DOI: 10.5061/dryad.6djh9w1fj
title: Differential SP4 expression and HSP60 abundance in buccal swabs from patients with schizophrenia

description: Schizophrenia (SCZ) is heterogenous and polygenic, making it difficult to
 diagnose and treat. This is unsurprising as diagnostic criteria are solely
 based on behavioral markers. There is a critical need for easy-to-collect
 biomarkers that aid in treatment. To identify potential biomarkers, we
 recruited SCZ patients and controls. Using buccal cell lysates, we
 performed real-time quantitative PCR and identified significant
 differences in Sp4 mRNA between patients and controls. Targeted mass
 spectrometry identified increased heat shock protein 60 (HSP60) in SCZ
 samples. To determine the utility of Sp4 mRNA and HSP60 protein as
 biomarkers, we evaluated their relationship with symptom severity and
 aberrant cognitive processes. Correlational analyses revealed that
 elevated Sp4 mRNA and HSP60 protein define a subgroup of SCZ patients who
 demonstrate symptomology and poor memory. These data support buccal cell
 Sp4 mRNA and HSP60 protein as easy-to-collect, candidate SCZ biomarkers
 for a subset of patients.
description: # Differential SP4 expression and HSP60 abundance in buccal swabs from
 patients with schizophrenia **Short title:** SP4 and HSP60 biomarkers in
 schizophrenia patients **Journal:** *Science Advances* (submitted /
 revision package) **Dataset DOI**:10.5061/dryad.6djh9w1fj.zip ## Overview
 This README describes all data files associated with the manuscript,
 including raw experimental outputs, processed datasets, and a consolidated
 master summary dataset used for all statistical analyses. The dataset
 includes molecular, cognitive, and clinical measures derived from buccal
 swabs and behavioral assessments in patients with schizophrenia and
 control subjects. All statistical analyses, normalization procedures, and
 model specifications are described in detail in the main text and the
 Materials and Methods section of the manuscript. No analysis scripts or
 proprietary analysis workspaces are provided. All datasets are supplied in
 non-proprietary CSV format with NA used to denote missing or
 non-applicable values. A single master summary file consolidates all
 de-identified participant-level variables used for correlation analyses,
 hierarchical regression models, and generation of all figures and
 supplementary tables. ## Software used • Microsoft Excel-compatible CSV
 files — raw and processed tabular data\ • QIAGEN Digital Insights software
 — RT-qPCR data processing, quality assessment, and targeted proteomics
 data handling Important clarification: Raw RT-qPCR output files include
 numerous machine-generated and quality-control variables produced by the
 instrument software. Only analysis-relevant variables were used for
 downstream analyses. These curated variables are compiled in the master
 summary dataset, which represents the authoritative, analysis-ready
 version of the data used for all reported results. ## File organization •
 qRT-PCR — raw RT-qPCR plate-level output files (CSV) • AXCPT_Data — AX-CPT
 participant-level raw task output files and summary data (CSV) • JOVI_Data
 — JOVI participant-level raw task output files and summary data (CSV) •
 HSP60_tMS — targeted mass spectrometry raw abundance and normalized HSP60
 data (CSV) • Supplementary — supplementary figures, tables, and validation
 source files • Crosta_Master_Summary_Data.csv — consolidated,
 analysis-ready dataset All CSV files contain no embedded formulas,
 formatting, or merged cells. Blank cells in original outputs have been
 replaced with NA.  ### List of Submitted Files
 **Crosta_Master_Summary_Data.csv** Consolidated, analysis-ready dataset
 containing all de-identified participant-level demographic, molecular,
 cognitive, and clinical variables used in all statistical analyses.
 **Crosta_Figure1_RTqPCR.zip**: (Figure 1 - RT-qPCR of SP4, NOS1AP,
 Dexras1) Raw RT-qPCR plate-level output files exported from QIAGEN Digital
 Insights software. Files contain machine-generated Ct values and
 quality-control metrics. Blank cells have been replaced with NA.
 `RTqPCR_Plate01_Raw.csv` `RTqPCR_Plate02_Raw.csv...`
 `RTqPCR_Plate09_Raw.csv` `RTqPCR_Plate10_Raw.csv`
 **Crosta_Figure2_AXCPT.zip** (AXCPT_Data - Figure 2 — AX Continuous
 Performance Task) Raw participant-level AX-CPT task output files. One CSV
 file per participant containing unprocessed CNTRACS/E-Prime output,
 including trial-level accuracy and reaction time data.
 `AXCPT_C[ID]_raw.csv` Control participants C01-C29, excluding C04 and C27.
 `AXCPT_P[ID]_raw.csv` Patient participants P02-P35, excluding P01, P15-16,
 P23-24, P29, P31-32. `axcpt_scores_summary.csv` Participant-level summary
 dataset containing averaged accuracy, error rates, and reaction times
 (milliseconds) for AX, AY, BX, and BY trial types.
 **Crosta_Figure4_tMS.zip** (HSP60_tMS - Figure 4 — targeted mass
 spectrometry) `tMS_abundance.csv` Raw HSP60 protein abundance values
 measured by targeted mass spectrometry. `tMS_normalization.csv` Normalized
 HSP60 abundance values used for statistical analyses.- JOVI_Data -
 Supplementary Figure 1 — JOVI task
 **Crosta_SupplementaryFigure1_JOVI.zip** (Raw participant-level JOVI task
 output files) One CSV file per participant containing unprocessed
 CNTRACS/E-Prime output, including trial-level responses, accuracy, and
 reaction times. `JOVI_C[ID]_raw.csv`: Control participants C01-C29,
 excluding C04 and C27. `JOVI_P[ID]_raw.csv`: Patient participants P02-P35,
 excluding P01, P15-16, P23-24, P29, P31-32) `JOVI_scores_Summary.csv`
 (JOVI summary file): Condition-level summary dataset (conditions 1–8)
 containing percent correct and mean reaction time (milliseconds) for
 correct responses. **Crosta_SupplementaryFigure2_RTqPCR_SP4.zip**
 (Supplementary Figure 2 — Orthogonal SP4 primer RT-qPCR)
 `RTqPCR_SP4-Origen.csv` `RTqPCR_SP4-RTP1.csv` `RTqPCR_SP4-TF.csv` Each
 file contains participant-level Ct mean, Delta Ct, and Delta Delta Ct
 values. 
 **Crosta_SupplementaryFigure4_Western_Blot_Analysis_of_HSP60.zip**
 (Supplementary Figure 4 — Western blot validation) `250110-Western Blot
 Analysis of HSP60 in Human Frontal Cortex_Determining Linear Range of
 HSP60_Buccal Swab Western Blot.pdf`
 **Crosta_Supplementary_Tables_Correlations.zip** (Supplementary tables)
 `Supplementary_Table_4_Correlations.csv`
 `Supplementary_Table_5_Multiple_Linear_Regression.csv` ### Participant
 identifiers • C### = control subject • P### = patient with schizophrenia
 All participant identifiers are fully de-identified and consistent across
 all datasets. ### Master summary dataset (central analysis file) A single
 CSV file consolidates demographic, molecular, cognitive, and clinical
 variables used in all statistical analyses reported in the manuscript.
 File • Filename: Crosta_Master_Summary_Data.csv • Rows: Individual
 participants • Columns: Defined below This dataset was used for: •
 Correlation analyses • Hierarchical multiple linear regression analyses •
 Generation of all summary statistics and figures **Data dictionary —
 Crosta_Master_Summary_Data.csv** **Participant and demographic variables**
 SubjectID - De-identified participant identifier (C### = control
 participant; P### = participant with schizophrenia). Age - Range of years
 that fits each participant's age at the time of experiment. Unit:
 5-year-buckets. Sex - binarized to 1 or 2 Race - Self-reported ethnicity
 category (1 = Asian; 2 = Black or African American; 3 = Hispanic or
 Latino, 4 = White). **Buccal swab molecular biomarkers (unitless)**
 SP4mRNA - Relative SP4 mRNA expression measured by RT-qPCR using the
 comparative Ct method. Values represent ΔΔCt-derived expression normalized
 to GAPDH and plate-specific control samples. Dexras1mRNA - Relative
 Dexras1 (RASD1) mRNA expression measured by RT-qPCR and normalized to
 GAPDH using the comparative Ct method. NOS1APmRNA - Relative NOS1AP mRNA
 expression measured by RT-qPCR and normalized to GAPDH using the
 comparative Ct method. HSP60_tMS_Normalized - Normalized abundance of
 HSP60 protein measured by targeted mass spectrometry. Values were
 normalized relative to control samples within analytical batches.
  **Memory performance (HVLT-R)** HVLTRTotalRecallRaw - Total number of
 words correctly recalled across learning trials of the Hopkins Verbal
 Learning Test–Revised. HVLTRDelayedRecallRaw - Number of words correctly
 recalled following the delay period.\ HVLTRRetentionRaw - Percentage of
 retained words calculated from delayed recall relative to learning
 performance. HVLTRRDIRaw - Recognition Discrimination Index, reflecting
 the ability to distinguish target words from distractors. **Cognitive
 control and goal maintenance (AX-CPT)** AXCPT_AX_ErrorRate - Proportion
 (0-1) of incorrect responses on AX trials. AXCPT_AY_ErrorRate - Proportion
 (0–1) of incorrect responses on AY trials. AXCPT_BX_ErrorRate - Proportion
 (0–1) of incorrect responses on BX trials. AXCPT_BY_ErrorRate - Proportion
 (0–1) of incorrect responses on BY trials. AXCPT_AX_ReactionTime_ms - Mean
 reaction time for correct responses on AX trials. AXCPT_AY_ReactionTime_ms
 - Mean reaction time for correct responses on AY trials.
 AXCPT_BX_ReactionTime_ms - Mean reaction time for correct responses on BX
 trials. AXCPT_BY_ReactionTime_ms - Mean reaction time for correct
 responses on BY trials. **Symptom severity (PANSS)** All PANSS variables
 are unitless composite scores. PANSS_Positive - Positive symptom factor
 score derived from the Positive and Negative Syndrome Scale.
 PANSS_Negative - Negative symptom factor score derived from the Positive
 and Negative Syndrome Scale. PANSS_Cognitive - Cognitive/disorganization
 factor score derived from PANSS items. PANSS_Excitement - Excitement
 factor score derived from PANSS items. PANSS_Depression
 - Depression/anxiety factor score derived from PANSS items.
 PANSS_Disorganization - Disorganization symptom cluster score based on
 Cuesta & Peralta classification. PANSS_Anergia - Anergia symptom
 cluster score reflecting reduced motivation and energy.
 PANSS_ThoughtDisturbance - Thought disturbance symptom cluster score.
 PANSS_Activation - Activation symptom cluster score reflecting agitation
 and hostility. PANSS_ParanoidBelligerence - Paranoid/belligerence symptom
 cluster score. PANSS_Depression_Cluster - Depression symptom cluster
 score. **Visual perception and integration (JOVI)**
 JOVI_percentcorrect_0deg - Percentage of correct responses at 0°
 orientation jitter. JOVI_percentcorrect_7_8deg - Percentage of correct
 responses at 7–8° orientation jitter. JOVI_percentcorrect_9_10deg
 - Percentage of correct responses at 9–10° orientation jitter.
 JOVI_percentcorrect_11_12deg - Percentage of correct responses at 11–12°
 orientation jitter. JOVI_percentcorrect_13_14deg - Percentage of correct
 responses at 13–14° orientation jitter. JOVI_percentcorrect_15_16deg
 - Percentage of correct responses at 15–16° orientation jitter.
 JOVI_percentcorrect_LineCatch - Percentage of correct responses on line
 catch trials.\ JOVI_percentcorrect_NoBackgroundCatch - Percentage of
 correct responses on no-background catch trials. JOVI_ReactionTime_0deg_ms
 - Mean reaction time for correct responses at 0° orientation jitter.
 JOVI_ReactionTime_7_8deg_ms - Mean reaction time for correct responses at
 7–8° orientation jitter. JOVI_ReactionTime_9_10deg_ms - Mean reaction time
 for correct responses at 9–10° orientation jitter.
 JOVI_ReactionTime_11_12deg_ms - Mean reaction time for correct responses
 at 11–12° orientation jitter. JOVI_ReactionTime_13_14deg_ms - Mean
 reaction time for correct responses at 13–14° orientation jitter.
 JOVI_ReactionTime_15_16deg_ms - Mean reaction time for correct responses
 at 15–16° orientation jitter. JOVI_ReactionTime_LineCatch_ms - Mean
 reaction time for correct responses on line catch trials.
 JOVI_ReactionTime_NoBackgroundCatch_ms - Mean reaction time for correct
 responses on no-background catch trials. ### Description of the data and
 file structure: Data Dictionary **File: Crosta_Figure1_RTqPCR.zip:**
 RT-qPCR of SP4, NOS1AP, and Dexras1 **Description: Data for Figure 1:
 RT-qPCR of SP4, NOS1AP, and Dexras1 in the manuscript.** RT-qPCR data for
 SP4, NOS1AP, and Dexras1 mRNA expression in buccal swab samples are
 provided as CSV files corresponding to individual qPCR plates (10 total)
 within the qRT-PCR/ directory. Each plate-level workbook contains raw
 instrument outputs exported from the qPCR analysis software, including
 mean quantification cycle values (Cq Mean, corresponding to Ct Mean),
 technical replicate information, and machine-generated quality-control
 metadata. RT-qPCR data processing and quality assessment were performed
 using QIAGEN Digital Insights software. Raw RT-qPCR output files contain
 numerous instrument-generated columns related to amplification
 performance, melt curve characteristics, and baseline thresholding. Only a
 subset of these columns was used for downstream analyses.
 Analysis-relevant values were extracted, processed, and compiled into
 analysis-ready datasets. Each reaction was run in triplicate. Positive
 controls (human brain cDNA) and negative controls (no-template/water
 controls) were included during assay validation and quality assessment but
 are not included in the deposited analysis-ready datasets, as they were
 not used in statistical analyses. **Contents: 10 plate-level raw output
 files (RTqPCR_Plate01_Raw.csv...RTqPCR_Plate10_Raw.csv) and
 RTqPCR_Data_Summary.csv** RTqPCR_Data_Summary.csv contains an
 analysis-ready summary of RT-qPCR measurements used to generate Figure 1.
 Data are aggregated at the participant level, with one row per participant
 and gene target. Values in this file were derived from raw plate-level
 RT-qPCR output files after quality control and normalization. **Variables
 for raw output files:** Well Position - Position of the reaction well on
 the qPCR plate (e.g., A1, B3). Used to identify the physical location of
 each reaction. Omit - Flag indicating whether the reaction was excluded
 from analysis by the instrument software.\ Values: TRUE = omitted; FALSE =
 included. Sample_Name - De-identified sample identifier corresponding to a
 participant or control material. C### = control participant; P### =
 patient. Dilution (e.g., 1:10) indicates RNA input dilution. Target_Name
 - Gene amplified in the reaction. Includes GAPDH (housekeeping gene), SP4,
 NOS1AP, Dexras1, or control reactions (e.g., water). Task - Reaction
 classification assigned by the qPCR software.\ “Unknown” indicates a
 biological sample; “NTC” indicates a no-template control. Reporter
 - Fluorescent reporter dye used to detect amplification (e.g., SYBR
 Green). Quencher - Fluorescent quencher associated with the reporter dye.
 For SYBR Green assays, this value may be NA or constant. Quantity
 - Estimated quantity of amplified target based on standard curve
 calculations, when applicable.\ Unit: arbitrary units defined by the
 instrument software. Quantity Mean - Mean estimated quantity across
 technical replicates.\ Unit: arbitrary units. Quantity SD - Standard
 deviation of quantity estimates across technical replicates.\ Unit:
 arbitrary units. RQ - Relative quantity calculated by the software,
 typically normalized to a reference sample or control.\ Unit: relative
 (unitless). RQ Min - Minimum relative quantity value across technical
 replicates.\ Unit: relative (unitless). RQ Max - Maximum relative quantity
 value across technical replicates.\ Unit: relative (unitless). CT - Cycle
 threshold (Ct) value for the individual reaction well. Ct is the PCR cycle
 at which fluorescence exceeds background threshold.\ Unit: cycles
 (unitless numeric value). Ct_Mean - Mean cycle threshold (Ct) across
 technical triplicates. Ct is the PCR cycle at which fluorescence exceeds
 background threshold.\ Unit: cycles (unitless numeric value). Ct SD
 - Standard deviation of Ct values across technical replicates.\ Unit:
 cycles. Delta Ct - Difference between Ct value of the target gene and Ct
 value of the housekeeping gene (GAPDH) for the same sample.\ Unit: cycles.
 Delta_Ct_Mean - Difference between Ct_Mean of the target gene and Ct_Mean
 of GAPDH for the same sample. Represents within-sample normalization.\
 Unit: cycles (unitless numeric value). Delta Ct Mean - Mean Delta Ct
 across technical replicates.\ Unit: cycles. Delta Ct SD - Standard
 deviation of Delta Ct values across technical replicates.\ Unit: cycles.
 Delta Ct SE - Standard error of the mean of Delta Ct values across
 technical replicates.\ Unit: cycles. Delta_Delta_Ct - Difference between
 the sample’s Delta_Ct_Mean and the mean Delta Ct of control samples run on
 the same qPCR plate. Plate-specific controls were used to correct for
 inter-plate variability.\ Unit: cycles. Automatic Ct Threshold - Indicator
 specifying whether the Ct threshold was automatically determined by the
 software.\ Values: TRUE/FALSE. Ct Threshold - Fluorescence threshold value
 used to calculate Ct during the exponential phase of amplification.\ Unit:
 fluorescence units (arbitrary). Automatic Baseline - Indicator specifying
 whether the baseline range was automatically determined by the software.\
 Values: TRUE/FALSE. Baseline Start - PCR cycle number at which the
 baseline calculation begins.\ Unit: cycles. Baseline End - PCR cycle
 number at which the baseline calculation ends.\ Unit: cycles. Amp Status
 - Amplification status assigned by the software.\ Values include “Amp”
 (successful amplification), “No Amp” (no amplification), or
 “Inconclusive”. Comments - Free-text comments generated by the software
 regarding amplification quality or issues. Cq Conf - Calculated confidence
 score for the Ct (Cq) value. Values near 1 indicate high confidence;
 values near 0 indicate failed or unreliable amplification.\ Unit: relative
 confidence (0–1). MTP - Multiplex flag indicating whether the reaction was
 multiplexed.\ Values: TRUE/FALSE. EXPFAIL - Experimental failure flag
 assigned by the software.\ TRUE indicates a failed reaction. NOAMP - Flag
 indicating no detectable amplification.\ TRUE indicates absence of
 amplification. THOLDFAIL - Threshold failure flag indicating abnormal
 threshold determination.\ Values: TRUE/FALSE. Tm1 - Primary melting
 temperature (Tm) of the amplified product determined from melt curve
 analysis.\ Unit: degrees Celsius (°C). CQCONF - Binary confidence flag for
 Ct value.\ Y = confident Ct; N = not confident. Tm2 - Secondary melting
 temperature peak, if present.\ Unit: degrees Celsius (°C). HIGHSD - Flag
 indicating high standard deviation among technical replicates.\ Values:
 TRUE/FALSE. Tm3 - Additional melting temperature peak detected during melt
 curve analysis.\ Unit: degrees Celsius (°C). OUTLIERRG - Flag indicating
 that the reaction was identified as a statistical outlier by the
 software.\ Values: TRUE/FALSE. Tm4 - Additional melting temperature peak,
 if detected.\ Unit: degrees Celsius (°C). NA - Indicates that a value is
 not applicable (e.g., housekeeping gene rows do not have Delta Ct or Delta
 Delta Ct values, or control reactions without amplification). *Variables
 for* *RTqPCR_Data_Summary.csv:* Plate Number - Numeric identifier of the
 RT-qPCR plate on which the sample was processed. Plates were analyzed
 independently, and control samples within each plate were used as the
 reference for ΔΔCt calculations. Subject_ID - De-identified participant
 identifier (C## = control participant, P## = participant with
 schizophrenia). Ct Mean GAPDH - Mean cycle threshold (Ct) value for the
 housekeeping gene GAPDH, averaged across technical replicates for the
 given subject on the specified plate. Ct values represent the PCR cycle at
 which fluorescence crossed the detection threshold (unitless). Ct Mean
 SP4  - Mean cycle threshold (Ct) value for SP4 mRNA across technical
 triplicates. Ct is the PCR cycle at which fluorescence exceeds background
 threshold.\ Unit: cycles (unitless numeric value). Ct Mean Dexras - Mean
 cycle threshold (Ct) value for Dextas1 mRNA across technical triplicates.
 Ct is the PCR cycle at which fluorescence exceeds background threshold.\
 Unit: cycles (unitless numeric value). Ct Mean NOS1AP - Mean cycle
 threshold (Ct) value for NOS1AP mRNA across technical triplicates. Ct is
 the PCR cycle at which fluorescence exceeds background threshold.\ Unit:
 cycles (unitless numeric value). Delta Ct Mean SP4 - Difference between
 Ct_Mean of SP4 mRNA and Ct_Mean of GAPDH for the same sample. Represents
 within-sample normalization.\ Unit: cycles (unitless numeric value). Delta
 Ct Mean Dexras - Difference between Ct_Mean of Dexras mRNA and Ct_Mean of
 GAPDH for the same sample. Represents within-sample normalization.\ Unit:
 cycles (unitless numeric value). Delta Ct Mean NOS1AP - Difference between
 Ct_Mean of NOS1AP mRNA and Ct_Mean of GAPDH for the same sample.
 Represents within-sample normalization.\ Unit: cycles (unitless numeric
 value). Delta Delta Ct SP4 - This value represents relative SP4 expression
 normalized to plate-specific controls. Difference between the sample’s
 Delta_Ct_Mean of SP4 mRNA and the mean Delta Ct of control samples run on
 the same qPCR plate. Plate-specific controls were used to correct for
 inter-plate variability.\ Unit: cycles. Delta Delta Ct Dexras - This value
 represents relative Dexras1 expression normalized to plate-specific
 controls. Difference between the sample’s Delta_Ct_Mean of Dexras1 mRNA
 and the mean Delta Ct of control samples run on the same qPCR plate.
 Plate-specific controls were used to correct for inter-plate variability.\
 Unit: cycles. Delta Delta Ct NOS1AP - This value represents relative
 NOS1AP expression normalized to plate-specific controls. Difference
 between the sample’s Delta_Ct_Mean of NOS1AP mRNA and the mean Delta Ct of
 control samples run on the same qPCR plate. Plate-specific controls were
 used to correct for inter-plate variability.\ Unit: cycles. NA values -
 Indicates that a value was not available or not applicable for that
 subject–gene combination (e.g., target not amplified, failed quality
 control, or reference gene only). 
 
 **File: Crosta_Figure2_AXCPT.zip**:AXCPT data for patients and controls
 Description: Data for Figure 2: **AX Continuous Performance Task in the
 manuscript** AX-CPT behavioral data assessing cognitive control and goal
 maintenance are provided in CSV format within the AXCPT_Data/ directory.
 Two complementary data products are included: participant-level raw task
 output files and a consolidated, analysis-ready summary dataset.
 **Contents:  53 individual raw data files
 (AXCPT_C01_raw.csv...AXCPT_P35_raw.csv) and axcpt_scores_summary.csv**
 Participant-level raw AX-CPT data in the raw data files are provided as
 individual Excel workbooks (AXCPT_Cxx_raw.csv and AXCPT_Pxx_raw.csv),
 where each file corresponds to a single subject (C### = control; P### =
 patient with schizophrenia). These files contain trial-by-trial task
 output exported directly from the CNTRACS AX-CPT task software (E-Prime
 format), including detailed information on task events, stimulus
 presentation, responses, reaction times, and device metadata. Each raw
 file includes a set of machine-generated variables reflecting practice and
 test blocks, cue and probe events, trial types (AX, AY, BX, BY), response
 accuracy, and timing measures. All values in the summary dataset were
 derived by aggregating trial-level data from the participant-level raw
 AX-CPT files. Missing or non-applicable values are explicitly coded as NA.
 All statistical analyses reported in the manuscript were performed
 exclusively using this consolidated summary dataset. Participant
 identifiers and group assignments are consistent across raw and summary
 files. **Variables for raw files:** ExperimentName - Name of the E-Prime
 experiment file used to administer the AX Continuous Performance Task
 (AX-CPT). Subject - De-identified participant identifier. Session
 - Session number for the participant. DataFile.Basename - Base filename of
 the raw E-Prime data file generated during task execution.
 Display.RefreshRate - Refresh rate of the display monitor used during task
 presentation, in Hertz (Hz). ExperimentVersion - Version identifier of the
 AX-CPT task. Group - Diagnostic group identifier assigned within the task
 software. Handedness - Participant-reported handedness as recorded by the
 task software. RandomSeed - Random number generator seed used to
 initialize trial order and stimulus presentation. RuntimeCapabilities
 - Capabilities of the runtime environment detected by the E-Prime
 software. RuntimeVersion - Version of the E-Prime runtime software used
 during data collection. RuntimeVersionExpected - Expected runtime version
 specified by the experiment configuration. StudioVersion - Version of
 E-Prime Studio used to create the task. SubjectCharacterString - Internal
 subject identifier string generated by the software. ThankYou.DEVICE
 - Marker indicating presentation of the task completion or “thank you”
 screen. Title.DEVICE - Marker indicating presentation of the title or
 introductory screen. Block - Block number within the task structure.
 EndofPractice.ACC - Accuracy during the final practice trial (1 = correct,
 0 = incorrect). EndofPractice.CRESP - Correct response code for the final
 practice trial. EndofPractice.DEVICE - Device marker associated with the
 end-of-practice event. EndofPractice.DurationError - Flag indicating a
 timing irregularity during the end-of-practice event.
 EndofPractice.OnsetDelay - Delay before onset of the end-of-practice
 screen, in milliseconds. EndofPractice.OnsetTime - Onset time of the
 end-of-practice screen, in milliseconds. EndofPractice.OnsetToOnsetTime
 - Time between consecutive onset events during end-of-practice, in
 milliseconds. EndofPractice.RESP - Participant response recorded during
 the end-of-practice event. EndofPractice.RT - Reaction time recorded
 during the end-of-practice event, in milliseconds. EndofPractice.RTTime
 - Absolute timestamp of the end-of-practice reaction time, in
 milliseconds. EndPractice1.DEVICE - Device marker indicating termination
 of the practice phase. InstructScreens - Indicator for instructional
 screen presentation. InstructScreens.Cycle - Cycle number associated with
 instructional screen presentation. InstructScreens.Sample - Sample index
 associated with instructional screen presentation. Pause.DEVICE - Marker
 indicating presentation of a pause screen. Practice - Indicator for
 practice trial execution. Practice.Cycle - Cycle number associated with
 practice trials. Practice.Sample - Sample index associated with practice
 trials. PracticeReady.DEVICE - Marker indicating readiness screen prior to
 practice trials. Procedure[Block] - Procedure name executed at the block
 level. Ready.DEVICE - Marker indicating presentation of a readiness screen
 prior to test blocks. Running[Block] - Indicator of block-level execution
 state. Slide01.DEVICE - Marker indicating presentation of slide 01.
 Slide02Build1.DEVICE / Slide02Build8.DEVICE - Markers indicating
 presentation of sequential build elements within slide 02.
 Slide02Build1.RESP – Slide02Build8.RESP - Participant responses associated
 with slide 02 build elements. Slide03CardPractice.DEVICE - Marker
 indicating presentation of card-based practice slide.
 Slide04ToTrials.DEVICE - Marker indicating transition from instruction to
 trials. Slide05Sounds1.DEVICE / Slide05Sounds4.DEVICE - Markers indicating
 sound cue presentation events. Slide05Sounds4.RESP - Participant response
 associated with the fourth sound cue. Test - Indicator for execution of
 test trials. Test.Cycle - Cycle number associated with test trials.
 Test.Sample - Sample index associated with test trials. Trial - Sequential
 trial number. CorrectRespCue - Correct response associated with the cue
 stimulus. CorrectRespTarg - Correct response associated with the probe
 (target) stimulus. Cue - Cue stimulus presented on the trial. Cue.ACC
 - Cue accuracy (1 = correct, 0 = incorrect). Cue.CRESP - Correct response
 code for the cue. Cue.DEVICE - Device marker associated with cue
 presentation. Cue.DurationError - Flag indicating abnormal timing during
 cue presentation. Cue.OffsetTime - Offset time of the cue stimulus, in
 milliseconds. Cue.OnsetDelay - Delay before cue onset, in milliseconds.
 Cue.OnsetTime - Onset time of the cue stimulus, in milliseconds.
 Cue.OnsetToOnsetTime - Time between consecutive cue onsets, in
 milliseconds. Cue.RESP - Participant response to the cue stimulus. Cue.RT
 - Reaction time to the cue stimulus, in milliseconds. Cue.RTTime
 - Absolute timestamp of cue reaction time, in milliseconds. Cue.StartTime
 - Start time of cue presentation, in milliseconds.
 CueFeedback.DurationError / CueFeedback.OnsetToOnsetTime - Variables
 describing timing, duration, and execution of feedback following cue
 responses, including onset, offset, delays, and timing errors (all time
 values in milliseconds). CueList - Identifier for the cue stimulus list.
 CueMask.StartTime - Start time of cue masking event, in milliseconds.
 Interval - Inter-stimulus interval duration, in milliseconds. Prac1
 - Indicator for an additional practice-related trial or event. Prac1.Cycle
 - Cycle number associated with the additional practice event. Prac1.Sample
 - Sample index associated with the additional practice event. Probe.ACC
 - Probe (target) accuracy (1 = correct, 0 = incorrect). Probe.CRESP
 - Correct response code for the probe stimulus. Probe.DEVICE - Device
 marker associated with probe presentation. Probe.OffsetTime - Offset time
 of the probe stimulus, in milliseconds. Probe.OnsetTime - Onset time of
 the probe stimulus, in milliseconds. Probe.RESP - Participant response to
 the probe stimulus. Probe.RT - Reaction time to the probe stimulus, in
 milliseconds. Probe.RTTime - Absolute timestamp of probe reaction time, in
 milliseconds. Probe.StartTime - Start time of probe presentation, in
 milliseconds. ProbeFeedback.ActionDelay / ProbeFeedback.TimingMode - \
 Variables describing timing, duration, execution, and timing mode of
 feedback following probe responses (all time values in milliseconds).
 Procedure[Trial] - Procedure name executed at the trial level.
 Running[Trial] - Indicator of trial-level execution state. Target - Target
 stimulus presented on the trial. TargetList - Identifier for the target
 stimulus list. Trials1to36, Trials1to36b, Trials1to36c, Trials1to36d
 - Identifiers for grouped trial sets defined by the task structure.
 Trials1to36.Cycle – Trials1to36d.Sample - Cycle and sample indices
 associated with grouped trial sets. TrialType - Trial classification (AX,
 AY, BX, or BY), defining cue–probe combinations used in AX-CPT analyses.
 NA - Indicates non-applicable values for task phases without responses.
 **Variables for axcpt_scores_summary:** subject_ID - De-identified
 participant identifier (C### = control subject, P### = patient with
 schizophrenia). Average_of_Probe.ACC - Mean accuracy across all probe
 trials.\ Unit: proportion (0–1). Average_of_Probe.RT - Mean reaction time
 for correct probe responses.\ Unit: milliseconds. AX_mean_error_rate,
 AY_mean_error_rate, BX_mean_error_rate, BY_mean_error_rate - Proportion of
 incorrect responses for each trial type.\ Unit: proportion (0–1).
 AX_mean_RT, AY_mean_RT, BX_mean_RT, BY_mean_RT - Mean reaction time for
 correct responses by trial type.\ Unit: milliseconds. 
 
 **File: Crosta_Figure4_tMS.zip** **Description: Data for Figure 4: HSP60
 targeted mass spectrometry results in the manuscript** Targeted mass
 spectrometry (tMS) was used to quantify HSP60 protein abundance in buccal
 cell lysates from patients with schizophrenia and control subjects. To
 ensure clarity, accessibility, and reuse, raw mass spectrometry output and
 normalized values used for statistical analyses are provided in two
 separate CSV files. **Contents: two files: tMS_abundance.csv:** Raw
 targeted mass spectrometry signal corresponding to HSP60 protein abundance
 and **tMS_normalization.csv: **HSP60 abundance normalized relative to the
 mean control abundance within the same analytical batch. **Variables for
 tMS_abundance.csv:** Sample - Well or sample position identifier used
 during targeted mass spectrometry acquisition. Subject_ID - De-identified
 participant identifier (C### = control subject, P### = patient with
 schizophrenia). HSP60_Abundance - Raw targeted mass spectrometry signal
 corresponding to HSP60 protein abundance.\ Unit: instrument intensity
 (arbitrary units). **Variables for tMS_normalization.csv:** Subject_ID
 - De-identified participant identifier (C### = control subject, P### =
 patient with schizophrenia). HSP60_Abundance - Raw HSP60 abundance value
 (copied from raw file). HSP60_normalized - HSP60 abundance normalized
 relative to the mean control abundance within the same analytical batch.\
 Unit: relative abundance (unitless). 
 
 ##### **Supplementary Figures and Tables**
 File: Crosta_SupplementaryFigure1_JOVI.zip **Data for Supplementary Figure
 1: Jittered-Orientation Visual Integration (JOVI) task in the manuscript**
 JOVI task data are provided as raw participant-level files and a
 consolidated summary file. **Contents: 54 files of raw data from JOVI task
 (JOVI_C01_Raw.csv...JOVI_P35_Raw.csv) and JOVI_scores_Summary.csv** Raw
 JOVI files are provided as CSV files named JOVI_Cxx_raw.csv or
 JOVI_Pxx_raw.csv. These files contain unprocessed CNTRACS/E-Prime output
 and include experiment metadata, stimulus presentation variables, trial
 identifiers, response accuracy, and reaction time measurements.
 **Variables for raw files:**  ExperimentName - Name of the E-Prime
 experiment file used to administer the Jittered Orientation Visual
 Integration (JOVI) task. Subject - De-identified participant identifier
 assigned by the experimental software. Session - Session number for the
 participant. CNTRACSID - Internal CNTRACS study identifier associated with
 the testing session. DataFile.Basename - Base filename of the E-Prime data
 file generated during task execution. Display.RefreshRate - Monitor
 refresh rate during stimulus presentation (Hz). ExperimentVersion
 - Version number of the JOVI task used. Group - Diagnostic group
 identifier assigned by the task software. RandomSeed - Random number
 generator seed used to initialize trial order. RuntimeCapabilities
 - Capabilities of the runtime environment detected by the software.
 RuntimeVersion - Version of the runtime software used during task
 execution. RuntimeVersionExpected - Expected runtime version specified by
 the task configuration. StudioVersion - Version of E-Prime Studio used to
 build the task. Block - Block number within the task. MasterList
 - Identifier for the master stimulus list used for trial presentation.
 MasterList.Cycle - Cycle number within the master stimulus list.
 MasterList.Sample - Sample index within the master stimulus list.
 PleasantnessDisplay.ACC - Accuracy flag for responses during the
 pleasantness rating display (1 = correct, 0 = incorrect).
 PleasantnessDisplay.CRESP - Correct response code for the pleasantness
 display. PleasantnessDisplay.RESP - Participant response during the
 pleasantness display. PleasantnessDisplay.RT - Reaction time for the
 pleasantness display response (milliseconds). PleasantnessDisplay.RTTime
 - Absolute timestamp of the pleasantness display reaction time
 (milliseconds). Procedure[Block] - Procedure state at the block level.
 Running[Block] - Execution state at the block level. Trial - Sequential
 trial number within the session. answer - Expected correct answer for the
 trial. Block10list – Block24list, Block1list – Block9list\ Indicators
 specifying membership of the current trial in predefined stimulus lists
 associated with different task conditions or difficulty levels. These
 fields are generated automatically by the task structure. correctresponse
 - Correct response associated with the stimulus presented on the trial.
 criticaltrials - Indicator of whether the trial is designated as a
 critical (analysis-relevant) trial. criticaltrials.Cycle - Cycle number
 within the critical trials list. criticaltrials.Sample - Sample index
 within the critical trials list. delta - Angular offset or jitter applied
 to the stimulus orientation on the trial (degrees). ISI.ACC - Accuracy
 flag for inter-stimulus interval events (1 = correct, 0 = incorrect).
 ISI.CRESP - Correct response code for the inter-stimulus interval.
 ISI.RESP - Participant response during the inter-stimulus interval. ISI.RT
 - Reaction time during the inter-stimulus interval (milliseconds). leftegs
 - Indicator for trials presenting left-oriented contour elements.
 leftegs.Cycle - Cycle number within the left-oriented element list.
 leftegs.Sample - Sample index within the left-oriented element list.
 orientation - Orientation direction of the stimulus (e.g., left or right).
 practicetrials - Indicator for practice trials. practicetrials.Cycle
 - Cycle number within the practice trials list. practicetrials.Sample
 - Sample index within the practice trials list. pracwithfeedbacklist
 - Indicator for practice trials presented with feedback.
 pracwithfeedbacklist.Cycle - Cycle number within the
 practice-with-feedback list. pracwithfeedbacklist.Sample - Sample index
 within the practice-with-feedback list. Procedure[Trial] - Procedure state
 at the individual trial level. responseinput.ACC - Accuracy of the
 participant’s response to the stimulus (1 = correct, 0 = incorrect).
 responseinput.CRESP - Correct response code for the stimulus.
 responseinput.RESP - Participant’s recorded response. responseinput.RT
 - Reaction time for the stimulus response (milliseconds). rightegs
 - Indicator for trials presenting right-oriented contour elements.
 rightegs.Cycle - Cycle number within the right-oriented element list.
 rightegs.Sample - Sample index within the right-oriented element list.
 Running[Trial] - Execution state at the trial level. size - Stimulus size
 condition used for the trial. stimuli - Filename or identifier of the
 image stimulus presented on the trial. NA - Indicates that a value was not
 applicable or not generated for a given trial (e.g., non-critical trials,
 practice trials, or software-generated placeholders). **Variables for
 JOVI_scores_Summary.csv:** Patient_ID - De-identified participant
 identifier (C### = control subject, P### = patient with schizophrenia).
 CONDITION - Stimulus condition (1–8). Percent_Correct - Percentage of
 correct responses per condition.\ Unit: percent (0–100).
 Mean_RT_For_Correct_Responses - Mean reaction time for correct responses
 per condition.\ Unit: milliseconds. 
 
 **File: Crosta_SupplementaryFigure2_RTqPCR_SP4.zip** **Description: Data
 for Supplementary Figure 2: RT-qPCR of SP4 in the manuscript** RT-qPCR
 validation of SP4 expression using three independent primer sets.
 **Contents:** **three CSV files of raw data for three primer sets:
 RTqPCR_SP4-Origen.csv, RTqPCR_SP4-RTP1.csv, and RTqPCR_SP4-TF.csv**
 **Variables:** Subject_ID - De-identified participant identifier (C### =
 control subject, P### = patient with schizophrenia). CT_Mean_GAPDH - Mean
 cycle threshold (Ct) value for GAPDH, averaged across technical
 triplicates for the sample. Represent the PCR cycle number at which
 fluorescence crossed the detection threshold.\ Unit: cycles. CT_Mean_Gene
 - Mean cycle threshold (Ct) value for SP4 mRNA measured using the SP4-Gene
 (Origene/RTP1/TF) primer set, averaged across technical triplicates.\
 Unit: cycles. DeltaCt_Mean_Gene - Mean ΔCt value for SP4-TF, calculated
 as: ΔCt = (Ct Mean SP4-Gene) − (Ct Mean GAPDH). This value represents
 SP4-Gene (Origene/RTP1/TF) expression normalized to the GAPDH internal
 control within the same sample. \ Unit: cycles. DeltaDeltaCt_Gene - ΔΔCt
 value for SP4-Gene (Origene/RTP1/TF) expression, calculated as: ΔΔCt =
 (ΔCt of the sample) − (mean ΔCt of control subjects on the same qPCR
 plate). This value represents plate-specific normalization of SP4
 expression relative to controls. \ Unit: cycles. NA - Indicates that a
 ΔΔCt value could not be computed, typically because a valid plate-matched
 control reference was unavailable for that sample. 
 
 **File: Crosta_SupplementaryFigure4_Western_Blot_Analysis_of_HSP60.zip**
 **Description: Data for Supplementary Figure 4: Western blot data for
 HSP60 in the manuscript** Western blot linear-range determination and full
 blot images. Data are provided as a PDF file containing representative
 blots and corresponding validation information. Quantitative analyses
 derived from these experiments are reported in the manuscript. **Contents:
 one powerpoint file of Western blots and quantitation.** **Variables:** No
 tabular raw data files are associated with this supplementary figure. 
 
 **Files: Crosta_Supplementary_Tables_Correlations.zip** **Description:
 Data for Supplementary Tables 4–5 in the manuscript** **Contents: Two
 Excel spreadsheets - Crosta et al Supplementary Table 4.Correlations.cvs
 and Crosta et al Supplementary Table 5.Linear Regressions.cvs**
 Correlation and hierarchical regression outputs with Benjamini–Hochberg
 FDR correction (Excel) 
 
 **External proteomics repository** Proteomics data are deposited with the
 ProteomeXchange Consortium (PRIDE): * **Dataset ID:** PXD055067 * **DOI:**
 10.6019/PXD055067 
 
 **Reproducibility statement** All statistical analyses, normalization
 procedures, and model specifications are described in detail in the main
 manuscript and Materials and Methods section. The Master Summary Excel
 file represents the complete, analysis-ready dataset used to generate all
 reported results. ## Human subjects data We received explicit consent from
 our participants to publish the de-identified data in the public domain,
 and explain all data have codes with no link to names or identifying
 information.