Elizabeth Worthey

Recent advances in spatial transcriptomics have enabled the profiling of increasingly larger numbers of genes while retaining single-cell and subcellular resolution in situ . However, standardized bioinformatics workflows for analyzing these datasets have lagged behind, with existing pipelines focusing primarily on image processing and cell segmentation. To address this gap, we present nf_xpatial, a best-practices Nextflow pipeline for the downstream analysis of 10x Genomics Xenium data. The pipeline performs quality control, filtering, log and cell area normalization, multi-sample integration, and both expression-driven and spatially informed clustering across systematic parameter sweeps, allowing users to evaluate and compare clustering resolutions and spatial modeling parameters within a single reproducible run. Overall, nf_xpatial streamlines the processing of Xenium data from platform outputs to integrated single-cell and spatial clustering datasets, providing a standardized starting point from which biologists can finetune parameters and proceed to hypothesis-driven spatial analyses. Availability and implementation: The source code and detailed documentation are freely available at https://github.com/U-BDS/nf_xpatial under the GPL-3 license. SUPPLEMENTARY INFORMATION: Supplementary data is provided.

Background: Chorangiomas, benign capillary lesions of the placenta, occur in ~1% of births, typically as solitary nodules. Multiple chorangioma syndrome is rare and increases risk of fetal heart failure, hydrops fetalis, and intrauterine death due to placental hemodynamic disruption. While genetic and hypoxic factors have been suggested in chorangioma development, direct molecular evidence is lacking. Here, we present a unique case of multiple chorangiomas confined to half of a shared placenta in monozygotic monochorionic diamniotic twins, providing a rare opportunity to dissect molecular drivers of chorangioma formation. Methods: Formalin-fixed paraffin-embedded tissue samples from chorangioma, affected and unaffected villi, and decidua from MCDA twins were subjected to whole-genome and bulk RNA sequencing. Germline and somatic small, structural, and copy number variants were identified. Clonal evolution analysis was conducted using PyClone-VI and ClonEvol. Mutational signature profiling was performed with SigProfilerExtractor to characterize molecular drivers of pathology. RNA-Seq (100 M reads/sample) was processed using the nf-core RNA-Seq pipeline, with differential expression analysis via DESeq2 to identify transcriptomic changes and mutational signatures. Quality control and artifact filtering were applied to mitigate FFPE-induced sequencing errors. Results: We identified a likely pathogenic early embryonic or germline EPAS1 frameshift deletion, suggesting impaired placental oxygen regulation and VEGF-driven angiogenesis. Chorangioma-affected tissue harbored pathogenic COL1A1, FBXO11, and TRIM71 somatic mutations, with elevated Leptin expression and oxidative stress signatures. In contrast, the unaffected twin’s placental territory carried a pathogenic MUTYH variant and repair deficiency-associated mutational signatures. These findings reveal distinct molecular processes in each placental domain and suggest a predisposing genetic alteration. Conclusions: Our study provides novel insights into the molecular basis of multiple chorangioma syndrome. To our knowledge, it is the first study to propose a molecular mechanism and the first to propose interaction of germline and somatic variants in syndrome pathobiology. Identification of molecular signatures linked to malignancy suggests potential overlap with oncogenic pathways that, if confirmed, would extend understanding of placental biology. These findings highlight the genetic-environmental interplay in placental pathology, with implications for preeclampsia, intrauterine growth restriction, and fetal vascular malperfusion.

Anoikis resistance, or evasion of cell death triggered by matrix detachment, is a hallmark of cancer cell survival and metastasis. We showed that repeated exposure to suspension stress followed by recovery under attached conditions leads to development of anoikis resistance. The acquisition of anoikis resistance was associated with enhanced invasion, chemoresistance, and immune evasion in vitro and distant metastasis in vivo. This acquired anoikis resistance was not genetic, persisting for a finite duration without detachment stress, but was sensitive to CDK8/19 mediator kinase inhibition that could also reverse anoikis resistance. Transcriptomic analysis revealed that CDK8/19 kinase inhibition induces bidirectional transcriptional changes in both sensitive and resistant cells, disrupting the balanced reprogramming required for anoikis adaptation and resistance by reversing some resistance-associated pathways and enhancing others. Both anoikis resistance and in vivo metastatic growth of ovarian cancers are sensitive to CDK8/19 inhibition, thereby providing a therapeutic opportunity to both prevent and suppress ovarian cancer metastasis.

Background: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling and heterogeneous disorder lacking validated biomarkers or targeted therapies. Clinical variability and elusive pathophysiology hinder progress toward effective diagnostics and treatment. Core symptoms include persistent fatigue, post-exertional malaise, unrefreshing sleep, cognitive dysfunction, and pain. We tested whether an individualized, “n-of-1” genomic and transcriptomic framework combined with comprehensive, participant-informed phenotyping could reveal molecular signatures unique to each patient. Methods: Clinical-grade whole-genome sequencing was conducted in 31 affected individuals from 25 families, with RNA-seq performed on a subset (16 affected, 7 unaffected) using blood samples. Machine-learning assisted variant triage, transcript-aware damage prediction, and expert review identified pathogenic or likely pathogenic variants in 8 of 25 probands (32%) and 12 of 31 affected individuals (39%). Results: Findings revealed marked genetic heterogeneity, including large-effect rare and more common variants. Implicated pathways included ATP generation, oxidative phosphorylation, fatty acid oxidation; regulation of glycolysis, amino acid and lipid turnover; ion and solute homeostasis; synaptic signaling, excitability, oxygen transport, and muscle integrity, resilience, and post-exertional recovery; previously implicated processes. Plausible modifiers influencing disease onset, severity, and relapsing–remitting patterns and possibly explaining intrafamilial variability and inconsistent findings across studies, were also identified. Despite gene-level diversity, downstream effects converged on impaired energy production, reduced stress resilience, and vulnerability to post-exertional metabolic failure; disruptions consistent with core ME/CFS symptoms of exertional intolerance, cognitive fog, and fatigue. Conclusions: Our findings support the hypothesis that at least a subset of ME/CFS cases represent distinct molecular disorders that converge on shared physiological pathways. Validation in larger, more diverse cohorts will be essential to test this hypothesis and establish generalizability, but increase size alone is unlikely to resolve causation in a disorder defined by rarity, heterogeneity, and molecular complexity. We suggest that progress will require experimental designs that integrate individual-level genomic data with deep, participant-informed deep phenotyping, capturing the combined effects of rare and common variants and environmental modifiers on disease expression and progression. We believe that an individualized precision medicine framework will uncover molecular drivers and modifiers of ME/CFS previously obscured by heterogeneity, enabling biologically informed stratification, improved trial design, biomarker discovery, and targeted interventions in this historically neglected condition.

Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order to overcome the higher sequencing errors to correctly identify cellular barcodes and unique molecular identifiers. Improvements in Oxford Nanopore sequencing, and development of novel computational methods have removed this requirement. Though these methods now exist, the limited availability of modular and portable workflows remains a challenge. Here we present, nf-core/scnanoseq, a secondary analysis pipeline for long-read single-cell and single-nuclei RNA that delivers gene and transcript-level quantification. The scnanoseq pipeline is implemented using Nextflow and is built upon the nf-core framework, enabling portability across computational environments, scalability and reproducibility of results across pipeline runs. The nf-core/scnanoseq workflow follows best practices for analyzing single-cell and single-nuclei data, performing barcode detection and correction, genome and transcriptome read alignment, unique molecular identifier deduplication, gene and transcript quantification, and extensive quality control reporting. AVAILABILITY OF DATA AND MATERIALS nf-core/scnanoseq is available at https://github.com/nf-core/scnanoseq under the MIT License and the documentation is available at https://nf-co.re/scnanoseq. The downstream analytical code for validation analysis is available at https://github.com/U-BDS/scnanoseq_analysis and all dataset sources have been disclosed under the methods section for each respective dataset.

Background Chorangiomas, benign proliferative capillary lesions in the placenta, occur in approximately 1% of births, typically as a solitary nodule. In rare cases, multiple nodules develop, posing risks of fetal heart failure, hydrops fetalis, and intrauterine death due to altered placental hemodynamics. Although genetic and hypoxic factors have been hypothesized to drive aberrant angiogenesis, definitive evidence has been lacking. We report on a unique case of multiple chorangiomas in half of a shared placenta in monozygotic, monochorionic diamniotic (MCDA) twins, providing an unprecedented opportunity to explore impacts that molecular variation has on chorangioma formation. Results Whole genome and bulk RNA sequencing supported identification of early embryonic or germline and somatic variation. It revealed a likely pathogenic heterozygous frameshift deletion in EPAS1, a hypoxia-sensing transcription factor, with an early embryonic or germline origin. This variant likely impaired placental oxygen regulation and angiogenesis through its impact on VEGF-related pathways. Deleterious somatic mutations in COL1A1, FBXO11, and TRIM71 were observed within the chorangioma-affected tissue, along with increased expression of Leptin and DNA damage signatures consistent with oxidative stress. In contrast, the unaffected twin’s placental territory showed a different pattern of pathogenic somatic variation with the presence of a known pathogenic variant in MUTYH and signs of repair deficiencies. These findings highlight the presence of predisposing events and distinct molecular processes within each domain of the shared placenta. We propose that these molecular events, combined with environmental factors intensified by the MCDA pregnancy, likely contributed to chorangioma development.. Conclusions Our study provides novel insights into the molecular basis of multiple chorangioma syndrome. To our knowledge, this is the first molecular evidence implicating both germline and somatic genetic involvement in this condition. The identification of molecular signatures previously associated with malignancy suggests that chorangiomas may share pathways with oncogenic processes. These findings highlight the importance of considering both genetic and environmental interactions in placental pathologies, offering potential implications for understanding and managing complex vascular and placental conditions, including preeclampsia, intrauterine growth restriction, and fetal vascular malperfusion.

Accurate diagnosis for the 400 million people with rare diseases is critical for healthcare decisions, prognosis, understanding disease mechanisms, and identification of treatments. Despite advances in genome sequencing, barriers such as high interpretation costs, diagnostic expertise, throughput associated delays, and uncertain variant classifications persist, with demand exceeding capacity. Many variant classification methods focus narrowly on specific consequences, leading to the use of complex integrative pipelines that often overlook transcript variability and lack prediction transparency. To overcome these limitations, we introduce DITTO. This transparent, transcript-aware machine-learning method demonstrates superior overall performance in accuracy, recall, and precision when compared to existing tools. DITTO is publicly available at https://github.com/uab-cgds-worthey/DITTO

Aim: The study aim was to determine caregiver interest and planned utilization of pharmacogenomic (PGx) results for their child with Prader-Willi syndrome. Methods: Caregivers consented to PGx test...

Anoikis resistance or evasion of cell death triggered by matrix detachment is a hallmark of cancer cell survival and metastasis. We show that repeated exposure to suspension stress followed by recovery under attached conditions leads to development of anoikis resistance. The acquisition of anoikis resistance is associated with enhanced invasion, chemoresistance, and immune evasion in vitro and distant metastasis in vivo. This acquired anoikis resistance is not genetic, persisting for a finite duration without detachment stress, but is sensitive to CDK8/19 Mediator kinase inhibition that can also reverse anoikis resistance. Transcriptomic analysis reveals that CDK8/19 kinase inhibition induces bidirectional transcriptional changes in both sensitive and resistant cells, disrupting the balanced reprogramming required for anoikis adaptation and resistance by reversing some resistance associated pathways and enhancing others. Both anoikis resistance and in vivo metastatic growth of ovarian cancers are sensitive to CDK8/19 inhibition, thereby providing a therapeutic opportunity to both prevent and suppress ovarian cancer metastasis.