SUB0000337401S
SCOPE OF WORK UCLA CO-INVESTIGATOR (REXACH) WILL ANALYZE RAW RNA SEQUENCING DATA PROVIDED BY UF AND UCSF. DATA TYPES INCLUDE SORTED CELL RNA SEQUENCING AND BULK RNA SEQUENCING FROM IPSC CULTURES, TRANSGENIC MOUSE MODELS AND DE-IDENTIFIED HUMAN BLOOD SAMPLES. UCLA WILL CLEAN AND PROCESS THE SEQUENCING DATA INCLUDING NORMALIZATION, BATCH CORRECTION, AND OUTLIER REMOVAL. WE WILL PERFORM ANALYSES TO CAREFULLY DETECT AND MITIGATE THE INFLUENCE OF TECHNICAL FACTORS ON DATA, ACCORDING TO HIGH DATA QUALITY STANDARDS. WE WILL PERFORM DIFFERENTIAL GENE EXPRESSION, WEIGHTED GENE CO-EXPRESSION AND BIOINFORMATIC ANALYSES TO CHARACTERIZE EFFECTS OF GRN HAPLOINSUFFIENCY ON MICROGLIA AND MONOCYTE AT THE TRANSCRIPTOMIC LEVEL. WE WILL SELECT GENE REGULATORS FOR FUNCTIONAL VALIDATION AND CONTRIBUTE TO FUNCTIONAL VALIDATION EXPERIMENTS. UCLA WILL PROVIDE DATA BACK TO THE COLLABORATING STUDY PIS (FINKBEINER AND TANSEY). UCLA WILL ALSO PARTICIPATE IN QUARTERLY MEETINGS WITH STUDY PIS TO DISCUSS INTERVAL PROGRESS AND RESULTS. UCLA WILL ALSO PROVIDE STUDY PIS DATA FOR THE ANNUAL NIH PROGRESS REPORTS. UCLA WILL CONTRIBUTE DATA, ANALYSES, FIGURES AND PARTICIPATE IN WRITING ANY MANUSCRIPTS RESULTING FROM THIS COLLABORATIVE WORK. UCLA WILL ENSURE COMPLIANCE WITH ALL NIH GUIDELINES FOR DATA SHARING, PROTECTION OF HUMAN SUBJECTS, AND ETHICS. THE HANDLING OF FIXED AND FROZEN BRAIN TISSUE AND DE-IDENTIFIED GENETIC AND GENE EXPRESSION DATA WILL BE PERFORMED IN ACCORDANCE WITH ETHICAL GUIDELINES AND REGULATIONS FOR THE RESEARCH USE OF HUMAN BRAIN TISSUE SET FORTH BY THE NIH THE UK HEALTH DEPARTMENTÂ S HUMAN TISSUE AUTHORITY CODE OF PRACTICE TO ENSURE THE HIGHEST STANDARD FOR DATA PROTECTION, NO PERSONAL IDENTIFYING INFORMATION WILL BE PROVIDED OR BE ACCESSIBLE TO THE REXACH LAB WITH RESPECT TO ANY OF THESE DATA. ALL OF THE WORK WILL BE DONE IN ACCORDANCE WITH THE NEW HEALTH INSURANCE PORTABILITY AND ACCOUNTABILITY ACT (HIPAA), WHICH SAFEGUARDS THE HEALTH INFORMATION OF INDIVIDUALS OBTAINING HEALTHCARE IN THE UNITED STATES. WE ARE IN FULL COMPLIANCE WITH THESE REGULATIONS. UCLA WILL ENSURE COMPLIANCE WITH ALL MTA AGREEMENTS PREPARED WITH THE STUDY COLLABORATORS REGARDING MATERIAL TRANSFER OF RAW DATA AND PROCESSED DATA, AND INTELLECTUAL PROPERTY. WE WILL COMPLY WITH ALL ASPECTS OF THE DATA SHARING PLAN PROVIDED WITH THIS GRANT APPLICATION, INCLUDING ASSISTING IN MAKING ALL DE-IDENTIFIED SEQUENCING DATA PUBLICLY AVAILABLE AT TIME OF PUBLICATION THROUGH DBGAP OR AN ALTERNATIVE REPOSITORY IN COMPLIANCE WITH NIH REQUIREMENTS.
University Of California, LOS Angeles
Project Grant RF1NS128800
$215.1k 2/25/24 SUB0000337301S
DR. STEVEN FINKBEINER WILL LEAD STUDIES IN AIM 1 OF THIS MULTI-PI R01 APPLICATION. HIS STUDIES WILL EMPLOY HUMAN INDUCED PLURIPOTENT STEM CELLS (IPSC) FROM FRONTOTEMPORAL DEMENTIA (FTD) PATIENTS WITH MUTATIONS IN THE C9ORF72 OR GRN (PROGRANULIN) GENES, OR CONTROLS INCLUDING COGNATE ISOGENIC LINES, DIFFERENTIATED TO FOREBRAIN NEURONS (I-NEURONS), OR MICROGLIA (I-MG) OR MONOCYTE (I-MO). HIS STUDIES WILL FOCUS ON UNDERSTANDING THE ROLE OF CENTRAL AND PERIPHERAL IMMUNE CELLS IN NEURODEGENERATION IN FTD USING HIS LONGITUDINAL IMAGING TECHNOLOGY ROBOTIC MICROSCOPY (RM). INITIAL STUDIES WILL DETERMINE IF CENTRAL I-MG OR PERIPHERAL I-MOS FROM FTD PATIENTS ARE HYPERACTIVE IN A CELL AUTONOMOUS MANNER. HYPERACTIVITY WILL BE ASSESSED BY MORPHOLOGICAL CHANGES, INCREASES IN PRODUCTION OF CYTOKINES AND PROLIFERATION. IN COCULTURING EXPERIMENTS, HE WILL ALSO DETERMINE IF THE ABNORMAL ACTIVITY OF FTD I-MG OR I-MOS IS INFLUENCED BY I-NEURONS FROM CONTROLS OR FTD PATIENTS IN A NON-CELL AUTONOMOUS MANNER AND WHETHER FTD I-MG OR I-MOS LABELED WITH ONE COLORED BIOSENSOR CAN ACCELERATE DEGENERATION OF CONTROL AND FTD I-NEURONS DETECTED WITH A DIFFERENT COLORED SENSOR. HE WILL ALSO TEST IF THE ABNORMAL ACTIVITY OF FTD-GRN I-MGS OR I-MOS AND THE DEGENERATION OF FTD-GRN I-NEURONS CAN BE RESCUED BY A SMALL MOLECULE TRAP1 INHIBITOR NVP-HSP990 AND/OR A FOXO1 INHIBITOR, AS1842856. THESE DRUGS INCREASE PROGRANULIN PRODUCTION IN CELLS AND WILL BE USED TO ESTABLISH THAT THE DISEASE PHENOTYPES OF EACH CELL TYPE (I-MG, I-MO AND INEURONS) ARE DEPENDENT ON PROGRANULIN DEFICIENCY. IN SUBSEQUENT STUDIES, DR. FINKBEINER WILL INVESTIGATE THE MECHANISMS OF THE ABNORMAL ACTIVITY OF CENTRAL AND/OR PERIPHERAL IMMUNE CELLS IN FTD. HE WILL TEST IF FTD I-MG AND I-MOS EXHIBIT ALTERATIONS IN THE AUTOPHAGY-LYSOSOMAL PATHWAY RESULTING IN IMPAIRED PROTEIN DEGRADATIVE MECHANISMS IN THE CELLS. HE WILL EMPLOY RM AND HIS OPTICAL PULSE LABELING TECHNOLOGY TO DETERMINE IF AUTOPHAGIC FLUX, PROTEASOME ACTIVITY AND LYSOSOMAL FUNCTION IS IMPAIRED IN THE HUMAN FTD IMMUNE CELLS AND WHETHER IMPAIRED PROTEIN DEGRADATION RESULTS IN THE INCREASED EXPRESSION AND CELLULAR AGGREGATION OF TDP43, A TOXIC PROTEIN LINKED TO NEURODEGENERATION IN FTD. IF LYSOSOMAL FUNCTION IS IMPAIRED, HE WILL USE A RANGE OF DIFFERENT BIOSENSORS TO INVESTIGATE HOW IT IS IMPAIRED. HE WILL ALSO DETERMINE IF A CRITICAL FUNCTION OF THE IMMUNE CELLS, PHAGOCYTOSIS IS ALTERED IN FTD. IN ADDITION TO STUDIES IN TWO DIMENSIONAL CULTURES, DR. FINKBEINER WILL STUDY THE ROLE OF IMMUNE CELLS IN NEURODEGENERATION USING 3-DIMENSIONAL HUMAN CEREBRAL ORGANOIDS. THE ORGANOIDS PRESENT A MORE NATURAL CELLULAR ENVIRONMENT TO STUDY IMMUNE CELL-NEURONAL INTERACTIONS SIMILAR TO HUMAN BRAIN. HE WILL USE METHODS RECENTLY DEVELOPED IN HIS LAB TO GENERATE BRAIN ORGANOIDS FROM HUMAN IPSCS AND MONITOR I-NEURONAL FUNCTIONS IN THE ORGANOIDS USING A NEW BIOSENSOR GEDI. HE WILL IMPLANT EITHER I-MGS OR I-MOS INTO THE HUMAN ORGANOIDS, AND MONITOR THEIR INFILTRATION, PROLIFERATION AND MATURATION USING RM AND BIOSENSORS UNIQUELY EXPRESSED IN THE IMMUNE CELLS PRIOR TO IMPLANTATION. HE WILL VISUALIZE BY RM IF THE FTD I-MG OR I-MO CLUSTER AROUND NEURONS AND USING THE GEDI PROBE DETERMINE WHETHER THEY AFFECT THE SURVIVAL OF THE NEURONS.
J.david Gladstone Institutes
Project Grant RF1NS128800
$339.1k 11/7/23 SUB00003373S
DR. STEVEN FINKBEINER WILL LEAD STUDIES IN AIM 1 OF THIS MULTI-PI R01 APPLICATION. HIS STUDIES WILL EMPLOY HUMAN INDUCED PLURIPOTENT STEM CELLS (IPSC) FROM FRONTOTEMPORAL DEMENTIA (FTD) PATIENTS WITH MUTATIONS IN THE C9ORF72 OR GRN (PROGRANULIN) GENES, OR CONTROLS INCLUDING COGNATE ISOGENIC LINES, DIFFERENTIATED TO FOREBRAIN NEURONS (I-NEURONS), OR MICROGLIA (I-MG) OR MONOCYTE (I-MO). HIS STUDIES WILL FOCUS ON UNDERSTANDING THE ROLE OF CENTRAL AND PERIPHERAL IMMUNE CELLS IN NEURODEGENERATION IN FTD USING HIS LONGITUDINAL IMAGING TECHNOLOGY ROBOTIC MICROSCOPY (RM). INITIAL STUDIES WILL DETERMINE IF CENTRAL I-MG OR PERIPHERAL I-MOS FROM FTD PATIENTS ARE HYPERACTIVE IN A CELL AUTONOMOUS MANNER. HYPERACTIVITY WILL BE ASSESSED BY MORPHOLOGICAL CHANGES, INCREASES IN PRODUCTION OF CYTOKINES AND PROLIFERATION. IN COCULTURING EXPERIMENTS, HE WILL ALSO DETERMINE IF THE ABNORMAL ACTIVITY OF FTD I-MG OR I-MOS IS INFLUENCED BY I-NEURONS FROM CONTROLS OR FTD PATIENTS IN A NON-CELL AUTONOMOUS MANNER AND WHETHER FTD I-MG OR I-MOS LABELED WITH ONE COLORED BIOSENSOR CAN ACCELERATE DEGENERATION OF CONTROL AND FTD I-NEURONS DETECTED WITH A DIFFERENT COLORED SENSOR. HE WILL ALSO TEST IF THE ABNORMAL ACTIVITY OF FTD-GRN I-MGS OR I-MOS AND THE DEGENERATION OF FTD-GRN I-NEURONS CAN BE RESCUED BY A SMALL MOLECULE TRAP1 INHIBITOR NVP-HSP990 AND/OR A FOXO1 INHIBITOR, AS1842856. THESE DRUGS INCREASE PROGRANULIN PRODUCTION IN CELLS AND WILL BE USED TO ESTABLISH THAT THE DISEASE PHENOTYPES OF EACH CELL TYPE (I-MG, I-MO AND INEURONS) ARE DEPENDENT ON PROGRANULIN DEFICIENCY. IN SUBSEQUENT STUDIES, DR. FINKBEINER WILL INVESTIGATE THE MECHANISMS OF THE ABNORMAL ACTIVITY OF CENTRAL AND/OR PERIPHERAL IMMUNE CELLS IN FTD. HE WILL TEST IF FTD I-MG AND I-MOS EXHIBIT ALTERATIONS IN THE AUTOPHAGY-LYSOSOMAL PATHWAY RESULTING IN IMPAIRED PROTEIN DEGRADATIVE MECHANISMS IN THE CELLS. HE WILL EMPLOY RM AND HIS OPTICAL PULSE LABELING TECHNOLOGY TO DETERMINE IF AUTOPHAGIC FLUX, PROTEASOME ACTIVITY AND LYSOSOMAL FUNCTION IS IMPAIRED IN THE HUMAN FTD IMMUNE CELLS AND WHETHER IMPAIRED PROTEIN DEGRADATION RESULTS IN THE INCREASED EXPRESSION AND CELLULAR AGGREGATION OF TDP43, A TOXIC PROTEIN LINKED TO NEURODEGENERATION IN FTD. IF LYSOSOMAL FUNCTION IS IMPAIRED, HE WILL USE A RANGE OF DIFFERENT BIOSENSORS TO INVESTIGATE HOW IT IS IMPAIRED. HE WILL ALSO DETERMINE IF A CRITICAL FUNCTION OF THE IMMUNE CELLS, PHAGOCYTOSIS IS ALTERED IN FTD. IN ADDITION TO STUDIES IN TWO DIMENSIONAL CULTURES, DR. FINKBEINER WILL STUDY THE ROLE OF IMMUNE CELLS IN NEURODEGENERATION USING 3-DIMENSIONAL HUMAN CEREBRAL ORGANOIDS. THE ORGANOIDS PRESENT A MORE NATURAL CELLULAR ENVIRONMENT TO STUDY IMMUNE CELL-NEURONAL INTERACTIONS SIMILAR TO HUMAN BRAIN. HE WILL USE METHODS RECENTLY DEVELOPED IN HIS LAB TO GENERATE BRAIN ORGANOIDS FROM HUMAN IPSCS AND MONITOR I-NEURONAL FUNCTIONS IN THE ORGANOIDS USING A NEW BIOSENSOR GEDI. HE WILL IMPLANT EITHER I-MGS OR I-MOS INTO THE HUMAN ORGANOIDS, AND MONITOR THEIR INFILTRATION, PROLIFERATION AND MATURATION USING RM AND BIOSENSORS UNIQUELY EXPRESSED IN THE IMMUNE CELLS PRIOR TO IMPLANTATION. HE WILL VISUALIZE BY RM IF THE FTD I-MG OR I-MO CLUSTER AROUND NEURONS AND USING THE GEDI PROBE DETERMINE WHETHER THEY AFFECT THE SURVIVAL OF THE NEURONS.
J.david Gladstone Institutes
Project Grant RF1NS128800
$339.1k 11/22/22 SUB00003374S
SCOPE OF WORK UCLA CO-INVESTIGATOR (REXACH) WILL ANALYZE RAW RNA SEQUENCING DATA PROVIDED BY UF AND UCSF. DATA TYPES INCLUDE SORTED CELL RNA SEQUENCING AND BULK RNA SEQUENCING FROM IPSC CULTURES, TRANSGENIC MOUSE MODELS AND DE-IDENTIFIED HUMAN BLOOD SAMPLES. UCLA WILL CLEAN AND PROCESS THE SEQUENCING DATA INCLUDING NORMALIZATION, BATCH CORRECTION, AND OUTLIER REMOVAL. WE WILL PERFORM ANALYSES TO CAREFULLY DETECT AND MITIGATE THE INFLUENCE OF TECHNICAL FACTORS ON DATA, ACCORDING TO HIGH DATA QUALITY STANDARDS. WE WILL PERFORM DIFFERENTIAL GENE EXPRESSION, WEIGHTED GENE CO-EXPRESSION AND BIOINFORMATIC ANALYSES TO CHARACTERIZE EFFECTS OF GRN HAPLOINSUFFIENCY ON MICROGLIA AND MONOCYTE AT THE TRANSCRIPTOMIC LEVEL. WE WILL SELECT GENE REGULATORS FOR FUNCTIONAL VALIDATION AND CONTRIBUTE TO FUNCTIONAL VALIDATION EXPERIMENTS. UCLA WILL PROVIDE DATA BACK TO THE COLLABORATING STUDY PIS (FINKBEINER AND TANSEY). UCLA WILL ALSO PARTICIPATE IN QUARTERLY MEETINGS WITH STUDY PIS TO DISCUSS INTERVAL PROGRESS AND RESULTS. UCLA WILL ALSO PROVIDE STUDY PIS DATA FOR THE ANNUAL NIH PROGRESS REPORTS. UCLA WILL CONTRIBUTE DATA, ANALYSES, FIGURES AND PARTICIPATE IN WRITING ANY MANUSCRIPTS RESULTING FROM THIS COLLABORATIVE WORK. UCLA WILL ENSURE COMPLIANCE WITH ALL NIH GUIDELINES FOR DATA SHARING, PROTECTION OF HUMAN SUBJECTS, AND ETHICS. THE HANDLING OF FIXED AND FROZEN BRAIN TISSUE AND DE-IDENTIFIED GENETIC AND GENE EXPRESSION DATA WILL BE PERFORMED IN ACCORDANCE WITH ETHICAL GUIDELINES AND REGULATIONS FOR THE RESEARCH USE OF HUMAN BRAIN TISSUE SET FORTH BY THE NIH THE UK HEALTH DEPARTMENTÂ S HUMAN TISSUE AUTHORITY CODE OF PRACTICE TO ENSURE THE HIGHEST STANDARD FOR DATA PROTECTION, NO PERSONAL IDENTIFYING INFORMATION WILL BE PROVIDED OR BE ACCESSIBLE TO THE REXACH LAB WITH RESPECT TO ANY OF THESE DATA. ALL OF THE WORK WILL BE DONE IN ACCORDANCE WITH THE NEW HEALTH INSURANCE PORTABILITY AND ACCOUNTABILITY ACT (HIPAA), WHICH SAFEGUARDS THE HEALTH INFORMATION OF INDIVIDUALS OBTAINING HEALTHCARE IN THE UNITED STATES. WE ARE IN FULL COMPLIANCE WITH THESE REGULATIONS. UCLA WILL ENSURE COMPLIANCE WITH ALL MTA AGREEMENTS PREPARED WITH THE STUDY COLLABORATORS REGARDING MATERIAL TRANSFER OF RAW DATA AND PROCESSED DATA, AND INTELLECTUAL PROPERTY. WE WILL COMPLY WITH ALL ASPECTS OF THE DATA SHARING PLAN PROVIDED WITH THIS GRANT APPLICATION, INCLUDING ASSISTING IN MAKING ALL DE-IDENTIFIED SEQUENCING DATA PUBLICLY AVAILABLE AT TIME OF PUBLICATION THROUGH DBGAP OR AN ALTERNATIVE REPOSITORY IN COMPLIANCE WITH NIH REQUIREMENTS.
University Of California, LOS Angeles
Project Grant RF1NS128800
$138.3k 10/11/22