Felix Horns

All Publications

• Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses. Science (New York, N.Y.) Shrock, E. L., Timms, R. T., Kula, T., Mena, E. L., West, A. P., Guo, R., Lee, I., Cohen, A. A., McKay, L. G., Bi, C., Leng, Y., Fujimura, E., Horns, F., Li, M., Wesemann, D. R., Griffiths, A., Gewurz, B. E., Bjorkman, P. J., Elledge, S. J. 2023; 380 (6640): eadc9498

  Abstract

  Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 immunodominant "public epitopes" at high resolution and characterizing several of their cognate antibodies, we concluded that germline-encoded sequences in antibodies drive recurrent recognition. Systematic analysis of antibody-antigen structures uncovered 18 human and 21 partially overlapping mouse germline-encoded amino acid-binding (GRAB) motifs within heavy and light V gene segments that in case studies proved critical for public epitope recognition. GRAB motifs represent a fundamental component of the immune system's architecture that promotes recognition of pathogens and leads to species-specific public antibody responses that can exert selective pressure on pathogens.

  View details for DOI 10.1126/science.adc9498

  View details for PubMedID 37023193

• Lineage tracing reveals fate bias and transcriptional memory in human B cells. Life science alliance Swift, M., Horns, F., Quake, S. R. 2023; 6 (3)

  Abstract

  We combined single-cell transcriptomics and lineage tracing to understand fate choice in human B cells. Using the antibody sequences of B cells, we tracked clones during in vitro differentiation. Clonal analysis revealed a subset of IgM+ B cells which were more proliferative than other B-cell types. Whereas the population of B cells adopted diverse states during differentiation, clones had a restricted set of fates available to them; there were two times more single-fate clones than expected given population-level cell-type diversity. This implicated a molecular memory of initial cell states that was propagated through differentiation. We then identified the genes which had strongest coherence within clones. These genes significantly overlapped known B-cell fate determination programs, suggesting the genes which determine cell identity are most robustly controlled on a clonal level. Persistent clonal identities were also observed in human plasma cells from bone marrow, indicating that these transcriptional programs maintain long-term cell identities in vivo. Thus, we show how cell-intrinsic fate bias influences differentiation outcomes in vitro and in vivo.

  View details for DOI 10.26508/lsa.202201792

  View details for PubMedID 36639222

• Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science (New York, N.Y.) Li, H., Janssens, J., De Waegeneer, M., Kolluru, S. S., Davie, K., Gardeux, V., Saelens, W., David, F. P., Brbic, M., Spanier, K., Leskovec, J., McLaughlin, C. N., Xie, Q., Jones, R. C., Brueckner, K., Shim, J., Tattikota, S. G., Schnorrer, F., Rust, K., Nystul, T. G., Carvalho-Santos, Z., Ribeiro, C., Pal, S., Mahadevaraju, S., Przytycka, T. M., Allen, A. M., Goodwin, S. F., Berry, C. W., Fuller, M. T., White-Cooper, H., Matunis, E. L., DiNardo, S., Galenza, A., O'Brien, L. E., Dow, J. A., FCA Consortium, Jasper, H., Oliver, B., Perrimon, N., Deplancke, B., Quake, S. R., Luo, L., Aerts, S., Agarwal, D., Ahmed-Braimah, Y., Arbeitman, M., Ariss, M. M., Augsburger, J., Ayush, K., Baker, C. C., Banisch, T., Birker, K., Bodmer, R., Bolival, B., Brantley, S. E., Brill, J. A., Brown, N. C., Buehner, N. A., Cai, X. T., Cardoso-Figueiredo, R., Casares, F., Chang, A., Clandinin, T. R., Crasta, S., Desplan, C., Detweiler, A. M., Dhakan, D. B., Dona, E., Engert, S., Floc'hlay, S., George, N., Gonzalez-Segarra, A. J., Groves, A. K., Gumbin, S., Guo, Y., Harris, D. E., Heifetz, Y., Holtz, S. L., Horns, F., Hudry, B., Hung, R., Jan, Y. N., Jaszczak, J. S., Jefferis, G. S., Karkanias, J., Karr, T. L., Katheder, N. S., Kezos, J., Kim, A. A., Kim, S. K., Kockel, L., Konstantinides, N., Kornberg, T. B., Krause, H. M., Labott, A. T., Laturney, M., Lehmann, R., Leinwand, S., Li, J., Li, J. S., Li, K., Li, K., Li, L., Li, T., Litovchenko, M., Liu, H., Liu, Y., Lu, T., Manning, J., Mase, A., Matera-Vatnick, M., Matias, N. R., McDonough-Goldstein, C. E., McGeever, A., McLachlan, A. D., Moreno-Roman, P., Neff, N., Neville, M., Ngo, S., Nielsen, T., O'Brien, C. E., Osumi-Sutherland, D., Ozel, M. N., Papatheodorou, I., Petkovic, M., Pilgrim, C., Pisco, A. O., Reisenman, C., Sanders, E. N., Dos Santos, G., Scott, K., Sherlekar, A., Shiu, P., Sims, D., Sit, R. V., Slaidina, M., Smith, H. E., Sterne, G., Su, Y., Sutton, D., Tamayo, M., Tan, M., Tastekin, I., Treiber, C., Vacek, D., Vogler, G., Waddell, S., Wang, W., Wilson, R. I., Wolfner, M. F., Wong, Y. E., Xie, A., Xu, J., Yamamoto, S., Yan, J., Yao, Z., Yoda, K., Zhu, R., Zinzen, R. P. 2022; 375 (6584): eabk2432

  Abstract

  For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

  View details for DOI 10.1126/science.abk2432

  View details for PubMedID 35239393

• Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons. eLife Xie, Q., Brbic, M., Horns, F., Kolluru, S. S., Jones, R. C., Li, J., Reddy, A. R., Xie, A., Kohani, S., Li, Z., McLaughlin, C. N., Li, T., Xu, C., Vacek, D., Luginbuhl, D. J., Leskovec, J., Quake, S. R., Luo, L., Li, H. 2021; 10

  Abstract

  Neurons undergo substantial morphological and functional changes during development to form precise synaptic connections and acquire specific physiological properties. What are the underlying transcriptomic bases? Here, we obtained the single-cell transcriptomes of Drosophila olfactory projection neurons (PNs) at four developmental stages. We decoded the identity of 21 transcriptomic clusters corresponding to 20 PN types and developed methods to match transcriptomic clusters representing the same PN type across development. We discovered that PN transcriptomes reflect unique biological processes unfolding at each stage-neurite growth and pruning during metamorphosis at an early pupal stage; peaked transcriptomic diversity during olfactory circuit assembly at mid-pupal stages; and neuronal signaling in adults. At early developmental stages, PN types with adjacent birth order share similar transcriptomes. Together, our work reveals principles of cellular diversity during brain development and provides a resource for future studies of neural development in PNs and other neuronal types.

  View details for DOI 10.7554/eLife.63450

  View details for PubMedID 33427646

• Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila. eLife McLaughlin, C. N., Brbić, M. n., Xie, Q. n., Li, T. n., Horns, F. n., Kolluru, S. S., Kebschull, J. M., Vacek, D. n., Xie, A. n., Li, J. n., Jones, R. C., Leskovec, J. n., Quake, S. R., Luo, L. n., Li, H. n. 2021; 10

  Abstract

  Recognition of environmental cues is essential for the survival of all organisms. Transcriptional changes occur to enable the generation and function of the neural circuits underlying sensory perception. To gain insight into these changes, we generated single-cell transcriptomes of Drosophila olfactory- (ORNs), thermo-, and hygro-sensory neurons at an early developmental and adult stage using single-cell and single-nucleus RNA sequencing. We discovered that ORNs maintain expression of the same olfactory receptors across development. Using receptor expression and computational approaches, we matched transcriptomic clusters corresponding to anatomically and physiologically defined neuron types across multiple developmental stages. We found that cell-type-specific transcriptomes partly reflected axon trajectory choices in development and sensory modality in adults. We uncovered stage-specific genes that could regulate the wiring and sensory responses of distinct ORN types. Collectively, our data reveal transcriptomic features of sensory neuron biology and provide a resource for future studies of their development and physiology.

  View details for DOI 10.7554/eLife.63856

  View details for PubMedID 33555999

• Memory B Cell Activation, Broad Anti-influenza Antibodies, and Bystander Activation Revealed by Single-Cell Transcriptomics. Cell reports Horns, F., Dekker, C. L., Quake, S. R. 2020; 30 (3): 905

  Abstract

  Antibody memory protects humans from many diseases. Protective antibody memory responses require activation of transcriptional programs, cell proliferation, and production of antigen-specific antibodies, but how these aspects of the response are coordinated is poorly understood. We profile the molecular and cellular features of the antibody response to influenza vaccination by integrating single-cell transcriptomics, longitudinal antibody repertoire sequencing, and antibody binding measurements. Single-cell transcriptional profiling reveals a program of memory B cell activation characterized by CD11c and T-bet expression associated with clonal expansion and differentiation toward effector function. Vaccination elicits an antibody clone, which rapidly acquired broad high-affinity hemagglutinin binding during affinity maturation. Unexpectedly, many antibody clones elicited by vaccination do not bind vaccine, demonstrating non-specific activation of bystander antibodies by influenza vaccination. These results offer insight into how molecular recognition, transcriptional programs, and clonal proliferation are coordinated in the human B cell repertoire during memory recall.

  View details for DOI 10.1016/j.celrep.2019.12.063

  View details for PubMedID 31968262

• Single-Cell Transcriptomes Reveal Diverse Regulatory Strategies for Olfactory Receptor Expression and Axon Targeting. Current biology : CB Li, H. n., Li, T. n., Horns, F. n., Li, J. n., Xie, Q. n., Xu, C. n., Wu, B. n., Kebschull, J. M., McLaughlin, C. N., Kolluru, S. S., Jones, R. C., Vacek, D. n., Xie, A. n., Luginbuhl, D. J., Quake, S. R., Luo, L. n. 2020

  Abstract

  The regulatory mechanisms by which neurons coordinate their physiology and connectivity are not well understood. The Drosophila olfactory receptor neurons (ORNs) provide an excellent system to investigate this question. Each ORN type expresses a unique olfactory receptor, or a combination thereof, and sends their axons to a stereotyped glomerulus. Using single-cell RNA sequencing, we identified 33 transcriptomic clusters for ORNs and mapped 20 to their glomerular types, demonstrating that transcriptomic clusters correspond well with anatomically and physiologically defined ORN types. Each ORN type expresses hundreds of transcription factors. Transcriptome-instructed genetic analyses revealed that (1) one broadly expressed transcription factor (Acj6) only regulates olfactory receptor expression in one ORN type and only wiring specificity in another type, (2) one type-restricted transcription factor (Forkhead) only regulates receptor expression, and (3) another type-restricted transcription factor (Unplugged) regulates both events. Thus, ORNs utilize diverse strategies and complex regulatory networks to coordinate their physiology and connectivity.

  View details for DOI 10.1016/j.cub.2020.01.049

  View details for PubMedID 32059767

• Cloning antibodies from single cells in pooled sequence libraries by selective PCR. PloS one Horns, F., Quake, S. R. 2020; 15 (8): e0236477

  Abstract

  Antibodies function by binding to antigens. Antibodies must be cloned and expressed to determine their binding characteristics, but current methods for high-throughput antibody sequencing yield antibody DNA pooled from many cells and do not readily permit cloning of antibodies from single B cells. We present a strategy for retrieving and cloning antibody DNA from single cells within a pooled library of cells. Our strategy, called selective PCR for antibody retrieval (SPAR), takes advantage of the unique sequence barcodes attached to individual cDNA molecules during sample preparation to enable specific amplification by PCR of antibody heavy- and light-chain cDNA originating from a single cell. We show through computational analysis that most human antibodies sequenced using typical high-throughput methods can be retrieved using SPAR, and experimentally demonstrate retrieval of full-length antibody variable region cDNA from three cells within pools of ~5,000 cells. SPAR enables rapid low-cost cloning and expression of native human antibodies from pooled single-cell sequence libraries for functional characterization.

  View details for DOI 10.1371/journal.pone.0236477

  View details for PubMedID 32756607

• Signatures of selection in the human antibody repertoire: Selective sweeps, competing subclones, and neutral drift PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Horns, F., Vollmers, C., Dekker, C. L., Quake, S. R. 2019; 116 (4): 1261–66

  View details for DOI 10.1073/pnas.1814213116

  View details for Web of Science ID 000456336100030

• Signatures of selection in the human antibody repertoire: Selective sweeps, competing subclones, and neutral drift. Proceedings of the National Academy of Sciences of the United States of America Horns, F., Vollmers, C., Dekker, C. L., Quake, S. R. 2019

  Abstract

  Antibodies are created and refined by somatic evolution in B cell populations, which endows the human immune system with the ability to recognize and eliminate diverse pathogens. However, the evolutionary processes that sculpt antibody repertoires remain poorly understood. Here, using an unbiased repertoire-scale approach, we show that the population genetic signatures of evolution are evident in human B cell lineages and reveal how antibodies evolve somatically. We measured the dynamics and genetic diversity of B cell responses in five adults longitudinally before and after influenza vaccination using high-throughput antibody repertoire sequencing. We identified vaccine-responsive B cell lineages that carry signatures of selective sweeps driven by positive selection, and discovered that they often display evidence for selective sweeps favoring multiple subclones. We also found persistent B cell lineages that exhibit stable population dynamics and carry signatures of neutral drift. By exploiting the relationship between B cell fitness and antibody binding affinity, we demonstrate the potential for using phylogenetic approaches to identify antibodies with high binding affinity. This quantitative characterization reveals that antibody repertoires are shaped by an unexpectedly broad spectrum of evolutionary processes and shows how signatures of evolutionary history can be harnessed for antibody discovery and engineering.

  View details for PubMedID 30622180

• Massive Expansion of Gypsy-Like Retrotransposons in Microbotryum Fungi GENOME BIOLOGY AND EVOLUTION Horns, F., Petit, E., Hood, M. E. 2017; 9 (2): 363-371

  View details for DOI 10.1093/gbe/evx011

  View details for Web of Science ID 000396058400013

  View details for PubMedID 28164239

• Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing. Cell Li, H. n., Horns, F. n., Wu, B. n., Xie, Q. n., Li, J. n., Li, T. n., Luginbuhl, D. J., Quake, S. R., Luo, L. n. 2017; 171 (5): 1206–20.e22

  Abstract

  The definition of neuronal type and how it relates to the transcriptome are open questions. Drosophila olfactory projection neurons (PNs) are among the best-characterized neuronal types: different PN classes target dendrites to distinct olfactory glomeruli, while PNs of the same class exhibit indistinguishable anatomical and physiological properties. Using single-cell RNA sequencing, we comprehensively characterized the transcriptomes of most PN classes and unequivocally mapped transcriptomes to specific olfactory function for six classes. Transcriptomes of closely related PN classes exhibit the largest differences during circuit assembly but become indistinguishable in adults, suggesting that neuronal subtype diversity peaks during development. Transcription factors and cell-surface molecules are the most differentially expressed genes between classes and are highly informative in encoding cell identity, enabling us to identify a new lineage-specific transcription factor that instructs PN dendrite targeting. These findings establish that neuronal transcriptomic identity corresponds with anatomical and physiological identity defined by connectivity and function.

  View details for PubMedID 29149607

• Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching ELIFE Horns, F., Vollmers, C., Croote, D., Mackey, S. F., Swan, G. E., Dekker, C. L., Davis, M. M., Quake, S. R. 2016; 5

  View details for DOI 10.7554/eLife.16578

  View details for Web of Science ID 000380927400001

• Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching. eLife Horns, F., Vollmers, C., Croote, D., Mackey, S. F., Swan, G. E., Dekker, C. L., Davis, M. M., Quake, S. R. 2016; 5

  Abstract

  Antibody class switching is a feature of the adaptive immune system which enables diversification of the effector properties of antibodies. Even though class switching is essential for mounting a protective response to pathogens, the in vivo patterns and lineage characteristics of antibody class switching have remained uncharacterized in living humans. Here we comprehensively measured the landscape of antibody class switching in human adult twins using antibody repertoire sequencing. The map identifies how antibodies of every class are created and delineates a two-tiered hierarchy of class switch pathways. Using somatic hypermutations as a molecular clock, we discovered that closely related B cells often switch to the same class, but lose coherence as somatic mutations accumulate. Such correlations between closely related cells exist when purified B cells class switch in vitro, suggesting that class switch recombination is directed toward specific isotypes by a cell-autonomous imprinted state.

  View details for DOI 10.7554/eLife.16578

  View details for PubMedID 27481325

  View details for PubMedCentralID PMC4970870