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Article: Brain-derived cell-free DNA.

Southwood, Dean / Singh, Sanyukta / Chatterton, Zac

2022 Volume 17, Issue 10, Page(s) 2213–2214

Language	English
Publishing date	2022-03-04
Publishing country	India
Document type	Journal Article
ZDB-ID	2388460-5
ISSN	1876-7958 ; 1673-5374
ISSN (online)	1876-7958
ISSN	1673-5374
DOI	10.4103/1673-5374.335794
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Article: Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration.

Rademacher, Katerina / Doric, Zak / Haddad, Dominik / Mamaligas, Aphroditi / Liao, Szu-Chi / Creed, Rose B / Kano, Kohei / Chatterton, Zac / Fu, Yuhong / Garcia, Joseph H / Vance, Victoria / Sei, Yoshitaka / Kreitzer, Anatol / Halliday, Glenda M / Nelson, Alexandra B / Margolis, Elyssa B / Nakamura, Ken

bioRxiv : the preprint server for biology

2024

Abstract: Parkinson's disease (PD) is characterized by the death of substantia nigra (SNc) dopamine (DA) neurons, but the pathophysiological mechanisms that precede and drive their death remain unknown. The activity of DA neurons is likely altered in PD, but we ... ...

Abstract	Parkinson's disease (PD) is characterized by the death of substantia nigra (SNc) dopamine (DA) neurons, but the pathophysiological mechanisms that precede and drive their death remain unknown. The activity of DA neurons is likely altered in PD, but we understand little about if or how chronic changes in activity may contribute to degeneration. To address this question, we developed a chemogenetic (DREADD) mouse model to chronically increase DA neuron activity, and confirmed this increase using
Language	English
Publishing date	2024-04-10
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.05.588321
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Article ; Online: Reply: CYLD variants in frontotemporal dementia associated with severe memory impairment in a Portuguese cohort.

Oyston, Lisa J / Chatterton, Zac / Hallupp, Marianne / Rajan, Neil / Kwok, John B / Dobson-Stone, Carol

Brain : a journal of neurology

2020 Volume 143, Issue 8, Page(s) e68

MeSH term(s)	Amyotrophic Lateral Sclerosis ; Deubiquitinating Enzyme CYLD ; Frontotemporal Dementia/complications ; Frontotemporal Dementia/genetics ; Humans ; Memory Disorders/etiology ; Pick Disease of the Brain ; Portugal/epidemiology
Chemical Substances	CYLD protein, human (EC 3.4.19.12) ; Deubiquitinating Enzyme CYLD (EC 3.4.19.12)
Language	English
Publishing date	2020-07-14
Publishing country	England
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	80072-7
ISSN	1460-2156 ; 0006-8950
ISSN (online)	1460-2156
ISSN	0006-8950
DOI	10.1093/brain/awaa184
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Article ; Online: Rationale and Design of the "DIagnostic and Prognostic Precision Algorithm for behavioral variant Frontotemporal Dementia" (DIPPA-FTD) Study: A Study Aiming to Distinguish Early Stage Sporadic FTD from Late-Onset Primary Psychiatric Disorders.

de Boer, Sterre C M / Riedl, Lina / Fenoglio, Chiara / Rue, Ishana / Landin-Romero, Ramon / Matis, Sophie / Chatterton, Zac / Galimberti, Daniela / Halliday, Glenda / Diehl-Schmid, Janine / Piguet, Olivier / Pijnenburg, Yolande A L / Ducharme, Simon

Journal of Alzheimer's disease : JAD

2023 Volume 97, Issue 2, Page(s) 963–973

Abstract: Background: The behavioral variant of frontotemporal dementia (bvFTD) is very heterogeneous in pathology, genetics, and disease course. Unlike Alzheimer's disease, reliable biomarkers are lacking and sporadic bvFTD is often misdiagnosed as a primary ... ...

Abstract	Background: The behavioral variant of frontotemporal dementia (bvFTD) is very heterogeneous in pathology, genetics, and disease course. Unlike Alzheimer's disease, reliable biomarkers are lacking and sporadic bvFTD is often misdiagnosed as a primary psychiatric disorder (PPD) due to overlapping clinical features. Current efforts to characterize and improve diagnostics are centered on the minority of genetic cases. Objective: The multi-center study DIPPA-FTD aims to develop diagnostic and prognostic algorithms to help distinguish sporadic bvFTD from late-onset PPD in its earliest stages. Methods: The prospective DIPPA-FTD study recruits participants with late-life behavioral changes, suspect for bvFTD or late-onset PPD diagnosis with a negative family history for FTD and/or amyotrophic lateral sclerosis. Subjects are invited to participate after diagnostic screening at participating memory clinics or recruited by referrals from psychiatric departments. At baseline visit, participants undergo neurological and psychiatric examination, questionnaires, neuropsychological tests, and brain imaging. Blood is obtained to investigate biomarkers. Patients are informed about brain donation programs. Follow-up takes place 10-14 months after baseline visit where all examinations are repeated. Results from the DIPPA-FTD study will be integrated in a data-driven approach to develop diagnostic and prognostic models. Conclusions: DIPPA-FTD will make an important contribution to early sporadic bvFTD identification. By recruiting subjects with ambiguous or prodromal diagnoses, our research strategy will allow the characterization of early disease stages that are not covered in current sporadic FTD research. Results will hopefully increase the ability to diagnose sporadic bvFTD in the early stage and predict progression rate, which is pivotal for patient stratification and trial design.
MeSH term(s)	Humans ; Frontotemporal Dementia/genetics ; Prospective Studies ; Prognosis ; Neuropsychological Tests ; Biomarkers ; Acetamides ; Isothiocyanates
Chemical Substances	2-(3,4-dichlorophenyl)-N-methyl-N-(1-(3-isothiocyanatophenyl)-2-(1-pyrrolidinyl)ethyl)acetamide (155512-49-5) ; Biomarkers ; Acetamides ; Isothiocyanates
Language	English
Publishing date	2023-12-24
Publishing country	Netherlands
Document type	Multicenter Study ; Journal Article
ZDB-ID	1440127-7
ISSN	1875-8908 ; 1387-2877
ISSN (online)	1875-8908
ISSN	1387-2877
DOI	10.3233/JAD-230829
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Article: Bisulfite Amplicon Sequencing Can Detect Glia and Neuron Cell-Free DNA in Blood Plasma.

Chatterton, Zac / Mendelev, Natalia / Chen, Sean / Carr, Walter / Kamimori, Gary H / Ge, Yongchao / Dwork, Andrew J / Haghighi, Fatemeh

Frontiers in molecular neuroscience

2021 Volume 14, Page(s) 672614

Abstract: Sampling the live brain is difficult and dangerous, and withdrawing cerebrospinal fluid is uncomfortable and frightening to the subject, so new sources of real-time analysis are constantly sought. Cell-free DNA (cfDNA) derived from glia and neurons ... ...

Abstract	Sampling the live brain is difficult and dangerous, and withdrawing cerebrospinal fluid is uncomfortable and frightening to the subject, so new sources of real-time analysis are constantly sought. Cell-free DNA (cfDNA) derived from glia and neurons offers the potential for wide-ranging neurological disease diagnosis and monitoring. However, new laboratory and bioinformatic strategies are needed. DNA methylation patterns on individual cfDNA fragments can be used to ascribe their cell-of-origin. Here we describe bisulfite sequencing assays and bioinformatic processing methods to identify cfDNA derived from glia and neurons. In proof-of-concept experiments, we describe the presence of both glia- and neuron-cfDNA in the blood plasma of human subjects following mild trauma. This detection of glia- and neuron-cfDNA represents a significant step forward in the translation of liquid biopsies for neurological diseases.
Language	English
Publishing date	2021-07-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452967-9
ISSN	1662-5099
ISSN	1662-5099
DOI	10.3389/fnmol.2021.672614
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Article: A potential patient stratification biomarker for Parkinson´s disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells.

Naaldijk, Yahaira / Fernández, Belén / Fasiczka, Rachel / Fdez, Elena / Leghay, Coline / Croitoru, Ioana / Kwok, John B / Boulesnane, Yanisse / Vizeneux, Amelie / Mutez, Eugenie / Calvez, Camille / Destée, Alain / Taymans, Jean-Marc / Aragon, Ana Vinagre / Yarza, Alberto Bergareche / Padmanabhan, Shalini / Delgado, Mario / Alcalay, Roy N / Chatterton, Zac /

Dzamko, Nicolas / Halliday, Glenda / Ruiz-Martínez, Javier / Chartier-Harlin, Marie-Christine / Hilfiker, Sabine

NPJ Parkinson's disease

2024 Volume 10, Issue 1, Page(s) 12

Abstract: Parkinson´s disease (PD) is a common neurodegenerative movement disorder and leucine-rich repeat kinase 2 (LRRK2) is a promising therapeutic target for disease intervention. However, the ability to stratify patients who will benefit from such treatment ... ...

Abstract	Parkinson´s disease (PD) is a common neurodegenerative movement disorder and leucine-rich repeat kinase 2 (LRRK2) is a promising therapeutic target for disease intervention. However, the ability to stratify patients who will benefit from such treatment modalities based on shared etiology is critical for the success of disease-modifying therapies. Ciliary and centrosomal alterations are commonly associated with pathogenic LRRK2 kinase activity and can be detected in many cell types. We previously found centrosomal deficits in immortalized lymphocytes from G2019S-LRRK2 PD patients. Here, to investigate whether such deficits may serve as a potential blood biomarker for PD which is susceptible to LRKK2 inhibitor treatment, we characterized patient-derived cells from distinct PD cohorts. We report centrosomal alterations in peripheral cells from a subset of early-stage idiopathic PD patients which is mitigated by LRRK2 kinase inhibition, supporting a role for aberrant LRRK2 activity in idiopathic PD. Centrosomal defects are detected in R1441G-LRRK2 and G2019S-LRRK2 PD patients and in non-manifesting LRRK2 mutation carriers, indicating that they accumulate prior to a clinical PD diagnosis. They are present in immortalized cells as well as in primary lymphocytes from peripheral blood. These findings indicate that analysis of centrosomal defects as a blood-based patient stratification biomarker may help nominate idiopathic PD patients who will benefit from LRRK2-related therapeutics.
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2819218-7
ISSN	2373-8057
ISSN	2373-8057
DOI	10.1038/s41531-023-00624-8
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Article ; Online: Author Correction: DUSP5 is methylated in CIMP-high colorectal cancer but is not a major regulator of intestinal cell proliferation and tumorigenesis.

Tögel, Lars / Nightingale, Rebecca / Wu, Rui / Chüeh, Anderly C / Al-Obaidi, Sheren / Luk, Ian / Dávalos-Salas, Mercedes / Chionh, Fiona / Murone, Carmel / Buchanan, Daniel D / Chatterton, Zac / Sieber, Oliver M / Arango, Diego / Tebbutt, Niall C / Williams, David / Dhillon, Amardeep S / Mariadason, John M

Scientific reports

2023 Volume 13, Issue 1, Page(s) 2422

Language	English
Publishing date	2023-02-10
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-29328-y
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Article ; Online: Age-Dependent Changes to Sphingolipid Balance in the Human Hippocampus are Gender-Specific and May Sensitize to Neurodegeneration.

Couttas, Timothy A / Kain, Nupur / Tran, Collin / Chatterton, Zac / Kwok, John B / Don, Anthony S

Journal of Alzheimer's disease : JAD

2018 Volume 63, Issue 2, Page(s) 503–514

Abstract: The greatest risk factor for developing Alzheimer's disease (AD) is aging. The major genetic risk factor for AD is the ɛ4 allele of the APOE gene, encoding the brain's major lipid transport protein, apolipoprotein E (ApoE). The research community is yet ... ...

Abstract	The greatest risk factor for developing Alzheimer's disease (AD) is aging. The major genetic risk factor for AD is the ɛ4 allele of the APOE gene, encoding the brain's major lipid transport protein, apolipoprotein E (ApoE). The research community is yet to decipher why the ApoE4 variant pre-disposes to AD, and how aging causes the disease. Studies have shown deregulated levels of sphingolipids, including decreased levels of the neuroprotective signaling lipid sphingosine 1-phosphate (S1P), and increased ceramide content, in brain tissue and serum of people with pre-clinical or very early AD. In this study we investigated whether sphingolipid levels are affected as a function of age or APOE genotype, in the hippocampus of neurologically normal subjects over the age of 65. Lipids were quantified in 80 postmortem tissue samples using liquid chromatography tandem mass spectrometry (LC-MS/MS). Sphingolipid levels were not significantly affected by the presence of one ɛ4 or ɛ2 allele. However, ceramide, sphingomyelin, and sulfatide content was very significantly correlated with age in the hippocampus of males. On the other hand, S1P, normalized to its non-phosphorylated precursor sphingosine, was inversely correlated with age in females. Our results therefore establish gender-specific differences in sphingolipid metabolism in the aging human brain. Ceramide is a pro-apoptotic lipid, and heavily implicated as a driver of insulin resistance in metabolic tissues. S1P is a neuroprotective lipid that supports glutamatergic neurotransmission. Increasing ceramide and decreasing S1P levels may contribute significantly to a pro-neurodegenerative phenotype in the aging brain.
MeSH term(s)	Aged ; Aged, 80 and over ; Aging/genetics ; Aging/metabolism ; Apolipoproteins E/genetics ; Female ; Hippocampus/metabolism ; Humans ; Male ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/metabolism ; Sex Characteristics ; Sphingolipids/metabolism
Chemical Substances	Apolipoproteins E ; Sphingolipids
Language	English
Publishing date	2018-04-16
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1440127-7
ISSN	1875-8908 ; 1387-2877
ISSN (online)	1875-8908
ISSN	1387-2877
DOI	10.3233/JAD-171054
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Article ; Online: Cerebrospinal fluid liquid biopsy for detecting somatic mosaicism in brain.

Ye, Zimeng / Chatterton, Zac / Pflueger, Jahnvi / Damiano, John A / McQuillan, Lara / Harvey, Anthony Simon / Malone, Stephen / Do, Hongdo / Maixner, Wirginia / Schneider, Amy / Nolan, Bernadette / Wood, Martin / Lee, Wei Shern / Gillies, Greta / Pope, Kate / Wilson, Michael / Lockhart, Paul J / Dobrovic, Alexander / Scheffer, Ingrid E /

Bahlo, Melanie / Leventer, Richard J / Lister, Ryan / Berkovic, Samuel F / Hildebrand, Michael S

Brain communications

2021 Volume 3, Issue 1, Page(s) fcaa235

Abstract: Brain somatic mutations are an increasingly recognized cause of epilepsy, brain malformations and autism spectrum disorders and may be a hidden cause of other neurodevelopmental and neurodegenerative disorders. At present, brain mosaicism can be detected ...

Abstract	Brain somatic mutations are an increasingly recognized cause of epilepsy, brain malformations and autism spectrum disorders and may be a hidden cause of other neurodevelopmental and neurodegenerative disorders. At present, brain mosaicism can be detected only in the rare situations of autopsy or brain biopsy. Liquid biopsy using cell-free DNA derived from cerebrospinal fluid has detected somatic mutations in malignant brain tumours. Here, we asked if cerebrospinal fluid liquid biopsy can be used to detect somatic mosaicism in non-malignant brain diseases. First, we reliably quantified cerebrospinal fluid cell-free DNA in 28 patients with focal epilepsy and 28 controls using droplet digital PCR. Then, in three patients we identified somatic mutations in cerebrospinal fluid: in one patient with subcortical band heterotopia the
Language	English
Publishing date	2021-01-21
Publishing country	England
Document type	Journal Article
ISSN	2632-1297
ISSN (online)	2632-1297
DOI	10.1093/braincomms/fcaa235
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Article ; Online: Validation of DNA methylation biomarkers for diagnosis of acute lymphoblastic leukemia.

Chatterton, Zac / Burke, Daniel / Emslie, Kerry R / Craig, Jeffery M / Ng, Jane / Ashley, David M / Mechinaud, Francoise / Saffery, Richard / Wong, Nicholas C

Clinical chemistry

2014 Volume 60, Issue 7, Page(s) 995–1003

Abstract: Background: DNA methylation biomarkers capable of diagnosis and subtyping have been found for many cancers. Fifteen such markers have previously been identified for pediatric acute lymphoblastic leukemia (ALL). Validation of these markers is necessary ... ...

Abstract	Background: DNA methylation biomarkers capable of diagnosis and subtyping have been found for many cancers. Fifteen such markers have previously been identified for pediatric acute lymphoblastic leukemia (ALL). Validation of these markers is necessary to assess their clinical utility for molecular diagnostics. Substantial efficiencies could be achieved with these DNA methylation markers for disease tracking with potential to replace patient-specific genetic testing. Methods: We evaluated DNA methylation of promoter regions of TLX3 (T-cell leukemia homeobox) and FOXE3 (forkhead box E3) in bone marrow biopsies from 197 patients classified as leukemic (n = 95) or clear of the disease (n = 102) by MALDI-TOF. Using a single nucleotide extension assay (methylSABER), we tested 10 bone marrow biopsies collected throughout the course of patient chemotherapy. Using reference materials, diagnostic thresholds and limits of detection were characterized for both methods. Results: Reliable detection of DNA methylation of TLX3 and FOXE3 segregated ALL from those clear of disease with minimal false-negative and false-positive results. The limit of detection with MALDI-TOF was 1000-5000 copies of methylated allele. For methylSABER, the limit of detection was 10 copies of methylated TLX3, which enabled monitoring of minimal residual disease in ALL patients. Conclusions: Mass spectrometry procedures can be used to regionally multiplex and detect rare DNA methylation events, establish DNA methylation loci as clinically applicable biomarkers for disease diagnosis, and track pediatric ALL.
MeSH term(s)	Adolescent ; Case-Control Studies ; Child ; Child, Preschool ; DNA Methylation ; False Negative Reactions ; False Positive Reactions ; Female ; Forkhead Transcription Factors/genetics ; Gene Dosage ; Genetic Markers ; Homeodomain Proteins/genetics ; Humans ; Infant ; Limit of Detection ; Male ; Neoplasm, Residual/diagnosis ; Neoplasm, Residual/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/diagnosis ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics ; Promoter Regions, Genetic ; Reference Standards ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Chemical Substances	FOXE3 protein, human ; Forkhead Transcription Factors ; Genetic Markers ; Homeodomain Proteins ; TLX3 protein, human
Language	English
Publishing date	2014-05-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Validation Studies
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1373/clinchem.2013.219956
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