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Broadly effective metabolic and immune recovery with C5 inhibition in CHAPLE disease

Abstract

Complement hyperactivation, angiopathic thrombosis and protein-losing enteropathy (CHAPLE disease) is a lethal disease caused by genetic loss of the complement regulatory protein CD55, leading to overactivation of complement and innate immunity together with immunodeficiency due to immunoglobulin wasting in the intestine. We report in vivo human data accumulated using the complement C5 inhibitor eculizumab for the medical treatment of patients with CHAPLE disease. We observed cessation of gastrointestinal pathology together with restoration of normal immunity and metabolism. We found that patients rapidly renormalized immunoglobulin concentrations and other serum proteins as revealed by aptamer profiling, re-established a healthy gut microbiome, discontinued immunoglobulin replacement and other treatments and exhibited catch-up growth. Thus, we show that blockade of C5 by eculizumab effectively re-establishes regulation of the innate immune complement system to substantially reduce the pathophysiological manifestations of CD55 deficiency in humans.

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Fig. 1: The treatment effect of eculizumab in CHAPLE disease.
Fig. 2: GI, circulatory, hematologic and metabolic manifestations of CHAPLE disease with or without eculizumab.
Fig. 3: Serum eculizumab concentration and total C5 and functional complement inhibition during the induction and maintenance phases of treatment.
Fig. 4: Blood concentrations of complement proteins and their activated products before and during eculizumab treatment.
Fig. 5: Microbiota composition shifts in eculizumab-treated patients with CHAPLE disease.
Fig. 6: Serum proteins altered in patients and response to eculizumab therapy.

Data availability

The microbiome sequencing data is linked to the National Center for Biotechnology Information (NCBI) BioProject ID PRJNA629392. The raw data, including the adat file used to generate proteomic analyses, the data analysis codes used for microbiome analyses and all other data that support the findings of this study, are available from the corresponding authors upon request to the extent allowed by all laws and institutional policies regarding confidentiality of patient clinical information. The following datasets were used in the study: Peditools; string db; maxikraken2 (v_1903_140GB) database; gnomAD v.2.1.1; and 1000genome.

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Acknowledgements

This work was supported in part by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, BCBB Support Services Contract HHSN316201300006W/HHSN27200002, and The Marmara University, Scientific Research Projects Committee (BAPKO, grant no. SAG-C-TUP-230119-0018). We thank the Turkish National Society of Allergy and Clinical Immunology (TNSACI) for supporting travel expenses for the screening studies. We thank C. Kemper of the National Heart, Lung and Blood Institute for thoughtful editing of the final manuscript. We thank M. Quiñones, the Center for Human Immunology and the NIAID Microbiome Program, NIAID, NIH, for research support. We also thank A. Kiykim for patient care, A. Dalga and I. Tatli for technical assistance and H. Su and X. He for advice and assistance; D. Comrie, S. Kubo and J. Ravell for critical reading of the manuscript; and R. Kissinger for artwork. We thank important colleagues at Regeneron: A. N. Thomas for sample processing; C. Huang for biomarker analysis; H. Qiu, and E. Sook Yen for eculizumab analysis; and C. H. Lai, L. DeStefano and K. Donohue for total C5 analysis. Molecular graphics and analyses were performed with UCSF ChimeraX, developed by the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco, with support from NIH R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, NIAID.

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A.O. and M.J.L. designed the trial and supervised all activities. A.O., M.J.L., I.V.-C., R. Apps, F.C., M.-D.W. and P.S. analyzed and interpreted data. O.H., J.T. and Y.B. supervised activities and interpreted data. R. Apps, G.F., B.S., Y.G.N., K.D.-N. and G.A. conducted experiments. Y.Z., A.L.S., C.L., C.A. and C.L.D. performed genetic sequencing and data analyses. A.O., S.B., E.K.-A., S.B.E., N.K., M.S., E. Tutar, D.E., B.A., S.S., F.O., D.K.U., A.I., O.B.S., G.K., E. Topal, E.S., R.H.J.H., S.N.G., A.B., I.O. and B.D. provided patient care and collected data. D.E., E. Tutar, R. Artan and B.A. conducted gastrointestinal interventions. C.C. made histopathology evaluations. R.E. provided radiological assessment. A.O., S.D.C. and M.J.L. wrote the paper. All authors reviewed, edited and approved the manuscript.

Corresponding authors

Correspondence to Ahmet Ozen or Michael J. Lenardo.

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Competing interests

The authors M.J.L. and A.O. have a pending patent on C5 inhibitor treatment of CHAPLE. B.S. is a former SomaLogic, Inc. (Boulder, CO, USA) employee and a company shareholder. O.H., Y.G.N., M.-D.W. and K.D.-N. are employees of Regeneron Pharmaceuticals Inc., a biopharma company. There are no conflicts of interest to report for the remaining coauthors.

Additional information

Peer review information Nature Immunology thanks Kevin Marchbank, Stuart Tangye and Chack-Yung Yu for their contribution to the peer review of this work. Peer reviewer reports are available. L. A. Dempsey was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Demographic, clinical and laboratory characteristics of the patients with CHAPLE disease enrolled in the study.

Reference ranges are indicated in parenthesis. NA: Not assessed, NP: New patient, WBC: White blood count, ANC: Absolute neutrophil count, ALC: Absolute lymphocyte count lymphocyte count, Hgb: Hemoglobin, Plt: Platelet count. CD55 NCBI Reference Sequence: NM_000574. * the lowest values in the past (more than 1 year before therapy) are indicated in the ‘past’ columns. ** the highest values in the past (more than 1 year before therapy) are indicated in the ‘past’ columns. The serum immunoglobulins compared to age-matched serum immunoglobulin reference ranges of Turkish children (Ref. 67). Peri-Tx: peri-treatment, referring to the past 12 months before the start of eculizumab until the end of the observation period.

Extended Data Fig. 2 Clinical symptoms, laboratory findings and growth percentiles of CHAPLE patients prior to and on eculizumab treatment.

Past: In the lifetime of the patient. Peri-Tx: Peri-treatment, referring to the past 12 months before the start of eculizumab until the end of the observation period. Current refers to the most recent measurement or the observation period when a particular patient has been on regular eculizumab Tx. + present, - absent, N/A: Not assessed. * We detected a recanalization of the narrowed segment in the thrombotic vessel in P5 during the follow up exam on eculizumab. However, there was no documented recovery of any of the thromboembolic complications in other patients during the indicated periods of follow up. ** P12 had ischemic gliotic foci in brain imaging. As identified by appropriate imaging including abdominal ultrasonography (USG) and/or doppler USG, and/or vascular imaging using a computed tomography or magnetic resonance imaging. § Growth percentiles not presented in certain columns; P2 was an adult during the peri-Tx period, and data not available in P14 and P15 for respective periods. Abdominal pain cannot be assessed in P13 due to verbal immaturity and corresponding assessment was made for discomfort and abnormal crying behavior.

Extended Data Fig. 3 Medical interventions received by CHAPLE patients prior to and during eculizumab treatment.

Past: In the lifetime of the patient. Peri-Tx: Peri-treatment, referring to the past 12 months before the start of eculizumab until the end of the observation period. Current refers to the most recent measurement or the presence of a finding during the observation period when a particular patient has been on regular eculizumab Tx. *A repeat bowel surgery had been planned in P8 prior to eculizumab. Likewise, P3 had been planned to undergo bowel surgery before eculizumab. P15 underwent 2 separate bowel resection surgeries and received 39 days of intensive care support during the postoperative period, including mechanical ventilation. ** ‘Other invasive intervention’ includes placement of a central access device in P8 to deliver frequent albumin transfusions; intracardiac blood clot removal surgery, chest tube placement to drain pneumothorax and a cranial surgery to alleviate brain hemorrhage in P4; a percutaneous endoscopic gastrostomy port to support enteral nutrition in P12; a transjugular intrahepatic portosystemic shunt (TIPS) to relieve portal hypertension in P16. P8 received intravenous (IV) antibiotics for sepsis and metronidazole for Giardia lamblia enteritis in the past. P4 and P12 experienced cardiovascular problems during the induction period of eculizumab, leading to dose skipping or termination of treatment, respectively. Eculizumab Tx was restarted in P12 after a period off- therapy, with no recurrence of similar manifestations. Fecal assessment during diarrheal episodes revealed Cryptosporidium parvum in P1 and P13 prior to eculizumab, who were treated with nitazoxanide uneventfully. The column for past medication before 1 year prior to eculizumab is blank for P13 due to young age and onset of symptoms during the past year. § Respiratory support refers to mechanical ventilation and/or oxygen treatment. PLE: Protein-losing enteropathy.

Extended Data Fig. 4 The effect of dose spacing between injections on albumin, trough eculizumab concentration, and complement markers during the maintenance therapy.

Blood samples were obtained prior to each injection. The horizontal line on left y axis shows lower range for albumin. Calculated mean ± S.D. values for dose intervals during the indicated time spans, or between two consecutive injections are presented in days. ECMb: eculizumab.

Extended Data Fig. 5 Variable dose spacing or interrupted therapy.

a, Normal serum protein levels sustained when switching from biweekly doses to monthly eculizumab injections in P1. Timing of eculizumab doses in relation to serum albumin and total protein concentrations for P1 in top panel, and immunoglobulin isotypes IgG, IgM and IgG in the bottom panel. b. Timeline plotting the incidence and severity of the indicated symptoms in P4 in relation to timing of eculizumab injection at various dosing intervals. Serum albumin levels plotted at the top of the figure with the horizontal bar showing normal range. Each arrow above the x-axis shows an eculizumab injection with the accompanying numbers illustrating days from the previous dose. The top line shows inability to feed (F) ranging from normal appetite (white) to intake completely abandoned (dark purple). The second line shows the presence (purple) or absence (white) of facial edema (E) in purple whereas the third line shows stool formation (S) on a scale from firm (white) to watery (dark gray). The fourth line quantifies the number of bowel movements (M) from 0-1 (white) to >11 (black). The fifth and sixth lines show the incidences of vomiting (V) from none (white) to >3 times per day (dark blue) and severity of nausea (N) from none (white) to severe (green), respectively. The last line shows severity of abdominal pain (P), ranging from none (white) to severe (dark brown). c. Serum albumin, total protein (T. protein), immunoglobulin G (IgG), and vitamin B12 concentrations for P3 before and after treatment at t = 0. Horizontal yellow bars for indicated parameters show normal range. Vertical dashed lines show eculizumab injections and purple bars dose skipping periods with the indicated numbers showing intervals between two consecutive injections.

Extended Data Fig. 6 Biological significance of proteomic changes in serum.

a, Top-ranking pathways (Wikipathways) plotted against normalized enrichment score (Ref. 68,69). Note, the enrichment of the pathways did not reach adjusted statistical significance level of false discovery rate (FDR) < 0.05. b, Enrichment plots from pre-ranked analysis of log2 fold changes (FC) in protein abundances of patients with respect to age-matched controls, showing rank-based ordering of proteins belonging to immunoglobulin Pfam domain PF13927 at baseline. Similar plots are generated for indicated Post-treatment (Post-Tx) timepoints using log2 FC in protein abundances calculated with respect to patient baseline values. PF13927, found to be enriched in the STRING analysis (Ref. 70), was added to the Wikipathways gene set to compute the normalized enrichment score (NES) and FDR.

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Ozen, A., Kasap, N., Vujkovic-Cvijin, I. et al. Broadly effective metabolic and immune recovery with C5 inhibition in CHAPLE disease. Nat Immunol 22, 128–139 (2021). https://doi.org/10.1038/s41590-020-00830-z

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