- Email: [email protected]
BACE1, THE BETA-SECRETASE ENZYME: A LEADING THERAPEUTIC TARGET FOR ALZHEIMER'S DISEASE
P162
EC-01-03
Podium Presentations: Sunday, July 24, 2016
BACE1, THE BETA-SECRETASE ENZYME: A LEADING THERAPEUTIC TARGET FOR ALZHEIMER’S DISEASE
Robert J. Vassar, Northwestern University, Chicago, IL, USA. Contact e-mail: [email protected]
Abstract not available. EC-01-04
PHYSIOLOGICAL SUBSTRATES OF BACE1 AND ADAM10: SAFETY ISSUES OR BIOMARKERS?
Stefan Lichtenthaler, Technical University of Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.. Contact e-mail: [email protected] Background: The beta-secretase BACE1 is a major drug target in Alzheimer’s disease (AD), but also has other functions, e.g. in myelination and axon targeting. BACE1-deficient mice have additional phenotypes in the brain and several BACE1 substrates, referred to as the BACE1 degradome, are emerging in the CNS. This raises the possibility that therapeutic BACE1 inhibition may have mechanism-based side-effects. Additionally, most BACE1 inhibitors also block the homologous protease BACE2 and, thus, may interfere with BACE2 function. Methods: We developed methods for whole proteome analysis of murine tissue, including CSF Results: We used the novel methods to identify BACE1 substrate candidates in murine CSF, but also in neurons and brains. Selected substrate candidates were validated and functionally and mechanistically characterized. Two of the candidates are seizure protein 6 (SEZ6) and SEZ6-like (SEZ6L), which control neurite outgrowth and synapse formation. Both proteins were validated as BACE1 substrates in vitro and in vivo. In CSF, SEZ6 and SEZ6L were found to be suitable markers for measuring BACE1 inhibition in vivo. Conclusions: BACE1 has broad functions in the CNS. The presentation will discuss the implication of the substrates a) for the safety of BACE1 inhibitors and b) for the use as companion diagnostics to monitor BACE inhibition in vivo. SUNDAY, JULY 24, 2016 FEATURED RESEARCH SESSIONS F1-01 THE ALZHEIMER’S DISEASE SEQUENCING PROJECT (ADSP): GENE DISCOVERY IN ACTION F1-01-01
STRUCTURAL VARIATION (SV) IN HETEROGENOUS WHOLE-GENOME SEQUENCING DATA FROM 111 FAMILIES AT RISK FOR ALZHEIMER DISEASE: ALZHEIMER DISEASE SEQUENCING PROJECT SV STUDY
Li Charlie Xia, Stanford University, Stanford, CA, USA; University of Pennsylvania, Philadelphia, PA, USA. Contact e-mail: [email protected] Background: The Alzheimer Disease Sequencing Project (ADSP) is a national initiative to identify novel genetic variants involved in determining risk of late-onset Alzheimer disease (AD). Methods: Structural variation was characterized in 111 families of multiple ethnicities comprising 578 individuals diagnosed with or at risk for AD. We developed a statistical framework that leverages pedigree information to assess accuracy and optimize structural variant (SV) calls. The kinship coefficient was used to filter SVs showing excess heterozygosity. We also formulated a metric called the D-score which is an outgroup-based measure of sib-sharing to filter SVs identified by calling algorithms that detect insertion and deletion breakpoints, but do not render genotypes. These
metrics also permitted assessment of reliability of individual calling programs for various SV sizes. An in silico procedure was devised to “spike-in” SVs of varying purity into real sequenced libraries, accommodating multi-library designs, and applied it to three samples that were sequenced at all three centers. This comprehensive QC process allowed benchmarking SV callers across the widely differing libraries and combining these callers in a library-specific way for improved specificity and sensitivity. Candidate SV regions were further refined using an ensemble of 12 SV callers with local assembly to provide precise breakpoints for subsequent calling of genotypes. Results: We identified a high-confidence set of deletions, insertions, and complex variants larger than 20 base pairs (bp) genotyped across all 578 individuals. These variants were prioritized based on predicted functional impact and overlap with known AD genes and linkage regions. Thus far, we detected, and confirmed by sequencing, a 44 bp ABCA7 deletion in 11 members (all have AD) of 5 of 67 CaribbeanHispanic families. This finding is consistent with our recent AD association finding of this deletion in a sample containing >2,800 African Americans which results in a frameshift and truncating mutation that could interfere with protein function. Conclusions: A carefully developed pipeline for detecting, genotyping, and filtering SVs from family-based whole genome sequence data permitted discovery of a robust association of AD risk with a rare 44 bp deletion in ABCA7. A more comprehensive analysis of these data is underway. F1-01-02
ALZHEIMER’S DISEASE SEQUENCING PROJECT: SEARCH FOR ALZHEIMER’S DISEASE RESILIENCE GENES THAT MAY MODIFY DISEASE SUSCEPTIBILITY IN SPECIFIC APOE GENOTYPE BACKGROUNDS
Eduardo Marcora1, Alan E. Renton1, Gary W. Beecham2, Eric Boerwinkle3,4, Laura Cantwell5, Carlos Cruchaga6,7,8, Rebecca Cweibel5, Adam Felsenfeld9, Myriam Fornage4,10, Manav Kapoor1, Keoni Kauwe11, Mugdha Khaladkar5, Dan Kobolt12,13,14, Yiyi Ma15, Richard Mayeux16, Marilyn Miller17, Adam C. Naj18, Amanda B. Partch18, Margaret A. Pericak-Vance2, Gerard D. Schellenberg18, Sudha Seshadri15,19,20, Badri N. Vardarajan16, Li-San Wang18, Joshua C. Bis21, Lindsay A. Farrer15, Alison M. Goate1, 1 Icahn School of Medicine at Mount Sinai, New York, NY, USA; 2University of Miami Miller School of Medicine, Miami, FL, USA; 3Baylor College of Medicine, Houston, TX, USA; 4University of Texas Health Science Center at Houston, Houston, TX, USA; 5University of Pennsylvania, Philadelphia, PA, USA; 6Washington University in St. Louis, Saint Louis, MO, USA; 7 Washington University School of Medicine, St. Louis, MO, USA; 8Knight Alzheimer Disease Center, St. Louis, MO, USA; 9Division of Genome Sciences, National Human Genome Research Institute, Bethesda, MD, USA; 10 University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA; 11Brigham Young University, Provo, UT, USA; 12 Washington University in St. Louis, St. Louis, MO, USA; 13Washington University, St. Louis, MO, USA; 14The Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; 15Boston University, Boston, MA, USA; 16Columbia University, New York, NY, USA; 17Division of Neuroscience, National Institute on Aging, Bethesda, MD, USA; 18 University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; 19The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA; 20Boston University School of Medicine, Boston, MA, USA; 21University of Washington, Seattle, WA, USA. Contact e-mail: [email protected] Background: Common variation at the APOE locus is the strongest known genetic risk factor for Alzheimer’s disease (AD).
EC-01-03
Podium Presentations: Sunday, July 24, 2016
BACE1, THE BETA-SECRETASE ENZYME: A LEADING THERAPEUTIC TARGET FOR ALZHEIMER’S DISEASE
Robert J. Vassar, Northwestern University, Chicago, IL, USA. Contact e-mail: [email protected]
Abstract not available. EC-01-04
PHYSIOLOGICAL SUBSTRATES OF BACE1 AND ADAM10: SAFETY ISSUES OR BIOMARKERS?
Stefan Lichtenthaler, Technical University of Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.. Contact e-mail: [email protected] Background: The beta-secretase BACE1 is a major drug target in Alzheimer’s disease (AD), but also has other functions, e.g. in myelination and axon targeting. BACE1-deficient mice have additional phenotypes in the brain and several BACE1 substrates, referred to as the BACE1 degradome, are emerging in the CNS. This raises the possibility that therapeutic BACE1 inhibition may have mechanism-based side-effects. Additionally, most BACE1 inhibitors also block the homologous protease BACE2 and, thus, may interfere with BACE2 function. Methods: We developed methods for whole proteome analysis of murine tissue, including CSF Results: We used the novel methods to identify BACE1 substrate candidates in murine CSF, but also in neurons and brains. Selected substrate candidates were validated and functionally and mechanistically characterized. Two of the candidates are seizure protein 6 (SEZ6) and SEZ6-like (SEZ6L), which control neurite outgrowth and synapse formation. Both proteins were validated as BACE1 substrates in vitro and in vivo. In CSF, SEZ6 and SEZ6L were found to be suitable markers for measuring BACE1 inhibition in vivo. Conclusions: BACE1 has broad functions in the CNS. The presentation will discuss the implication of the substrates a) for the safety of BACE1 inhibitors and b) for the use as companion diagnostics to monitor BACE inhibition in vivo. SUNDAY, JULY 24, 2016 FEATURED RESEARCH SESSIONS F1-01 THE ALZHEIMER’S DISEASE SEQUENCING PROJECT (ADSP): GENE DISCOVERY IN ACTION F1-01-01
STRUCTURAL VARIATION (SV) IN HETEROGENOUS WHOLE-GENOME SEQUENCING DATA FROM 111 FAMILIES AT RISK FOR ALZHEIMER DISEASE: ALZHEIMER DISEASE SEQUENCING PROJECT SV STUDY
Li Charlie Xia, Stanford University, Stanford, CA, USA; University of Pennsylvania, Philadelphia, PA, USA. Contact e-mail: [email protected] Background: The Alzheimer Disease Sequencing Project (ADSP) is a national initiative to identify novel genetic variants involved in determining risk of late-onset Alzheimer disease (AD). Methods: Structural variation was characterized in 111 families of multiple ethnicities comprising 578 individuals diagnosed with or at risk for AD. We developed a statistical framework that leverages pedigree information to assess accuracy and optimize structural variant (SV) calls. The kinship coefficient was used to filter SVs showing excess heterozygosity. We also formulated a metric called the D-score which is an outgroup-based measure of sib-sharing to filter SVs identified by calling algorithms that detect insertion and deletion breakpoints, but do not render genotypes. These
metrics also permitted assessment of reliability of individual calling programs for various SV sizes. An in silico procedure was devised to “spike-in” SVs of varying purity into real sequenced libraries, accommodating multi-library designs, and applied it to three samples that were sequenced at all three centers. This comprehensive QC process allowed benchmarking SV callers across the widely differing libraries and combining these callers in a library-specific way for improved specificity and sensitivity. Candidate SV regions were further refined using an ensemble of 12 SV callers with local assembly to provide precise breakpoints for subsequent calling of genotypes. Results: We identified a high-confidence set of deletions, insertions, and complex variants larger than 20 base pairs (bp) genotyped across all 578 individuals. These variants were prioritized based on predicted functional impact and overlap with known AD genes and linkage regions. Thus far, we detected, and confirmed by sequencing, a 44 bp ABCA7 deletion in 11 members (all have AD) of 5 of 67 CaribbeanHispanic families. This finding is consistent with our recent AD association finding of this deletion in a sample containing >2,800 African Americans which results in a frameshift and truncating mutation that could interfere with protein function. Conclusions: A carefully developed pipeline for detecting, genotyping, and filtering SVs from family-based whole genome sequence data permitted discovery of a robust association of AD risk with a rare 44 bp deletion in ABCA7. A more comprehensive analysis of these data is underway. F1-01-02
ALZHEIMER’S DISEASE SEQUENCING PROJECT: SEARCH FOR ALZHEIMER’S DISEASE RESILIENCE GENES THAT MAY MODIFY DISEASE SUSCEPTIBILITY IN SPECIFIC APOE GENOTYPE BACKGROUNDS
Eduardo Marcora1, Alan E. Renton1, Gary W. Beecham2, Eric Boerwinkle3,4, Laura Cantwell5, Carlos Cruchaga6,7,8, Rebecca Cweibel5, Adam Felsenfeld9, Myriam Fornage4,10, Manav Kapoor1, Keoni Kauwe11, Mugdha Khaladkar5, Dan Kobolt12,13,14, Yiyi Ma15, Richard Mayeux16, Marilyn Miller17, Adam C. Naj18, Amanda B. Partch18, Margaret A. Pericak-Vance2, Gerard D. Schellenberg18, Sudha Seshadri15,19,20, Badri N. Vardarajan16, Li-San Wang18, Joshua C. Bis21, Lindsay A. Farrer15, Alison M. Goate1, 1 Icahn School of Medicine at Mount Sinai, New York, NY, USA; 2University of Miami Miller School of Medicine, Miami, FL, USA; 3Baylor College of Medicine, Houston, TX, USA; 4University of Texas Health Science Center at Houston, Houston, TX, USA; 5University of Pennsylvania, Philadelphia, PA, USA; 6Washington University in St. Louis, Saint Louis, MO, USA; 7 Washington University School of Medicine, St. Louis, MO, USA; 8Knight Alzheimer Disease Center, St. Louis, MO, USA; 9Division of Genome Sciences, National Human Genome Research Institute, Bethesda, MD, USA; 10 University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA; 11Brigham Young University, Provo, UT, USA; 12 Washington University in St. Louis, St. Louis, MO, USA; 13Washington University, St. Louis, MO, USA; 14The Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; 15Boston University, Boston, MA, USA; 16Columbia University, New York, NY, USA; 17Division of Neuroscience, National Institute on Aging, Bethesda, MD, USA; 18 University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; 19The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA; 20Boston University School of Medicine, Boston, MA, USA; 21University of Washington, Seattle, WA, USA. Contact e-mail: [email protected] Background: Common variation at the APOE locus is the strongest known genetic risk factor for Alzheimer’s disease (AD).