040] was derived from pre-treatment samples of the I-SPY2 trial, which is an ongoing multicentric randomized Phase II neoadjuvant platform trial for high-risk stage II or III BC. Six hundred eighty-four pretreatment samples were included in this analysis: 274 corresponded to HR+/MP-H1, 105 to HR+/MP-H2, and 305 to TN/MP-H2, accounting for 7 experimental plus a control arm. We used principal component and distance analyses, differentially expressed genes (analysis performed for pairwise comparisons of the 3 subtypes, a linear model, log fold-change and moderated-t p-values relative to a minimum fold-change threshold of fc = 1.5), gene set enrichment analysis using KEGG and GO, and Ingenuity Pathway Analysis, as well as 32 previously defined qualifying biomarkers to study similarities in biology between the subgroups. Results: On principal component and distance analyses, results reveal close similarity between HR+/MP-H2 and TN/MP-H2 indicating shared transcriptomic features. Gene expression analysis revealed that HR+/MP-H2 tumors resemble TN/MP-H2 more than HR+/MP-H1 cancers. Differential gene expression analysis revealed that HR+/MP-H2 and TN/MP-H2 cancers presented only two differentially expressed genes, compared to HR+/MP-H1 and HR+/MP-H2, which presented 577 differentially expressed genes. Upon pathway analysis, HR+/MP-H1 cancers presented the most significant upregulation in the glucocorticoid receptor signaling, DHCR24, and HOTAIR pathways, compared to HR+/MP-H2 cancers. Furthermore, HR+/MP-H2 and TN/MP-H2 shared enrichment of DNA repair and cell cycle pathways. In addition, various biomarkers were analyzed, and among the most representative shared biomarkers for HR+/MP-H2 and TN/MP-H2 were immune features, higher proliferation, and a lower expression of ESR1 co-expressed genes as compared to HR+/MP-H1 cancers. The rates of pathologic complete response were 41% for TN/MP-H2, 31% for HR+/MP-H2, and 11% HR+/MP-H1 cancers among all included patients. Conclusions: A subset of HR+ cancers defined by MP-H2 status closely resemble TN in molecular and clinical features. The similarity of pCR rates for MP-2 observed within either HR+/HER2- and TN is supported by our findings of similarity of active biology between HR+/MP-2 and TN/MP-2. These findings have implications for understanding the biology of HR+/MP-H2 BCs and optimizing treatment strategies.

Comparative proteomic analysis of dental pulp from supernumerary and normal permanent teeth

ObjectivesTo obtain and compare the protein profiles of supernumerary and normal permanent dental pulp tissues.Materials and methodsDental pulp tissues were obtained from supernumerary and normal permanent teeth. Proteins were extracted and analyzed by liquid chromatography-tandem mass spectrometry (LC/MS-MS). Protein identification and quantification from MS data was performed with MaxQuant. Statistical analysis was conducted using Metaboanalyst to identify differentially expressed proteins (DEPs) (P-value < 0.05, fold-change > 2). Gene Ontology enrichment analyses were performed with gProfiler.ResultsA total of 3,534 proteins were found in normal dental pulp tissue and 1,093 in supernumerary dental pulp tissue, with 174 DEPs between the two groups. This analysis revealed similar functional characteristics in terms of cellular component organization, cell differentiation, developmental process, and response to stimulus, alongside exclusive functions unique to normal permanent dental pulp tissues such as healing, vascular development and cell death. Upon examination of DEPs, these proteins were associated with the processes of wound healing and apoptosis.ConclusionsThis study provides a comprehensive understanding of the protein profile of dental pulp tissue, including the first such profiling of supernumerary permanent dental pulp. There are functional differences between the proteomic profiles of supernumerary and normal permanent dental pulp tissue, despite certain biological similarities between the two groups. Differences in protein expression were identified, and the identified DEPs were linked to the healing and apoptosis processes.Clinical relevanceThis discovery enhances our knowledge of supernumerary and normal permanent pulp tissue, and serves as a valuable reference for future studies on supernumerary teeth.

High frequency of MEFV disease-causing variants in children with very-early-onset inflammatory bowel disease.

Biological similarities between inflammatory bowel disease (IBD) and familial Mediterranean fever (FMF) have been described in humans and animal models suggesting a possible common genetic basis. FMF is caused by variants in the MEFV gene which encodes pyrin, an immune regulator. This study aimed to investigate the carrier rate of disease-causing MEFV variants in children of different ethnicities diagnosed with very-early-onset IBD (VEO-IBD). The study included 23 children diagnosed with VEO-IBD who had undergone whole exome sequencing. The exomes were evaluated for MEFV monoallelic and biallelic disease-causing variants and compared to exome sequencing data of 250 probands with suspected monogenic diseases other than IBD. Of the 23 children diagnosed with VEO-IBD, 12 (52%) were carriers of at least one MEFV disease-causing variant, which was threefold higher than in individuals without IBD. The most frequent variants identified were p.M694V and p.E148Q (42% each). The allelic frequency of MEFV variants was found to be higher across the VEO-IBD group in 13 of 14 ethnicities compared to the control group. The study suggests that disease-causing variants in the MEFV gene should be sought in cases of VEO-IBD. However, the clinical importance of this finding is yet to be defined. There are biological similarities between inflammatory bowel disease and familial Mediterranean fever, suggesting a possible genetic relationship. Children less than 6 years old clinically diagnosed with inflammatory bowel disease have a threefold higher rate of disease-causing variants in the MEFV gene than controls. Monogenic testing in children with very-early-onset inflammatory bowel disease should include a search for MEFV variants.

Radiolabelling and preclinical characterisation of [89Zr]Zr-Df-ATG-101 bispecific to PD-L1/4–1BB

PurposeATG-101, a bispecific antibody that simultaneously targets the immune checkpoint PD-L1 and the costimulatory receptor 4-1BB, activates exhausted T cells upon PD-L1 crosslinking. Previous studies demonstrated promising anti-tumour efficacy of ATG-101 in preclinical models. Here, we labelled ATG-101 with 89Zr to confirm its tumour targeting effect and tissue biodistribution in a preclinical model. We also evaluated the use of immuno-PET to study tumour uptake of ATG-101 in vivo.MethodsATG-101, anti-PD-L1, and an isotype control were conjugated with p-SCN-Deferoxamine (Df). The Df-conjugated antibodies were radiolabelled with 89Zr, and their radiochemical purity, immunoreactivity, and serum stability were assessed. We conducted PET/MRI and biodistribution studies on [89Zr]Zr-Df-ATG-101 in BALB/c nude mice bearing PD-L1-expressing MDA-MB-231 breast cancer xenografts for up to 10 days after intravenous administration of [89Zr]Zr-labelled antibodies. The specificity of [89Zr]Zr-Df-ATG-101 was evaluated through a competition study with unlabelled ATG-101 and anti-PD-L1 antibodies.ResultsThe Df-conjugation and [89Zr]Zr -radiolabelling did not affect the target binding of ATG-101. Biodistribution and imaging studies demonstrated biological similarity of [89Zr]Zr-Df-ATG-101 and [89Zr]Zr-Df-anti-PD-L1. Tumour uptake of [89Zr]Zr-Df-ATG-101 was clearly visualised using small-animal PET imaging up to 7 days post-injection. Competition studies confirmed the specificity of PD-L1 targeting in vivo.Conclusion[89Zr]Zr-Df-ATG-101 in vivo distribution is dependent on PD-L1 expression in the MDA-MB-231 xenograft model. Immuno-PET with [89Zr]Zr-Df-ATG-101 provides real-time information about ATG-101 distribution and tumour uptake in vivo. Our data support the use of [89Zr]Zr-Df-ATG-101 to assess tumour and tissue uptake of ATG-101.

Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastaticdisease.

It is important to identify molecular features that improve prostate cancer (PCa) risk stratification before radical treatment with curative intent. Molecular analysis of historical diagnostic formalin-fixed paraffin-embedded (FFPE) prostate biopsies from cohorts with post-radiotherapy (RT) long-term clinical follow-up has been limited. Utilizing parallel sequencing modalities, we performed a proof-of-principle sequencing analysis of historical diagnostic FFPE prostate biopsies. We compared patients with (i) stable PCa (sPCa)postprimary or salvage RT,(ii) progressing PCa (pPCa) post-RT,and (iii) de novo metastatic PCa(mPCa). A cohort of 19 patients with diagnostic prostate biopsies (n = 6 sPCa, n = 5 pPCa, n = 8 mPCa) and mean 4 years 10 months follow-up (diagnosed 2009-2016) underwent nucleic acid extraction from demarcated malignancy. Samples underwent 3'RNA sequencing (3'RNAseq) (n = 19), nanoString analysis (n = 12), and Illumina 850k methylation (n = 8) sequencing. Bioinformatic analysis was performed to coherently identify differentially expressed genes and methylated genomic regions (MGRs). Eighteen of 19 samples provided useable 3'RNAseq data. Principal component analysis (PCA) demonstrated similar expression profiles between pPCa and mPCa cases, versus sPCa. Coherently differentially methylated probes between these groups identified ~600 differentially MGRs. The top 50 genes with increased expression in pPCa patients were associated with reduced progression-free survival post-RT (p < 0.0001) in an external cohort. 3'RNAseq, nanoString and 850k-methylation analyses are each achievable from historical FFPE diagnostic pretreatment prostate biopsies, unlocking the potential to utilize large cohorts of historic clinical samples. Profiling similarities between individuals with pPCa and mPCa suggests biological similarities and historical radiological staging limitations, which warrant further investigation.