Daniel Hoces Burga

All Publications

• A synthetic biology approach to engineering circuits in immune cells. Immunological reviews Hoces, D., Miguens Blanco, J., Hernandez-Lopez, R. A. 2023

  Abstract

  A synthetic circuit in a biological system involves the designed assembly of genetic elements, biomolecules, or cells to create a defined function. These circuits are central in synthetic biology, enabling the reprogramming of cellular behavior and the engineering of cells with customized responses. In cancer therapeutics, engineering T cells with circuits have the potential to overcome the challenges of current approaches, for example, by allowing specific recognition and killing of cancer cells. Recent advances also facilitate engineering integrated circuits for the controlled release of therapeutic molecules at specified locations, for example, in a solid tumor. In this review, we discuss recent strategies and applications of synthetic receptor circuits aimed at enhancing immune cell functions for cancer immunotherapy. We begin by introducing the concept of circuits in networks at the molecular and cellular scales and provide an analysis of the development and implementation of several synthetic circuits in T cells that have the goal to overcome current challenges in cancer immunotherapy. These include specific targeting of cancer cells, increased T-cell proliferation, and persistence in the tumor microenvironment. By harnessing the power of synthetic biology, and the characteristics of certain circuit architectures, it is now possible to engineer a new generation of immune cells that recognize cancer cells, while minimizing off-target toxicities. We specifically discuss T-cell circuits for antigen density sensing. These circuits allow targeting of solid tumors that share antigens with normal tissues. Additionally, we explore designs for synthetic circuits that could control T-cell differentiation or T-cell fate as well as the concept of synthetic multicellular circuits that leverage cellular communication and division of labor to achieve improved therapeutic efficacy. As our understanding of cell biology expands and novel tools for genome, protein, and cell engineering are developed, we anticipate further innovative approaches to emerge in the design and engineering of circuits in immune cells.

  View details for DOI 10.1111/imr.13244

  View details for PubMedID 37464881

• Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota ELIFE Hoces, D., Greter, G., Arnoldini, M., Staubli, M. L., Moresi, C., Sintsova, A., Berent, S., Kolinko, I., Bansept, F., Woller, A., Hafliger, J., Martens, E., Hardt, W., Sunagawa, S., Loverdo, C., Slack, E. 2023; 12

  Abstract

  Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. In this study, we used genetically barcoded Bacteroides thetaiotaomicron (B. theta) strains to quantify population bottlenecks experienced by a B. theta population during colonization of the mouse gut. As expected, this reveals an inverse relationship between microbiota complexity and the probability that an individual wildtype B. theta clone will colonize the gut. The polysaccharide capsule of B. theta is important for resistance against attacks from other bacteria, phage, and the host immune system, and correspondingly acapsular B. theta loses in competitive colonization against the wildtype strain. Surprisingly, the acapsular strain did not show a colonization defect in mice with a low-complexity microbiota, as we found that acapsular strains have an indistinguishable colonization probability to the wildtype strain on single-strain colonization. This discrepancy could be resolved by tracking in vivo growth dynamics of both strains: acapsular B.theta shows a longer lag phase in the gut lumen as well as a slightly slower net growth rate. Therefore, as long as there is no niche competitor for the acapsular strain, this has only a small influence on colonization probability. However, the presence of a strong niche competitor (i.e., wildtype B. theta, SPF microbiota) rapidly excludes the acapsular strain during competitive colonization. Correspondingly, the acapsular strain shows a similarly low colonization probability in the context of a co-colonization with the wildtype strain or a complete microbiota. In summary, neutral tagging and detailed analysis of bacterial growth kinetics can therefore quantify the mechanisms of colonization resistance in differently-colonized animals.

  View details for DOI 10.7554/eLife.81212

  View details for Web of Science ID 000952320300001

  View details for PubMedID 36757366

  View details for PubMedCentralID PMC10014078

• "EvoVax" - A rationally designed inactivated Salmonella Typhimurium vaccine induces strong and long-lasting immune responses in pigs. Vaccine Lentsch, V., Aslani, S., Echtermann, T., Preet, S., Cappio Barazzone, E., Hoces, D., Moresi, C., Kummerlen, D., Slack, E. 2023; 41 (38): 5545-5552

  Abstract

  Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm) poses a considerable threat to public health due to its zoonotic potential. Human infections are mostly foodborne, and pork and pork products are ranked among the top culprits for transmission. In addition, the high percentage of antibiotic resistance, especially in monophasic S.Tm, limits treatment options when needed. Better S.Tm control would therefore be of benefit both for farm animals and for safety of the human food chain. A promising pre-harvest intervention is vaccination. In this study we tested safety and immunogenicity of an oral inactivated S.Tm vaccine, which has been recently shown to generate an "evolutionary trap" and to massively reduce S.Tm colonization and transmission in mice. We show that this vaccine is highly immunogenic and safe in post-weaning pigs and that administration of a single oral dose results in a strong and long-lasting serum IgG response. This has several advantages over existing - mainly live - vaccines against S.Tm, both in improved seroconversion and reduced risk of vaccine-strain persistence and reversion to virulence.

  View details for DOI 10.1016/j.vaccine.2023.07.059

  View details for PubMedID 37517910

• Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle. PLoS biology Hoces, D., Lan, J., Sun, W., Geiser, T., Staubli, M. L., Cappio Barazzone, E., Arnoldini, M., Challa, T. D., Klug, M., Kellenberger, A., Nowok, S., Faccin, E., Macpherson, A. J., Stecher, B., Sunagawa, S., Zenobi, R., Hardt, W., Wolfrum, C., Slack, E. 2022; 20 (9): e3001743

  Abstract

  The capacity of the intestinal microbiota to degrade otherwise indigestible diet components is known to greatly improve the recovery of energy from food. This has led to the hypothesis that increased digestive efficiency may underlie the contribution of the microbiota to obesity. OligoMM12-colonized gnotobiotic mice have a consistently higher fat mass than germ-free (GF) or fully colonized counterparts. We therefore investigated their food intake, digestion efficiency, energy expenditure, and respiratory quotient using a novel isolator-housed metabolic cage system, which allows long-term measurements without contamination risk. This demonstrated that microbiota-released calories are perfectly balanced by decreased food intake in fully colonized versus gnotobiotic OligoMM12 and GF mice fed a standard chow diet, i.e., microbiota-released calories can in fact be well integrated into appetite control. We also observed no significant difference in energy expenditure after normalization by lean mass between the different microbiota groups, suggesting that cumulative small differences in energy balance, or altered energy storage, must underlie fat accumulation in OligoMM12 mice. Consistent with altered energy storage, major differences were observed in the type of respiratory substrates used in metabolism over the circadian cycle: In GF mice, the respiratory exchange ratio (RER) was consistently lower than that of fully colonized mice at all times of day, indicative of more reliance on fat and less on glucose metabolism. Intriguingly, the RER of OligoMM12-colonized gnotobiotic mice phenocopied fully colonized mice during the dark (active/eating) phase but phenocopied GF mice during the light (fasting/resting) phase. Further, OligoMM12-colonized mice showed a GF-like drop in liver glycogen storage during the light phase and both liver and plasma metabolomes of OligoMM12 mice clustered closely with GF mice. This implies the existence of microbiota functions that are required to maintain normal host metabolism during the resting/fasting phase of circadian cycle and which are absent in the OligoMM12 consortium.

  View details for DOI 10.1371/journal.pbio.3001743

  View details for PubMedID 36126044

• A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nature microbiology Diard, M., Bakkeren, E., Lentsch, V., Rocker, A., Bekele, N. A., Hoces, D., Aslani, S., Arnoldini, M., Böhi, F., Schumann-Moor, K., Adamcik, J., Piccoli, L., Lanzavecchia, A., Stadtmueller, B. M., Donohue, N., van der Woude, M. W., Hockenberry, A., Viollier, P. H., Falquet, L., Wüthrich, D., Bonfiglio, F., Loverdo, C., Egli, A., Zandomeneghi, G., Mezzenga, R., Holst, O., Meier, B. H., Hardt, W. D., Slack, E. 2021; 6 (7): 830-841

  Abstract

  The ability of gut bacterial pathogens to escape immunity by antigenic variation-particularly via changes to surface-exposed antigens-is a major barrier to immune clearance1. However, not all variants are equally fit in all environments2,3. It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here, we demonstrate this phenomenon using Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm). A dominant surface antigen of S.Tm is its O-antigen: a long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase variation4,5. We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen-specific immunoglobulin A and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naive mice. Through the use of rationally designed oral vaccines, we induced immunoglobulin A responses blocking all of these trajectories. This selected for Salmonella mutants carrying deletions of the O-antigen polymerase gene wzyB. Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents or complement) and predation (bacteriophages) and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off in S.Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.

  View details for DOI 10.1038/s41564-021-00911-1

  View details for PubMedID 34045711

  View details for PubMedCentralID PMC7611113

• High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains MICROBIOME Zund, M., Ruscheweyh, H., Field, C. M., Meyer, N., Cuenca, M., Hoces, D., Hardt, W., Sunagawa, S. 2021; 9 (1): 77

  Abstract

  Temperate phages influence the density, diversity and function of bacterial populations. Historically, they have been described as carriers of toxins. More recently, they have also been recognised as direct modulators of the gut microbiome, and indirectly of host health and disease. Despite recent advances in studying prophages using non-targeted sequencing approaches, methodological challenges in identifying inducible prophages in bacterial genomes and quantifying their activity have limited our understanding of prophage-host interactions.We present methods for using high-throughput sequencing data to locate inducible prophages, including those previously undiscovered, to quantify prophage activity and to investigate their replication. We first used the well-established Salmonella enterica serovar Typhimurium/p22 system to validate our methods for (i) quantifying phage-to-host ratios and (ii) accurately locating inducible prophages in the reference genome based on phage-to-host ratio differences and read alignment alterations between induced and non-induced prophages. Investigating prophages in bacterial strains from a murine gut model microbiota known as Oligo-MM12 or sDMDMm2, we located five novel inducible prophages in three strains, quantified their activity and showed signatures of lateral transduction potential for two of them. Furthermore, we show that the methods were also applicable to metagenomes of induced faecal samples from Oligo-MM12 mice, including for strains with a relative abundance below 1%, illustrating its potential for the discovery of inducible prophages also in more complex metagenomes. Finally, we show that predictions of prophage locations in reference genomes of the strains we studied were variable and inconsistent for four bioinformatic tools we tested, which highlights the importance of their experimental validation.This study demonstrates that the integration of experimental induction and bioinformatic analysis presented here is a powerful approach to accurately locate inducible prophages using high-throughput sequencing data and to quantify their activity. The ability to generate such quantitative information will be critical in helping us to gain better insights into the factors that determine phage activity and how prophage-bacteria interactions influence our microbiome and impact human health. Video abstract.

  View details for DOI 10.1186/s40168-021-01033-w

  View details for Web of Science ID 000636295500001

  View details for PubMedID 33781335

  View details for PubMedCentralID PMC8008629

• Regulatory T cell expansion resolves after effective strongyloidiasis treatment in subjects with HTLV-1 co-infection PARASITOLOGY INTERNATIONAL Hoces, D., Barros, N., Woll, F., Bauer, A., Clinton White, A., Montes, M. 2020; 76: 102092

  Abstract

  Regulatory T-cells (Tregs) are increased in patients with HTLV-1/Strongyloides stercoralis co-infection, and they may modify otherwise protective antigen-specific cytokine production. We hypothesized that effective anti-helminthic treatment would decrease Tregs and restore antigen-specific cytokine responses.We enrolled 19 patients with Strongyloides larvae in their stool by Baerman's test. Six were positive and 13 negative for antibody to HTLV-1 by ELISA, with positive tests confirmed by immunoblot. Before treatment, co-infected subjects had higher Tregs percentages and lower antigen-stimulated IL-5 levels compared to subjects with Strongyloides without HTLV-1. All patients were treated with ivermectin. After effective treatment, Tregs percentages decreased in patients with HTLV-1; however, antigen-specific IL-5 production remained blunted in co-infected subjects.These results suggest that treating strongyloidiasis infection decreases circulating Tregs, but antigen-specific cytokine remains altered. This may reflect blunting of sensitization by Tregs.

  View details for DOI 10.1016/j.parint.2020.102092

  View details for Web of Science ID 000528164100035

  View details for PubMedID 32120049

• Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. Nature microbiology Wotzka, S. Y., Kreuzer, M., Maier, L., Arnoldini, M., Nguyen, B. D., Brachmann, A. O., Berthold, D. L., Zünd, M., Hausmann, A., Bakkeren, E., Hoces, D., Gül, E., Beutler, M., Dolowschiak, T., Zimmermann, M., Fuhrer, T., Moor, K., Sauer, U., Typas, A., Piel, J., Diard, M., Macpherson, A. J., Stecher, B., Sunagawa, S., Slack, E., Hardt, W. D. 2019; 4 (12): 2164-2174

  Abstract

  The microbiota confers colonization resistance, which blocks Salmonella gut colonization1. As diet affects microbiota composition, we studied whether food composition shifts enhance susceptibility to infection. Shifting mice to diets with reduced fibre or elevated fat content for 24 h boosted Salmonella Typhimurium or Escherichia coli gut colonization and plasmid transfer. Here, we studied the effect of dietary fat. Colonization resistance was restored within 48 h of return to maintenance diet. Salmonella gut colonization was also boosted by two oral doses of oleic acid or bile salts. These pathogen blooms required Salmonella's AcrAB/TolC-dependent bile resistance. Our data indicate that fat-elicited bile promoted Salmonella gut colonization. Both E. coli and Salmonella show much higher bile resistance than the microbiota. Correspondingly, competitive E. coli can be protective in the fat-challenged gut. Diet shifts and fat-elicited bile promote S. Typhimurium gut infections in mice lacking E. coli in their microbiota. This mouse model may be useful for studying pathogen-microbiota-host interactions, the protective effect of E. coli, to analyse the spread of resistance plasmids and assess the impact of food components on the infection process.

  View details for DOI 10.1038/s41564-019-0568-5

  View details for PubMedID 31591555

  View details for PubMedCentralID PMC6881180

• Growing, evolving and sticking in a flowing environment: understanding IgA interactions with bacteria in the gut IMMUNOLOGY Hoces, D., Arnoldini, M., Diard, M., Loverdo, C., Slack, E. 2020; 159 (1): 52-62

  Abstract

  Immunology research in the last 50 years has made huge progress in understanding the mechanisms of anti-bacterial defense of deep, normally sterile, tissues such as blood, spleen and peripheral lymph nodes. In the intestine, with its dense commensal microbiota, it seems rare that this knowledge can be simply translated. Here we put forward the idea that perhaps it is not always the theory of immunology that is lacking to explain mucosal immunity, but rather that we have overlooked crucial parts of the mucosal immunological language required for its translation: namely intestinal and bacterial physiology. We will try to explain this in the context of intestinal secretory antibodies (mainly secretory IgA), which have been described to prevent, to alter, to not affect, or to promote colonization of the intestine and gut-draining lymphoid tissues, and where effector mechanisms have remained elusive. In fact, these apparently contradictory outcomes can be generated by combining the basic premises of bacterial agglutination with an understanding of bacterial growth (i.e. secretory IgA-driven enchained growth), fluid handling and bacterial competition in the gut lumen.

  View details for DOI 10.1111/imm.13156

  View details for Web of Science ID 000498817800001

  View details for PubMedID 31777063

  View details for PubMedCentralID PMC6904610

• Do Memory CD4 T Cells Keep Their Cell-Type Programming: Plasticity versus Fate Commitment? T-Cell Heterogeneity, Plasticity, and Selection in Humans COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY Sallusto, F., Cassotta, A., Hoces, D., Foglierini, M., Lanzavecchia, A. 2018; 10 (3)

  Abstract

  The wide range of effector and memory T cells is instrumental for immune regulation and tailored mechanisms of protection against pathogens. Here, we will focus on human CD4 T cells and discuss T-cell plasticity and intraclonal diversification in the context of a progressive and selective model of CD4 T-cell differentiation.

  View details for DOI 10.1101/cshperspect.a029421

  View details for Web of Science ID 000426466500007

  View details for PubMedID 28432133

  View details for PubMedCentralID PMC5830897

• Missed opportunities for HIV control: Gaps in HIV testing for partners of people living with HIV in Lima, Peru PLOS ONE Vasquez, A. L., Errea, R. A., Hoces, D., Echevarria, J., Gonzalez-Lagos, E., Gotuzzo, E. 2017; 12 (8): e0181412

  Abstract

  Based on the hypothesis that HIV programs struggle to deliver health services that harmonize necessities of treatment and prevention, we described the outcomes of routinely provided HIV testing to partners of people living with HIV (PLWH) through a secondary analysis of routine data collected at a public hospital in Lima, Peru.Among PLWH enrolled in the study center's HIV program between 2005 and 2014, we identified index cases (IC): PLWH who reported a unique partner not previously enrolled. We grouped partners according to their HIV status as reported by IC and collected data on HIV testing, clinical characteristics and admissions. The main outcome was the frequency of HIV testing among partners with reported unknown/seronegative HIV status.Out of 1586 PLWH who reported a unique partner at enrollment, 171 had a previously enrolled partner, leaving 1415 (89%) IC. HIV status of the partner was reported as unknown in 571 (40%), seronegative in 325 (23%) and seropositive in 519 (37%). Out of 896 partners in the unknown/seronegative group, 72 (8%) had HIV testing, 42/72 (58%) tested within three months of IC enrollment. Among the 49/72 (68%) who tested positive for HIV, 33 (67%) were enrolled in the HIV program. The proportion in WHO clinical stage IV was lower in enrolled partners compared to IC (37% vs 9%, p = 0.04). Non-tested partners (824) were likely reachable by the hospital, as 297/824 (36%) of their IC were admitted in the study center at least once, 51/243 (21%) female IC had received pregnancy care at the study center, and 401/692 (64%) of IC on antiretroviral therapy had achieved viral suppression, implying frequent visits to the hospital for pill pick-up.In this setting, HIV testing of partners of PLWH was suboptimal, illustrating missed opportunities for HIV control. Integration of HIV strategies in primarily clinical-oriented services is a challenging need.

  View details for DOI 10.1371/journal.pone.0181412

  View details for Web of Science ID 000407548800006

  View details for PubMedID 28806412

  View details for PubMedCentralID PMC5555572

• Assessing the HIV Care Continuum in Latin America: progress in clinical retention, cART use and viral suppression JOURNAL OF THE INTERNATIONAL AIDS SOCIETY Rebeiro, P. F., Cesar, C., Shepherd, B. E., De Boni, R. B., Cortes, C. P., Rodriguez, F., Belaunzaran-Zamudio, P., Pape, J. W., Padgett, D., Hoces, D., McGowan, C. C., Cahn, P. 2016; 19: 20636

  Abstract

  We assessed trends in HIV Care Continuum outcomes associated with delayed disease progression and reduced transmission within a large Latin American cohort over a decade: clinical retention, combination antiretroviral therapy (cART) use and viral suppression (VS).Adults from Caribbean, Central and South America network for HIV epidemiology clinical cohorts in seven countries contributed data between 2003 and 2012. Retention was defined as two or more HIV care visits annually, >90 days apart. cART was defined as prescription of three or more antiretroviral agents annually. VS was defined as HIV-1 RNA <200 copies/mL at last measurement annually. cART and VS denominators were subjects with at least one visit annually. Multivariable modified Poisson regression was used to assess temporal trends and examine associations between age, sex, HIV transmission mode, cohort, calendar year and time in care.Among 18,799 individuals in retention analyses, 14,380 in cART analyses and 13,330 in VS analyses, differences existed between those meeting indicator definitions versus those not by most characteristics. Retention, cART and VS significantly improved from 2003 to 2012 (63 to 77%, 74 to 91% and 53 to 82%, respectively; p<0.05, each). Female sex (risk ratio (RR)=0.97 vs. males) and injection drug use as HIV transmission mode (RR=0.83 vs. male sexual contact with males (MSM)) were significantly associated with lower retention, but unrelated with cART or VS. MSM (RR=0.96) significantly decreased the probability of cART compared with heterosexual transmission.HIV Care Continuum outcomes improved over time in Latin America, though disparities for vulnerable groups remain. Efforts must be made to increase retention, cART and VS, while engaging in additional research to sustain progress in these settings.

  View details for DOI 10.7448/IAS.19.1.20636

  View details for Web of Science ID 000376174300001

  View details for PubMedID 27065108

  View details for PubMedCentralID PMC4827101

• CD4 Response Up to 5 Years After Combination Antiretroviral Therapy in Human Immunodeficiency Virus-Infected Patients in Latin America and the Caribbean OPEN FORUM INFECTIOUS DISEASES Luz, P. M., Belaunzaran-Zamudio, P. F., Crabtree-Ramirez, B., Caro-Vega, Y., Hoces, D., Rebeiro, P. F., Blevins, M., Pape, J. W., Cortes, C. P., Padgett, D., Cahn, P., Veloso, V. G., McGowan, C. C., Grinsztejn, B., Shepherd, B. E., Carribbean Cent South Amer Network 2015; 2 (2): ofv079

  Abstract

  We describe CD4 counts at 6-month intervals for 5 years after combination antiretroviral therapy initiation among 12 879 antiretroviral-naive human immunodeficiency virus-infected adults from Latin America and the Caribbean. Median CD4 counts increased from 154 cells/mm(3) at baseline (interquartile range [IQR], 60-251) to 413 cells/mm(3) (IQR, 234-598) by year 5.

  View details for DOI 10.1093/ofid/ofv079

  View details for Web of Science ID 000365786200030

  View details for PubMedID 26180829

  View details for PubMedCentralID PMC4498272