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Deep molecular profiling of synovial biopsies in the STRAP trial identifies signatures predictive of treatment response to biologic therapies in rheumatoid arthritis.
Approximately 40% of patients with rheumatoid arthritis do not respond to individual biologic therapies, while biomarkers predictive of treatment response are lacking. Here we analyse RNA-sequencing (RNA-Seq) of pre-treatment synovial tissue from the biopsy-based, precision-medicine STRAP trial (n = 208), to identify gene response signatures to the randomised therapies: etanercept (TNF-inhibitor), tocilizumab (interleukin-6 receptor inhibitor) and rituximab (anti-CD20 B-cell depleting antibody). Machine learning models applied to RNA-Seq predict clinical response to etanercept, tocilizumab and rituximab at the 16-week primary endpoint with area under receiver operating characteristic curve (AUC) values of 0.763, 0.748 and 0.754 respectively (n = 67-72) as determined by repeated nested cross-validation. Prediction models for tocilizumab and rituximab are validated in an independent cohort (R4RA): AUC 0.713 and 0.786 respectively (n = 65-68). Predictive signatures are converted for use with a custom synovium-specific 524-gene nCounter panel and retested on synovial biopsy RNA from STRAP patients, demonstrating accurate prediction of treatment response (AUC 0.82-0.87). The converted models are combined into a unified clinical decision algorithm that has the potential to transform future clinical practice by assisting the selection of biologic therapies.
Contrasting modes of cultural evolution: Kra-Dai languages and weaving technologies
We investigate and compare the evolution of two aspects of culture, languages and weaving technologies, amongst the Kra-Dai (Tai-Kadai) peoples of southwest China and southeast Asia, using Bayesian Markov-Chain Monte Carlo methods to uncover phylogenies. The results show that languages and looms evolved in related but different ways, and bring some new insights into the diaspora of the Kra-Dai speakers across southeast Asia. We found that the languages and looms used by Hlai speakers of Hainan are outgroups in both linguistic and loom phylogenies, and that the looms used by speakers of closely related languages tend to belong to similar types. However, we also found discrepancies at a deep level between linguistic subgroups and loom types, in particular among widely dispersed South-Western Tai speakers, and we discuss possible reasons for this.
Viridans Streptococcal Biofilm Evades Immune Detection and Contributes to Inflammation and Rupture of Atherosclerotic Plaques.
BACKGROUND: Bacterial DNA from the oral cavity, respiratory tract, gut, and skin has been detected in atherosclerotic plaques, suggesting a role in chronic inflammation linked to atherosclerosis. Chronic bacterial infections often form biofilms resistant to antibiotics and immune detection, giving rise to a new generation of virulent bacteria in suitable conditions. This study explores the role of the immune system in bacterial-induced inflammation of atherosclerotic plaques. METHODS: Coronary plaques from 121 sudden death victims and endarterectomy samples from 96 surgical patients were analyzed using bacterial real-time quantitative polymerase chain reaction, immunohistochemistry, and genome-wide expression analysis. TLR (toll-like receptor) signaling was examined in bacterial-activated TLR cell lines. RESULTS: Of the bacteria detected, oral viridans group streptococcal DNA was the most common, being found in 42.1% of coronary plaques and 42.9% of endarterectomies. Immunopositivity for viridans streptococci correlated with severe atherosclerosis (P<0.0001) in both series and death from coronary heart disease (P=0.021) or myocardial infarction (P=0.042). Viridans streptococci colonized the core of the atheroma as a biofilm unrecognized by macrophages of the innate immune system. In contrast, immunopositive streptococci that appeared to have originated from the biofilm infiltrated the ruptured fibrous cap of the atheroma in endarterectomy samples and coronary plaques and were detected by pattern-recognizing receptors and coexpressed with the adaptive immune response. Among the viridans streptococcal strains, TLR2 was the most activated bacterial-signaling pathway. Genome-wide expression analysis of endarterectomy samples showed upregulation of bacterial recognition pathways. CONCLUSIONS: Latent chronic bacterial inflammation evades immune detection and may contribute to the pathogenesis of complicated atherosclerotic plaques and fatal myocardial infarction.
Defining the genetic determinants of CD8+ T cell receptor repertoire in the context of immune checkpoint blockade.
The relationship between genetic variation and CD8+ T cell receptor (TCR) repertoire usage in patients receiving immune checkpoint blockade (ICB) therapy for cancer is unexplored. We have conducted a genome-wide and human leukocyte antigen (HLA)-focused analysis of CD8+ TCR repertoire to identify genetic determinants of variable gene (V-gene) and CDR3 K-nucleotide oligomer usage from samples taken before and after ICB (n = 250). We identify 11 cis and 10 trans V-gene associations, primarily to the MHC, that meet genome-wide significance. TCR clones containing HLA associated V-genes were less stable across treatment, while, at the single-cell level, genetically associated clones demonstrate subset enrichment and increased tumor reactivity expression profiles. Notably, patients with HLA-matched TCR clones demonstrate improved overall survival. Our work indicates a complex relationship between genotype and TCR repertoire in the context of ICB treatment, with implications for understanding factors relating to therapeutic response and patient outcomes.
Development and Validation of a Type 1 Diabetes Multi-Ancestry Polygenic Score.
OBJECTIVE: Polygenic scores strongly predict type 1 diabetes risk, but most scores were developed in European-ancestry populations. In this study, we developed a multi-ancestry polygenic score to accurately predict type 1 diabetes risk across diverse populations. RESEARCH DESIGN AND METHODS: We used recent multi-ancestry genome-wide association studies to create a type 1 diabetes multi-ancestry polygenic score (T1D MAPS). We trained the score in the Mass General Brigham (MGB) Biobank (372 individuals with type 1 diabetes) and tested the score in the All of Us program (86 individuals with type 1 diabetes). We evaluated the area under the receiver operating characteristic curve (AUC), and we compared the AUC to two published single-ancestry scores: T1D GRS2EUR and T1D GRSAFR. We also developed an updated score (T1D MAPS2) that combines T1D GRS2EUR and T1D MAPS. RESULTS: Among individuals with non-European ancestry, the AUC of T1D MAPS was 0.90, significantly higher than T1D GRS2EUR (0.82, P = 0.04) and T1D GRSAFR (0.82, P = 0.007). Among individuals with European ancestry, the AUC of T1D MAPS was slightly lower than T1D GRS2EUR (0.89 vs. 0.91, P = 0.02). However, T1D MAPS2 performed equivalently to T1D GRS2EUR in European ancestry (0.91 vs. 0.91, P = 0.45) while still performing better in non-European ancestry (0.90 vs. 0.82, P = 0.04). CONCLUSIONS: A novel polygenic score improves type 1 diabetes risk prediction in non-European ancestry while maintaining high predictive power in European ancestry. These findings advance the accuracy of type 1 diabetes genetic risk prediction across diverse populations.
Paired analysis of host and pathogen genomes identifies determinants of human tuberculosis.
Infectious disease is the result of interactions between host and pathogen and can depend on genetic variations in both. We conduct a genome-to-genome study of paired human and Mycobacterium tuberculosis genomes from a cohort of 1556 tuberculosis patients in Lima, Peru. We identify an association between a human intronic variant (rs3130660, OR = 10.06, 95%CI: 4.87 - 20.77, P = 7.92 × 10-8) in the FLOT1 gene and a subclavaluee of Mtb Lineage 2. In a human macrophage infection model, we observe hosts with the rs3130660-A allele exhibited stronger interferon gene signatures. The interacting strains have altered redox states due to a thioredoxin reductase mutation. We investigate this association in a 2020 cohort of 699 patients recruited during the COVID-19 pandemic. While the prevalence of the interacting strain almost doubled between 2010 and 2020, its infection is not associated with rs3130660 in this recent cohort. These findings suggest a complex interplay among host, pathogen, and environmental factors in tuberculosis dynamics.
Genomic and Serological Rheumatoid Arthritis Biomarkers, MUC5B Promoter Variant, and Interstitial Lung Abnormalities.
RATIONALE: Rheumatoid arthritis (RA) has been implicated in interstitial lung disease (ILD) as majority of studies have been comprised of patients with known RA. However, it remains unclear whether an underlying risk for RA in combination with genetic risk for pulmonary fibrosis is associated with radiological markers of early lung injury and fibrosis in broader population samples. OBJECTIVE: Determine whether genetic and serological biomarkers of RA risk in combination with the MUC5B (rs35705950) risk allele (T) are associated with interstitial lung abnormalities (ILA) on computed tomography (CT) scans. METHODS: Associations of RA-risk HLA-DRB1 alleles (*04:01, *04:08, *04:05, *04:04, *10:01) and serum RA autoantibodies with ILA in the Multi-Ethnic Study of Atherosclerosis (MESA, n=4,018) and COPDGene (n=5,963) cohorts were modeled using logistic regression and adjusted for age, sex, self-reported race and ethnicity, smoking history, body mass index, and principal components of genetic ancestry. RESULTS: The prevalence of an RA risk HLA-DRB1 allele was 16.5% and 21.9% in MESA and COPDGene, respectively. ILA was present in 3.9% and 11% in MESA and COPDGene, respectively. An RA risk HLA-DRB1 allele was not significantly associated with ILA in MESA and COPDGene. In MESA, higher serum levels of IgA rheumatoid factor (RF) and anti-cyclic citrullinated peptide were associated with an odds ratio (OR) for ILA of 1.20 (95% CI 1.07-1.35) and 1.19 (95% CI 1.04-1.37), respectively. Among smokers without baseline ILA, per doubling of IgM RF was associated with an OR for ILA 10 years later of 1.25 (95% CI 1.08-1.43). Associations were not significantly different by MUC5B risk allele status. CONCLUSIONS: RA-related HLA-DRB1 alleles were not associated with ILA, whereas higher serum levels of IgM RF among smokers without baseline ILA were associated with subsequent ILA.
History of tuberculosis disease is associated with genetic regulatory variation in Peruvians.
A quarter of humanity is estimated to have been exposed to Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n = 63) or did not progress to TB (controls, n = 63). Transcriptomic profiling of monocyte-derived DCs and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Four genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma.
Burkitt lymphoma (BL) is responsible for many childhood cancers in sub-Saharan Africa, where it is linked to recurrent or chronic infection by Epstein-Barr virus or Plasmodium falciparum. However, whether human leukocyte antigen (HLA) polymorphisms, which regulate immune response, are associated with BL has not been well investigated, which limits our understanding of BL etiology. Here we investigate this association among 4,645 children aged 0-15 years, 800 with BL, enrolled in Uganda, Tanzania, Kenya, and Malawi. HLA alleles are imputed with accuracy >90% for HLA class I and 85-89% for class II alleles. BL risk is elevated with HLA-DQA1*04:01 (adjusted odds ratio [OR] = 1.61, 95% confidence interval [CI] = 1.32-1.97, P = 3.71 × 10-6), with rs2040406(G) in HLA-DQA1 region (OR = 1.43, 95% CI = 1.26-1.63, P = 4.62 × 10-8), and with amino acid Gln at position 53 versus other variants in HLA-DQA1 (OR = 1.36, P = 2.06 × 10-6). The associations with HLA-DQA1*04:01 (OR = 1.29, P = 0.03) and rs2040406(G) (OR = 1.68, P = 0.019) persist in mutually adjusted models. The higher risk rs2040406(G) variant for BL is associated with decreased HLA-DQB1 expression in eQTLs in EBV transformed lymphocytes. Our results support the role of HLA variation in the etiology of BL and suggest that a promising area of research might be understanding the link between HLA variation and EBV control.
Broad Impact of Bowel Urgency in Ulcerative Colitis and Crohn's Disease: US, European, and Japanese Patient and Healthcare Professional Perspectives from the Communicating Needs and Features of IBD Experiences (CONFIDE) Survey.
INTRODUCTION: Bowel urgency affects the quality of life of patients with Crohn's disease (CD) and ulcerative colitis (UC). This study used data from the Communicating Needs and Features of IBD Experiences (CONFIDE) survey to explore patient and healthcare professional (HCP) perceptions on the broad impacts of bowel urgency on patients' emotions and daily lives. METHODS: Online, quantitative, cross-sectional surveys were conducted among patients with moderate-to-severe UC or CD (defined based on previous treatment, steroid use, and/or hospitalization) and HCPs specialized in gastroenterology in Europe (France, Germany, Italy, Spain, UK), United States (US), and Japan. Data were summarized using descriptive statistics. RESULTS: The analysis included 200 US, 556 European, and 124 Japanese patients with UC and 215 US, 547 European, and 99 Japanese patients with CD; and 200 US, 503 European, and 100 Japanese HCPs. Patients experiencing bowel urgency in the past month and HCPs reported high emotional (up to: 97% patients, 97% HCPs) and daily life (up to: 85% patients, 97% HCPs) impacts due to bowel urgency in the US, Europe, and Japan. In all geographies, these impacts were similar among patients with UC and CD. Although patients and HCPs reported a broad impact of bowel urgency, HCPs perceived a higher impact than patients, but it was not among the top three most impactful symptoms on HCPs' treatment decisions. CONCLUSIONS: Bowel urgency affects the emotions and daily life of patients with UC or CD in the US, Europe, and Japan. A multidisciplinary approach is required to enhance care and develop suitable treatment strategies.
Mass cytometry as a tool in target validation and drug discovery.
Mass cytometry provides highly multiparametric data at a single cell level, coupling the specificity and sensitivity of time-of-flight mass spectrometry with the single-cell throughput of flow cytometry. It offers great value in interrogating the potentially heterogenous impact that a drug may have on a biological system, allowing an investigator to capture not just changes in cell behavior, but how these changes may differ between cell subtypes. In this chapter, we review the technical details of the platform as well as its limitations, before describing our approach to planning and running a mass cytometry experiment. A series of method modules, spanning the staining process through to data cleaning, are described that are then combined to create three separate experiments. The first experiment illustrates a core process in mass cytometry: the validation and titration of a metal-conjugated antibody reporter. The second experiment explores the impact of a kinase inhibitor on cell cycle and apoptosis pathways of a human myeloma cell line. And the third experiment exploits the multiparametric capability of mass cytometry, by exploring the differential expression changes in a transcription factor upon drug treatment across the cellular compartments of a peripheral blood mononuclear cell sample.
The effects of lacosamide, pregabalin, and tapentadol on peripheral nerve excitability: A randomized, double-blind, placebo-controlled, crossover, multi-center trial in healthy subjects.
BACKGROUND: Chronic pain is a leading cause of disability globally, with limited treatment options and frequent adverse effects. The IMI-PainCare-BioPain project aimed to enhance analgesic drug development by standardizing biomarkers. This study, IMI2-PainCare-BioPain-RCT1, evaluated the effects of lacosamide, pregabalin, and tapentadol on peripheral nerve excitability in healthy subjects through a randomized, double-blind, placebo-controlled crossover trial. METHODS: The study included 43 healthy participants aged 18-45 years. Participants underwent four treatment periods where they received single doses of lacosamide (200 mg), pregabalin (150 mg), tapentadol (100 mg), or placebo. High-frequency stimulation was applied to induce hyperalgesia. The two primary endpoints were changes in Strength Duration Time Constant (SDTC) in large sensory and motor fibers between lacosamide and placebo periods at the first post-dose timepoint compared to baseline (60 min). Other predefined endpoints included recovery cycle, threshold electrotonus (TEd), and S2 accommodation as well as effects of pregabalin and tapentadol. RESULTS: Lacosamide statistically significantly reduced SDTC in large sensory fibers (mean reduction 0.04 (95% CI 0.01-0.08), p = 0.012) and in motor fibers (mean reduction 0.04 (95% CI 0.00-0.07), p = 0.039) but had no effect on small sensory fibers at the first timepoint compared to placebo. There were no effects of pregabalin and tapentadol on SDTC. Of other predefined endpoints, lacosamide produced statistically significant changes in subexcitability, S2 accommodation TEd(peak), and TEd40(Accom) in large sensory fibers. No statistically significant changes were observed in refractoriness, relative refractory period, or accommodation half-time at the first timepoint compared to placebo. CONCLUSIONS: This study demonstrates that nerve excitability testing can detect pharmacodynamic effects on large myelinated fibers in healthy subjects. Lacosamide statistically significantly reduced peripheral nerve excitability, particularly in large sensory fibers.
ctDNA to Predict Treatment Response in Head and Neck Squamous Cell Carcinoma: A Systematic Review.
OBJECTIVE: To investigate the potential role of plasma circulating tumor DNA (ctDNA) in predicting treatment response in HPV-positive and HPV-negative Head and Neck Squamous Cell Carcinoma (HNSCC). DATA SOURCES: Medline, PubMed, Cochrane databases (Cochrane Library, Cochrane Central Register of Controlled Trials) and EMBASE databases were searched in accordance with the standard PICOTS model. REVIEW METHODS: Search results were independently reviewed by two primary authors. Disagreements were adjudicated by the senior author. Studies were excluded according to defined exclusion criteria. Studies were assessed for quality in accordance with the REMARK guidelines. Data were then extracted, and findings were discussed narratively. RESULTS: From a total of 1026 articles initially retrieved, 18 papers were included in the final review. Study quality was suboptimal, with a median REMARK score of 12.65/20. Short follow-up (median 24.5 months) and modest cohort sizes (median 59 patients) were observed. Most studies (13/18) investigated HPV ctDNA alone, and ctDNA detection methods varied considerably between studies. Broadly, studies showed that ctDNA monitoring has a high negative predictive value (91.7%) for residual and recurrent disease. Persistently positive ctDNA corresponded with poorer outcomes overall, but there was variability in the positive predictive value between studies, which was mitigated by consecutive testing. CONCLUSION: These results suggest there is potential for ctDNA utility in surveillance for both HPV-positive and HPV-negative HNSCC patients; however, better adherence to reporting guidelines will enable meta-analysis.