Sofia Elena Luna

All Publications

• Enhancement of erythropoietic output by Cas9-mediated insertion of a natural variant in haematopoietic stem and progenitor cells. Nature biomedical engineering Luna, S. E., Camarena, J., Hampton, J. P., Majeti, K. R., Charlesworth, C. T., Soupene, E., Selvaraj, S., Jia, K., Sheehan, V. A., Cromer, M. K., Porteus, M. H. 2024

  Abstract

  Some gene polymorphisms can lead to monogenic diseases, whereas other polymorphisms may confer beneficial traits. A well-characterized example is congenital erythrocytosis-the non-pathogenic hyper-production of red blood cells-that is caused by a truncated erythropoietin receptor. Here we show that Cas9-mediated genome editing in CD34+ human haematopoietic stem and progenitor cells (HSPCs) can recreate the truncated form of the erythropoietin receptor, leading to substantial increases in erythropoietic output. We also show that combining the expression of the cDNA of a truncated erythropoietin receptor with a previously reported genome-editing strategy to fully replace the HBA1 gene with an HBB transgene in HSPCs (to restore normal haemoglobin production in cells with a β-thalassaemia phenotype) gives the edited HSPCs and the healthy red blood cell phenotype a proliferative advantage. Combining knowledge of human genetics with precise genome editing to insert natural human variants into therapeutic cells may facilitate safer and more effective genome-editing therapies for patients with genetic diseases.

  View details for DOI 10.1038/s41551-024-01222-6

  View details for PubMedID 38886504

  View details for PubMedCentralID 46538

• A simultaneous knockout knockin genome editing strategy in HSPCs potently inhibits CCR5- and CXCR4-tropic HIV-1 infection. Cell stem cell Dudek, A. M., Feist, W. N., Sasu, E. J., Luna, S. E., Ben-Efraim, K., Bak, R. O., Cepika, A. M., Porteus, M. H. 2024; 31 (4): 499-518.e6

  Abstract

  Allogeneic hematopoietic stem and progenitor cell transplant (HSCT) of CCR5 null (CCR5Δ32) cells can be curative for HIV-1-infected patients. However, because allogeneic HSCT poses significant risk, CCR5Δ32 matched bone marrow donors are rare, and CCR5Δ32 transplant does not confer resistance to the CXCR4-tropic virus, it is not a viable option for most patients. We describe a targeted Cas9/AAV6-based genome editing strategy for autologous HSCT resulting in both CCR5- and CXCR4-tropic HIV-1 resistance. Edited human hematopoietic stem and progenitor cells (HSPCs) maintain multi-lineage repopulation capacity in vivo, and edited primary human T cells potently inhibit infection by both CCR5-tropic and CXCR4-tropic HIV-1. Modification rates facilitated complete loss of CCR5-tropic replication and up to a 2,000-fold decrease in CXCR4-tropic replication without CXCR4 locus disruption. This multi-factor editing strategy in HSPCs could provide a broad approach for autologous HSCT as a functional cure for both CCR5-tropic and CXCR4-tropic HIV-1 infections.

  View details for DOI 10.1016/j.stem.2024.03.002

  View details for PubMedID 38579682

• Factors Influencing Parental Willingness to Consent to a Survey Study for Patients in the Pediatric Emergency Department. Pediatric emergency care Fischer, K., Smith, G. B., Luna, S. E., Jamro-Comer, E., Leupold, O., Ahmed, H., Govindji, S., Ahmad, F. 2024

  Abstract

  To identify factors that impact parental willingness to consent to research studies conducted for their children during visits to pediatric emergency departments (EDs).Parents and guardians of children receiving care in our pediatric ED were approached and asked if they would be willing to let their child participate in a research study requiring the child to complete an electronic questionnaire. No such questionnaire existed, however, because the primary purpose was to ascertain the parent's willingness to let their child participate. All parents were debriefed and informed of the true purpose of the study and asked to complete a survey themselves to help understand factors that influenced their initial decision of whether to consent. Bivariate tests and logistic regression were used to evaluate unadjusted and adjusted associations between parent and patient characteristics and parental consent decision.We approached 431 eligible parents about the hypothetical research study involving their children, and 386 (89.6%) consented for their children to participate. After the debriefing, 392 (91.0%) parents consented to complete the parental survey. We observed statistically significant associations between shorter length of ED stay to approach for consent for the study (P = 0.048) as well as longer travel time (P = 0.03) and willingness to consent in bivariate analysis, though this did not hold in regression analysis. Regression analysis revealed parents of children who have previously participated in research had 79 times lower odds of consenting to participate in our study adjusted for parent race, ethnicity, actual and perceived length of stay, traveltime to the ED, and altruism.A high proportion of parents consented to their child participating in research in our ED with previous child participation in research being associated with lower odds of parental consent even when adjusted for other factors. Our findings may inform future research practices and studies investigating parental perceptions and motivations surrounding research studies.

  View details for DOI 10.1097/PEC.0000000000003126

  View details for PubMedID 38412522

• Using Inducible Signaling Receptors to Increase Erythropoietic Output from Genome-Edited Hematopoietic Stem Cells Majeti, K. R., Shah, A. P., Luna, S. E., Soupene, E., Chu, S. N., Sharma, D., Porteus, M., Cromer, K. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-189791

  View details for Web of Science ID 001159740304238

• Using Human Genetics to Develop Strategies to Increase Erythropoietic Output from Genome-Edited Hematopoietic Stem and Progenitor Cells Luna, S. E., Camarena, J., Hampton, J. P., Majeti, K. R., Charlesworth, C. T., Soupene, E., Sheehan, V. A., Cromer, K., Porteus, M. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-174170

  View details for Web of Science ID 001159900800204

• High-efficiency transgene integration by homology-directed repair in human primary cells using DNA-PKcs inhibition. Nature biotechnology Selvaraj, S., Feist, W. N., Viel, S., Vaidyanathan, S., Dudek, A. M., Gastou, M., Rockwood, S. J., Ekman, F. K., Oseghale, A. R., Xu, L., Pavel-Dinu, M., Luna, S. E., Cromer, M. K., Sayana, R., Gomez-Ospina, N., Porteus, M. H. 2023

  Abstract

  Therapeutic applications of nuclease-based genome editing would benefit from improved methods for transgene integration via homology-directed repair (HDR). To improve HDR efficiency, we screened six small-molecule inhibitors of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a key protein in the alternative repair pathway of non-homologous end joining (NHEJ), which generates genomic insertions/deletions (INDELs). From this screen, we identified AZD7648 as the most potent compound. The use of AZD7648 significantly increased HDR (up to 50-fold) and concomitantly decreased INDELs across different genomic loci in various therapeutically relevant primary human cell types. In all cases, the ratio of HDR to INDELs markedly increased, and, in certain situations, INDEL-free high-frequency (>50%) targeted integration was achieved. This approach has the potential to improve the therapeutic efficacy of cell-based therapies and broaden the use of targeted integration as a research tool.

  View details for DOI 10.1038/s41587-023-01888-4

  View details for PubMedID 37537500

  View details for PubMedCentralID 3694601

• Engineering Human Hematopoietic Stem and Progenitor Cells for Lineage-Specific Expression of Galactocerebrosidase Using Genome Editing Amorin, N. A., Golden, L., Poletto, E., Johnston, N., Feist, W., Menezes, T., Kikuta, K., Luna, S., Charlton, C., Kashuv, T., Gomez-Ospina, N. CELL PRESS. 2023: 782

  View details for Web of Science ID 001045144203407

• Establishing Multilayered Genetic Resistance to HIV-1 by Engineering Hematopoietic Stem and Progenitor Cells for B Cell Specific Secretion of Therapeutic Antibodies Feist, W., Luna, S., Ben-Efraim, K., Interrante, M., Amorin, N. A., Johnston, N., Dudek, A., Porteus, M. H. CELL PRESS. 2023: 115-116

  View details for Web of Science ID 001045144200214

• Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis. Nature Weinstock, J. S., Gopakumar, J., Burugula, B. B., Uddin, M. M., Jahn, N., Belk, J. A., Bouzid, H., Daniel, B., Miao, Z., Ly, N., Mack, T. M., Luna, S. E., Prothro, K. P., Mitchell, S. R., Laurie, C. A., Broome, J. G., Taylor, K. D., Guo, X., Sinner, M. F., von Falkenhausen, A. S., Kääb, S., Shuldiner, A. R., O'Connell, J. R., Lewis, J. P., Boerwinkle, E., Barnes, K. C., Chami, N., Kenny, E. E., Loos, R. J., Fornage, M., Hou, L., Lloyd-Jones, D. M., Redline, S., Cade, B. E., Psaty, B. M., Bis, J. C., Brody, J. A., Silverman, E. K., Yun, J. H., Qiao, D., Palmer, N. D., Freedman, B. I., Bowden, D. W., Cho, M. H., DeMeo, D. L., Vasan, R. S., Yanek, L. R., Becker, L. C., Kardia, S. L., Peyser, P. A., He, J., Rienstra, M., Van der Harst, P., Kaplan, R., Heckbert, S. R., Smith, N. L., Wiggins, K. L., Arnett, D. K., Irvin, M. R., Tiwari, H., Cutler, M. J., Knight, S., Muhlestein, J. B., Correa, A., Raffield, L. M., Gao, Y., de Andrade, M., Rotter, J. I., Rich, S. S., Tracy, R. P., Konkle, B. A., Johnsen, J. M., Wheeler, M. M., Smith, J. G., Melander, O., Nilsson, P. M., Custer, B. S., Duggirala, R., Curran, J. E., Blangero, J., McGarvey, S., Williams, L. K., Xiao, S., Yang, M., Gu, C. C., Chen, Y. I., Lee, W. J., Marcus, G. M., Kane, J. P., Pullinger, C. R., Shoemaker, M. B., Darbar, D., Roden, D. M., Albert, C., Kooperberg, C., Zhou, Y., Manson, J. E., Desai, P., Johnson, A. D., Mathias, R. A., Blackwell, T. W., Abecasis, G. R., Smith, A. V., Kang, H. M., Satpathy, A. T., Natarajan, P., Kitzman, J. O., Whitsel, E. A., Reiner, A. P., Bick, A. G., Jaiswal, S. 2023

  Abstract

  Mutations in a diverse set of driver genes increase the fitness of haematopoietic stem cells (HSCs), leading to clonal haematopoiesis1. These lesions are precursors for blood cancers2-6, but the basis of their fitness advantage remains largely unknown, partly owing to a paucity of large cohorts in which the clonal expansion rate has been assessed by longitudinal sampling. Here, to circumvent this limitation, we developed a method to infer the expansion rate from data from a single time point. We applied this method to 5,071 people with clonal haematopoiesis. A genome-wide association study revealed that a common inherited polymorphism in the TCL1A promoter was associated with a slower expansion rate in clonal haematopoiesis overall, but the effect varied by driver gene. Those carrying this protective allele exhibited markedly reduced growth rates or prevalence of clones with driver mutations in TET2, ASXL1, SF3B1 and SRSF2, but this effect was not seen in clones with driver mutations in DNMT3A. TCL1A was not expressed in normal or DNMT3A-mutated HSCs, but the introduction of mutations in TET2 or ASXL1 led to the expression of TCL1A protein and the expansion of HSCs in vitro. The protective allele restricted TCL1A expression and expansion of mutant HSCs, as did experimental knockdown of TCL1A expression. Forced expression of TCL1A promoted the expansion of human HSCs in vitro and mouse HSCs in vivo. Our results indicate that the fitness advantage of several commonly mutated driver genes in clonal haematopoiesis may be mediated by TCL1A activation.

  View details for DOI 10.1038/s41586-023-05806-1

  View details for PubMedID 37046083

  View details for PubMedCentralID 4624443