Suman Ranjan Das

Successful hematopoietic cell transplant requires immunosuppression to prevent graft-versus-host disease (GVHD), a lethal, T cell–mediated complication. The phase 3 BMT CTN 1703 trial demonstrated superior GVHD-free/relapse-free survival for posttransplant cyclophosphamide (PT-Cy)–based GVHD prophylaxis versus tacrolimus/methotrexate (Tac/MTX), but the T cell biology underpinning these outcomes remains unknown. To determine this, 324 patients were coenrolled onto BMT CTN 1801 to investigate the distinct T cell immune reconstitution pathways of these regimens, including extensive evaluation of T cell receptor (TCR) repertoire, via sequencing of 2359 longitudinal samples and 180,432,350 T cells. Multimodal T cell analysis revealed that PT-Cy was associated with pan–T cell deletion followed by delayed T cell expansion from a smaller founder population compared with Tac/MTX. This created a T cell diversity bottleneck, leading to reduced TCR repertoire diversity for 2 years posttransplant. Reduced TCR diversity, more common in patients receiving PT-Cy, was linked to protection against chronic GVHD when patients were analyzed without regard to study arm. Leveraging donor- and host-specific TCR clonal analysis, we determined that PT-Cy–mediated T cell depletion also depleted pathogen-specific TCRs, rendering PT-Cy patients more likely to lack detectable graft-derived pathogen-specific TCRs early after transplant, which was associated with an increased risk of severe infection. This study reveals how distinct immunosuppression strategies uniquely remodel T cell immunity and shape divergent transplant outcomes.

BACKGROUND: Joint use of multiple molecular layers can be useful to prioritize targets for mechanistic studies. Application of this approach to coronary disease in large populations is an emerging field. METHODS: We used reported circulating proteomic data (Somascan aptamer-based) from ≈3000 individuals in the CARDIA study (Coronary Artery Risk Development in Young Adults), measuring association with prevalent and 10-year incident coronary artery calcium (CAC) score. We used a multiparametric approach to prioritize circulating protein-CAC associations via genomics of circulating protein levels and coronary artery transcription. RESULTS: Proteins linked to prevalent/incident CAC in CARDIA implicated pathogenic mechanisms of vascular disease, including fibrosis and inflammation (GDF-15 [growth/differentiation factor 15], CDCP1 [CUB domain–containing protein 1], GSN [gelsolin], THBS2 [thrombospondin-2], chemokines, RNAS6 [ribonuclease K6]), oxidative lipid metabolism (CILP2; cartilage intermediate layer protein 2), extracellular matrix remodeling and signaling (MMPs [matrix metalloproteinases], TIMP-1 [tissue inhibitor of metalloproteinases 1], integrins), calcification (Notch 1, ARHGAP36 [Rho GTPase-activating protein 36]), and metabolism (GIP [gastric inhibitory polypeptide]), as well as new proteins not previously reported. Using proteome-wide association study genetic approaches, several targets with nominal evidence in CAC proteomics were associated with atherosclerosis or myocardial infarction in over 300K individuals, including PCSK9 (proprotein convertase subtilisin/kexin type 9) and APOC1. Finally, the coronary artery–specific transcriptome-wide association study of CAC yielded genes with previously implicated mechanistic roles in vascular homeostasis, inflammation, and metabolism, as well as genes without previously described function in CAC. Overlap across CAC proteomics and transcriptome-wide association study highlighted genes involved in vascular inflammation (S100A9), cardiac development (HES1 [transcription factor HES-1]), vessel wall structure (SPARCL1 [SPARC-like protein 1]), and vascular dysfunction or plaque (NOTCH3 [neurogenic locus notch homolog protein 3], TNFSF12 [tumor necrosis factor ligand superfamily member 12], S100A12 [protein S100-A12]). CONCLUSIONS: These results report population-level multiomics in human coronary calcification, presenting a method to identify disease-relevant targets through integration of human genetic approaches with multiomics.

Viral comorbidities elicit complex host responses by activating redox-sensitive signaling pathways, prominently those regulated by NADPH oxidase (Nox) enzymes. Nox are critical components of host defense, generating reactive oxygen species (ROS) that modulate key cellular signaling cascades. Under normal physiological conditions, Nox activity is tightly controlled; however, viral infections frequently disrupt this regulation, leading to aberrant upregulation of specific Nox isoforms. Elevated expression of individual Nox enzymes has been observed in infections such as influenza A and hepatitis C virus, while simultaneous activation of multiple Nox isoforms occurs in HIV and SARS-CoV infections. Similar patterns of dual or multi-isoform Nox activation are also reported in complex disease states, including diabetes, thrombosis, and fibrosis. MicroRNAs play a crucial role in this process by selectively regulating Nox isoform expression during viral infection, thereby remodeling the host redox environment. Nox-derived ROS influence multiple downstream signaling pathways, including SMAD, MAPK, CXCR-mediated signaling, and the JNK/ERK axis, promoting inflammation and fibrosis that worsen viral disease outcomes. Additionally, several FDA-approved drugs, investigational agents, and microRNA-based therapeutics show promise in modulating Nox activity. Therefore, this article substantiates how viral infections reprogram host transcriptomic and redox signaling networks, contributing to viral pathogenesis and offering potential therapeutic intervention strategies.

Prenatal exposure to ambient air pollutants has been associated with adverse child health across different populations. In the absence of direct air pollution exposure measures, epigenetic biomarkers can serve as indicators of cumulative exposure. Previously, we developed a methodological pipeline to build a prediction model to distinguish infants highly exposed to air pollutants in utero based on DNA methylation in cord blood samples. Here, we test and refine this pipeline using data from multiple pregnancy cohort sites included in the Environmental influences on Child Health Outcomes (ECHO) Cohort. Levels of prenatal exposure to fine particulate matter (PM2.5), nitrogen dioxide (NO2), and 8-hour maximum ozone (O3) were modeled using geocoded address data and machine learning. DNA methylation was measured using 450K or EPIC arrays. Training and validation sets were created and matched based on exposure level, cohort site, and array type to test the performance of the pipeline prediction model using area under the curve metrics. Among the three exposures, epigenetic-based predictions of PM2.5 and NO2 produced higher area under the curve values (0.64–0.68 and 0.62–0.95, respectively) than those for O3 (0.50–0.75). We identified differences in the performance of the pipeline model across geographical regions, exposure windows, and thresholds used to distinguish “high” and “low” air pollutant exposure. Overall, this pipeline enabled the estimation of air pollution from DNA methylation data, though careful consideration of model inputs is required. Further studies will test the performance of the CpG sites identified by the pipeline to predict child health outcomes.

Background: Symptomatic Clostridioides difficile infection (CDI) can cause significant morbidity and mortality. Conversely, patients can be colonized with toxigenic C. difficile in the absence of symptoms, termed asymptomatic colonization. We previously demonstrated that the presence and function of C. difficile toxins do not differentiate between asymptomatic colonization and CDI in children, suggesting the influence of other factors. This study aimed to interrogate the intestinal microbiome and butyrate in stool samples from children with CDI and asymptomatic colonization. Methods: Design: case-control study. Setting: tertiary care children's hospital. Participants and measures: asymptomatic children had stool tested for C. difficile by nucleic-acid amplification-based testing (NAAT) and were considered colonized if positive (n = 50). Residual stool was also obtained from symptomatic children who tested positive for C. difficile by NAAT (n = 55). The microbiome was assessed via 16S rRNA sequencing and butyrate via liquid chromatography-mass spectrometry. Results: Compared with clinical covariates and comorbidities, C. difficile symptom status (ie, asymptomatic colonization vs symptomatic CDI) demonstrated the strongest differential abundance association on gut microbes. Symptomatic CDI was associated with increased abundance of Escherichia/Shigella (Benjamini–Hochberg adjusted q = 3.94 × 10−5), Haemophilus (q = 0.022), and Gemella (q = 0.085), and depleted abundance of gut commensals such as Faecalibacterium (q = 0.041), Blautia (q = 0.041), and Bifidobacterium (q = 0.063). We also observed depletion in the abundance of microbial butyrate producers and fecal butyrate in participants with symptomatic CDI versus asymptomatic colonization. Conclusions: The gut microbiota and butyrate differ between participants with asymptomatic C. difficile colonization and symptomatic CDI, suggesting their potential role in symptom development.

Background: Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections and hospitalization in infants and children. Whole genome sequencing (WGS) plays a critical role in understanding the evolution and epidemiology of RSV. Limited studies have been conducted in Central America and the Caribbean, and none have specifically focused on lineages involved in recent outbreaks. Furthermore, no assays currently exist to evaluate the sensitivity of the RSV fusion protein to monoclonal antibodies. Methods: In Panama, an epidemiological surveillance system tracks RSV activity through the collection of nasopharyngeal samples from patients with acute respiratory infections. Between January 2018 and July 2024, 303 RSV‐positive samples were analyzed by RT‐qPCR. RSV‐B was the dominant subgroup in 2018, but following years had alternating dominance between RSV‐A and RSV‐B. Of the 303 samples, 115 underwent WGS. Additionally, neutralization assays were done using different Anti‐F Monoclonal Antibodies. Results: In RSV‐A, 11 lineages were identified, with 3 to 5 cocirculating during each annual outbreak, and a shift in predominance from A.D .1 (2019) to A.D .5.2 (2023–2024). In RSV‐B, two lineages circulated: B.D.4.1.1 (2018–2020) and its descendant B.D.E.1, which predominated from 2021 onward. Several monoclonal antibodies, including nirsevimab's precursor MEDI8897*, effectively neutralized the RSV strains in neutralization assays. Conclusions: Although Panama has not yet implemented a preventive therapy for RSV, this step could modify outbreak dynamics. The findings from this study provide a baseline reference prior to the implementation of preventive therapies against RSV in Panama and the region, facilitating the assessment of potential changes in the evolutionary dynamics of the virus.

Background and Aims: Symptomatic Clostridioides difficile infection (CDI) can cause significant morbidity and mortality. Conversely, patients can be colonized with toxigenic C. difficile in the absence of symptoms, termed asymptomatic colonization. We previously demonstrated that the presence and function of C. difficile toxins do not differentiate between asymptomatic colonization and CDI in children, suggesting the influence of other factors. This study aimed to interrogate the intestinal microbiome and butyrate in stool samples from children with CDI and asymptomatic colonization. Methods: Design: Case-control study Setting: Tertiary care children’s hospital Participants and measures: Asymptomatic children had stool tested for C. difficile by nucleic-acid amplification-based testing (NAAT) and were considered colonized if positive (N=50). Residual stool was also obtained from symptomatic children who tested positive for C. difficile by NAAT (N=55). The microbiome was assessed via 16S rRNA sequencing and butyrate via liquid chromatography-mass spectrometry. Results: Compared to clinical co-variates and comorbidities, C. difficile symptom status (i.e., asymptomatic colonization versus symptomatic CDI) demonstrated the strongest differential abundance association on gut microbes. Symptomatic CDI was associated with increased abundance of Escherichia/Shigella (Benjamini-Hochberg adjusted q=3.94×10 ⁻⁵ ), Haemophilus (q=0.022), and Gemella (q=0.085), and depleted abundance of gut commensals such as Faecalibacterium (q=0.041), Blautia (q=0.041), and Bifidobacterium (q=0.063). We also observed depletion in the abundance of microbial butyrate producers and fecal butyrate in participants with symptomatic CDI versus asymptomatic colonization. Conclusion: The gut microbiota and butyrate differ between participants with asymptomatic C. difficile colonization and symptomatic CDI, suggesting their potential role in symptom development.

Background: Persons with HIV (PWH) on contemporary antiretroviral therapy (ART) are at elevated risk for developing age-related cardiometabolic diseases. We hypothesized that integrative analysis of cross-tissue, multimodal data from PWH could provide insight into molecular programming that defines cardiometabolic phenotypes in this high-risk group. Methods: We enrolled 93 PWH without diabetes who were virologically suppressed on contemporary ART and obtained measures of insulin resistance, glucose intolerance, and adiposity. We performed circulating lipidomics, proteomics, and metabolomics, as well as subcutaneous adipose tissue (SAT) bulk transcriptomics, and used multiomics factor analysis (MOFA) to perform integrative analyses of these datasets. Results: The median age was 43 years, median body mass index 30.8 kg/m2, 81% were male, and 56% were self-identified non-Hispanic White. We identified a specific MOFA factor associated with visceral adipose tissue volume (ρ = −0.43), homeostasis model assessment 2 insulin resistance score (ρ = −0.52), liver density (ρ = 0.43), and other cardiometabolic risk factors, which explained more variance in the SAT transcriptome and circulating lipidome compared with the circulating proteome and metabolome. Gene set enrichment analysis of this factor showed extracellular matrix and inflammatory pathways that primarily mapped to SAT myeloid cells and adipose progenitor cells using single-cell deconvolution. Lipidomic analysis showed that this factor was significantly enriched for triacylglycerol and diacylglycerol species. Conclusions: Our multiomic analysis demonstrated coordinated, multitissue molecular reprogramming in virologically suppressed PWH with elevated cardiometabolic disease risk. Longitudinal studies of PWH with assessments of adipose tissue and lipid handling are necessary to understand mechanisms of cardiometabolic disease in PWH. Clinical Trials Registration. NCT04451980.