Alma-Martina Cepika

All Publications

• 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

• Epigenetic signature and key transcriptional regulators of human antigen-specific type 1 regulatory T cells Biorxiv Cepika, A., Amaya, L., Waichler, C., Narula, M., Mantilla, M. M., Thomas, B. C., Chen, P. P., Freeborn, R. A., Pavel-Dinu, M., Nideffer, J. F., Porteus, M., Bacchetta, R., Muller, F., Greenleaf, W. J., Chang, H. Y., Roncarolo, M. 2024

  View details for DOI 10.1101/2024.03.07.582969

• T-ALLO10 INFUSION AFTER A.DEPLETED-HSCT IN CHILDREN AND YOUNG ADULTS WITH HEMATOLOGIC MALIGNANCIES: IMPROVED IMMUNE RECONSTITUTION IN THE ABSENCE OF SEVERE GVHD Bertaina, A., Bacchetta, R., Shyr, D., Saini, G., Lee, J., Kristovich, K., Agarwal-Hashmi, R., Klein, O., Melsop, K., Tate, K., Barbarito, G., Oppizzi, L., Chen, P., Cepika, A., Roncarolo, M. SPRINGERNATURE. 2023: 232-234

  View details for Web of Science ID 001110902800295

• AML/T cell interactomics uncover correlates of patient outcomes and the key role of ICAM1 in T cell killing of AML. bioRxiv : the preprint server for biology Sayitoglu, E. C., Luca, B. A., Boss, A. P., Thomas, B. C., Freeborn, R. A., Uyeda, M. J., Chen, P. P., Nakauchi, Y., Waichler, C., Lacayo, N., Bacchetta, R., Majeti, R., Gentles, A. J., Cepika, A. M., Roncarolo, M. G. 2023

  Abstract

  T cells are important for the control of acute myeloid leukemia (AML), a common and often deadly malignancy. We observed that some AML patient samples are resistant to killing by human engineered cytotoxic CD4 + T cells. Single-cell RNA-seq of primary AML samples and CD4 + T cells before and after their interaction uncovered transcriptional programs that correlate with AML sensitivity or resistance to CD4 + T cell killing. Resistance-associated AML programs were enriched in AML patients with poor survival, and killing-resistant AML cells did not engage T cells in vitro . Killing-sensitive AML potently activated T cells before being killed, and upregulated ICAM1 , a key component of the immune synapse with T cells. Without ICAM1, killing-sensitive AML became resistant to killing to primary ex vivo -isolated CD8 + T cells in vitro , and engineered CD4 + T cells in vitro and in vivo . Thus, ICAM1 on AML acts as an immune trigger, allowing T cell killing, and could affect AML patient survival in vivo .AML is a common leukemia with sub-optimal outcomes. We show that AML transcriptional programs correlate with susceptibility to T cell killing. Killing resistance-associated AML programs are enriched in patients with poor survival. Killing-sensitive, but not resistant AML activate T cells and upregulate ICAM1 that binds to LFA-1 on T cells, allowing immune synapse formation which is critical for AML elimination.

  View details for DOI 10.1101/2023.09.21.558911

  View details for PubMedID 37790561

  View details for PubMedCentralID PMC10542521

• Therapeutics and Diagnostics Discovery: Cell and Gene Therapy A Practical Guide to Drug Development in Academia Roncarolo, M., Cepika, A., Bacchetta, R. Springer Cham. 2023; 2: 75-81

  View details for DOI 10.1007/978-3-031-34724-5_2

• Alloantigen-specific type 1 regulatory T cells suppress through CTLA-4 and PD-1 pathways and persist long-term in patients. Science translational medicine Chen, P. P., Cepika, A., Agarwal-Hashmi, R., Saini, G., Uyeda, M. J., Louis, D. M., Cieniewicz, B., Narula, M., Amaya Hernandez, L. C., Harre, N., Xu, L., Thomas, B. C., Ji, X., Shiraz, P., Tate, K. M., Margittai, D., Bhatia, N., Meyer, E., Bertaina, A., Davis, M. M., Bacchetta, R., Roncarolo, M. G. 2021; 13 (617): eabf5264

  Abstract

  [Figure: see text].

  View details for DOI 10.1126/scitranslmed.abf5264

  View details for PubMedID 34705520

• Tregopathies: Monogenic diseases resulting in regulatory T-cell deficiency. The Journal of allergy and clinical immunology Cepika, A., Sato, Y., Liu, J. M., Uyeda, M. J., Bacchetta, R., Roncarolo, M. G. 2018; 142 (6): 1679–95

  Abstract

  Monogenic diseases of the immune system, also known as inborn errors of immunity, are caused by single-gene mutations resulting in immune deficiency and dysregulation. More than 350 diseases have been described to date, and the number is rapidly expanding, with increasing availability of next-generation sequencing facilitating the diagnosis. The spectrum of immune dysregulation is wide, encompassing deficiencies in humoral, cellular, innate, and adaptive immunity; phagocytosis; and the complement system, which lead to autoinflammation and autoimmunity. Multiorgan autoimmunity is a dominant symptom when genetic mutations lead to defects in molecules essential for the development, survival, and/or function of regulatory T (Treg) cells. Studies of "Tregopathies" are providing critical mechanistic information on Treg cell biology, the role of Treg cell-associated molecules, and regulation of peripheral tolerance in human subjects. The pathogenic immune networks underlying these diseases need to be dissected to apply and develop immunomodulatory treatments and design curative treatments using cell and gene therapy. Here we review the pathogenetic mechanisms, clinical presentation, diagnosis, and current and future treatments of major known Tregopathies caused by mutations in FOXP3, CD25, cytotoxic Tlymphocyte-associated antigen 4 (CTLA4), LPS-responsive and beige-like anchor protein (LRBA), and BTB domain and CNC homolog 2 (BACH2) and gain-of-function mutations in signal transducer and activator oftranscription 3 (STAT3). We also discuss deficiencies in genesencoding STAT5b and IL-10 or IL-10 receptor aspotential Tregopathies.

  View details for DOI 10.1016/j.jaci.2018.10.026

  View details for PubMedID 30527062

• A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis JOURNAL OF EXPERIMENTAL MEDICINE Cepika, A., Banchereau, R., Segura, E., Ohouo, M., Cantarel, B., Goller, K., Cantrell, V., Ruchaud, E., Gatewood, E., Phuong Nguyen, Gu, J., Anguiano, E., Zurawski, S., Baisch, J. M., Punaro, M., Baldwin, N., Obermoser, G., Palucka, K., Banchereau, J., Amigorena, S., Pascual, V. 2017; 214 (11): 3449–66

  Abstract

  The etiology of sporadic human chronic inflammatory diseases remains mostly unknown. To fill this gap, we developed a strategy that simultaneously integrates blood leukocyte responses to innate stimuli at the transcriptional, cellular, and secreted protein levels. When applied to systemic juvenile idiopathic arthritis (sJIA), an autoinflammatory disease of unknown etiology, this approach identified gene sets associated with specific cytokine environments and activated leukocyte subsets. During disease remission and off treatment, sJIA patients displayed dysregulated responses to TLR4, TLR8, and TLR7 stimulation. Isolated sJIA monocytes underexpressed the IL-1 inhibitor aryl hydrocarbon receptor (AHR) at baseline and accumulated higher levels of intracellular IL-1β after stimulation. Supporting the demonstration that AHR down-regulation skews monocytes toward macrophage differentiation, sJIA monocytes differentiated in vitro toward macrophages, away from the dendritic cell phenotype. This might contribute to the increased incidence of macrophage activation syndrome in these patients. Integrated analysis of high-dimensional data can thus unravel immune alterations predisposing to complex inflammatory diseases.

  View details for PubMedID 28935693

  View details for PubMedCentralID PMC5679164

• Epigenetic Profiling of PTPN11 Mutant JMML Hematopoietic Stem and Progenitor Cells Reveals an Aberrant Histone Landscape. Cancers Sinha, R., Dvorak, M., Ganesan, A., Kalesinskas, L., Niemeyer, C. M., Flotho, C., Sakamoto, K. M., Lacayo, N., Patil, R. V., Perriman, R., Cepika, A. M., Liu, Y. L., Kuo, A., Utz, P. J., Khatri, P., Bertaina, A. 2023; 15 (21)

  Abstract

  Juvenile myelomonocytic leukemia (JMML) is a deadly pediatric leukemia driven by RAS pathway mutations, of which >35% are gain-of-function in PTPN11. Although DNA hypermethylation portends severe clinical phenotypes, the landscape of histone modifications and chromatin profiles in JMML patient cells have not been explored. Using global mass cytometry, Epigenetic Time of Flight (EpiTOF), we analyzed hematopoietic stem and progenitor cells (HSPCs) from five JMML patients with PTPN11 mutations. These data revealed statistically significant changes in histone methylation, phosphorylation, and acetylation marks that were unique to JMML HSPCs when compared with healthy controls. Consistent with these data, assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis revealed significant alterations in chromatin profiles at loci encoding post-translational modification enzymes, strongly suggesting their mis-regulated expression. Collectively, this study reveals histone modification pathways as an additional epigenetic abnormality in JMML patient HSPCs, thereby uncovering a new family of potential druggable targets for the treatment of JMML.

  View details for DOI 10.3390/cancers15215204

  View details for PubMedID 37958378

• Discovery of Key Transcriptional Regulators of Alloantigen-Inducible Tregs Used for Cell Therapy Cepika, A., Amaya, L., Waichler, C., Narula, M., Thomas, B. C., Chen, P. P., Mantilla, M. M., Pavel-Dinu, M., Freeborn, R., Porteus, M. H., Bacchetta, R., Mueller, F., Greenleaf, W. J., Chang, H. Y., Roncarolo, M. CELL PRESS. 2023: 370-371

  View details for Web of Science ID 001045144201371

• SATB1 chromatin loops regulate Megakaryocyte/Erythroid Progenitor Expansion by facilitating HSP70 and GATA1 induction. Stem cells (Dayton, Ohio) Wilkes, M. C., Chae, H. D., Scanlon, V., Cepika, A. M., Wentworth, E. P., Saxena, M., Eskin, A., Chen, Z., Glader, B., Roncarolo, M. G., Nelson, S. F., Sakamoto, K. M. 2023

  Abstract

  Diamond Blackfan Anemia (DBA) is an inherited bone marrow failure syndrome associated with severe anemia, congenital malformations and increased risk of developing cancer. The chromatin-binding SATB1 is downregulated in Megakaryocyte/Erythroid Progenitors (MEPs) in patients and cell models of DBA, leading to a reduction in MEP expansion. Here we demonstrate that SATB1 expression is required for the upregulation of the critical erythroid factors HSP70 and GATA1 that accompanies MEP differentiation. SATB1 binding to specific sites surrounding the HSP70 genes, promotes chromatin loops that are required for induction of HSP70, which in turn promotes GATA1 induction. This demonstrates that SATB1, although gradually downregulated during myelopoiesis, maintains a biological function in early myeloid progenitors.

  View details for DOI 10.1093/stmcls/sxad025

  View details for PubMedID 36987811

• Case report: Refractory Evans syndrome in two patients with spondyloenchondrodysplasia with immune dysregulation treated successfully with JAK1/JAK2 inhibition. Frontiers in immunology Gernez, Y., Narula, M., Cepika, A., Valdes Camacho, J., Hoyte, E. G., Mouradian, K., Glader, B., Singh, D., Sathi, B., Rao, L., Tolin, A. L., Weinberg, K. I., Lewis, D. B., Bacchetta, R., Weinacht, K. G. 2023; 14: 1328005

  Abstract

  Biallelic mutations in the ACP5 gene cause spondyloenchondrodysplasia with immune dysregulation (SPENCDI). SPENCDI is characterized by the phenotypic triad of skeletal dysplasia, innate and adaptive immune dysfunction, and variable neurologic findings ranging from asymptomatic brain calcifications to severe developmental delay with spasticity. Immune dysregulation in SPENCDI is often refractory to standard immunosuppressive treatments. Here, we present the cases of two patients with SPENCDI and recalcitrant autoimmune cytopenias who demonstrated a favorable clinical response to targeted JAK inhibition over a period of more than 3 years. One of the patients exhibited steadily rising IgG levels and a bone marrow biopsy revealed smoldering multiple myeloma. A review of the literature uncovered that approximately half of the SPENCDI patients reported to date exhibited increased IgG levels. Screening for multiple myeloma in SPENCDI patients with rising IgG levels should therefore be considered.

  View details for DOI 10.3389/fimmu.2023.1328005

  View details for PubMedID 38347954

• T-allo10 Infusion after αβ depleted-HSCT in Children and Young Adults with Hematologic Malignancies: Improved Immune Reconstitution in the Absence of Severe GvHD 2023 Tandem Meetings of ASTCT and CIBMTR Bertaina, A., Bacchetta, R., Shyr, D. C., Saini, G., Lee, J., Kristovich, K., Agarwal-Hashmi, R., Klein, O. R., Melsop, K., Tate, K., Barbarito, G., Opizzi, L., Chen, P., Cepika, A., Roncarolo, M. 2023: S209

  View details for DOI 10.1016/S2666-6367(23)00340-8

• Unraveling Transcriptomic Profiles of Pediatric Acute Myeloid Leukemia Cells Sensitive or Resistant to Cytotoxic Killing by Engineered TR1-like Cells Sayitoglu, E., Luca, B., Thomas, B., Cieniewicz, B., Uyeda, M., Chen, P., Cepika, A., Gentles, A., Roncarolo, M. CELL PRESS. 2022: 153

  View details for Web of Science ID 000794043700315

• Downregulation of SATB1 by miRNAs Reduces Megakaryocyte/Erythroid Progenitor Expansion in pre-clinical models of Diamond Blackfan Anemia Experimental Hematology Wilkes, M. C., Scanlon, V., Shibuya, A., Cepika, A., Eskin, A., Chen, Z., Narla, A., Glader, B., Roncarolo, M., Nelson, S. F., Sakamoto, K. M. 2022

  View details for DOI 10.1016/j.exphem.2022.04.005

• 296 - Phase 1/1b Study of T-allo10 Infusion after HLA-Partially Matched αβ depleted-HSCT in Children and Young Adults with Hematologic Malignancies: Preliminary Results 2022 Tandem Meetings of ASTCT and CIBMTR Bertaina, A., Bacchetta, R., Shyr, D. C., Saini, G., Kristovich, K., Agarwal, R., Klein, O., Melsop, K., Tate, K., Barbarito, G., Chen, P., Cepika, A., Roncarolo, M. 2022: S232

  View details for DOI 10.1016/S2666-6367(22)00456-0

• Adoptively Transferred, In Vitro-Generated Alloantigen-Specific Type 1 Regulatory T (Tr1) Cells Persist Long-Term In Vivo Cepika, A., Chen, P. P., Agarwal, R., Saini, G., Louis, D. M., Amaya-Hernandez, L. C., Xu, L., Shiraz, P., Tate, K. M., Margittai, D., Bhatia, N., Meyer, E., Bertaina, A., Davis, M. M., Bacchetta, R., Roncarolo, M. CELL PRESS. 2021: 73

  View details for Web of Science ID 000645188700142

• Engineered Type 1 Regulatory T Cells Have a Cytotoxic Profile and Kill Pediatric Acute Myeloid Leukemia Cells Sayitoglu, E., Uyeda, M., Liu, J. M., Cieniewicz, B., Chen, P., Lacayo, N., Cepika, A., Roncarolo, M. CELL PRESS. 2021: 317

  View details for Web of Science ID 000645188700642

• A case of Spondyloenchondrodysplasia with immune dysregulation presenting as Systemic Lupus Erythematous Camacho, J., Singh, D., Bacchetta, R., Weinberg, K., Cepika, A., Narula, M., Lewis, D. B., Gernez, Y., Weinacht, K. SPRINGER/PLENUM PUBLISHERS. 2021: S18–S19

  View details for Web of Science ID 000639851600028

• Pre-clinical development and molecular characterization of an engineered type 1 regulatory T-cell product suitable for immunotherapy. Cytotherapy Liu, J. M., Chen, P., Uyeda, M. J., Cieniewicz, B., Sayitoglu, E. C., Thomas, B. C., Sato, Y., Bacchetta, R., Cepika, A. M., Roncarolo, M. G. 2021

  Abstract

  Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative therapeutic approach for many hematological disorders. However, allo-HSCT is frequently accompanied by a serious side effect: graft-versus-host disease (GVHD). The clinical use of allo-HSCT is limited by the inability of current immunosuppressive regimens to adequately control GvHD without impairing the graft-versus-leukemia effect (GvL) conferred by transplanted healthy immune cells. To address this, the authors have developed an engineered type 1 regulatory T-cell product called CD4IL-10 cells. CD4IL-10 cells are obtained through lentiviral transduction, which delivers the human IL10 gene into purified polyclonal CD4+ T cells. CD4IL-10 cells may provide an advantage over standard-of-care immunosuppressants because of the ability to suppress GvHD through continuous secretion of IL-10 and enhance the GvL effect in myeloid malignancies through targeted killing of malignant myeloid cells.Here the authors established a production process aimed at current Good Manufacturing Practice (cGMP) production for CD4IL-10 cells.The authors demonstrated that the CD4IL-10 cell product maintains the suppressive and cytotoxic functions of previously described CD4IL-10 cells. In addition, RNA sequencing analysis of CD4IL-10 identified novel transcriptome changes, indicating that CD4IL-10 cells primarily upregulate cytotoxicity-related genes. These include four molecules with described roles in CD8+ T and natural killer cell-mediated cytotoxicity: CD244, KLRD1, KLRC1 and FASLG. Finally, it was shown that CD4IL-10 cells upregulate IL-22, which mediates wound healing and tissue repair, particularly in the gut.Collectively, these results pave the way toward clinical translation of the cGMP-optimized CD4IL-10 cell product and uncover new molecules that have a role in the clinical application of CD4IL-10 cells.

  View details for DOI 10.1016/j.jcyt.2021.05.010

  View details for PubMedID 34404616

• BHLHE40 Regulates IL-10 and IFN-γ Production in T Cells but Does Not Interfere With Human Type 1 Regulatory T Cell Differentiation Frontiers in Immunology Uyeda, M. J., Freeborn, R. A., Cieniewicz, B., Romano, R., Chen, P. P., Liu, J. M., Thomas, B., Lee, E., Cepika, A., Bacchetta, R., Roncarolo, M. 2021

  View details for DOI 10.3389/fimmu.2021.683680

• Engineered Type-1 Regulatory T Cells as Cellular Therapy for Treatment of Immune Mediated Diseases Liu, J. M., Chen, P., Cieniewicz, B., Cepika, A., Bacchetta, R., Roncarolo, M. AMER ASSOC IMMUNOLOGISTS. 2020

  View details for Web of Science ID 000589972400598

• Engineered type 1 regulatory T cells designed for clinical use kill primary pediatric acute myeloid leukemia cells Haematologica Cieniewicz, B., Uyeda, M. J., Chen, P. P., Sayitoglu, E. C., Liu, J. M., Andolfi, G., Greenthal, K., Bertaina, A., Gregori, S., Bacchetta, R., Lacayo, N. J., Cepika, A., Roncarolo, M. 2020

  View details for DOI 10.3324/haematol.2020.263129

• Alloantigen-specific Tr1 cells designed to prevent GvHD have a distinct molecular identity and suppress through CTLA-4 and PD-1 Society for Immunotherapy of Cancer’s (SITC) 35th Anniversary Annual Meeting Cepika, A., Chen, P. P., Uyeda, M. J., Cieniewicz, B., Narula, M., Amaya, L., Louis, D. M., Xu, L., Ji, X., Bertaina, A., Agarwal-Hashmi, R., Davis, M. M., Meyer, E., Bacchetta, R., Roncarolo, M. 2020: A159–A159

  View details for DOI 10.1136/jitc-2020-SITC2020.0146

• Longitudinal profiling of human blood transcriptome in healthy and lupus pregnancy JOURNAL OF EXPERIMENTAL MEDICINE Hong, S., Banchereau, R., Maslow, B. L., Guerra, M. M., Cardenas, J., Baisch, J., Branch, D., Porter, T., Sawitzke, A., Laskin, C. A., Buyon, J. P., Merrill, J., Sammaritano, L. R., Petri, M., Gatewood, E., Cepika, A., Ohouo, M., Obermoser, G., Anguiano, E., Kim, T., Nulsen, J., Nehar-Belaid, D., Mankenship, D., Turner, J., Banchereau, J., Salmon, J. E., Pascual, V. 2019; 216 (5): 1154–69

  View details for DOI 10.1084/jem.20190185

  View details for Web of Science ID 000466981400016

• Engineered Type-1 Regulatory T Cells for Treatment of Graft-versus-Host Disease in Allogeneic Hematopoietic Stem Cell Transplant Recipients Liu, J. H., Chen, P., Cieniewicz, B., Cepika, A., Bacchetta, R., Roncarolo, M. CELL PRESS. 2019: 459

  View details for Web of Science ID 000464381005080

• IL1 Receptor Antagonist Controls Transcriptional Signature of Inflammation in Patients with Metastatic Breast Cancer CANCER RESEARCH Wu, T., Xu, K., Martinek, J., Young, R. R., Banchereau, R., George, J., Turner, J., Kim, K., Zurawski, S., Wang, X., Blankenship, D., Brookes, H. M., Marches, F., Obermoser, G., Lavecchio, E., Levin, M. K., Bae, S., Chung, C., Smith, J. L., Cepika, A., Oxley, K. L., Snipes, G. J., Banchereau, J., Pascual, V., O'Shaughnessy, J., Palucka, A. 2018; 78 (18): 5243–58

  Abstract

  Inflammation affects tumor immune surveillance and resistance to therapy. Here, we show that production of IL1β in primary breast cancer tumors is linked with advanced disease and originates from tumor-infiltrating CD11c+ myeloid cells. IL1β production is triggered by cancer cell membrane-derived TGFβ. Neutralizing TGFβ or IL1 receptor prevents breast cancer progression in humanized mouse model. Patients with metastatic HER2- breast cancer display a transcriptional signature of inflammation in the blood leukocytes, which is attenuated after IL1 blockade. When present in primary breast cancer tumors, this signature discriminates patients with poor clinical outcomes in two independent public datasets (TCGA and METABRIC).Significance: IL1β orchestrates tumor-promoting inflammation in breast cancer and can be targeted in patients using an IL1 receptor antagonist. Cancer Res; 78(18); 5243-58. ©2018 AACRSee related commentary by Dinarello, p. 5200.

  View details for PubMedID 30012670

• Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics ANNUAL REVIEW OF IMMUNOLOGY, VOL 35 Banchereau, R., Cepika, A., Banchereau, J., Pascual, V., Littman, D. R., Yokoyama, W. M. 2017; 35: 337–70

  Abstract

  Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice. Herein, we review the use of transcriptomics to define mechanistic, diagnostic, and predictive signatures in human autoimmunity and autoinflammation. We discuss some of the analytical approaches applied to extract biological knowledge from high-dimensional data sets. Finally, we touch upon emerging applications of transcriptomics to study eQTLs, B and T cell repertoire diversity, and isoform usage.

  View details for PubMedID 28142321

• Timing of Influenza Vaccine Response in Patients That Receive Autologous Hematopoietic Cell Transplantation Sokol, K. A., Kim-Schulze, S., Robins, H., Obermoser, G., Blankenship, D., Qi, J., Patel, M., Kakon, N., Ueno, H., Anguiano, E., Priest, E., Cepika, A., Emerson, R., Albrecht, R., Garcia-Sastre, A., Palucka, K., Marches, R., Sanders, C., Duboff, M., Osman, K., Merad, M. 2017: S143–S144

  View details for DOI 10.1016/j.bbmt.2016.12.266

• Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients CELL Banchereau, R., Hong, S., Cantarel, B., Baldwin, N., Baisch, J., Edens, M., Cepika, A., Acs, P., Turner, J., Anguiano, E., Vinod, P., Kahn, S., Obermoser, G., Blankenship, D., Wakeland, E., Nassi, L., Gotte, A., Punaro, M., Liu, Y., Banchereau, J., Rossello-Urgell, J., Wright, T., Pascual, V. 2016; 165 (3): 551–65

  Abstract

  Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by loss of tolerance to nucleic acids and highly diverse clinical manifestations. To assess its molecular heterogeneity, we longitudinally profiled the blood transcriptome of 158 pediatric patients. Using mixed models accounting for repeated measurements, demographics, treatment, disease activity (DA), and nephritis class, we confirmed a prevalent IFN signature and identified a plasmablast signature as the most robust biomarker of DA. We detected gradual enrichment of neutrophil transcripts during progression to active nephritis and distinct signatures in response to treatment in different nephritis subclasses. Importantly, personalized immunomonitoring uncovered individual correlates of disease activity that enabled patient stratification into seven groups, supported by patient genotypes. Our study uncovers the molecular heterogeneity of SLE and provides an explanation for the failure of clinical trials. This approach may improve trial design and implementation of tailored therapies in genetically and clinically complex autoimmune diseases. PAPERCLIP.

  View details for PubMedID 27040498

  View details for PubMedCentralID PMC5426482

• Transcriptional specialization of human dendritic cell subsets in response to microbial vaccines NATURE COMMUNICATIONS Banchereau, R., Baldwin, N., Cepika, A., Athale, S., Xue, Y., Yu, C. I., Metang, P., Cheruku, A., Berthier, I., Gayet, I., Wang, Y., Ohouo, M., Snipes, L., Xu, H., Obermoser, G., Blankenship, D., Oh, S., Ramilo, O., Chaussabel, D., Banchereau, J., Palucka, K., Pascual, V. 2014; 5: 5283

  Abstract

  The mechanisms by which microbial vaccines interact with human APCs remain elusive. Herein, we describe the transcriptional programs induced in human DCs by pathogens, innate receptor ligands and vaccines. Exposure of DCs to influenza, Salmonella enterica and Staphylococcus aureus allows us to build a modular framework containing 204 transcript clusters. We use this framework to characterize the responses of human monocytes, monocyte-derived DCs and blood DC subsets to 13 vaccines. Different vaccines induce distinct transcriptional programs based on pathogen type, adjuvant formulation and APC targeted. Fluzone, Pneumovax and Gardasil, respectively, activate monocyte-derived DCs, monocytes and CD1c+ blood DCs, highlighting APC specialization in response to vaccines. Finally, the blood signatures from individuals vaccinated with Fluzone or infected with influenza reveal a signature of adaptive immunity activation following vaccination and symptomatic infections, but not asymptomatic infections. These data, offered with a web interface, may guide the development of improved vaccines.

  View details for PubMedID 25335753

• RNA recognition by human TLR8 can lead to autoimmune inflammation JOURNAL OF EXPERIMENTAL MEDICINE Guiducci, C., Gong, M., Cepika, A., Xu, Z., Tripodo, C., Bennett, L., Crain, C., Quartier, P., Cush, J. J., Pascual, V., Coffman, R. L., Barrat, F. J. 2013; 210 (13): 2903–19

  Abstract

  Studies on the role of the RNA receptor TLR8 in inflammation have been limited by its different function in human versus rodents. We have generated multiple lines of transgenic mice expressing different levels of human TLR8. The high copy number chimeras were unable to pass germline; developed severe inflammation targeting the pancreas, salivary glands, and joints; and the severity of the specific phenotypes closely correlated with the huTLR8 expression levels. Mice with relatively low expression levels survived and bred successfully but had increased susceptibility to collagen-induced arthritis, and the levels of huTLR8 correlated with proinflammatory cytokines in the joints of the animals. At the cellular level, huTLR8 signaling exerted a DC-intrinsic effect leading to up-regulation of co-stimulatory molecules and subsequent T cell activation. A pathogenic role for TLR8 in human diseases was suggested by its increased expression in patients with systemic arthritis and the correlation of TLR8 expression with the elevation of IL-1β levels and disease status. We found that the consequence of self-recognition via TLR8 results in a constellation of diseases, strikingly distinct from those related to TLR7 signaling, and points to specific inflammatory diseases that may benefit from inhibition of TLR8 in humans.

  View details for DOI 10.1084/jem.20131044

  View details for Web of Science ID 000328742600010

  View details for PubMedID 24277153

  View details for PubMedCentralID PMC3865472

• Systems approaches to human autoimmune diseases CURRENT OPINION IN IMMUNOLOGY Banchereau, R., Cepika, A., Pascual, V. 2013; 25 (5): 598–605

  Abstract

  Systemic autoimmune diseases result from interactions between genes and environmental triggers that lead to dysregulation of both innate and adaptive immunity. Systems biology approaches enable the global characterization of complex systems at the DNA, RNA and protein levels. Recent technological breakthroughs such as deep sequencing or high-throughput proteomics are revealing novel inflammatory pathways involved in autoimmunity. Herein, we review recent developments, challenges and promising avenues in the use of systems approaches to understand human systemic autoimmune and autoinflammatory diseases.

  View details for PubMedID 24055331

  View details for PubMedCentralID PMC3924714

• Systems Scale Interactive Exploration Reveals Quantitative and Qualitative Differences in Response to Influenza and Pneumococcal Vaccines IMMUNITY Obermoser, G., Presnell, S., Domico, K., Xu, H., Wang, Y., Anguiano, E., Thompson-Snipes, L., Ranganathan, R., Zeitner, B., Bjork, A., Anderson, D., Speake, C., Ruchaud, E., Skinner, J., Alsina, L., Sharma, M., Dutartre, H., Cepika, A., Israelsson, E., Phuong Nguyen, Quynh-Anh Nguyen, Harrod, A., Zurawski, S. M., Pascual, V., Ueno, H., Nepom, G. T., Quinn, C., Blankenship, D., Palucka, K., Banchereau, J., Chaussabel, D. 2013; 38 (4): 831–44

  Abstract

  Systems immunology approaches were employed to investigate innate and adaptive immune responses to influenza and pneumococcal vaccines. These two non-live vaccines show different magnitudes of transcriptional responses at different time points after vaccination. Software solutions were developed to explore correlates of vaccine efficacy measured as antibody titers at day 28. These enabled a further dissection of transcriptional responses. Thus, the innate response, measured within hours in the peripheral blood, was dominated by an interferon transcriptional signature after influenza vaccination and by an inflammation signature after pneumococcal vaccination. Day 7 plasmablast responses induced by both vaccines was more pronounced after pneumococcal vaccination. Together, these results suggest that comparing global immune responses elicited by different vaccines will be critical to our understanding of the immune mechanisms underpinning successful vaccination.

  View details for DOI 10.1016/j.immuni.2012.12.008

  View details for Web of Science ID 000330942100023

  View details for PubMedID 23601689

  View details for PubMedCentralID PMC3681204

• Immunodeficiency, autoinflammation and amylopectinosis in humans with inherited HOIL-1 and LUBAC deficiency NATURE IMMUNOLOGY Boisson, B., Laplantine, E., Prando, C., Giliani, S., Israelsson, E., Xu, Z., Abhyankar, A., Israel, L., Trevejo-Nunez, G., Bogunovic, D., Cepika, A., MacDuff, D., Chrabieh, M., Hubeau, M., Bajolle, F., Debre, M., Mazzolari, E., Vairo, D., Agou, F., Virgin, H. W., Bossuyt, X., Rambaud, C., Facchetti, F., Bonnet, D., Quartier, P., Fournet, J., Pascual, V., Chaussabel, D., Notarangelo, L. D., Puel, A., Israel, A., Casanova, J., Picard, C. 2012; 13 (12): 1178-+

  Abstract

  We report the clinical description and molecular dissection of a new fatal human inherited disorder characterized by chronic autoinflammation, invasive bacterial infections and muscular amylopectinosis. Patients from two kindreds carried biallelic loss-of-expression and loss-of-function mutations in HOIL1 (RBCK1), a component of the linear ubiquitination chain assembly complex (LUBAC). These mutations resulted in impairment of LUBAC stability. NF-κB activation in response to interleukin 1β (IL-1β) was compromised in the patients' fibroblasts. By contrast, the patients' mononuclear leukocytes, particularly monocytes, were hyper-responsive to IL-1β. The consequences of human HOIL-1 and LUBAC deficiencies for IL-1β responses thus differed between cell types, consistent with the unique association of autoinflammation and immunodeficiency in these patients. These data suggest that LUBAC regulates NF-κB-dependent IL-1β responses differently in different cell types.

  View details for DOI 10.1038/ni.2457

  View details for Web of Science ID 000311217900011

  View details for PubMedID 23104095

  View details for PubMedCentralID PMC3514453

• Decrease in circulating DNA, IL-10 and BAFF levels in newly-diagnosed SLE patients after corticosteroid and chloroquine treatment CELLULAR IMMUNOLOGY Cepika, A., Juresa, D., Vergles, J., Malenica, B., Santak, M., Kapitanovic, S., Mayer, M., Anic, B., Sentic, M., Gagro, A. 2012; 276 (1-2): 196–203

  Abstract

  Arsenal of pattern-recognition receptors alongside antibody production machinery make B cells vulnerable to autoimmune response if an autoantigen elicits both pathways in a self-sustained fashion. Systemic lupus erythematosus is an autoimmune disease characterized by autoantibodies to DNA, RNA and related structures. Murine studies demonstrated autoreactive B cell activation upon TLR9 stimulation with DNA-containing immune complexes. This activation could be abolished with chloroquine, a drug used in SLE treatment that also blocks TLR9 signaling. We investigated whether chloroquine modulates TLR9 expression, circulating DNA levels and B cell-related cytokines in newly discovered, untreated SLE patients. TLR9 was measured in peripheral blood B cells by flow cytometry, serum DNA by real-time PCR, and IL-10 and BAFF by ELISA before treatment, after 3weeks on corticosteroids, and 3months after introduction of chloroquine. We found that circulating DNA is higher in SLE patients than in controls in every time-point and decreases significantly after chloroquine treatment. Untreated patients had higher serum IL-10 than controls or patients on corticosteroids. Also, corticosteroids decreased and chloroquine completely abolished CpG-mediated CD86 upregulation on B cells and IL-10 secretion in PBMC culture. Providing the TLR9 pathway activation demonstrates its importance in pathogenesis of human SLE, this data supports continuation of chloroquine in SLE treatment protocol. In addition, observed modulation of cytokine and DNA levels after immunomodulatory treatment prompts for inclusion of untreated patients in studies of human immune disorders.

  View details for DOI 10.1016/j.cellimm.2012.05.009

  View details for Web of Science ID 000307260800026

  View details for PubMedID 22703694

• Monocyte Response to LPS after Exposure to Corticosteroids and Chloroquine with Implications for Systemic Lupus Erythematosus SCANDINAVIAN JOURNAL OF IMMUNOLOGY Cepika, A., Bendelja, K., Vergles, J. M., Malenica, B., Kapitanovic, S., Gagro, A. 2010; 72 (5): 434–43

  Abstract

  Essential part of a response to infection is early pathogen recognition and adequate initiation of innate immunity. One of the hallmarks of systemic lupus erythematosus (SLE) is reduced resistance to infection despite overall hyperactivity of the immune system. Immunosuppressive drugs (high-dose corticosteroids and cytotoxic agents) are independent risk factors for infection in SLE, with bacteria as predominant cause. To investigate whether less aggressive immunomodulatory treatment may still affect recognition and response to Gram-negative bacteria, we measured TLR4 expression in monocytes of untreated SLE patients and patients on chloroquine and low-dose steroid therapy and examined the drugs' influence on monocyte TLR4 expression in peripheral blood mononuclear cell (PBMC) culture. Additionally, we determined whether induction of monocyte NF-κB signalling, TNF-α and IL-6 production with lipopolysaccharide (LPS), a TLR4 ligand, can be altered with dexamethasone, chloroquine or both. There was no statistically significant difference in TLR4 expression between patients with SLE and controls, even though treated SLE patients tended to have lower frequency of TLR4(+) monocytes and TLR4 mean fluorescence intensity than healthy controls. However, neither dexamethasone nor chloroquine had major influence on TLR4 expression in vitro or suppressed LPS-induced NF-κB activation in monocytes, although dexamethasone decreased TNF-α and IL-6 production. Therefore, even if low-dose steroids or chloroquine do not seem to affect TLR4 expression and signalling, steroids might decrease cytokine production in response to LPS.

  View details for DOI 10.1111/j.1365-3083.2010.02450.x

  View details for Web of Science ID 000282570500007

  View details for PubMedID 21039738

• Expression of chemokine receptor CX(3)CR1 in infants with respiratory syncytial virus bronchiolitis PEDIATRIC ALLERGY AND IMMUNOLOGY Cepika, A., Gagro, A., Bace, A., Tjesic-Drinkovic, D., Kelecic, J., Baricic-Voskresensky, T., Matic, M., Drazenovic, V., Marinic, I., Mlinaric-Galinovic, G., Tjesic-Drinkovic, D., Vrtar, Z., Rabatic, S. 2008; 19 (2): 148–56

  Abstract

  Respiratory syncytial virus (RSV) glycoprotein G mimics fractalkine, a CX(3)C chemokine, which mediates chemotaxis of leukocytes expressing its receptor, CX(3)CR1. The aim of this study was to examine the relationship between RSV infection and expression of perforin and IFN-gamma in CX(3)CR1-expressing peripheral blood CD8(+) T cells. Samples were collected from infants with RSV bronchiolitis, both in the acute and convalescence phase (n = 12), and from their age- and sex-matched healthy controls (n = 15). Perforin expression and IFN-gamma secretion in CX(3)CR1(+) CD8(+) T cells were assessed by four-color flow cytometry. The NF-kappaB p50 and p65 subunit levels were also determined as markers of RSV-induced inflammation. Study results showed perforin and CX(3)CR1 expression to be significantly lower in the convalescent phase of infected infants than in healthy controls. There was no significant difference in IFN-gamma secretion and NF-kappaB binding activity between two time-points in RSV-infected infants, or when compared with healthy controls. Infants with prolonged wheezing had lower acute-phase CX(3)CR1 levels in peripheral blood. These data indicate existence of an event persisting after acute RSV infection that is able to modulate effector functions of cytotoxic T cells, and also link disease severity with CX(3)CR1 expression.

  View details for PubMedID 18257903

• The effect of chloroquine add-on therapy on TLR9 expression in systemic lupus erythematosus Cepika, A., Soldo-Juresa, D., Morovic-Vergles, J., Malenica, B., Gagro, A. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2008: S93–S94

  View details for DOI 10.1016/j.clim.2008.03.262

  View details for Web of Science ID 000255533200267

• Effect of steroids on the frequency of regulatory T Cells and expression of FOXP3 in a patient with systemic lupus erythematosus: a two-year follow-up LUPUS Cepika, A., Marinic, I., Morovic-Vergles, J., Soldo-Juresa, D., Gagro, A. 2007; 16 (5): 374–77

  View details for DOI 10.1177/0961203307077990

  View details for Web of Science ID 000248089800012

  View details for PubMedID 17576742

• Determination of intracellular protein expression Methods in Molecular Biology Cepika, A., Gagro, A. Rudjer Bošković Institute. 2007: 798–803
• ELISPOT Methods in Molecular Biology Cepika, A., Gagro, A. Rudjer Bošković Institute. 2007: 696–702
• Determination of cytokines by flow cytometry Methods in Molecular Biology Cepika, A., Gagro, A. Rudjer Bošković Institute. 2007: 694–696
• Type I cytokine profiles of human naive and memory B lymphocytes: a potential for memory cells to impact polarization IMMUNOLOGY Gagro, A., Servis, D., Cepika, A. M., Toellner, K. M., Grafton, G., Taylor, D. R., Branica, S., Gordon, J. 2006; 118 (1): 66–77

  Abstract

  B cells bifurcating along 'type 1' or 'type 2' pathways under the influence of polarizing cytokines can, in turn, influence the direction of an immune response. Here, we compare the capacity of human B cells residing within naïve and memory compartments to participate in type 1 polarizing responses. B-cell receptor (BCR) engagement provided the main signal for interleukin (IL)-12Rbeta1 expression in the two subsets: this was potentiated by CD154 together with interferon-gamma (IFN-gamma) but inhibited by IL-12. IL-12Rbeta2 could be induced on a minority of B cells by the same signals, and also by IFN-gamma alone. WSX-1, a receptor for IL-27, was expressed in both subsets with no evidence for its regulation by the signals studied. While neither subset was capable of secreting much IL-12 p70, memory B cells could produce a small amount of IL-12 p40 on CD40 ligation. Memory B cells also, exclusively, expressed IL-23 p19 mRNA on BCR triggering. Importantly, products of appropriately stimulated memory--but not naive--B cells were shown to promote the synthesis of IFN-gamma in uncommitted T-helper cells. The data indicate an equal capacity for naïve and memory B cells to respond within a type 1 polarizing environment. Although poorly equipped for initiating type 1 responses, B cells--by virtue of the memory subset--reveal a capacity for their maintenance and amplification following T-dependent signalling.

  View details for PubMedID 16630024

• The role of immune system in control of the influenza pandemic Infektološki glasnik Gagro, A., Cepika, A., Kosor, E., Marinić, I., Kuzman, I., Jeren, T., Draženović, V., Rakušić, S., Mlinarić-Galinović, G. 2006; 26 (1): 13-18