{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003215","ANALYSIS_ID":"AN005272","PROJECT_ID":"PR002005","VERSION":"1","CREATED_ON":"May 21, 2024, 2:05 pm"},

"PROJECT":{"PROJECT_TITLE":"Protein restriction slows the development and progression of Alzheimer''s disease in mice","PROJECT_TYPE":"MS targeted lipidomics","PROJECT_SUMMARY":"Dietary protein is a critical regulator of metabolic health and aging. Low protein diets are associated with healthy aging in humans, and many independent groups of researchers have shown that dietary protein restriction (PR) extends the lifespan and healthspan of mice. Here, we examined the effect of PR on metabolic health and the development and progression of Alzheimer’s disease (AD) in the 3xTg mouse model of AD. We found that PR has metabolic benefits for 3xTg mice and non-transgenic controls of both sexes, promoting leanness and glycemic control in 3xTg mice and rescuing the glucose intolerance of 3xTg females. We found that PR induces sex-specific alterations in circulating metabolites and in the brain lipidome, downregulating sphingolipid subclasses including ceramides, glucosylceramides, and sphingomyelins in 3xTg females. Consumption of a PR diet starting at 6 months of age reduced AD pathology in conjunction with reduced mTORC1 activity, increased autophagy, and had cognitive benefits for 3xTg mice. Finally, PR improved the survival of 3xTg mice. Our results demonstrate that PR slows the progression of AD at molecular and pathological levels, preserves cognition in this mouse model of AD, and suggests that PR or pharmaceutical interventions that mimic the effects of this diet may hold promise as a treatment for AD.","INSTITUTE":"University of Wisconsin-Madison","LAST_NAME":"Simcox","FIRST_NAME":"Judith","ADDRESS":"433 Babcock Dr, Madison, WI, 53706, USA","EMAIL":"jsimcox@wisc.edu","PHONE":"-"},

"STUDY":{"STUDY_TITLE":"Protein restriction slows the development and progression of Alzheimer''s disease in mice","STUDY_SUMMARY":"Dietary protein is a critical regulator of metabolic health and aging. Low protein diets are associated with healthy aging in humans, and many independent groups of researchers have shown that dietary protein restriction (PR) extends the lifespan and healthspan of mice. Here, we examined the effect of PR on metabolic health and the development and progression of Alzheimer’s disease (AD) in the 3xTg mouse model of AD. We found that PR has metabolic benefits for 3xTg mice and non-transgenic controls of both sexes, promoting leanness and glycemic control in 3xTg mice and rescuing the glucose intolerance of 3xTg females. We found that PR induces sex-specific alterations in circulating metabolites and in the brain lipidome, downregulating sphingolipid subclasses including ceramides, glucosylceramides, and sphingomyelins in 3xTg females. Consumption of a PR diet starting at 6 months of age reduced AD pathology in conjunction with reduced mTORC1 activity, increased autophagy, and had cognitive benefits for 3xTg mice. Finally, PR improved the survival of 3xTg mice. Our results demonstrate that PR slows the progression of AD at molecular and pathological levels, preserves cognition in this mouse model of AD, and suggests that PR or pharmaceutical interventions that mimic the effects of this diet may hold promise as a treatment for AD.","INSTITUTE":"University of Wisconsin-Madison","LAST_NAME":"Simcox","FIRST_NAME":"Judith","ADDRESS":"433 Babcock Dr, Madison, WI, 53706, USA","EMAIL":"jsimcox@wisc.edu","PHONE":"-","TOTAL_SUBJECTS":"40","NUM_MALES":"20","NUM_FEMALES":"20"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"3xTg","GENDER":"Male and female","ANIMAL_FEED":"Control, TD.180161; PR, TD.10192"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"F1",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F1_pos_cer_dMRM_072023_063.d"}
},
{
"Subject ID":"-",
"Sample ID":"F2",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F2_pos_cer_dMRM_072023_011.d"}
},
{
"Subject ID":"-",
"Sample ID":"F3",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F3_pos_cer_dMRM_072023_033.d"}
},
{
"Subject ID":"-",
"Sample ID":"F4",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F4_pos_cer_dMRM_072023_015.d"}
},
{
"Subject ID":"-",
"Sample ID":"F5",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F5_pos_cer_dMRM_072023_025.d"}
},
{
"Subject ID":"-",
"Sample ID":"F6",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F6_pos_cer_dMRM_072023_061.d"}
},
{
"Subject ID":"-",
"Sample ID":"F7",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F7_pos_cer_dMRM_072023_065.d"}
},
{
"Subject ID":"-",
"Sample ID":"F8",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F8_pos_cer_dMRM_072023_023.d"}
},
{
"Subject ID":"-",
"Sample ID":"F9",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F9_pos_cer_dMRM_072023_079.d"}
},
{
"Subject ID":"-",
"Sample ID":"F10",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F10_pos_cer_dMRM_072023_081.d"}
},
{
"Subject ID":"-",
"Sample ID":"F11",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F11_pos_cer_dMRM_072023_047.d"}
},
{
"Subject ID":"-",
"Sample ID":"F12",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F12_pos_cer_dMRM_072023_057.d"}
},
{
"Subject ID":"-",
"Sample ID":"F13",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F13_pos_cer_dMRM_072023_075.d"}
},
{
"Subject ID":"-",
"Sample ID":"F14",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F14_pos_cer_dMRM_072023_051.d"}
},
{
"Subject ID":"-",
"Sample ID":"F15",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F15_pos_cer_dMRM_072023_059.d"}
},
{
"Subject ID":"-",
"Sample ID":"F16",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F16_pos_cer_dMRM_072023_031.d"}
},
{
"Subject ID":"-",
"Sample ID":"F17",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F17_pos_cer_dMRM_072023_089.d"}
},
{
"Subject ID":"-",
"Sample ID":"F18",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F18_pos_cer_dMRM_072023_009.d"}
},
{
"Subject ID":"-",
"Sample ID":"F19",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F19_pos_cer_dMRM_072023_071.d"}
},
{
"Subject ID":"-",
"Sample ID":"F20",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"F20_pos_cer_dMRM_072023_019.d"}
},
{
"Subject ID":"-",
"Sample ID":"M1",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M1_pos_cer_dMRM_072023_083.d"}
},
{
"Subject ID":"-",
"Sample ID":"M2",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M2_pos_cer_dMRM_072023_035.d"}
},
{
"Subject ID":"-",
"Sample ID":"M3",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M3_pos_cer_dMRM_072023_029.d"}
},
{
"Subject ID":"-",
"Sample ID":"M4",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M4_pos_cer_dMRM_072023_041.d"}
},
{
"Subject ID":"-",
"Sample ID":"M5",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M5_pos_cer_dMRM_072023_017.d"}
},
{
"Subject ID":"-",
"Sample ID":"M6",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M6_pos_cer_dMRM_072023_053.d"}
},
{
"Subject ID":"-",
"Sample ID":"M7",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M7_pos_cer_dMRM_072023_013.d"}
},
{
"Subject ID":"-",
"Sample ID":"M8",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M8_pos_cer_dMRM_072023_021.d"}
},
{
"Subject ID":"-",
"Sample ID":"M9",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M9_pos_cer_dMRM_072023_087.d"}
},
{
"Subject ID":"-",
"Sample ID":"M10",
"Factors":{"Sample source":"Brain","Genotype":"Non-transgenic","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M10_pos_cer_dMRM_072023_043.d"}
},
{
"Subject ID":"-",
"Sample ID":"M11",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M11_pos_cer_dMRM_072023_073.d"}
},
{
"Subject ID":"-",
"Sample ID":"M12",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M12_pos_cer_dMRM_072023_067.d"}
},
{
"Subject ID":"-",
"Sample ID":"M13",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M13_pos_cer_dMRM_072023_037.d"}
},
{
"Subject ID":"-",
"Sample ID":"M14",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M14_pos_cer_dMRM_072023_077.d"}
},
{
"Subject ID":"-",
"Sample ID":"M15",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M15_pos_cer_dMRM_072023_091.d"}
},
{
"Subject ID":"-",
"Sample ID":"M16",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M16_pos_cer_dMRM_072023_049.d"}
},
{
"Subject ID":"-",
"Sample ID":"M17",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M17_pos_cer_dMRM_072023_069.d"}
},
{
"Subject ID":"-",
"Sample ID":"M18",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M18_pos_cer_dMRM_072023_045.d"}
},
{
"Subject ID":"-",
"Sample ID":"M19",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M19_pos_cer_dMRM_072023_039.d"}
},
{
"Subject ID":"-",
"Sample ID":"M20",
"Factors":{"Sample source":"Brain","Genotype":"3xTg","Treatment":"Protein restriction"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"M20_pos_cer_dMRM_072023_027.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mice were euthanized by cervical dislocation after a 3 hour fast, and the right hemisphere was fixed in formalin for histology whereas the left hemisphere was snap-frozen for mass spectrometry analysis.","SAMPLE_TYPE":"Brain"},

"TREATMENT":{"TREATMENT_SUMMARY":"At the start of the experiment, mice were randomized to receive either a 21% protein diet (Control, TD.180161) or a 7% protein diet (PR, TD.10192) obtained from Envigo. Our diets were formulated to be isocaloric, meaning that any reduction in protein content was compensated for by adjusting the carbohydrate content and fat percent stayed constant."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Whole brain samples were pulverized and 20 mg were homogenized in 215 µL MeOH plus 10 µL of a 30 µM solution of each of the following internal standards: Cer d18:1(d7)_15:0 (Avanti #67492-15-3), Cer d18:1(d7)_16:0 (Avanti # 1840942-13-3), Cer d18:1(d7)_18:0 (Avanti #1840942-14-4), Cer d18:1(d7)_24:0 (Avanti #1840942-15-5), Cer d18:1(d7)_24:1 (Avanti # 1840942-16-6), and SM d18:1(d7)_18:1 (Avanti # 2342574-42-7). The samples were homogenized in bead tubes (1.4mm, Qiagen, #13113-50) in a Qiagen TissueLyzer II (catalog no.: 9244420) for 2 cycles in blocks chilled to 4°C. 250 µL H2O and 750 µL MTBE were then added, and the samples were inverted to mix and placed on ice. After 15 minutes, the samples were centrifuged at 4 °C at 16000 x g for 5 minutes, and 500 µL of the top organic phase was removed into a new tube and dried using a speedvac. Lipids were then resuspended in 150 µL IPA and stored at -20°C until analysis. An insoluble precipitate was also observed when the extracts were resuspended in IPA."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"For targeted sphingolipid separation","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)","SOLVENT_A":"60:40 acetonitrile:water; 10 mM ammonium formate; 0.1% formic acid","SOLVENT_B":"9:1:90 acetonitrile:water:isopropyl alcolhol; 10 mM ammonium formate; 0.1% formic acid","FLOW_GRADIENT":"The gradient began with 30% B and increased to 60% over 1.8 min, then increased to 80% until 7 min and 99% until 7.14 min, which was maintained until 10 min.","FLOW_RATE":"0.5 mL/min","COLUMN_TEMPERATURE":"60"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Agilent 6495 QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Data was processed in the Agilent MassHunter Wokstation, and sphingolipids were quantified by peak height based on the relative concentration of the appropriate internal standard within the samples."},

"MS_METABOLITE_DATA":{
"Units":"ng lipid/mg brain",

"Data":[{"Metabolite":"GlcCer 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