Supplemental Information Supplemental Table 1. Parallel group analysis patient medication breakdown Supplemental Table 1 Characteristics Antipsychotics (number) amisulpride aripiprazole clozapine haloperidol olanzapine paliperidone quetiapine risperidone ziprasidone zuclopenithixol amisulpride/clozapine amisulpride/risperidone ariprazole/clozapine clozapine/haloperidol clozapine/paliperidone clozapine/chlorpromazine olanzapine/paliperidone olanzapine/risperidone olanzapine/zuclopenithixol paliperidone/quetiapine quetiapine/risperidone quetiapine/ziprasidone quetiapine/zuclopenithixol Antidepressants (numbers) citalopram clomipramine desvenlaxafine doxepin duloxetine escitalopram fluoxetine lithium setraline sodium valproate venlaxafine citalopram/lithium escitalopram/ lithium escitalopram/mirtazapine fluoxetine/sodium valproate paroxetine/sodium valproate sodium valproate/venlaxafine Benzodiazepines^ (numbers) N Placebo first 39 N Raloxifene first 40 2 2 10 0 6 2 1 4 1 2 3 0 1 1 2 0 0 0 0 1 0 0 1 14 1 1 11 1 3 1 2 6 1 1 3 1 1 0 0 1 1 1 1 0 1 1 1 19 2 1 1 0 1 2 2 1 0 2 0 0 1 0 1 0 0 1 2 0 0 1 0 1 1 0 6 1 1 1 1 1 0 1 2 5 ^Benzodiazepines included diazepam, temazepam, oxazepam, and lorazepam 1 Supplemental Table 2. Demographic, Cognitive, and Symptom Characteristics of Healthy Controls Supplemental Table 2 Characteristics Age Education Sex (number) N Controls 87 31.9 (8.3) 87 87 14.6 (2.3) 46 41 male female 87 Race (number) 69 12 2 4 Caucasian Asian Caucasian/Asian Other Baseline Scores WAIS-III WTAR 87 87 107.0 (14.5) 108.1 (8.8) 87 87 87 70 87 10.9 (2.9) 11.9 (3.4) 10.4 (3.6) 25.6 (8.7) 42.2 (11.3) Cognitive Tests WAIS-LNS WMS-LM I WMS-LM II TMT-A COWAT Symptom Tests PANSS Positive Negative General Total n/a n/a n/a n/a DASS SF-36v2 Total SQLS Total Depression 81 Anxiety 81 Stress 81 81 81 3.6 (5.5) 2.9 (4.1) 6.7 (7.8) 140.9 (10.7) 23.2 (11.2) Unless otherwise specified, numbers refer to means and SD in parenthesis WAIS-III Wechsler Adult Intelligence Scale, WTAR Wechsler Test of Adult Reading,WAIS- LNS Letter Number Sequencing, WMS-LM I Wechsler Memory Scale Logical Memory I,WMS- LM II Wechsler Memory Scale Logical Memory II, TMT-A trail making test A, COWAT Controlled Oral Word Association Test, PANSS Positive and Negative Syndrome Scale, DASS Depression Anxiety and Stress Scale, SF-36v2 Short Form 36 Version 2 Health Survey Questionnaire, SQLS Schizophrenia Quality of Life Scale. 2 Supplemental Table 3. Crossover hormone and coagulation panel changes with raloxifene versus placebo treatment Supplemental Table 3 N Reference Ranges Hormone Panel Luteinizing Hormone Follicle Stimulating Hormone Coagulation Panel Prothrombin Time International Normalised Ratio Antithrombin III M/F Placebo Mean Mean Difference Difference (SD) (SD) M F -0.5 (1.6) 1.5 (8.3) -0.7 (1.2) 0.4 (3.4) M [0-10]/ F [0-84] mIU/ml M [0-12]/ F [0-90] mIU/ml 44/27 43/27 M/F [12-15] sec M/F [0.8-1.1] M/F [80-135 %] 36/16 -0.2 (0.6) 0.1 (0.4) 43/26 -0.03 (0.09) 0.00 (0.08) 39/24 0.9 (5.9) 2.0 (23.9) Raloxifene Mean Mean Difference Difference (SD) (SD) M F 0.6 (2.1) 2 (7.1) 1.0 (1.4) 1.9 (6.4) 0.3 (0.5) 0.04 (0.08) -8.0 (7.9) 0.1 (0.6) 0.02 (0.05) -6.8 (21.8) Condition Condition*Sex p-value p-value 0.44 p<0.01 0.73 0.80 0.08 0.02 0.02 0.12 0.08 0.99 A review of changes on blood panel measures, including the coagulation panel, did not generally show any clinically relevant blood changes, however, one patient who appeared normal at baseline showed a 48% decline in Antithrombin III after raloxifene treatment, which returned to normal in follow-up blood work 6 weeks later. 3 Supplemental Table 4. Period effects Supplemental Table 4 Period I Mean Difference (SD) Period II Mean Difference (SD) Mean Difference (SD) t df pvalue Cohen's d 0.1 (0.6) 0.6 (1.1) 0.5 (1.1) -0.4 (1.0) -0.1 (0.7) 0.1 (0.7) 0.1 (1.0) 0.1 (1.0) -0.2 (0.7) -0.0 (0.6) 0.0 (1.0) 0.5 (1.8) 0.4 (1.9) -0.2 (1.3) -0.0 (1.0) 0.3 2.3 1.7 -0.9 -0.0 70 70 70 47 69 0.75 0.02 0.09 0.38 0.97 0.0 0.5 0.4 0.2 0.2 Total -0.9 (2.5) -0.6 (3.4) -1.8 (4.5) -3.4 (8.0) 0.3 (2.8) -0.2 (3.2) 0.2 (4.7) 0.2 (8.0) -1.2 (4.3) -0.4 (5.4) -2.0 (7.4) -3.6 (13.1) -2.3 -0.7 -2.3 -2.3 70 70 70 70 0.03 0.49 0.03 0.02 0.5 0.1 0.4 0.5 Depression -1.8 (7.3) 0.8 (10.7) -2.6 (15.1) -1.4 69 0.16 0.3 -0.7 (11.1) -1.8 (14.5) 7.1 (23.3) -4.4 (20.3) 0.50 -1.0 2.5 -1.8 69 69 68 65 0.62 0.30 0.01 0.09 0.1 0.2 0.5 0.4 Measure Cognitive Tests WAIS-LNS WMS-LM I WMS-LM II TMT-A COWAT Symptom Tests PANSS Positive Negative General DASS Anxiety Stress SF-36v2 Total SQLS Total -1.3 (6.2) -1.6 (8.2) 4.3 (12.6) -4.0 (11.8) -0.6 (7.2) 0.2 (9.5) -2.8 (15.3) 0.4 (12.3) Cohen's d calculated as Mean Diff/ SD pooled cognitive measures are z-score adjusted WAIS-LNS Wechsler Adult Intelligence scale Letter Number Sequencing,WMS- LM I Wechsler Memory Scale Logical Memory I,WMS-LM II Wechsler Memory Scale Logical Memory II, TMT-A trail making test A, COWAT Controlled Oral Word Association Test, PANSS Positive and Negative Syndrome Scale, DASS Depression Anxiety and Stress Scale, SF-36v2 Short Form 36 Version 2 Health Survey Questionnaire, SQLS Schizophrenia Quality of Life Scale 4 Supplemental Table 5. Carryover effects Supplemental Table 5 Measure WAIS-LNS WMSR-LM I WMSR-LM II COWAT TMT-A PANSS positive PANSS negative PANSS general PANSS Total DASS depression DASS anxiety DASS stress SF-36v2 Total SQLS Total Mean Diff (SE) p-value -0.2 (0.2) 0.26 -0.9 (0.2) <0.01*** -0.9 (0.2) <0.01*** -0.2 (0.2) 0.29 0.8 (0.3) <0.01 -0.9 (0.7) 0.18 0.6 (0.9) 0.49 0.4 (1.3) 0.75 0.1 (2.2) 0.96 -0.7 (2.5) 0.77 0.3 (1.8) 0.88 -4.3 (2.4) 0.08 5.8 (4.5) 0.21 -0.3 (3.2) 0.93 ***p<0.001 Carryover calculated as placebo/raloxifene versus raloxifene placebo on (period 1 change score +period 2 change score) WAIS-LNS Wechsler Adult Intelligence scale Letter Number Sequencing, WMSR-LM I Wechsler Memory Scale Revised Logical Memory I, WMSR- LM II Wechsler Memory Scale Revised Logical Memory II, TMT-A trail making test A, COWAT Controlled Oral Word Association Test, PANSS Positive and Negative Syndrome Scale, DASS Depression Anxiety and Stress Scale, SF-36v2 Short Form 36 Version 2 Health Survey Questionnaire, SQLS Schizophrenia Quality of Life Scale. 5 Supplemental Table 6. Mixed (M)ANOVAs with sex and condition as between group factors Supplemental Table 6 Mixed (M)ANOVA OUTCOMES Mixed MANOVA: LMI, LMII, LNS, COWAT Between Subjects Condition Sex Condition*Sex Within Subjects Time Time *Condition Time * Sex Time * Condition * Sex Mixed ANOVA: TMT-A Time Time * Condition Time * Sex Time * Condition * Sex UNIVARIATE OUTCOMES Interaction Measure Univariate Analysis: LMI, LMII, LNS, COWAT Time * Condition LMI LMII LNS COWAT Time * Condition * Sex LMI LMII LNS COWAT W-L Value (hyp df, err df)=F p-value 1.0 F(4,72)=0.4 0.9 F(4,72)=1.0 1.0 F(4,72)=0.6 0.8 F(4,72)=4.8 0.8 F(4,72)=4.1 0.9 F(4,72)=1.0 0.8 F(4,72)=4.3 0.841 0.398 0.644 0.002 0.005 0.434 0.004 0.9 F(1,53)=6.2 0.9 F(1,53)=6.7 1.0 F(1,53)=2.4 1.0 F(1,53)=0.0 0.016 0.012 0.126 0.838 H-F Value (hyp df, err df)=F p-value 2.9 F(1,75)=5.5 1.1 F(1,75)=1.7 0.2 F(1,75)=1.2 1.7 F(1,75)=8.2 0.8 F(1,75)=1.6 0.1 F(1,75)=0.1 2.9 F(1,75)=5.5 2.9 F(1,75)=5.5 0.021 0.202 0.271 0.005 0.209 0.768 0.639 0.002 Two separate mixed (M)ANOVAS, one with z-transformed measures of LMI (Weschler Logical Memory I), LMII (Weschler Logical Memory II), LNS (WAIS-III Letter-Number-Sequencing), and COWAT (Controlled Oral Word Association Test), and the second repeated measure ANOVA with ztransformed TMT-A (Trail Making Test A). Both repeated measure (M) ANOVAS included condition (placebo v. raloxifene) and sex (male v. female) as between subject measures and time (baseline visit v. 6-week visit) as the within subject factor. Reported above are the multivariate outcomes for the separate (M)ANOVAS and univariate results for the MANOVA with LMI, LMII, LNS, and COWAT. W-L Value refers to Wilks' Lamda and H-F refers to Huynh-Feldt values. Negative mean differences of LMI, LMII, LNS, and COWAT and a positive mean difference of TMT-A indicate an improvement. 6 Supplemental Table 7. Lease significant difference pairwise comparisons for mixed (M)ANOVAs with sex and condition as between group factors Supplemental Table 7 placebo pMeasure Sex Mean Difference (SE) value Time*Condition Pairwise Comparisons LMI -0.2 (0.2) 0.240 LMII -0.4 (0.2) 0.074 LNS -0.2 (0.1) 0.087 COWAT 0.3 (0.1) 0.019 TMT-A -0.0 (0.2) 0.952 Time*Condition*Sex Pairwise Comparisons LMI male -0.4 (0.2) 0.027 female 0.0 (0.3) 0.934 LMII male -0.3 (0.2) 0.200 female -0.4 (0.3) 0.192 LNS male -0.3 (0.1) 0.032 female -0.1 (0.2) 0.534 COWAT male 0.1 (0.1) 0.562 female 0.5 (0.2) 0.015 TMT-A male 0.2 (0.2) 0.340 female -0.3 (0.3) 0.432 raloxifene Mean Difference (SE) p-value -0.8 (0.2) -0.7 (0.2) -0.0 (0.1) -0.2 (0.1) 0.7 (0.2) p<0.001 p<0.001 0.803 0.109 0.001 -0.7 (0.2) -0.8 (0.2) -0.7 (0.2) -0.7 (0.3) 0.0 (0.1) 0.0 (0.1) 0.1 (0.1) -0.5 (0.2) 0.9 (0.2) 0.5 (0.3) 0.002 0.001 0.005 0.011 0.818 0.898 0.382 0.004 0.001 0.073 Results of Least Significant Difference Pairwise comparisons for Time (baseline v. 6week visit) by Condition (raloxifene v. placebo) interaction and Time by condition by sex (male v. female) interaction for the two separate mixed (M)ANOVAS represented in supplemental table 6. Measures refer to LMI (Weschler Logical Memory I), LMII (Weschler Logical Memory II), LNS (WAIS-III Letter-Number-Sequencing), COWAT (Controlled Oral Word Association Test), and TMT-A (Trail Making Test A). Negative mean differences of LMI, LMII, LNS, and COWAT and a positive mean difference of TMT-A indicate an improvement. 7 Supplemental Table 8. Cognitive responders Supplemental Table 8 Characteristics Cognitive Tests WAIS-LNS WMSR-LM I WMSR-LM II TMT-A COWAT Total Unique Individuals Chi-square Number Needed to Treat Raloxifene first Placebo first n = 40 n=39 1 12 12 1 1 0 4 5 0 0 6 (15%) 16 (40%) 5.6 p=0.02 4 WAIS-LNS Wechsler Adult Intelligence scale Letter Number Sequencing, WMSR-LM I Wechsler Memory Scale Revised Logical Memory I, WMSR-LM II Wechsler Memory Scale Revised Logical Memory II, COWAT Controlled Oral Word Association Test, TMT-A Trail Making Test A. 8 Supplemental Table 9. Symptom responders Supplemental Table 9 No improvement Improvement Chi-square (df) p-value raloxifene 34 6 PANSS positive 1.4 (1) p=0.24 placebo 29 10 raloxifene 31 9 PANSS negative 0.3 (1) p=0.61 placebo 32 7 raloxifene 33 7 PANSS general 0.0 (1) p=0.96 placebo 32 7 raloxifene 35 5 PANSS total 0.1 (1) p=0.71 placebo 33 6 raloxifene 21 18 DAS depression 2.7 (1) p=0.10 placebo 28 11 raloxifene 22 17 DAS anxiety 0.9 (1) p=0.35 placebo 26 13 raloxifene 21 18 DAS stress 0.8 (1) p=0.36 placebo 25 14 raloxifene 34 5 SF-36v2 total 0.1 (1) p=0.71 placebo 32 6 raloxifene 23 15 SQLS total 0.2 (1) p=0.70 placebo 24 13 Raloxifene 31 (78%) Total Improved Placebo 30 (77%) Chi-square 0.0 (1) p=0.95 Number Needed to Treat 173 % change calculated as (week 6 minus baseline)/(baseline) PANSS Positive and Negative Syndrome Scale, DASS Depression Anxiety and Stress Scale, SF36v2 Short Form 36 Version 2 Health Survey Questionnaire, SQLS Schizophrenia Quality of Life Scale. Improvement defined as ≥ 20% symptom severity reduction. No improvement defined as <20% symptom severity reduction. 9 Supplemental Table 10. Cognitive and symptom outcomes in crossover analysis Supplemental Table 10 Measure Cognitive Outcomes Cognitive Tests X Treatment TMT-A X Treatment Symptom Outcomes PANSS X Treatment N Wilk’s Lambda F test p-value 70 48 0.9 0.9 (4,66)=1.8 (1,47)=4.3 0.14 0.04 71 (3,68)=1.3 0.28 DASS X Treatment 70 0.9 1.0 (3,67)=0.7 0.57 SF-36v2 X Treatment 69 1.0 (1,68)=0.0 0.88 SQLS X Treatment 66 1.0 (1,65)=0.8 0.37 Cognitive z-scores were used for cognitive analyses Cognitive Tests (Wechsler Adult Intelligence Scale Letter Number Sequencing, Wechsler Memory Scale Revised Logical Memory I, Wechsler Memory Scale Revised Logical Memory II, COWAT Controlled Oral Word Association Test), Treatment (raloxifene versus placebo), Time (1=baseline, 2=week 6), TMT-A (Trail Making Test A), PANSS (Positive and Negative Syndrome Scale [incl. positive, negative, and general subtests]), DASS (Depression Anxiety and Stress Scale), SF-36v2 (short form 36 version 2 health survey questionnaire, SQLS (Schizophrenia Quality of Life Scale Crossover Analysis and Results To assess the overall crossover design results, difference scores were calculated for each outcome measure for each phase (period 1: week 6 score minus baseline score, period 2: week 13 score minus week 6 score). These difference scores were combined for the raloxifene and placebo conditions, regardless of period. Treatment effects on cognition were analysed using a repeated measures MANOVA (with LNS, LM I, LM II, and COWAT as dependent variables) and a repeated measures ANOVA (with TMT-A as a dependent variable) with treatment condition (raloxifene versus placebo) as the within subjects measure. Treatment effects for symptom, emotional and functional measures were analysed using separate repeated measures MANOVAs (for PANSS and DASS) and repeated measures ANOVAs (for SF36-v2 and SQLS) with treatment condition (raloxifene versus placebo) as the within subjects factor. Treatment effects for the full 13-week crossover trial design revealed a significant treatment effect only on TMT-A, Wilk’s Lambda 0.9, (1, 47) = 4.3, p = 0.04, where the raloxifene condition showed a significant benefit, mean difference (SD) = -0.5, (1.0), relative to placebo, mean difference (SD) = -0.1, (0.7), (see table above). The crossover design analysis did not show any other significant effects of raloxifene in relation to cognitive, symptom, emotional, or functional measures. 10 Supplemental Figure 1. Example of Carryover Effect on Logical Memory I (LM I) Figure 1. A carryover effect is evident in the raloxifene/placebo (R/P) condition, where during the placebo treatment condition in phase II the group that was previously administered raloxifene does not return to their baseline. Wechsler Memory Scale Revised Logical Memory I is a measure of immediate verbal memory. WO = washout period. 11