Table 1.

Primary and secondary endpoints of the study with detailed explanation and arguments for choosing these endpoints.

	Endpoint	Explanation	comment
Primary	Safety assessment of abatacept in patients with chronic sarcoidosis depending on immunosuppressive regime, measured as number of infectious complications during treatment period	Number of infectious complications during treatment period of one year: -Opportunistic infectious -Infections requiring hospitalization -Infections requiring intravenous antibiotic treatment (including anti-fungal or anti-viral-drugs) -EBV reactivation	Immunosuppression harbors the risk of especially opportunistic infections. Therefore, infections were chosen as primary endpoint to assess safety. The above-mentioned definitions of monitored infections avoid the false-positive detection of infections or detection of minor infections like seasonal flue.
Secondary	Safety assessment of abatacept	- Rate of infections during treatment period compared to rate of similar infections in included patients within a one year period prior to study inclusion (where available) -Rates of adverse events (including non-infectious complications like allergic reactions) -Rates of serious adverse events	Individuals included in this study suffer from chronic sarcoidosis and received immunosuppressive therapies beforehand. Therefore, the complications of abatacept treatment must be compared to previous complications. Therefore, infections and other therapy-related complications will be retrospectively analysed for the year before study enrolment and compared to events during abatacept treatment.
	Assessment of patient reported outcome parameters during treatment with abatacept	Change in KSQ (King's sarcoidosis questionnaire) St. George Respiratory Questionnaire (SGRQ) Leicester Cough Questionnaire (LCQ)	Patient-related outcomes are increasingly recognized as relevant endpoints in clinical studies. Therefore, three questionnaires were included in the study to measure patient-related outcome as change during treatment. KSQ: This questionnaire comprises many issues that affect well-being of patients suffering from sarcoidosis including fatigue, excertional dyspnea, medication side effects and the influence of all these parameters on activities of daily life. A change of 6 points are considered clinically significant [42,61]. St. George Respiratory Questionnaire: This questionnaire is the most frequently used tool to assess patients' respiratory symptoms. Even though it has never been evaluated for sarcoidosis, it is often used and requested. The minimal important difference for interstitial lung diseases is considered to be 6 points change [62]. Leicester Cough Questionnaire: The Leicester Cough Questionnaire is a very recent questionnaire focusing on the symptom of cough, which often affects patients with sarcoidosis. Cough can hardly be treated and often leads to physical and psychical impairment of patients. The minimal important difference is 1.3 points [63].
	Efficacy assessment of treatment with Abatacept, measured as pulmonary function at regular visits (12, 24 36, 48 and 52 weeks)	TLC FVC DLCO SB DLCO/VA pO2 at rest and after 6MWT AaDO2 DSP	Sarcoidosis is mostly affecting the lung and lung functional impairments represent one major indication for therapy. TLC: The Total lung capacity reflects best changes of the lung volume because it measures vital capacity as well as residual volume. A change of 10% is considered to be clinical relevant FVC: The Forced Vital Capacity has been the most important lung function parameter in several studies for interstitial lung diseases. A change of 10% from baseline has been used in most studies. DLCOcSB: Diffusing capacity single breath (DLCOcSB) has been considered to be a good parameter for assessing sarcoidosis' impact on lung function and identifying patients at risk for progession. A 15% change is considered significant. DLCOc/VA: DLCOc/VA mirrors the diffusion capacity for oxygen and is considered a very sensitive marker for interstitial abnormalities in lung diseases and sarcoidosis. pO2at rest and after 6MWT: This parameter allows to monitor the oxygenation under rest and under exertion. Deterioration is defined as 50 m reduction of walking distance or as a decrease of >5 mmHg compared to baseline in the 6 min walk test. Distance saturation product (DSP): DSP is measured after 6MWT. It is calculated by the product of the walking distance and the oxygen saturation after the walk divided by 100. Therefore, this product integrates both components of the 6MWT, that is distance and saturation. AaDO2– alveolar arterial pO2difference: AaDO2 is calculated by the alveolar air equation and is a subtle maker of O2-diffusion impairment.
	Laboratory parameters	sIL2R Neopterin ACE IL17 Total white blood cell count B- and T-cell count Characterization of T- and B-cell subtypes mRNA measurement	Laboratory parameters have been used to monitor inflammatory activity of sarcoidosis, even though all markers have limitations. sIL2R: This parameter reflects inflammatory processes has been found in chronic sarcoidosis. It can be used for monitoring disease activity in sarcoidosis. Neopterin: This parameter reflects inflammatory processes as have been found in chronic sarcoidosis. It can be used for monitoring disease activity in sarcoidosis. ACE: ACE is in part produced by granulomas and can therefore be used to monitor granuloma burden in sarcoidosis. IL17: Interfering with CTLA is supposed to influence Th17-T-cells and thereby IL17 might be used to assess the influence of Abatacept on TH17 T-cells. mRNA measurement: With the use of Abatacept, we expect alterations of surface molecules on immune cells (e.g. T-cells, monocytes, macrophages). These alterations might be explained e.g. by (i) Abatacept-mediated internalization of surface molecules or by (ii) transcriptional/translational changes induced by Abatacept. The analysis of mRNA will help to dissect the underlying molecular mechanism. B- and T-cell count, characterization of T- and B-cell subtypes: As mentioned above, Abatacept is supposed to influence T-cell response in chronic sarcoidosis. Therefore, change of T-cell subtypes may reflect the biological response to Abatacept.
	Bronchoalveolar lavage parameters	Total cell count/100 ml lavage fluid Percentage of differential bronchoalveolar cells Subtypes of T-cells in bronchoalveolar lavage Surface molecules as markers of cell activation, e.g. HLA-DR, CD57 etc. Released cytokines by BAL cells TNF MIP-1a IL-12p40 CXCL10 (IP-10) IL10 TGFβ IFNγ, IL13 IL8 IL17 CCL18 mRNA measurement	BAL fluid and cell analysis of alveolar cells have been proven to deepen the understanding of alveolar inflammation as ongoing in sarcoidosis. Therefore, participants of this study will undergo bronchoscopy and BAL before starting abatacept and after one year of treatment. As abatacept influences T-cell/APC interaction, we expect changes in T-cell subtypes and lower inflammatory response of alveolar cells. Total cell count/100 ml lavage fluid: Total cell number is increased in most inflammatory processes affecting the alveolar compartment and is therefore an unspecific general marker of alveolar inflammation. Percentage of differential bronchoalveolar cells: As mentioned above, sarcoidosis is characterized by a lymphocytic alveolitis. Therefore, it can be expected that the percentage of lymphocytes decreases under successful treatment. Additional information can be drawn from the percentage of neutrophils because they predict a more aggressive course of sarcoidosis. Under Abatacept treatment, a reduction of neutrophils as sign of less inflammatory activity can be expected. Subtypes of T-cells in bronchoalveolar lavage: Abatacept influences T-cell subtype and it can be expected that the T-cell subtype in the alveolar compartment is changed after abatacept treatment. Expression of surface molecules as surrogates of cell activation: Several surface molecules on immune cells indicate their activation state (e.g. HLA-DR, CD57) and thereby might serve as markers of therapy success under Abatacept treatment. Cytokines produced by alveolar cells: Cells obtained by the bronchoalveolar lavage will be cultivated under suitable conditions and released cytokines in the supernatants will be measured, e.g. TNF, MIP-1a, IL-12p40, CXCL10 (IP-10), IL10, TGFβ, IFNγ IL13, IL8, IL17 and CCL18. mRNA measurement: With the use of Abatacept, we expect alterations of surface molecules on immune cells (e.g. T-cells, monocytes, macrophages). These alterations might be explained e.g. by (i) Abatacept-mediated internalization of surface molecules or by Refs. [64] (ii) transcriptional/translational changes induced by Abatacept. The analysis of mRNA will help to dissect the underlying molecular mechanism.
	Need of therapy escalation/modification	Daily steroid dose Need for steroid pulses (see below) Need for therapy modification (see below)	The two main goals of sarcoidosis treatment are (i) control of inflammatory activity that damages organs' function and [64] (ii) to achieve disease control by a minimum or no corticosteroid treatment. Therefore, the steroid doses used to control disease are a good surrogate for the therapeutic effect of Abatacept Daily steroid dose: Daily steroid doses will be monitored and compared to the steroid doses in the year before Abatacept treatment was started. Need for steroid pulses: Number of steroid pulses to control disease flairs and the dosage used will be monitored and compared to the dosage before. Need for therapy modification: Therapy modification (e.g. need of therapy interruption, therapy escalation) will be monitored.