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Content Supplement 1:…………………………………………………………………………….Page 2 the Detailed Information of Establishment and Assessment of Chronic Stress Model Content Supplement 1:…………………………………………………………………………….Page 2 The Detailed information of establishment and assessment of chronic stress model. Supplement 2:…………………………………………………………………………….Page 7 General data of the animals about body weight, food intake, biochemistry, inflammation and blood morphology. Supplement 3:…………………………………………………………………………….Page 12 Sample size calculation. Supplement 4:…………………………………………………………………………….Page 14 Limma of full length of DEPs with probe ID, logFC, pValue, adj.P.Val, t value and Gene Name. Supplement 5: ……………………………………………………………………………Page 122 Protein ID_Gene Name of DEPs. Supplement 6: ……………………………………………………………………………Page 164 Figure S2: Weighted Co-expression Network Construction. (A) Sample dendrogram and trait heatmap. (B) The eigengene dendrogram could cluster the 17 modules. (C) The scatter diagrams show the membership of the other nine modules vs. gene significance. Figure S3: Module Preservation Analysis. (A) The scatter diagrams show the membership of the other seven modules vs. gene significance. (B) Interactions of the 17 co-expression modules were analyzed with the selected genes; light colors represent high overlap and progressively darker red color indicates lower overlap. Blocks of lighter colors along the diagonal represent the co- expression modules. Figure S4: Enrichment analysis for the DEPs using Metascape. (A) Heatmap of enriched terms across input gene lists, colored by p-values. (B) The network of enriched terms represented as pie charts, where the charts are color-coded based on the identities of the gene lists. (C) The network of enriched terms colored by cluster ID, where nodes that share the same cluster ID are typically close to each other. (D) The network of enriched terms colored by p-values, where terms containing more genes tend to have a more significant p-value. (E) Summary of enrichment analysis using DisGeNET. (F) Summary of enrichment analysis using PaGenBase. 1 Supplement 1 2 Supplement 1: The Detailed information of establishment and assessment of chronic stress model. Methods: Detailed information of establishment of chronic stress model[1] Stress is defined as a threatened state provoked by physiologic, psychological, or environmental stressors [2]. As there is no standard stress procedure for rabbits, we adopted both social stress (referred to as unstable social environment model) and physiologic stress (referred to as rat chronic unpredicted mild stress model, CUMS) methods (Table S1). These two stress groups (CS group and AS+CS group) were assigned in a separate room to avoid interfering the non-stress groups (Normal group and AS group). To reduce gastrointestinal injuries, stress manipulation was conducted after feeding, at least half an hour later. Social stress procedures: animals were paired together in one cage for 4 hours per day and the pairings were exchanged within the own groups every week, forcing rabbits to continually reestablish social relationships [3]. The time that rabbits in other cage (as intruder) and in home cage during the entire experiments should be balanced. Physical stress procedures: continuous overnight illumination, 2 hours of white noise (a tone of 80 dB), and 2 hours of high-intensity stroboscopic illumination (300 flashes/min) were selected separately at different days. In order to reduce habituation, one foot shock (1mA) was added (several seconds/time, five times in total)[4]. The stress regime was started at the end of week 4 and lasted for 8 weeks. Table S1. Chronic stress procedures 3 Time Methods Monday Tuesday Wednesday Thursday Friday Saturday Social stress 4h 4h 4h 4h 4h 4h Physical stress Overnight illumination 12h - - White noise（80db） 2h - - Stroboscopic illumination 2h - - Foot shock（1mA） 5times - - Assessment of chronic stress animal model[1] The rabbits were carefully inspected after stress exposure. The fur scoring was recorded to reflect the basic health status (referred to as the standard of mouse) [5]. To obtain the information on the impact of the stressors on animal behavior in natural state, all rabbits were recorded for 10 min on video, between 8:00 am and 9:00 am, before the rabbits began eating. The video was recorded 3 - 4 times every week. The individual behavioral assessment of the same group was summed to provide a total score of each 4-week stress period. Fur score: 1 point represents clean, shiny, and tidy fur; 2 points represent dull and irregular fur, with a few minor wounds; 3 points represent less hair fur, more marked with minor wounds; and 4 points represent lack of hair, ruffled fur, with several minor wounds. Rabbits with obvious wounding were excluded from the study. Behavior score: it was observed that rabbit behaviors were mainly classified into inactivity, locomotor, grooming, and drinking. Inactivity was defined as rabbits sitting or huddling quietly in the cage. Locomotor behaviors comprised of cage exploration, walking, stretching out, and reacting to the other rabbits in the same room. Grooming behavior included licking their paws and using their paws to wipe and wash their face, 4 ears, trunk or hind quarters [6]. The behavioral activity of the 4 categories for each rabbit was scored as the percentage of 10-min observation period. The total percent time in each group was calculated every 4 weeks after stress exposure (at week 8 and week 12). Results: The CS animal model was established successfully, which was presented in our previous publication. And please see the “Assessments of chronic stress model” section in the “Results” (PMID: 29336364)[1]. References [1] Z. M. Yu, X. T. Deng, R. M. Qi, L. Y. Xiao, C. Q. Yang, and T. Gong, "Mechanism of Chronic Stress-induced Reduced Atherosclerotic Medial Area and Increased Plaque Instability in Rabbit Models of Chronic Stress," Chinese medical journal, vol. 131, no. 2, pp. 161-170, 2018. [2] P. H. Black and L. D. Garbutt, "Stress, inflammation and cardiovascular disease," Journal of psychosomatic research, vol. 52, no. 1, pp. 1-23, 2002. [3] P. M. McCabe, J. A. Gonzales, J. Zaias et al., "Social environment influences the progression of atherosclerosis in the watanabe heritable hyperlipidemic rabbit," Circulation, vol. 105, no. 3, pp. 354-359, 2002. [4] C. Rabasa, C. Muñoz-Abellán, N. Daviu, R. Nadal, and A. Armario, "Repeated 5 exposure to immobilization or two different footshock intensities reveals differential adaptation of the hypothalamic-pituitary-adrenal axis," Physiology & behavior, vol. 103, no. 2, pp. 125-133, 2011. [5] H. M. Savignac, N. P. Hyland, T. G. Dinan, and J. F. Cryan, "The effects of repeated social interaction stress on behavioural and physiological parameters in a stress-sensitive mouse strain," Behavioural brain research, vol. 216, no. 2, pp. 576-584, 2011. [6] V. J. Aloyo and K. D. Dave, "Behavioral response to emotional stress in rabbits: role of serotonin and serotonin2A receptors," Behavioural pharmacology, vol. 18, no. 7, pp. 651-659, 2007. 6 Supplement 2 7 Supplement 2: General data of the animals about body weight, food intake, biochemistry, inflammation and blood morphology Material and methods: Blood sampling, blood routine and biochemical assays Rabbit blood samples were obtained from the central ear artery between 7:00 a.m. and 9:00 a.m. every 4 weeks, after 12 h of fasting. Then take 0.4ml blood and put it into the EDTA anticoagulant tube. The serum samples separated by centrifugation at 4°C were stored in aliquots at −80°C. The relevant parameters of blood routine, such as white blood cell (WBC), red blood cell (RBC), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean erythrocyte hemoglobin concentration (MCHC), red cell distribution width (RDW), platelet (PLT), and mean platelet volume (MPV) were measured by enzymatic assays using a full blood count analyzer (Beckman, USA). The concentrations of total cholesterol (TC), triglyceride (TG), low‑density lipoprotein cholesterin (LDLC), and high‑density lipoprotein cholesterin (HDLC), alanine transaminase (ALT), aspartate transaminase (AST), blood glucose (GLU), blood urea (BUN), blood uric acid (URIC) were measured by an automated analyzer (Beckman, USA). Interleukin‑6 (IL‑6) were measured by commercially available enzyme‑linked immunosorbent assay (ELISA) kits (R and D Systems, Minneapolis, MN, USA). High‑sensitivity C‑reactive protein (hs‑CRP) was measured by enhanced immunoturbidimetric assay. 8 Wright staining Wright’s Giemsa staining kit was bought from the Servicebio (G1009). Use capillary pipette to absorb 5-7 UL of EDTA anticoagulant peripheral blood and drop blood to one end of the slide. The push piece and the slide form an Angle of 30 degrees, and push the blood to the other end of the slide with a uniform speed. Label the blood smear, put the blood smear flat on the staining frame, and drop liquid A to cover the whole blood membrane. After 1 minute, add liquid B, mix liquid A and B evenly. The ratio of liquid A and B is 1:2. After staining in a horizontal position for 5-10 minutes, lift the slide and shake it gently so that the dye is no longer attached to the blood membrane. Use the pure water to wash the dye solution on the tissue, waiting for natural drying. Rapid observation under microscope (Axio Zoom V16, ZEISS, Germany). Results: General data of the animals about body weight, food intake, biochemistry, inflammation The general data of body weight, food intake, biochemistry, inflammation of the animals was presented in the Table S2. There were no differences among the four groups at aspects of body weight, food intake, ALT, AST, BUN, URIC, WBC, RBC, MCV, MCH, RDW, PLT, MPV. Compared with the control group, the TC level in the AS (38.09±2.38 mmol/L) and AS+CS (43.96±0.67 mmol/L) groups was higher (P<0.05). The concentration of TG in the AS+CS (5.84±0.72 mmol/L) was higher than the control group (2.77±0.58 mmol/L) (P<0.05). Compared with the control group, the 9 LDLC level in the AS (17.25±1.22 mmol/L) and AS+CS (19.37±0.32 mmol/L) groups was higher (P<0.05).
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