Rafael Rivera Lugo

All Publications

• Reprogramming <i>Listeria monocytogenes</i> flavin metabolism to improve its therapeutic safety profile and broaden innate T-cell activation MBIO Chevee, V., Lobanovska, M., Rivera-Lugo, R., Guereca, L., Feng, Y., Anaya-Sanchez, A., Garcia Castillo, J., Huckins, A. M., Lemmens, E. E., Rae, C. S., Hardy, J. W., Carrington, R., Kotula, J. W., Portnoy, D. A. 2025: e0365225

  Abstract

  Listeria monocytogenes is a facultative intracellular bacterial pathogen that is a potent inducer of cell-mediated immunity, which has led to the development of attenuated, Listeria-based cancer vaccines. L. monocytogenes strains, such as live-attenuated double-deleted Listeria (LADD), lacking two key virulence factors, ΔactA and ΔinlB, have been used safely in clinical trials and showed promising anti-tumor activity. Despite early clinical success, improving potency and safety by preventing extracellular bacterial growth is paramount for the development of further clinical applications. We describe a quadruple attenuated intracellular Listeria (QUAIL) strain that, in addition to ΔactAΔinlB, lacks ribC and ribF, which encode enzymes required for generating the essential flavin cofactors flavin mononucleotide (FMN) and flavin adenine nucleotide (FAD). QUAIL imported FMN and FAD during intracellular growth but was unable to grow extracellularly in blood or on vascular catheters in mice, which reduced its lethality. Despite its lack of extracellular growth, QUAIL maintained its immunoprotective properties, which were comparable to LADD. Furthermore, we showed that QUAIL can be engineered to synthesize riboflavin, leading to expansion and activation of mucosal-associated invariant T cells. Together, our data support the use of QUAIL as a promising therapeutic platform with an improved safety profile that is amenable to further modifications to expand its immune-activating potential.IMPORTANCEListeria-based live-attenuated cancer vaccines represent a promising therapy in many different pre-clinical tumor models and in clinical trials. Enhancing its anti-cancer immunity and increasing its safety profile will advance the clinical applications of Listeria vaccines. By manipulating Listeria monocytogenes flavin metabolism, we engineered a quadruple attenuated intracellular Listeria (QUAIL) vaccine candidate strain that has limited toxicity associated with extracellular growth in major extracellular niches in vivo, including blood and implanted catheter ports. Furthermore, we showed that QUAIL can be effectively programmed to engage innate-like T cells known as mucosal-associated invariant T cells, which could be harnessed for future cancer immunotherapies. The results presented here lay the foundation for further analysis of QUAIL as a safer, yet immunopotent L. monocytogenes vaccine or therapeutic vector.

  View details for DOI 10.1128/mbio.03652-25

  View details for Web of Science ID 001651587300001

  View details for PubMedID 41474325

• <i>Mycobacterium tuberculosis</i> triggers reduced inflammatory cytokine responses and virulence in mice lacking Tax1bp1 PLOS PATHOGENS Chin, J., Abeydeera, N., Repasy, T., Rivera-Lugo, R., Mitchell, G., Nguyen, V. Q., Zheng, W., Richards, A., Stevenson, E., Swaney, D. L., Krogan, N. J., Ernst, J. D., Cox, J. S., Budzik, J. M. 2025; 21 (10): e1012829

  Abstract

  Host responses - autophagy, cell death, and inflammation - limit the growth of bacterial pathogens while minimizing tissue damage. During the early stages of infection, Mycobacterium tuberculosis (Mtb) thwarts these and other innate immune defense mechanisms in alveolar macrophages (AMs) derived from the yolk sac; in later stages, it circumvents defenses in recruited mononuclear cells (MNCs) and survives within them despite additional cytokine stimulation from recruited T cells. The mechanisms that drive variable rates of Mtb growth in different macrophage subtypes and how Mtb manipulates inflammatory responses to grow within innate immune cells remain obscure. Here we explored the role of the host factor, Tax-1 binding protein 1 (Tax1bp1), an autophagy receptor that targets pathogens for degradation through selective autophagy and terminates pro-inflammatory cytokine responses. Unexpectedly, we found that Tax1bp1-deficient mice were less susceptible to Mtb infection, and generated reduced inflammatory cytokine responses, compared to wild-type mice; the same mutant mice exhibited decreased growth of, and inflammatory cytokine responses to, Listeria monocytogenes, suggesting that Tax1bp1 plays a role in host responses to multiple intracellular pathogens. Contrary to our previous ex vivo findings in bone marrow-derived macrophages (BMDMs), in vivo growth of Mtb in AMs and a subset of recruited MNCs was more limited in mice lacking Tax1bp1 relative to wild-type mice. To better understand these differences, we performed global protein abundance measurements in mock- and Mtb-infected AM samples ex vivo from wild-type mice. These experiments revealed that Tax1bp1 protein abundance does not significantly change early after infection in AMs but does in BMDMs; moreover, early after infection, Tax1bp1-deficiency reduced necrotic-like cell death -- an outcome that favors Mtb replication -- in AMs but not BMDMs. Together, these results show that deficiency of Tax1bp1 plays a crucial, cell type-specific role in linking the regulation of autophagy, cell death, and anti-inflammatory host responses and overall reducing bacterial growth.

  View details for DOI 10.1371/journal.ppat.1012829

  View details for Web of Science ID 001606537600001

  View details for PubMedID 41171885

  View details for PubMedCentralID PMC12588459

• Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages. bioRxiv : the preprint server for biology Chin, J., Abeydeera, N., Repasy, T., Rivera-Lugo, R., Mitchell, G., Nguyen, V. Q., Zheng, W., Richards, A., Swaney, D. L., Krogan, N. J., Ernst, J. D., Cox, J. S., Budzik, J. M. 2024

  Abstract

  Crosstalk between autophagy, host cell death, and inflammatory host responses to bacterial pathogens enables effective innate immune responses that limit bacterial growth while minimizing coincidental host damage. Mycobacterium tuberculosis (Mtb) thwarts innate immune defense mechanisms in alveolar macrophages (AMs) during the initial stages of infection and in recruited bone marrow-derived cells during later stages of infection. However, how protective inflammatory responses are achieved during Mtb infection and the variation of the response in different macrophage subtypes remain obscure. Here, we show that the autophagy receptor Tax1bp1 plays a critical role in enhancing inflammatory cytokine production and increasing the susceptibility of mice to Mtb infection. Surprisingly, although Tax1bp1 restricts Mtb growth during infection of bone marrow-derived macrophages (BMDMs) (Budzik et al. 2020) and terminates cytokine production in response to cytokine stimulation or viral infection, Tax1bp1 instead promotes Mtb growth in AMs, neutrophils, and a subset of recruited monocyte-derived cells from the bone marrow. Tax1bp1 also leads to increases in bacterial growth and inflammatory responses during infection of mice with Listeria monocytogenes, an intracellular pathogen that is not effectively targeted to canonical autophagy. In Mtb-infected AMs but not BMDMs, Tax1bp1 enhances necrotic-like cell death early after infection, reprogramming the mode of host cell death to favor Mtb replication in AMs. Tax1bp1's impact on host cell death is a mechanism that explains Tax1bp1's cell type-specific role in the control of Mtb growth. Similar to Tax1bp1-deficiency in AMs, the expression of phosphosite-deficient Tax1bp1 restricts Mtb growth. Together, these results show that Tax1bp1 plays a crucial role in linking the regulation of autophagy, cell death, and pro-inflammatory host responses and enhancing susceptibility to bacterial infection.

  View details for DOI 10.1101/2024.12.16.628616

  View details for PubMedID 39763950

  View details for PubMedCentralID PMC11702572