Lucie Rodriguez-Coffinet

All Publications

• Assessing AI's cognitive abilities for scientific discovery in the field of systems vaccinology. Science immunology Rodriguez-Coffinet, L., Kazmin, D., Pulendran, B. 2025; 10 (114): eadx1794

  Abstract

  The advent of large language models (LLMs) has transformed academic research by accelerating hypothesis generation and data analysis. LLMs can help researchers uncover patterns and insights from vast datasets to foster innovative scientific discovery. However, questions arise regarding the creative capacity of artificial intelligence (AI), especially in biologically complex fields such as vaccinology. This study evaluates the ability of LLMs to generate hypotheses, design experiments, and infer broader biological principles through a proposed framework called "The Creation Game." Using three case studies-general control nonderepressible 2 (GCN2)'s role in dendritic cell antigen presentation via stress response, sterol regulatory element-binding protein (SREBP)'s influence on metabolic responses, and Toll-like receptor 5 (TLR5)'s connection to microbiota-driven vaccine efficacy-we assessed AI's accuracy, logic, and creativity. The findings underscore the potential of LLMs to accelerate vaccine research while emphasizing the importance of ethical oversight. By complementing human creativity, AI could potentially transform hypothesis-driven science, paving the way for tailored vaccination strategies and deeper insights into human immunity.

  View details for DOI 10.1126/sciimmunol.adx1794

  View details for PubMedID 41348860

• Longitudinal gut microbial trajectories show differences in early life LPS exposure and IFNγ responses Arzoomand, A., Lou, T., Sahi, M., Rodriguez, L., Lakshmikanth, T., Bernhardsson, A., Ohlin, M., Mugabo, C., Gonzales, L., Barcenilla, H., Johnson, A., Schwenk, J., Brodin, P. OXFORD UNIV PRESS. 2025

  View details for DOI 10.1093/jimmun/vkaf283.1871

  View details for Web of Science ID 001627274100001

• Systems-level immunomonitoring in children with solid tumors to enable precision medicine. Cell Chen, Q., Zhao, B., Tan, Z., Hedberg, G., Wang, J., Gonzalez, L., Mugabo, C. H., Johnsson, A., Negrini, E., Paez, L. P., Rodriguez, L., James, A., Chen, Y., Mikes, J., Bernhardsson, A. K., Reitzner, S. M., von Walden, F., O'Neill, O., Barcenilla, H., Wang, C., Davis, M. M., Carlson, L., Pal, N., Blomgren, K., Repsilber, D., Herold, N., Lakshmikanth, T., Kogner, P., Ljungblad, L., Brodin, P. 2025

  Abstract

  Cancer is the leading cause of death from disease in children. Survival depends not only on surgery, cytostatic drugs, and radiation but also on systemic immune responses. Factors influencing these immune responses in children of different ages and tumor types are unknown. Novel immunotherapies can enhance anti-tumor immune responses, but few children have benefited, and markers of effective responses are lacking. Here, we present a systems-level analysis of immune responses in 191 children within a population-based cohort with diverse tumors and reveal that age and tumor type shape immune responses differently. Systemic inflammation and cytotoxic Tcell responses correlate with tumor mutation rates and immune cell infiltration. Clonally expanded Tcell responses are rarely detected in blood or tumors at diagnosis but are sometimes elicited during treatment. Expanded Tcells are similarly regulated in children and adults with more immunogenic cancers. This research aims to facilitate the development of precision immunotherapies for children with cancer.

  View details for DOI 10.1016/j.cell.2024.12.014

  View details for PubMedID 39837329

• Human milk feeding practices and serum immune profiles of one-year-old infants in the CHILD birth cohort study. The American journal of clinical nutrition Ames, S. R., Lotoski, L. C., Rodriguez, L., Brodin, P., Mandhane, P. J., Moraes, T. J., Simons, E., Turvey, S. E., Subbarao, P., Azad, M. B. 2025; 121 (1): 60-73

  Abstract

  Breastfeeding and human milk consumption are associated with immune system development; however, the underlying mechanisms and the impact of different infant feeding practices are unclear.This study aimed to investigate how current human milk feeding (HMF) status is related to infant immune biomarker profiles, as well as explore relationships with HMF history (i.e., duration, exclusivity, and method: directly from the breast or pumped and bottled).This observational birth cohort study involved 605 infants from the Canadian CHILD Cohort Study. Infant feeding was captured from hospital birth records and parent questionnaires. Ninety-two biomarkers reflecting immune system activity and development were measured in serum collected at 1 y (12.6 ± 1.4 mo) using the Olink Target 96 Inflammation panel. Associations were determined using multivariable regression (adjusted for sex, time until blood sample centrifugation, and study site).Nearly half (42.6%) of infants were still receiving HMF at the time of blood sampling. Compared with non-HMF infants, HMF infants had higher levels of serum fibroblast growth factor 21 (FGF-21, adjusted standardized β coefficient: 0.56; 95% CI: 0.41, 0.72), cluster of differentiation 244 (CD244, β: 0.35; 95% CI: 0.19, 0.50), chemokine ligand 6 (CXCL6, β: 0.34; 95% CI: 0.18, 0.50), and chemokine ligand 20 (CCL20, β: 0.26; 95% CI: 0.09, 0.42) and lower extracellular newly identified receptor for advanced glycation end-products binding protein (EN-RAGE, β: -0.16; 95% CI: -0.29, -0.03). Among non-HMF infants, serum interleukin 7 (IL-7) had a marginally positive association with past HMF duration (β: 0.05; 95% CI: 0.02, 0.08) that persisted for ≤5 mo post-HMF cessation. Exclusive HMF duration and HMF method (at 3 mo of age) were not associated with any biomarkers.Current HMF status and (to a lesser extent) HMF history are associated with several inflammation-associated biomarkers in 1-y-old infants. These results provide new evidence that HMF impacts immune activity and development and suggest hypotheses about the underlying mechanisms. They also highlight the importance of including current HMF status in immune system-focused infant serum proteomic studies.

  View details for DOI 10.1016/j.ajcnut.2024.10.021

  View details for PubMedID 39486685

  View details for PubMedCentralID PMC11747196

• Cytokine Profile in Children Following SARS-CoV-2 Infection: Preliminary Findings. The Pediatric infectious disease journal Buonsenso, D., Camporesi, A., Di Sante, G., Sali, M., Boza, M. D., Morello, R., Valentini, P., Raffaelli, F., Rodriguez, L., Gonzalez, L., Johnsson, A., Mugabo, C. H., Lakshmikanth, T., Brodin, P. 2025; 44 (1): 54-57

  Abstract

  We provide preliminary evidence that, also in children, Long coronavirus disease (COVID) may be characterized by a proinflammatory signature. Ten Long COVID patients, 7 convalescent subjects after COVID infection and 4 healthy controls were enrolled. When adjusted for sex, children with long COVID had statistically significant differences in the levels of Flt3L, CD5, uPA, CCL23, CD40 and TGFα. When adjusted for age, CCL23 levels remained statistically significant.

  View details for DOI 10.1097/INF.0000000000004558

  View details for PubMedID 39352145

  View details for PubMedCentralID PMC11627325

• Author Correction: Immune system adaptation during gender-affirming testosterone treatment. Nature Lakshmikanth, T., Consiglio, C., Sardh, F., Forlin, R., Wang, J., Tan, Z., Barcenilla, H., Rodriguez, L., Sugrue, J., Noori, P., Ivanchenko, M., Piñero Páez, L., Gonzalez, L., Habimana Mugabo, C., Johnsson, A., Ryberg, H., Hallgren, Å., Pou, C., Chen, Y., Mikeš, J., James, A., Dahlqvist, P., Wahlberg, J., Hagelin, A., Holmberg, M., Degerblad, M., Isaksson, M., Duffy, D., Kämpe, O., Landegren, N., Brodin, P. 2024; 634 (8033): E5

  View details for DOI 10.1038/s41586-024-08081-w

  View details for PubMedID 39317781

  View details for PubMedCentralID PMC11464365

• Immune system adaptation during gender-affirming testosterone treatment. Nature Lakshmikanth, T., Consiglio, C., Sardh, F., Forlin, R., Wang, J., Tan, Z., Barcenilla, H., Rodriguez, L., Sugrue, J., Noori, P., Ivanchenko, M., Piñero Páez, L., Gonzalez, L., Habimana Mugabo, C., Johnsson, A., Ryberg, H., Hallgren, Å., Pou, C., Chen, Y., Mikeš, J., James, A., Dahlqvist, P., Wahlberg, J., Hagelin, A., Holmberg, M., Degerblad, M., Isaksson, M., Duffy, D., Kämpe, O., Landegren, N., Brodin, P. 2024; 633 (8028): 155-164

  Abstract

  Infectious, inflammatory and autoimmune conditions present differently in males and females. SARS-CoV-2 infection in naive males is associated with increased risk of death, whereas females are at increased risk of long COVID1, similar to observations in other infections2. Females respond more strongly to vaccines, and adverse reactions are more frequent3, like most autoimmune diseases4. Immunological sex differences stem from genetic, hormonal and behavioural factors5 but their relative importance is only partially understood6-8. In individuals assigned female sex at birth and undergoing gender-affirming testosterone therapy (trans men), hormone concentrations change markedly but the immunological consequences are poorly understood. Here we performed longitudinal systems-level analyses in 23 trans men and found that testosterone modulates a cross-regulated axis between type-I interferon and tumour necrosis factor. This is mediated by functional attenuation of type-I interferon responses in both plasmacytoid dendritic cells and monocytes. Conversely, testosterone potentiates monocyte responses leading to increased tumour necrosis factor, interleukin-6 and interleukin-15 production and downstream activation of nuclear factor kappa B-regulated genes and potentiation of interferon-γ responses, primarily in natural killer cells. These findings in trans men are corroborated by sex-divergent responses in public datasets and illustrate the dynamic regulation of human immunity by sex hormones, with implications for the health of individuals undergoing hormone therapy and our understanding of sex-divergent immune responses in cisgender individuals.

  View details for DOI 10.1038/s41586-024-07789-z

  View details for PubMedID 39232147

  View details for PubMedCentralID PMC11374716

• Immune system perturbations in patients with long COVID. Trends in molecular medicine Rodriguez, L., Brodin, P. 2024; 30 (3): 200-201

  Abstract

  Klein et al. report multimodal analyses of immune cells, proteins, and physiological parameters in patients with long COVID (LC). At the group level, LC subjects exhibited elevated antibody responses to SARS-CoV-2, but also to herpes viruses, pointing to a general suppression of viral control mechanisms in LC.

  View details for DOI 10.1016/j.molmed.2023.12.008

  View details for PubMedID 38177028

• Antisecretory factor in breastmilk is associated with reduced incidence of sepsis in preterm infants. Pediatric research Gustafsson, A., Johansson, E., Henckel, E., Olin, A., Rodriguez, L., Brodin, P., Lange, S., Bohlin, K. 2024; 95 (3): 762-769

  Abstract

  Antisecretory Factor (AF) is a protein present in breastmilk that regulates inflammatory processes. We aimed to investigate the level of AF in mothers' own milk (MOM) in relation to sepsis and other neonatal morbidities in preterm infants.Samples of breastmilk and infant plasma were collected at 1, 4, and 12 weeks after birth from 38 mothers and their 49 infants born before 30 weeks gestation. AF-compleasome in MOM was determined by a sandwich enzyme-linked immunosorbent assay (ELISA) and inflammatory markers in infant plasma by a panel of 92 inflammatory proteins. Neonatal treatments and outcomes were recorded.The level of AF in MOM week 1 was lower for infants with later sepsis compared to no sepsis (p = 0.005). Corrected for nutritional intake of MOM, higher levels of AF decreased the risk for sepsis, OR 0.24. AF in MOM week 1 was negatively correlated to inflammatory proteins in infant plasma week 4, markedly IL-8, which was also associated with infant sepsis. Overall, higher AF levels in MOM was associated with fewer major morbidities of prematurity.Mother's milk containing high levels of antisecretory factor is associated with reduced risk for sepsis and inflammation in preterm infants.High level of antisecretory factor (AF) in mothers' own milk is associated with less risk for later sepsis in preterm infants. Receiving mothers' milk with low AF levels during the first week after birth is correlated with more inflammatory proteins in infant's plasma 2-4 weeks later. Human breastmilk has anti-inflammatory properties, and antisecretory factor in mothers' own milk is a component of potential importance for infants born preterm. The findings suggest that food supplementation with AF to mothers of preterm infants to increase AF-levels in breastmilk may be a means to decrease the risk of inflammatory morbidities of prematurity.

  View details for DOI 10.1038/s41390-023-02909-3

  View details for PubMedID 38001236

  View details for PubMedCentralID PMC10899102

• Age-dependent differences in efferocytosis determine the outcome of opsonophagocytic protection from invasive pathogens. Immunity Bee, G. C., Lokken-Toyli, K. L., Yeung, S. T., Rodriguez, L., Zangari, T., Anderson, E. E., Ghosh, S., Rothlin, C. V., Brodin, P., Khanna, K. M., Weiser, J. N. 2023; 56 (6): 1255-1268.e5

  Abstract

  In early life, susceptibility to invasive infection skews toward a small subset of microbes, whereas other pathogens associated with diseases later in life, including Streptococcus pneumoniae (Spn), are uncommon among neonates. To delineate mechanisms behind age-dependent susceptibility, we compared age-specific mouse models of invasive Spn infection. We show enhanced CD11b-dependent opsonophagocytosis by neonatal neutrophils improved protection against Spn during early life. The augmented function of neonatal neutrophils was mediated by higher CD11b surface expression at the population level due to dampened efferocytosis, which also resulted in more CD11bhi "aged" neutrophils in peripheral blood. Dampened efferocytosis during early life could be attributed to the lack of CD169+ macrophages in neonates and reduced systemic expressions of multiple efferocytic mediators, including MerTK. On experimentally impairing efferocytosis later in life, CD11bhi neutrophils increased and protection against Spn improved. Our findings reveal how age-dependent differences in efferocytosis determine infection outcome through the modulation of CD11b-driven opsonophagocytosis and immunity.

  View details for DOI 10.1016/j.immuni.2023.03.018

  View details for PubMedID 37059107

  View details for PubMedCentralID PMC10330046

• Achieving symptom relief in patients with myalgic encephalomyelitis by targeting the neuro-immune interface and optimizing disease tolerance. Oxford open immunology Rodriguez, L., Pou, C., Lakshmikanth, T., Zhang, J., Mugabo, C. H., Wang, J., Mikes, J., Olin, A., Chen, Y., Rorbach, J., Juto, J. E., Li, T. Q., Julin, P., Brodin, P. 2023; 4 (1): iqad003

  Abstract

  Myalgic encephalomyelitis (ME) previously also known as chronic fatigue syndrome is a heterogeneous, debilitating syndrome of unknown etiology responsible for long-lasting disability in millions of patients worldwide. The most well-known symptom of ME is post-exertional malaise, but many patients also experience autonomic dysregulation, cranial nerve dysfunction and signs of immune system activation. Many patients also report a sudden onset of disease following an infection. The brainstem is a suspected focal point in ME pathogenesis and patients with structural impairment to the brainstem often show ME-like symptoms. The brainstem is also where the vagus nerve originates, a critical neuro-immune interface and mediator of the inflammatory reflex which regulate systemic inflammation. Here, we report the results of a randomized, placebo-controlled trial using intranasal mechanical stimulation targeting nerve endings in the nasal cavity, likely from the trigeminal nerve, possibly activating additional centers in the brainstem of ME patients and correlating with a ∼30% reduction in overall symptom scores after 8 weeks of treatment. By performing longitudinal, systems-level monitoring of the blood immune system in these patients, we uncover signs of chronic immune activation in ME, as well as immunological correlates of improvement that center around gut-homing immune cells and reduced inflammation. The mechanisms of symptom relief remain to be determined, but transcriptional analyses suggest an upregulation of disease tolerance mechanisms. We believe that these results are suggestive of ME as a condition explained by a maladaptive disease tolerance response following infection.

  View details for DOI 10.1093/oxfimm/iqad003

  View details for PubMedID 37255930

  View details for PubMedCentralID PMC10148714

• Bifidobacteria-mediated immune system imprinting early in life. Cell Henrick, B. M., Rodriguez, L., Lakshmikanth, T., Pou, C., Henckel, E., Arzoomand, A., Olin, A., Wang, J., Mikes, J., Tan, Z., Chen, Y., Ehrlich, A. M., Bernhardsson, A. K., Mugabo, C. H., Ambrosiani, Y., Gustafsson, A., Chew, S., Brown, H. K., Prambs, J., Bohlin, K., Mitchell, R. D., Underwood, M. A., Smilowitz, J. T., German, J. B., Frese, S. A., Brodin, P. 2021; 184 (15): 3884-3898.e11

  Abstract

  Immune-microbe interactions early in life influence the risk of allergies, asthma, and other inflammatory diseases. Breastfeeding guides healthier immune-microbe relationships by providing nutrients to specialized microbes that in turn benefit the host's immune system. Such bacteria have co-evolved with humans but are now increasingly rare in modern societies. Here we show that a lack of bifidobacteria, and in particular depletion of genes required for human milk oligosaccharide (HMO) utilization from the metagenome, is associated with systemic inflammation and immune dysregulation early in life. In breastfed infants given Bifidobacterium infantis EVC001, which expresses all HMO-utilization genes, intestinal T helper 2 (Th2) and Th17 cytokines were silenced and interferon β (IFNβ) was induced. Fecal water from EVC001-supplemented infants contains abundant indolelactate and B. infantis-derived indole-3-lactic acid (ILA) upregulated immunoregulatory galectin-1 in Th2 and Th17 cells during polarization, providing a functional link between beneficial microbes and immunoregulation during the first months of life.

  View details for DOI 10.1016/j.cell.2021.05.030

  View details for PubMedID 34143954

• The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19. Cell Consiglio, C. R., Cotugno, N., Sardh, F., Pou, C., Amodio, D., Rodriguez, L., Tan, Z., Zicari, S., Ruggiero, A., Pascucci, G. R., Santilli, V., Campbell, T., Bryceson, Y., Eriksson, D., Wang, J., Marchesi, A., Lakshmikanth, T., Campana, A., Villani, A., Rossi, P., Landegren, N., Palma, P., Brodin, P. 2020; 183 (4): 968-981.e7

  Abstract

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is typically very mild and often asymptomatic in children. A complication is the rare multisystem inflammatory syndrome in children (MIS-C) associated with COVID-19, presenting 4-6 weeks after infection as high fever, organ dysfunction, and strongly elevated markers of inflammation. The pathogenesis is unclear but has overlapping features with Kawasaki disease suggestive of vasculitis and a likely autoimmune etiology. We apply systems-level analyses of blood immune cells, cytokines, and autoantibodies in healthy children, children with Kawasaki disease enrolled prior to COVID-19, children infected with SARS-CoV-2, and children presenting with MIS-C. We find that the inflammatory response in MIS-C differs from the cytokine storm of severe acute COVID-19, shares several features with Kawasaki disease, but also differs from this condition with respect to T cell subsets, interleukin (IL)-17A, and biomarkers associated with arterial damage. Finally, autoantibody profiling suggests multiple autoantibodies that could be involved in the pathogenesis of MIS-C.

  View details for DOI 10.1016/j.cell.2020.09.016

  View details for PubMedID 32966765

  View details for PubMedCentralID PMC7474869

• Unraveling the Immune Response in Severe COVID-19. Journal of clinical immunology Rodriguez, L., Brodin, P. 2020; 40 (7): 958-959

  View details for DOI 10.1007/s10875-020-00849-9

  View details for PubMedID 32827284

  View details for PubMedCentralID PMC7442888

• Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19. Cell reports. Medicine Rodriguez, L., Pekkarinen, P. T., Lakshmikanth, T., Tan, Z., Consiglio, C. R., Pou, C., Chen, Y., Mugabo, C. H., Nguyen, N. A., Nowlan, K., Strandin, T., Levanov, L., Mikes, J., Wang, J., Kantele, A., Hepojoki, J., Vapalahti, O., Heinonen, S., Kekäläinen, E., Brodin, P. 2020; 1 (5): 100078

  Abstract

  Severe disease of SARS-CoV-2 is characterized by vigorous inflammatory responses in the lung, often with a sudden onset after 5-7 days of stable disease. Efforts to modulate this hyperinflammation and the associated acute respiratory distress syndrome rely on the unraveling of the immune cell interactions and cytokines that drive such responses. Given that every patient is captured at different stages of infection, longitudinal monitoring of the immune response is critical and systems-level analyses are required to capture cellular interactions. Here, we report on a systems-level blood immunomonitoring study of 37 adult patients diagnosed with COVID-19 and followed with up to 14 blood samples from acute to recovery phases of the disease. We describe an IFNγ-eosinophil axis activated before lung hyperinflammation and changes in cell-cell co-regulation during different stages of the disease. We also map an immune trajectory during recovery that is shared among patients with severe COVID-19.

  View details for DOI 10.1016/j.xcrm.2020.100078

  View details for PubMedID 32838342

  View details for PubMedCentralID PMC7405891