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Mascheretti S, Arrigoni F, Toraldo A, Giubergia A, Andreola C, Villa M, Lampis V, Giorda R, Villa M, Peruzzo D. Alterations in neural activation in the ventral frontoparietal network during complex magnocellular stimuli in developmental dyslexia associated with READ1 deletion. BEHAVIORAL AND BRAIN FUNCTIONS : BBF 2024; 20:16. [PMID: 38926731 PMCID: PMC11210179 DOI: 10.1186/s12993-024-00241-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND An intronic deletion within intron 2 of the DCDC2 gene encompassing the entire READ1 (hereafter, READ1d) has been associated in both children with developmental dyslexia (DD) and typical readers (TRs), with interindividual variation in reading performance and motion perception as well as with structural and functional brain alterations. Visual motion perception -- specifically processed by the magnocellular (M) stream -- has been reported to be a solid and reliable endophenotype of DD. Hence, we predicted that READ1d should affect neural activations in brain regions sensitive to M stream demands as reading proficiency changes. METHODS We investigated neural activations during two M-eliciting fMRI visual tasks (full-field sinusoidal gratings controlled for spatial and temporal frequencies and luminance contrast, and sensitivity to motion coherence at 6%, 15% and 40% dot coherence levels) in four subject groups: children with DD with/without READ1d, and TRs with/without READ1d. RESULTS At the Bonferroni-corrected level of significance, reading skills showed a significant effect in the right polar frontal cortex during the full-field sinusoidal gratings-M task. Regardless of the presence/absence of the READ1d, subjects with poor reading proficiency showed hyperactivation in this region of interest (ROI) compared to subjects with better reading scores. Moreover, a significant interaction was found between READ1d and reading performance in the left frontal opercular area 4 during the 15% coherent motion sensitivity task. Among subjects with poor reading performance, neural activation in this ROI during this specific task was higher for subjects without READ1d than for READ1d carriers. The difference vanished as reading skills increased. CONCLUSIONS Our findings showed a READ1d-moderated genetic vulnerability to alterations in neural activation in the ventral attentive and salient networks during the processing of relevant stimuli in subjects with poor reading proficiency.
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Affiliation(s)
- Sara Mascheretti
- Department of Brain and Behavioral Sciences, University of Pavia, Piazza Botta, 6, Pavia (PV), 27100, PV, Italy.
- Child Psychopathology Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini (LC), Italy.
| | - Filippo Arrigoni
- Radiology and Neuroradiology Department, Children's Hospital V. Buzzi, Milan, Italy
| | - Alessio Toraldo
- Department of Brain and Behavioral Sciences, University of Pavia, Piazza Botta, 6, Pavia (PV), 27100, PV, Italy
- Milan Centre for Neuroscience (NeuroMI), Milan, Italy
| | - Alice Giubergia
- Neuroimaging Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini (LC), Italy
| | | | - Martina Villa
- Department of Psychological Sciences, University of Connecticut, Storrs, CT, USA
- The Connecticut Institute for Brain and Cognitive Sciences, University of Connecticut, Storrs, CT, USA
- Yale Child Study Center Language Sciences Consortium, New Haven, CT, USA
| | - Valentina Lampis
- Department of Brain and Behavioral Sciences, University of Pavia, Piazza Botta, 6, Pavia (PV), 27100, PV, Italy
- Child Psychopathology Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini (LC), Italy
| | - Roberto Giorda
- Molecular Biology Laboratory, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini (LC), Italy
| | - Marco Villa
- Molecular Biology Laboratory, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini (LC), Italy
| | - Denis Peruzzo
- Neuroimaging Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini (LC), Italy
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Schmock H, Stevenson MP, Hanebaum S, Vangkilde A, Rosengren A, Weinsheimer SM, Skovby F, Olesen C, Ullum H, Baaré WFC, Siebner HR, Didriksen M, Werge T, Olsen L, Jepsen JRM. Clinical segmentation in 22q11.2 deletion syndrome: Cognitive impairments and additional genetic load. J Psychiatr Res 2024; 177:153-161. [PMID: 39018710 DOI: 10.1016/j.jpsychires.2024.06.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/29/2024] [Accepted: 06/17/2024] [Indexed: 07/19/2024]
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) is associated with high psychiatric morbidity. However, large phenotypic heterogeneity hampers early detection of 22q11.2DS individuals at highest risk. Here, we investigated whether individuals with 22q11.2DS can be subdivided into clinically relevant subgroups based on their severity of cognitive impairments and whether such subgroups differ in polygenic risk. Using a cross-sectional design, we examined the number of lifetime psychiatric diagnoses and polygenic risk scores for schizophrenia in an unselected nationwide biobank cohort of individuals with 22q11.2DS (n = 183). Approximately 35% of this sample, aged 10-30 years, had a history with one or more psychiatric diagnosis. In a representative nested subgroup of 28 children and youth, we performed additional comprehensive cognitive evaluation and assessed psychiatric symptoms. Unsupervised hierarchical cluster analysis was performed to divide the subgroup of 22q11.2DS individuals, based on their performance on the cognitive testing battery. This produced two groups that did not differ in mean age or gender composition, but were characterized by low cognitive (LF) and high cognitive (HF) functional levels. The LF group, which had significantly lower global cognitive functioning scores, also displayed higher negative symptom scores; whereas, the HF group displayed lower rate of current psychiatric disorders than the LF group and the reminder of the biobank cohort. The polygenic risk score for schizophrenia was insignificantly lower for the low functioning group than for the high functioning group, after adjustment. Cognitive functioning may provide useful information on psychiatric risk.
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Affiliation(s)
- H Schmock
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
| | - Matt P Stevenson
- Lundbeck Foundation Center for Clinical Intervention and Neuropsychiatric Schizophrenia Research (CINS) and Center for Neuropsychiatric Schizophrenia Research (CNSR), Mental Health Center Glostrup, Copenhagen University Hospital, DK-2600 Glostrup, Copenhagen, Denmark
| | - S Hanebaum
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
| | - A Vangkilde
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
| | - A Rosengren
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
| | - S M Weinsheimer
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
| | - F Skovby
- Department of Clinical Genetics, Zealand University Hospital, DK-4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - C Olesen
- Department of Pediatrics, Aarhus University Hospital, DK-8000 Aarhus C, Denmark
| | - H Ullum
- Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - W F C Baaré
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, DK-2650 Hvidovre, Denmark
| | - H R Siebner
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, DK-2650 Hvidovre, Denmark; Child and Adolescent Mental Health Center, Copenhagen University Hospital, DK-2600 Glostrup, Copenhagen, Denmark
| | - M Didriksen
- H. Lundbeck A/S, Ottiliavej 9, DK-2500 Valby, Denmark
| | - T Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, DK-4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - L Olsen
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
| | - J R M Jepsen
- Lundbeck Foundation Center for Clinical Intervention and Neuropsychiatric Schizophrenia Research (CINS) and Center for Neuropsychiatric Schizophrenia Research (CNSR), Mental Health Center Glostrup, Copenhagen University Hospital, DK-2600 Glostrup, Copenhagen, Denmark; Child and Adolescent Mental Health Center, Copenhagen University Hospital, DK-2600 Glostrup, Copenhagen, Denmark.
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153
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Chang K, Jian X, Wu C, Gao C, Li Y, Chen J, Xue B, Ding Y, Peng L, Wang B, He L, Xu Y, Li C, Li X, Wang Z, Zhao X, Pan D, Yang Q, Zhou J, Zhu Z, Liu Z, Xia D, Feng G, Zhang Q, Wen Y, Shi Y, Li Z. The Contribution of Mosaic Chromosomal Alterations to Schizophrenia. Biol Psychiatry 2024:S0006-3223(24)01419-7. [PMID: 38942348 DOI: 10.1016/j.biopsych.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
BACKGROUND Mosaic chromosomal alterations (mCAs) are implicated in neuropsychiatric disorders, yet the contribution to schizophrenia (SCZ) risk for somatic copy number variations (sCNVs) emerging in early developmental stages is not fully established. METHODS We analyzed blood-derived genotype arrays from 9,715 SCZ patients and 28,822 controls of Chinese descent using a computational tool (MoChA) based on long-range chromosomal information to detect mCAs. We focused on probable early developmental sCNVs through stringent filtering. We assessed the sCNVs' burden across varying cell fraction (CF) cutoffs, as well as the frequency with which genes were involved in sCNVs. We integrated this data with the Psychiatric Genomics Consortium (PGC) dataset, which comprises 12,834 SCZ cases and 11,648 controls of European descent, and complemented it with genotyping data from postmortem brain tissue of 936 subjects (449 cases and 487 controls). RESULTS Patients with SCZ had a significantly higher somatic losses detection rate than control subjects (1.00% vs 0.52%; odds ratio (OR) = 1.91; 95% CI, 1.47-2.49; two-sided Fisher's exact test, p=1.49×10-6). Further analysis indicated that the ORs escalated proportionately (from 1.91 to 2.78) with the increment in CF cutoffs. Recurrent sCNVs associated with SCZ (OR>8; Fisher's exact test, p<0.05) were identified, including notable regions at 10q21.1 (ZWINT), 3q26.1 (SLITRK3), 1q31.1 (BRINP3) and 12q21.31-21.32 (MGAT4C and NTS) in the Chinese cohort, some regions validated with PGC data. Cross-tissue validation pinpointed somatic losses at loci like 1p35.3-35.2 and 19p13.3-13.2. CONCLUSIONS The study highlights mCAs' significant impact on SCZ, suggesting their pivotal role in the disorder's genetic etiology.
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Affiliation(s)
- Kaihui Chang
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China;; School of Basic Medicine, Qingdao University, Qingdao, 266003, China;; National Engineering Research Center of Innovation and Application of Minimally Invasive Instruments, Hangzhou 310016, China
| | - Xuemin Jian
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Chuanhong Wu
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China;; School of Basic Medicine, Qingdao University, Qingdao, 266003, China
| | - Chengwen Gao
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China
| | - Yafang Li
- School of Basic Medicine, Qingdao University, Qingdao, 266003, China
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China;; Shanghai Clinical Research Center for Mental Health, Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Baiqiang Xue
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China;; School of Public Health, Qingdao University, Qingdao, 266003, China
| | - Yonghe Ding
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China;; School of Public Health, Qingdao University, Qingdao, 266003, China
| | - Lixia Peng
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China;; School of Pharmacy, Qingdao University, Qingdao, 266003, China
| | - Baokun Wang
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China;; School of Pharmacy, Qingdao University, Qingdao, 266003, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yifeng Xu
- Shanghai Clinical Research Center for Mental Health, Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Changgui Li
- Shandong Provincial Key Laboratory of Metabolic Disease & the Metabolic Disease Institute of Qingdao University, Qingdao, 266003, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiangzhong Zhao
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China
| | - Dun Pan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qiangzhen Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Juan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Zijia Zhu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ze Liu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Disong Xia
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Guoyin Feng
- Shanghai Clinical Research Center for Mental Health, Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Qian Zhang
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China
| | - Yanqin Wen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yongyong Shi
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China;; School of Basic Medicine, Qingdao University, Qingdao, 266003, China;; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China;; Shanghai Clinical Research Center for Mental Health, Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China;; Shandong Provincial Key Laboratory of Metabolic Disease & the Metabolic Disease Institute of Qingdao University, Qingdao, 266003, China;; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, 200030, China;; Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China;; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, 200030, China;; Department of Psychiatry, the First Teaching Hospital of Xinjiang Medical University, Urumqi, 830054, China;; Changning Mental Health Center, Shanghai, 200042, China.
| | - Zhiqiang Li
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China;; School of Basic Medicine, Qingdao University, Qingdao, 266003, China;; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China;; School of Public Health, Qingdao University, Qingdao, 266003, China;; School of Pharmacy, Qingdao University, Qingdao, 266003, China;; Shandong Provincial Key Laboratory of Metabolic Disease & the Metabolic Disease Institute of Qingdao University, Qingdao, 266003, China;; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, 200030, China;.
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154
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Islam F, Lisoway A, Oh ES, Fiori LM, Magarbeh L, Elsheikh SSM, Kim HK, Kloiber S, Kennedy JL, Frey BN, Milev R, Soares CN, Parikh SV, Placenza F, Hassel S, Taylor VH, Leri F, Blier P, Uher R, Farzan F, Lam RW, Turecki G, Foster JA, Rotzinger S, Kennedy SH, Müller DJ. Integrative Genetic Variation, DNA Methylation, and Gene Expression Analysis of Escitalopram and Aripiprazole Treatment Outcomes in Depression: A CAN-BIND-1 Study. PHARMACOPSYCHIATRY 2024. [PMID: 38917846 DOI: 10.1055/a-2313-9979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Little is known about the interplay between genetics and epigenetics on antidepressant treatment (1) response and remission, (2) side effects, and (3) serum levels. This study explored the relationship among single nucleotide polymorphisms (SNPs), DNA methylation (DNAm), and mRNA levels of four pharmacokinetic genes, CYP2C19, CYP2D6, CYP3A4, and ABCB1, and its effect on these outcomes. METHODS The Canadian Biomarker Integration Network for Depression-1 dataset consisted of 177 individuals with major depressive disorder treated for 8 weeks with escitalopram (ESC) followed by 8 weeks with ESC monotherapy or augmentation with aripiprazole. DNAm quantitative trait loci (mQTL), identified by SNP-CpG associations between 20 SNPs and 60 CpG sites in whole blood, were tested for associations with our outcomes, followed by causal inference tests (CITs) to identify methylation-mediated genetic effects. RESULTS Eleven cis-SNP-CpG pairs (q<0.05) constituting four unique SNPs were identified. Although no significant associations were observed between mQTLs and response/remission, CYP2C19 rs4244285 was associated with treatment-related weight gain (q=0.027) and serum concentrations of ESCadj (q<0.001). Between weeks 2-4, 6.7% and 14.9% of those with *1/*1 (normal metabolizers) and *1/*2 (intermediate metabolizers) genotypes, respectively, reported ≥2 lbs of weight gain. In contrast, the *2/*2 genotype (poor metabolizers) did not report weight gain during this period and demonstrated the highest ESCadj concentrations. CITs did not indicate that these effects were epigenetically mediated. DISCUSSION These results elucidate functional mechanisms underlying the established associations between CYP2C19 rs4244285 and ESC pharmacokinetics. This mQTL SNP as a marker for antidepressant-related weight gain needs to be further explored.
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Affiliation(s)
- Farhana Islam
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Amanda Lisoway
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Edward S Oh
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Laura M Fiori
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Verdun, Quebec, Canada
| | - Leen Magarbeh
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Samar S M Elsheikh
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Helena K Kim
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Stefan Kloiber
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - James L Kennedy
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Benicio N Frey
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
- St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
| | - Roumen Milev
- Department of Psychiatry, Queen's University, Providence Care, Kingston, Ontario, Canada
| | - Claudio N Soares
- Department of Psychiatry, Queen's University, Providence Care, Kingston, Ontario, Canada
| | - Sagar V Parikh
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Franca Placenza
- Centre for Mental Health, University Health Network, Toronto, Ontario, Canada
| | - Stefanie Hassel
- Department of Psychiatry, University of Calgary, Calgary, Alberta, Canada; Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Valerie H Taylor
- Department of Psychiatry, University of Calgary, Calgary, Alberta, Canada; Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Francesco Leri
- Department of Psychology and Neuroscience, University of Guelph, Guelph, Ontario, Canada
| | - Pierre Blier
- The Royal Institute of Mental Health Research, Ottawa, Ontario, Canada
| | - Rudolf Uher
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Faranak Farzan
- Mechatronic Systems Engineering, Simon Fraser University, Surrey, British Columbia, Canada
| | - Raymond W Lam
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Verdun, Quebec, Canada
| | - Jane A Foster
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
- Centre for Mental Health, University Health Network, Toronto, Ontario, Canada
- St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
| | - Susan Rotzinger
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, St Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Sidney H Kennedy
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Centre for Mental Health, University Health Network, Toronto, Ontario, Canada
- Department of Psychiatry, St Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario, Canada
| | - Daniel J Müller
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Clinic of Würzburg, Würzburg, Germany
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155
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Zhang W, Wang X, Yang K, Zhang A, Yu L, Jiang Z, Hong X, Lei T, Cui Y. Psychometric Properties of the MOVES Scale for Tourette Syndrome and Comorbidities in a Chinese Cultural Context. Child Psychiatry Hum Dev 2024:10.1007/s10578-024-01734-x. [PMID: 38916698 DOI: 10.1007/s10578-024-01734-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
The Motor tic, Obsessions and Compulsions, Vocal tic Evaluation Survey (MOVES) is a widely used screening tool for Tourette syndrome (TS) and associated comorbidities. This study evaluated its applicability for children in China using 7,125 participants from the National Center for Children's Health (Beijing). Psychometric evaluations included exploratory and confirmatory factor analysis, yielding a 16-item, four-factor model that explained 55.11% of the variance and demonstrated good internal consistency (Cronbach's alpha = 0.88) and test-retest reliability (ICC = 0.86). The scale showed strong convergent, discriminant, and criterion-related validity and was significantly correlated with other established TS scales. The results affirm the reliability and validity of the MOVES for screening TS in Asian contexts, addressing a crucial gap in the region's TS assessment tools.
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Affiliation(s)
- Wenyan Zhang
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xianbin Wang
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Kai Yang
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Anyi Zhang
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Liping Yu
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Zhongliang Jiang
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xu Hong
- Cloud Services Innovation Laboratory, Institute of Intelligent Science and Technology, China Electronics Technology Group Corporation, Beijing, 100041, China
| | - Tianyuan Lei
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
| | - Yonghua Cui
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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Fazel Darbandi S, An JY, Lim K, Page NF, Liang L, Young DM, Ypsilanti AR, State MW, Nord AS, Sanders SJ, Rubenstein JLR. Five autism-associated transcriptional regulators target shared loci proximal to brain-expressed genes. Cell Rep 2024; 43:114329. [PMID: 38850535 PMCID: PMC11235582 DOI: 10.1016/j.celrep.2024.114329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/15/2023] [Accepted: 05/22/2024] [Indexed: 06/10/2024] Open
Abstract
Many autism spectrum disorder (ASD)-associated genes act as transcriptional regulators (TRs). Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify the regulatory targets of ARID1B, BCL11A, FOXP1, TBR1, and TCF7L2, ASD-associated TRs in the developing human and mouse cortex. These TRs shared substantial overlap in the binding sites, especially within open chromatin. The overlap within a promoter region, 1-2,000 bp upstream of the transcription start site, was highly predictive of brain-expressed genes. This signature was observed in 96 out of 102 ASD-associated genes. In vitro CRISPRi against ARID1B and TBR1 delineated downstream convergent biology in mouse cortical cultures. After 8 days, NeuN+ and CALB+ cells were decreased, GFAP+ cells were increased, and transcriptomic signatures correlated with the postmortem brain samples from individuals with ASD. We suggest that functional convergence across five ASD-associated TRs leads to shared neurodevelopmental outcomes of haploinsufficient disruption.
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Affiliation(s)
- Siavash Fazel Darbandi
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, South Korea; BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, South Korea
| | - Kenneth Lim
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicholas F Page
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lindsay Liang
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David M Young
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Athena R Ypsilanti
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - Stephan J Sanders
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA; Institute for Developmental and Regenerative Medicine, Old Road Campus, Roosevelt Dr., Headington, Oxford OX3 7TY, UK.
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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157
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Pottier C, Küçükali F, Baker M, Batzler A, Jenkins GD, van Blitterswijk M, Vicente CT, De Coster W, Wynants S, Van de Walle P, Ross OA, Murray ME, Faura J, Haggarty SJ, van Rooij JG, Mol MO, Hsiung GYR, Graff C, Öijerstedt L, Neumann M, Asmann Y, McDonnell SK, Baheti S, Josephs KA, Whitwell JL, Bieniek KF, Forsberg L, Heuer H, Lago AL, Geier EG, Yokoyama JS, Oddi AP, Flanagan M, Mao Q, Hodges JR, Kwok JB, Domoto-Reilly K, Synofzik M, Wilke C, Onyike C, Dickerson BC, Evers BM, Dugger BN, Munoz DG, Keith J, Zinman L, Rogaeva E, Suh E, Gefen T, Geula C, Weintraub S, Diehl-Schmid J, Farlow MR, Edbauer D, Woodruff BK, Caselli RJ, Donker Kaat LL, Huey ED, Reiman EM, Mead S, King A, Roeber S, Nana AL, Ertekin-Taner N, Knopman DS, Petersen RC, Petrucelli L, Uitti RJ, Wszolek ZK, Ramos EM, Grinberg LT, Gorno Tempini ML, Rosen HJ, Spina S, Piguet O, Grossman M, Trojanowski JQ, Keene DC, Lee-Way J, Prudlo J, Geschwind DH, Rissman RA, Cruchaga C, Ghetti B, Halliday GM, Beach TG, Serrano GE, Arzberger T, Herms J, Boxer AL, Honig LS, Vonsattel JP, Lopez OL, Kofler J, White CL, Gearing M, Glass J, Rohrer JD, Irwin DJ, Lee EB, Van Deerlin V, Castellani R, Mesulam MM, Tartaglia MC, Finger EC, Troakes C, Al-Sarraj S, Miller BL, Seelaar H, Graff-Radford NR, Boeve BF, Mackenzie IR, van Swieten JC, Seeley WW, Sleegers K, Dickson DW, Biernacka JM, Rademakers R. Deciphering Distinct Genetic Risk Factors for FTLD-TDP Pathological Subtypes via Whole-Genome Sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.24.24309088. [PMID: 38978643 PMCID: PMC11230325 DOI: 10.1101/2024.06.24.24309088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Frontotemporal lobar degeneration with neuronal inclusions of the TAR DNA-binding protein 43 (FTLD-TDP) is a fatal neurodegenerative disorder with only a limited number of risk loci identified. We report our comprehensive genome-wide association study as part of the International FTLD-TDP Whole-Genome Sequencing Consortium, including 985 cases and 3,153 controls, and meta-analysis with the Dementia-seq cohort, compiled from 26 institutions/brain banks in the United States, Europe and Australia. We confirm UNC13A as the strongest overall FTLD-TDP risk factor and identify TNIP1 as a novel FTLD-TDP risk factor. In subgroup analyses, we further identify for the first time genome-wide significant loci specific to each of the three main FTLD-TDP pathological subtypes (A, B and C), as well as enrichment of risk loci in distinct tissues, brain regions, and neuronal subtypes, suggesting distinct disease aetiologies in each of the subtypes. Rare variant analysis confirmed TBK1 and identified VIPR1 , RBPJL , and L3MBTL1 as novel subtype specific FTLD-TDP risk genes, further highlighting the role of innate and adaptive immunity and notch signalling pathway in FTLD-TDP, with potential diagnostic and novel therapeutic implications.
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158
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Kojima K, Tadaka S, Okamura Y, Kinoshita K. Two-stage strategy using denoising autoencoders for robust reference-free genotype imputation with missing input genotypes. J Hum Genet 2024:10.1038/s10038-024-01261-6. [PMID: 38918526 DOI: 10.1038/s10038-024-01261-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/16/2024] [Accepted: 05/13/2024] [Indexed: 06/27/2024]
Abstract
Widely used genotype imputation methods are based on the Li and Stephens model, which assumes that new haplotypes can be represented by modifying existing haplotypes in a reference panel through mutations and recombinations. These methods use genotypes from SNP arrays as inputs to estimate haplotypes that align with the input genotypes by analyzing recombination patterns within a reference panel, and then infer unobserved variants. While these methods require reference panels in an identifiable form, their public use is limited due to privacy and consent concerns. One strategy to overcome these limitations is to use de-identified haplotype information, such as summary statistics or model parameters. Advances in deep learning (DL) offer the potential to develop imputation methods that use haplotype information in a reference-free manner by handling it as model parameters, while maintaining comparable imputation accuracy to methods based on the Li and Stephens model. Here, we provide a brief introduction to DL-based reference-free genotype imputation methods, including RNN-IMP, developed by our research group. We then evaluate the performance of RNN-IMP against widely-used Li and Stephens model-based imputation methods in terms of accuracy (R2), using the 1000 Genomes Project Phase 3 dataset and corresponding simulated Omni2.5 SNP genotype data. Although RNN-IMP is sensitive to missing values in input genotypes, we propose a two-stage imputation strategy: missing genotypes are first imputed using denoising autoencoders; RNN-IMP then processes these imputed genotypes. This approach restores the imputation accuracy that is degraded by missing values, enhancing the practical use of RNN-IMP.
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Affiliation(s)
- Kaname Kojima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Yasunobu Okamura
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-0873, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-0873, Japan.
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
- Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
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159
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Badja C, Momen S, Koh GCC, Boushaki S, Roumeliotis TI, Kozik Z, Jones I, Bousgouni V, Dias JML, Krokidis MG, Young J, Chen H, Yang M, Docquier F, Memari Y, Valcarcel-Zimenez L, Gupta K, Kong LR, Fawcett H, Robert F, Zhao S, Degasperi A, Kumar Y, Davies H, Harris R, Frezza C, Chatgilialoglu C, Sarkany R, Lehmann A, Bakal C, Choudhary J, Fassihi H, Nik-Zainal S. Insights from multi-omic modeling of neurodegeneration in xeroderma pigmentosum using an induced pluripotent stem cell system. Cell Rep 2024; 43:114243. [PMID: 38805398 DOI: 10.1016/j.celrep.2024.114243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Xeroderma pigmentosum (XP) is caused by defective nucleotide excision repair of DNA damage. This results in hypersensitivity to ultraviolet light and increased skin cancer risk, as sunlight-induced photoproducts remain unrepaired. However, many XP patients also display early-onset neurodegeneration, which leads to premature death. The mechanism of neurodegeneration is unknown. Here, we investigate XP neurodegeneration using pluripotent stem cells derived from XP patients and healthy relatives, performing functional multi-omics on samples during neuronal differentiation. We show substantially increased levels of 5',8-cyclopurine and 8-oxopurine in XP neuronal DNA secondary to marked oxidative stress. Furthermore, we find that the endoplasmic reticulum stress response is upregulated and reversal of the mutant genotype is associated with phenotypic rescue. Critically, XP neurons exhibit inappropriate downregulation of the protein clearance ubiquitin-proteasome system (UPS). Chemical enhancement of UPS activity in XP neuronal models improves phenotypes, albeit inadequately. Although more work is required, this study presents insights with intervention potential.
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Affiliation(s)
- Cherif Badja
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK.
| | - Sophie Momen
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Gene Ching Chiek Koh
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Soraya Boushaki
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, 237 Fulham Road, London SW3 6JB, UK
| | - Zuza Kozik
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, 237 Fulham Road, London SW3 6JB, UK
| | - Ian Jones
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Vicky Bousgouni
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - João M L Dias
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Marios G Krokidis
- Institute of Nanoscience and Nanotechnology, N.C.S.R. "Demokritos", Agia Paraskevi Attikis, 15310 Athens, Greece; Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece
| | - Jamie Young
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Hongwei Chen
- Wellcome Sanger Institute, Hinxton CB10 1RQ, UK; Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Ming Yang
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - France Docquier
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK
| | - Yasin Memari
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Lorea Valcarcel-Zimenez
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Komal Gupta
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Li Ren Kong
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; NUS Centre for Cancer Research, N2CR, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore; Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Heather Fawcett
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Florian Robert
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Salome Zhao
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Andrea Degasperi
- Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Yogesh Kumar
- Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Helen Davies
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Rebecca Harris
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Robert Sarkany
- National Xeroderma Pigmentosum Service, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London SE1 7EH, UK
| | - Alan Lehmann
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Chris Bakal
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Jyoti Choudhary
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, 237 Fulham Road, London SW3 6JB, UK
| | - Hiva Fassihi
- National Xeroderma Pigmentosum Service, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London SE1 7EH, UK
| | - Serena Nik-Zainal
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK.
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160
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Zhao Y, Guo W, Zhou J, Wang X. Schizophrenia and risk preference: a bidirectional two-sample mendelian randomization study. Eur Arch Psychiatry Clin Neurosci 2024:10.1007/s00406-024-01853-5. [PMID: 38914854 DOI: 10.1007/s00406-024-01853-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
Increasing evidence shows that risk preference is associated with schizophrenia. However, the causality and direction of this association are not clear; Therefore, we used Mendelian randomization (MR) to examine the potential bidirectional relationship between risk preference and schizophrenia. Genome-wide association studies (GWAS) summary data on risk preference of 939,908 participants from the UK Biobank and 23andMe were used to identify general risk preference. Data from 320,404 subjects (76,755 cases and 243,649 controls) from The Psychiatric Genomics Consortium were used to identify schizophrenia. The weighted median (WM), the inverse variance weighted (IVW), and the Mendelian randomization-Egger (MR-Egger) methods were used for the MR analysis to estimate the causal effect and detect the directional pleiotropy. The GWAS summary data were respectively from two combined samples, containing 939,908 and 320,404 subjects of European ancestry. Mendelian randomization evidence suggested that risk preference was associated with increased onset of schizophrenia (OR = 2.84, 95CI%: 1.77-4.56, P = 1.58*10 - 5) and that schizophrenia was also associated with raised risk preference (OR = 1.11, 95CI%: 1.07-1.15, P = 7.98*10 - 8). With the use of large-scale GWAS data, robust evidence suggests an interaction between risk preference and schizophrenia. This also indicates that early identification of and intervention for increased risk preference may improve the prognosis of schizophrenia.
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Affiliation(s)
- Yixin Zhao
- Department of Psychiatry, National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Weilong Guo
- Department of Psychiatry, National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Jiansong Zhou
- Department of Psychiatry, National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
| | - Xiaoping Wang
- Department of Psychiatry, National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
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161
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Pletenev I, Bazarevich M, Zagirova D, Kononkova A, Cherkasov A, Efimova O, Tiukacheva E, Morozov K, Ulianov K, Komkov D, Tvorogova A, Golimbet V, Kondratyev N, Razin S, Khaitovich P, Ulianov S, Khrameeva E. Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome. Nucleic Acids Res 2024; 52:6234-6252. [PMID: 38647066 PMCID: PMC11194087 DOI: 10.1093/nar/gkae271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/21/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024] Open
Abstract
Chromatin architecture regulates gene expression and shapes cellular identity, particularly in neuronal cells. Specifically, polycomb group (PcG) proteins enable establishment and maintenance of neuronal cell type by reorganizing chromatin into repressive domains that limit the expression of fate-determining genes and sustain distinct gene expression patterns in neurons. Here, we map the 3D genome architecture in neuronal and non-neuronal cells isolated from the Wernicke's area of four human brains and comprehensively analyze neuron-specific aspects of chromatin organization. We find that genome segregation into active and inactive compartments is greatly reduced in neurons compared to other brain cells. Furthermore, neuronal Hi-C maps reveal strong long-range interactions, forming a specific network of PcG-mediated contacts in neurons that is nearly absent in other brain cells. These interacting loci contain developmental transcription factors with repressed expression in neurons and other mature brain cells. But only in neurons, they are rich in bivalent promoters occupied by H3K4me3 histone modification together with H3K27me3, which points to a possible functional role of PcG contacts in neurons. Importantly, other layers of chromatin organization also exhibit a distinct structure in neurons, characterized by an increase in short-range interactions and a decrease in long-range ones.
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Affiliation(s)
- Ilya A Pletenev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maria Bazarevich
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Diana R Zagirova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | - Anna D Kononkova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Alexander V Cherkasov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Olga I Efimova
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Eugenia A Tiukacheva
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow 141700, Russia
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- CNRS UMR9018, Institut Gustave Roussy, Villejuif 94805, France
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Kirill V Morozov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Kirill A Ulianov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Dmitriy Komkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna V Tvorogova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Vera E Golimbet
- Laboratory of Clinical Genetics, Mental Health Research Center, Moscow 115522, Russia
| | - Nikolay V Kondratyev
- Laboratory of Clinical Genetics, Mental Health Research Center, Moscow 115522, Russia
| | - Sergey V Razin
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Philipp Khaitovich
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Sergey V Ulianov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Ekaterina E Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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162
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Pramotton FM, Spitz S, Kamm RD. Challenges and Future Perspectives in Modeling Neurodegenerative Diseases Using Organ-on-a-Chip Technology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403892. [PMID: 38922799 DOI: 10.1002/advs.202403892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/01/2024] [Indexed: 06/28/2024]
Abstract
Neurodegenerative diseases (NDDs) affect more than 50 million people worldwide, posing a significant global health challenge as well as a high socioeconomic burden. With aging constituting one of the main risk factors for some NDDs such as Alzheimer's disease (AD) and Parkinson's disease (PD), this societal toll is expected to rise considering the predicted increase in the aging population as well as the limited progress in the development of effective therapeutics. To address the high failure rates in clinical trials, legislative changes permitting the use of alternatives to traditional pre-clinical in vivo models are implemented. In this regard, microphysiological systems (MPS) such as organ-on-a-chip (OoC) platforms constitute a promising tool, due to their ability to mimic complex and human-specific tissue niches in vitro. This review summarizes the current progress in modeling NDDs using OoC technology and discusses five critical aspects still insufficiently addressed in OoC models to date. Taking these aspects into consideration in the future MPS will advance the modeling of NDDs in vitro and increase their translational value in the clinical setting.
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Affiliation(s)
- Francesca Michela Pramotton
- Department of Mechanical Engineering and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sarah Spitz
- Department of Mechanical Engineering and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Roger D Kamm
- Department of Mechanical Engineering and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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163
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Jaykumar AB, Binns D, Taylor CA, Anselmo A, Birnbaum SG, Huber KM, Cobb MH. WNKs regulate mouse behavior and alter central nervous system glucose uptake and insulin signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.598125. [PMID: 38915673 PMCID: PMC11195145 DOI: 10.1101/2024.06.09.598125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Certain areas of the brain involved in episodic memory and behavior, such as the hippocampus, express high levels of insulin receptors and glucose transporter-4 (GLUT4) and are responsive to insulin. Insulin and neuronal glucose metabolism improve cognitive functions and regulate mood in humans. Insulin-dependent GLUT4 trafficking has been extensively studied in muscle and adipose tissue, but little work has demonstrated either how it is controlled in insulin-responsive brain regions or its mechanistic connection to cognitive functions. In this study, we demonstrate that inhibition of WNK (With-No-lysine (K)) kinases improves learning and memory in mice. Neuronal inhibition of WNK enhances in vivo hippocampal glucose uptake. Inhibition of WNK enhances insulin signaling output and insulin-dependent GLUT4 trafficking to the plasma membrane in mice primary neuronal cultures and hippocampal slices. Therefore, we propose that the extent of neuronal WNK kinase activity has an important influence on learning, memory and anxiety-related behaviors, in part, by modulation of neuronal insulin signaling.
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Affiliation(s)
- Ankita B. Jaykumar
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
| | - Derk Binns
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
| | - Clinton A. Taylor
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
| | - Anthony Anselmo
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
| | - Shari G. Birnbaum
- Departments of Peter O’Donnell Jr. Brain Institute and Psychiatry, UT Southwestern Medical Center, Dallas, USA
| | | | - Melanie H. Cobb
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
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164
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Tu Y, Xu B. Esketamine induces tripartite motif-containing protein 24 to improve cognitive dysfunction in Alzheimer's disease. Neurosci Lett 2024; 834:137836. [PMID: 38802052 DOI: 10.1016/j.neulet.2024.137836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Esketamine has been revealed to improve cognitive impairments under different conditions, while its function in Alzheimer's disease (AD) has not been well characterized. We expounded the effects and detailed mechanism of esketamine in triple transgenic AD (3xTg-AD) mice in the present study. The impaired spatial learning and memory retention of 3xTg-AD mice were ameliorated by esketamine, whereas tripartite motif-containing protein 24 (TRIM24) depletion reversed the ameliorative effects of esketamine in 3xTg-AD mice. Esketamine elevated the extent of PI3K and AKT phosphorylation in the hippocampus by promoting TRIM24 expression, and knockdown of TRIM24 impaired the PI3K/AKT pathway. AD-like mice had increased expression of pro-inflammatory molecules and elevated expression of GFAP and p-Tau. Esketamine reduced inflammation, but its therapeutic effect was reversed by TRIM24 knockdown. The PI3K/AKT pathway blockage exacerbated cognitive deficits and neuroinflammatory responses in mice. Thus, esketamine has the potential to improve the cognitive and memory functions of 3xTg-AD mice by repressing neuroinflammation by activating TRIM24 and the downstream PI3K/AKT pathway.
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Affiliation(s)
- Yingbing Tu
- Department of Anesthesia, Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou 215101, Jiangsu, PR China
| | - Bin Xu
- Department of Anesthesia, Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou 215101, Jiangsu, PR China.
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165
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Leger BS, Meredith JJ, Ideker T, Sanchez-Roige S, Palmer AA. Rare and common variants associated with alcohol consumption identify a conserved molecular network. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2024. [PMID: 39031522 DOI: 10.1111/acer.15399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 07/22/2024]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified hundreds of common variants associated with alcohol consumption. In contrast, genetic studies of alcohol consumption that use rare variants are still in their early stages. No prior studies of alcohol consumption have examined whether common and rare variants implicate the same genes and molecular networks, leaving open the possibility that the two approaches might identify distinct biology. METHODS To address this knowledge gap, we used publicly available alcohol consumption GWAS summary statistics (GSCAN, N = 666,978) and whole exome sequencing data (Genebass, N = 393,099) to identify a set of common and rare variants for alcohol consumption. We used gene-based analysis to implicate genes from common and rare variant analyses, which we then propagated onto a shared molecular network using a network colocalization procedure. RESULTS Gene-based analysis of each dataset implicated 294 (common variants) and 35 (rare variants) genes, including ethanol metabolizing genes ADH1B and ADH1C, which were identified by both analyses, and ANKRD12, GIGYF1, KIF21B, and STK31, which were identified in only the rare variant analysis, but have been associated with other neuropsychiatric traits. Network colocalization revealed significant network overlap between the genes identified via common and rare variants. The shared network identified gene families that function in alcohol metabolism, including ADH, ALDH, CYP, and UGT. Seventy-one of the genes in the shared network were previously implicated in neuropsychiatric or substance use disorders but not alcohol-related behaviors (e.g. EXOC2, EPM2A, and CACNG4). Differential gene expression analysis showed enrichment in the liver and several brain regions. CONCLUSIONS Genes implicated by network colocalization identify shared biology relevant to alcohol consumption, which also underlie neuropsychiatric traits and substance use disorders that are comorbid with alcohol use, providing a more holistic understanding of two disparate sources of genetic information.
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Affiliation(s)
- Brittany S Leger
- Program in Biomedical Sciences, University of California San Diego, La Jolla, California, USA
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA
| | - John J Meredith
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
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166
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García-González J, Garcia-Gonzalez S, Liou L, O'Reilly PF. The Gene Expression Landscape of Disease Genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.20.24309121. [PMID: 38947033 PMCID: PMC11213058 DOI: 10.1101/2024.06.20.24309121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Fine-mapping and gene-prioritisation techniques applied to the latest Genome-Wide Association Study (GWAS) results have prioritised hundreds of genes as causally associated with disease. Here we leverage these recently compiled lists of high-confidence causal genes to interrogate where in the body disease genes operate. Specifically, we combine GWAS summary statistics, gene prioritisation results and gene expression RNA-seq data from 46 tissues and 204 cell types in relation to 16 major diseases (including 8 cancers). In tissues and cell types with well-established relevance to the disease, the prioritised genes typically have higher absolute and relative (i.e. tissue/cell specific) expression compared to non-prioritised 'control' genes. Examples include brain tissues in psychiatric disorders (P-value < 1×10-7), microglia cells in Alzheimer's Disease (P-value = 9.8×10-3) and colon mucosa in colorectal cancer (P-value < 1×10-3). We also observe significantly higher expression for disease genes in multiple tissues and cell types with no established links to the corresponding disease. While some of these results may be explained by cell types that span multiple tissues, such as macrophages in brain, blood, lung and spleen in relation to Alzheimer's disease (P-values < 1×10-3), the cause for others is unclear and motivates further investigation that may provide novel insights into disease etiology. For example, mammary tissue in Type 2 Diabetes (P-value < 1×10-7); reproductive tissues such as breast, uterus, vagina, and prostate in Coronary Artery Disease (P-value < 1×10-4); and motor neurons in psychiatric disorders (P-value < 3×10-4). In the GTEx dataset, tissue type is the major predictor of gene expression but the contribution of each predictor (tissue, sample, subject, batch) varies widely among disease-associated genes. Finally, we highlight genes with the highest levels of gene expression in relevant tissues to guide functional follow-up studies. Our results could offer novel insights into the tissues and cells involved in disease initiation, inform drug target and delivery strategies, highlighting potential off-target effects, and exemplify the relative performance of different statistical tests for linking disease genes with tissue and cell type gene expression.
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Affiliation(s)
- Judit García-González
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York City, NY 10029, USA
| | - Saul Garcia-Gonzalez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York City, NY 10029, USA
- Center for Excellence in Youth Education, Icahn School of Medicine, Mount Sinai, New York City, NY 10029, USA
| | - Lathan Liou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York City, NY 10029, USA
| | - Paul F O'Reilly
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York City, NY 10029, USA
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167
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Lalagkas PN, Melamed RD. Shared genetics between breast cancer and predisposing diseases identifies novel breast cancer treatment candidates. RESEARCH SQUARE 2024:rs.3.rs-4536370. [PMID: 38947022 PMCID: PMC11213186 DOI: 10.21203/rs.3.rs-4536370/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background Current effective breast cancer treatment options have severe side effects, highlighting a need for new therapies. Drug repurposing can accelerate improvements to care, as FDA-approved drugs have known safety and pharmacological profiles. Some drugs for other conditions, such as metformin, an antidiabetic, have been tested in clinical trials for repurposing for breast cancer. Here, we exploit the genetics of breast cancer and linked predisposing diseases to propose novel drug repurposing. We hypothesize that if a predisposing disease contributes to breast cancer pathology, identifying the pleiotropic genes related to the risk of cancer could prioritize drug targets, among all drugs treating a predisposing disease. We aim to develop a method to not only prioritize drug repurposing, but also to highlight shared etiology explaining repurposing. Methods We compile breast cancer's predisposing diseases from literature. For each predisposing disease, we use GWAS summary statistics to identify genes in loci showing genetic correlation with breast cancer. Then, we use a network approach to link these shared genes to canonical pathways, and similarly for all drugs treating the predisposing disease, we link their targets to pathways. In this manner, we are able to prioritize a list of drugs based on each predisposing disease, with each drug linked to a set of implicating pathways. Finally, we evaluate our recommendations against drugs currently under investigation for breast cancer. Results We identify 84 loci harboring mutations with positively correlated effects between breast cancer and its predisposing diseases; these contain 194 identified shared genes. Out of the 112 drugs indicated for the predisposing diseases, 76 drugs can be linked to shared genes via pathways (candidate drugs for repurposing). Fifteen out of these candidate drugs are already in advanced clinical trial phases or approved for breast cancer (OR = 9.28, p = 7.99e-03, one-sided Fisher's exact test), highlighting the ability of our approach to identify likely successful candidate drugs for repurposing. Conclusions Our novel approach accelerates drug repurposing for breast cancer by leveraging shared genetics with its known risk factors. The result provides 59 novel candidate drugs alongside biological insights supporting each recommendation.
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168
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Van Rampelbergh J, Achenbach P, Leslie RD, Kindermans M, Parmentier F, Carlier V, Bovy N, Vanderelst L, Van Mechelen M, Vandepapelière P, Boitard C. First-in-human, double-blind, randomized phase 1b study of peptide immunotherapy IMCY-0098 in new-onset type 1 diabetes: an exploratory analysis of immune biomarkers. BMC Med 2024; 22:259. [PMID: 38902652 PMCID: PMC11191262 DOI: 10.1186/s12916-024-03476-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND IMCY-0098, a synthetic peptide developed to halt disease progression via elimination of key immune cells in the autoimmune cascade, has shown a promising safety profile for the treatment of type 1 diabetes (T1D) in a recent phase 1b trial. This exploratory analysis of data from that trial aimed to identify the patient biomarkers at baseline associated with a positive response to treatment and examined the associations between immune response parameters and clinical efficacy endpoints (as surrogates for mechanism of action endpoints) using an artificial intelligence-based approach of unsupervised explainable machine learning. METHODS We conducted an exploratory analysis of data from a phase 1b, dose-escalation, randomized, placebo-controlled study of IMCY-0098 in patients with recent-onset T1D. Here, a panel of markers of T cell activation, memory T cells, and effector T cell response were analyzed via descriptive statistics. Artificial intelligence-based analyses of associations between all variables, including immune responses and clinical responses, were performed using the Knowledge Extraction and Management (KEM®) v 3.6.2 analytical platform. RESULTS The relationship between all available patient data was investigated using unsupervised machine learning implemented in the KEM® environment. Of 15 associations found for the dose C group (450 μg subcutaneously followed by 3 × 225 μg subcutaneously), seven involved human leukocyte antigen (HLA) type, all of which identified improvement/absence of worsening of disease parameters in DR4+ patients and worsening/absence of improvement in DR4- patients. This association with DR4+ and non-DR3 was confirmed using the endpoints normalized area under the curve C-peptide from mixed meal tolerance tests where presence of DR4 HLA haplotype was associated with an improvement in both endpoints. Exploratory immune analysis showed that IMCY-0098 dose B (150 μg subcutaneously followed by 3 × 75 μg subcutaneously) and dose C led to an increase in presumed/potentially protective antigen-specific cytolytic CD4+ T cells and a decrease in pathogenic CD8+ T cells, consistent with the expected mechanism of action of IMCY-0098. The analysis identified significant associations between immune and clinical responses to IMCY-0098. CONCLUSIONS Promising preliminary efficacy results support the design of a phase 2 study of IMCY-0098 in patients with recent-onset T1D. TRIAL REGISTRATION ClinicalTrials.gov NCT03272269; EudraCT: 2016-003514-27.
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Affiliation(s)
| | - Peter Achenbach
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, Klinikum Rechts Der Isar, Munich, Germany
| | | | | | | | | | - Nicolas Bovy
- Imcyse S.A, Avenue Pré-Aily 14, Liège, 4031, Belgium
| | | | | | | | - Christian Boitard
- Inserm U1016, Cochin Institute, Paris, France
- Medical Faculty, Université de Paris, Paris, France
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169
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Johnson EC, Austin-Zimmerman I, Thorpe HHA, Levey DF, Baranger DAA, Colbert SMC, Demontis D, Khokhar JY, Davis LK, Edenberg HJ, Di Forti M, Sanchez-Roige S, Gelernter J, Agrawal A. Cross-ancestry genetic investigation of schizophrenia, cannabis use disorder, and tobacco smoking. Neuropsychopharmacology 2024:10.1038/s41386-024-01886-3. [PMID: 38906991 DOI: 10.1038/s41386-024-01886-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 06/23/2024]
Abstract
Individuals with schizophrenia frequently experience co-occurring substance use, including tobacco smoking and heavy cannabis use, and substance use disorders. There is interest in understanding the extent to which these relationships are causal, and to what extent shared genetic factors play a role. We explored the relationships between schizophrenia (Scz; European ancestry N = 161,405; African ancestry N = 15,846), cannabis use disorder (CanUD; European ancestry N = 886,025; African ancestry N = 120,208), and ever-regular tobacco smoking (Smk; European ancestry N = 805,431; African ancestry N = 24,278) using the largest available genome-wide studies of these phenotypes in individuals of African and European ancestries. All three phenotypes were positively genetically correlated (rgs = 0.17-0.62). Genetic instrumental variable analyses suggested the presence of shared heritable factors, but evidence for bidirectional causal relationships was also found between all three phenotypes even after correcting for these shared genetic factors. We identified 327 pleiotropic loci with 439 lead SNPs in the European ancestry data, 150 of which were novel (i.e., not genome-wide significant in the original studies). Of these pleiotropic loci, 202 had lead variants which showed convergent effects (i.e., same direction of effect) on Scz, CanUD, and Smk. Genetic variants convergent across all three phenotypes showed strong genetic correlations with risk-taking, executive function, and several mental health conditions. Our results suggest that both shared genetic factors and causal mechanisms may play a role in the relationship between CanUD, Smk, and Scz, but longitudinal, prospective studies are needed to confirm a causal relationship.
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Affiliation(s)
- Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
| | - Isabelle Austin-Zimmerman
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Hayley H A Thorpe
- Department of Anatomy and Cell Biology, Western University, London, ON, Canada
| | - Daniel F Levey
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - David A A Baranger
- Department of Psychological and Brain Sciences, Washington University in Saint Louis, St. Louis, MO, USA
| | - Sarah M C Colbert
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Jibran Y Khokhar
- Department of Anatomy and Cell Biology, Western University, London, ON, Canada
| | - Lea K Davis
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Marta Di Forti
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Sandra Sanchez-Roige
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
- Department of Psychiatry, UC San Diego School of Medicine, La Jolla, CA, USA
| | - Joel Gelernter
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
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170
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Jones EF, Howton TC, Flanary VL, Clark AD, Lasseigne BN. Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage. Mol Brain 2024; 17:40. [PMID: 38902764 PMCID: PMC11188239 DOI: 10.1186/s13041-024-01112-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/08/2024] [Indexed: 06/22/2024] Open
Abstract
Alternative splicing (AS) contributes to the biological heterogeneity between species, sexes, tissues, and cell types. Many diseases are either caused by alterations in AS or by alterations to AS. Therefore, measuring AS accurately and efficiently is critical for assessing molecular phenotypes, including those associated with disease. Long-read sequencing enables more accurate quantification of differentially spliced isoform expression than short-read sequencing approaches, and third-generation platforms facilitate high-throughput experiments. To assess differences in AS across the cerebellum, cortex, hippocampus, and striatum by sex, we generated and analyzed Oxford Nanopore Technologies (ONT) long-read RNA sequencing (lrRNA-Seq) C57BL/6J mouse brain cDNA libraries. From > 85 million reads that passed quality control metrics, we calculated differential gene expression (DGE), differential transcript expression (DTE), and differential transcript usage (DTU) across brain regions and by sex. We found significant DGE, DTE, and DTU across brain regions and that the cerebellum had the most differences compared to the other three regions. Additionally, we found region-specific differential splicing between sexes, with the most sex differences in DTU in the cortex and no DTU in the hippocampus. We also report on two distinct patterns of sex DTU we observed, sex-divergent and sex-specific, that could potentially help explain sex differences in the prevalence and prognosis of various neurological and psychiatric disorders in future studies. Finally, we built a Shiny web application for researchers to explore the data further. Our study provides a resource for the community; it underscores the importance of AS in biological heterogeneity and the utility of long-read sequencing to better understand AS in the brain.
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Affiliation(s)
- Emma F Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Timothy C Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Victoria L Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Amanda D Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Brittany N Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America.
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Patel D, McElroy JP, Weng DY, Sahar K, Reisinger SA, Freudenheim JL, Wewers MD, Shields PG, Song MA. Sex-related DNA methylation is associated with inflammation and gene expression in the lungs of healthy individuals. Sci Rep 2024; 14:14280. [PMID: 38902313 PMCID: PMC11190195 DOI: 10.1038/s41598-024-65027-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024] Open
Abstract
Lung cancer exhibits sex-biased molecular characteristics and epidemiological trends, suggesting a need for sex-specific approaches to understanding its etiology and treatment. DNA methylation alterations play critical roles in lung carcinogenesis and may serve as valuable biomarkers for precision medicine strategies. We employed the Infinium MethylationEPIC array to identify autosomal sex-related differentially methylated CpG sites (DM-CpGs) in lung epithelium of healthy individuals (32 females and 37 males) while controlling for age, BMI, and tobacco use. We correlated DM-CpGs with gene expression in lung epithelium and immune responses in bronchoalveolar lavage. We validated these DM-CpGs in lung tumors and adjacent normal tissue from The Cancer Genome Atlas (TCGA). Among 522 identified DM-CpGs, 61% were hypermethylated in females, predominantly located in promoter regions. These DM genes were implicated in cell-to-cell signaling, cellular function, transport, and lipid metabolism. Correlation analysis revealed sex-specific patterns between DM-CpGs and gene expression. Additionally, several DM-CpGs were correlated significantly with cytokines (IL-1β, IL-4, IL-12p70, and IFN-γ), macrophage, and lymphocyte counts. Also, some DM-CpGs were observed in TCGA lung adenocarcinoma, squamous cell carcinoma, and adjacent normal tissues. Our findings highlight sex-specific DNA methylation patterns in healthy lung epithelium and their associations with lung gene expression and lung immune biomarkers. These findings underscore the potential role of lung sex-related CpGs as epigenetic predispositions influencing sex disparities in lung cancer risk and outcomes, warranting further investigation for personalized lung cancer management strategies.
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Affiliation(s)
- Devki Patel
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Joseph P McElroy
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Daniel Y Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Kamel Sahar
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Sarah A Reisinger
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Mark D Wewers
- Pulmonary and Critical Care Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Peter G Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA.
- Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
| | - Min-Ae Song
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA.
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172
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Park C, Weerakkody JS, Schneider R, Miao S, Pitt D. CNS cell-derived exosome signatures as blood-based biomarkers of neurodegenerative diseases. Front Neurosci 2024; 18:1426700. [PMID: 38966760 PMCID: PMC11222337 DOI: 10.3389/fnins.2024.1426700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/07/2024] [Indexed: 07/06/2024] Open
Abstract
Molecular biomarkers require the reproducible capture of disease-associated changes and are ideally sensitive, specific and accessible with minimal invasiveness to patients. Exosomes are a subtype of extracellular vesicles that have gained attention as potential biomarkers. They are released by all cell types and carry molecular cargo that reflects the functional state of the cells of origin. These characteristics make them an attractive means of measuring disease-related processes within the central nervous system (CNS), as they cross the blood-brain barrier (BBB) and can be captured in peripheral blood. In this review, we discuss recent progress made toward identifying blood-based protein and RNA biomarkers of several neurodegenerative diseases from circulating, CNS cell-derived exosomes. Given the lack of standardized methodology for exosome isolation and characterization, we discuss the challenges of capturing and quantifying the molecular content of exosome populations from blood for translation to clinical use.
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Affiliation(s)
- Calvin Park
- Columbia University Irving Medical Center, Columbia University, New York, NY, United States
| | | | | | - Sheng Miao
- Yale School of Medicine, Yale University, New Haven, CT, United States
| | - David Pitt
- Yale School of Medicine, Yale University, New Haven, CT, United States
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173
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Coyle JT. Passing the torch: The ascendance of the glutamatergic synapse in the pathophysiology of schizophrenia. Biochem Pharmacol 2024:116376. [PMID: 38906225 DOI: 10.1016/j.bcp.2024.116376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/11/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
For nearly fifty years, the dopamine hypothesis has dominated our understanding of the pathophysiology of schizophrenia and provided the lone target for drug development. However, with the exception of clozapine, the dopamine D2 receptor antagonizing anti-psychotic drugs have little impact on the negative symptoms and cognitive deficits, aspects of the disorder that robustly predict outcome. Pathologic studies reveal cortical atrophy and wide-spread loss of glutamatergic synaptic spines, unexplained by dopaminergic malfunction. Recent genome-wide association studies indicate that at least thirty risk genes for schizophrenia encode proteins localized to the glutamatergic synapse and inhibit glutamate neurotransmission, especially at the NMDA receptor. To function, the NMDA receptor requires the binding of glycine (primarily in the cerebellum and brainstem) or D-serine (in forebrain) to the NR1 channel subunit of the NMDA receptor. Genetically silencing the gene (srr) encoding serine racemase, the biosynthetic enzyme for D-serine, results in forebrain NMDA receptor hypofunction. The srr-/- mice have 90 % loss of endogenous D-serine and approximately 70 % decrease in NMDA receptor function. Several animal models of schizophrenia are based on behavioral and pharmacologic strategies, which have negligible validity with regard to the fundamental etiology of schizophrenia. We summarize here the results of a mouse model, in which srr, one of the two dozen or more risk gene for schizophrenia that affect NMDA receptor function, has been inactivated. The srr-/- mice exhibit striking similarities to schizophrenia including cortical atrophy, loss of cortico-limbic glutamatergic synapses, increased sub-cortical dopamine release, EEG abnormalities, and cognitive impairments. The limited efficacy of drugs targeting the glutamatergic synapse on DSM-5 diagnosed criteria for schizophrenia used in clinical trials may reflect the fact that only 30 % of the patients have impaired glutamatergic neurotransmission, resulting from the genetic heterogeneity of the disorder.
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Affiliation(s)
- Joseph T Coyle
- Eben S Draper Professor of Psychiatry and Neuroscience Harvard Medical School (Emeritus), McLean Hospital, 115 Mill St, Belmont, MA 02478, United States.
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174
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Bledsoe X, Gamazon ER. A transcriptomic atlas of the human brain reveals genetically determined aspects of neuropsychiatric health. Am J Hum Genet 2024:S0002-9297(24)00208-8. [PMID: 38925120 DOI: 10.1016/j.ajhg.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Regulation of gene expression is a vital component of neurological homeostasis. Cataloging the consequences of endogenous gene expression on the physical structure and connectivity of the brain offers a means of unifying trait-associated genetic variation with trait-associated neurological features. We perform tissue-specific transcriptome-wide association studies (TWASs) on over 3,400 neuroimaging phenotypes in the UK Biobank (N = 33,224) using our joint-tissue imputation (JTI)-TWAS method. We identify highly significant associations between predicted expression for 7,192 genes and a wide variety of measures of the brain derived from magnetic resonance imaging (MRI). Our approach generates reproducible results in internal and external replication datasets. Genetically determined expression alone is sufficient for high-fidelity reconstruction of brain structure and organization. We demonstrate complementary benefits of cross-tissue and single-tissue analyses toward an integrated neurobiology and provide evidence that gene expression outside the central nervous system provides unique insights into brain health. As an application, we provide evidence suggesting that the genetically regulated expression of schizophrenia risk genes causally affects over 73% of neurological phenotypes that are altered in individuals with schizophrenia (as identified by neuroimaging studies). Imaging features associated with neuropsychiatric traits can provide valuable insights into underlying pathophysiology. By linking neuroimaging-derived phenotypes with expression levels of specific genes, this resource represents a powerful gene prioritization schema that can improve our understanding of brain function, development, and disease. The use of multiple different cortical and subcortical atlases in the resource facilitates direct integration of these data with findings from a diverse range of clinical neuroimaging studies.
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Affiliation(s)
- Xavier Bledsoe
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Eric R Gamazon
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Memory & Alzheimer's Center, Nashville, TN, USA.
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175
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Si S, Liu H, Xu L, Zhan S. Identification of novel therapeutic targets for chronic kidney disease and kidney function by integrating multi-omics proteome with transcriptome. Genome Med 2024; 16:84. [PMID: 38898508 PMCID: PMC11186236 DOI: 10.1186/s13073-024-01356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a progressive disease for which there is no effective cure. We aimed to identify potential drug targets for CKD and kidney function by integrating plasma proteome and transcriptome. METHODS We designed a comprehensive analysis pipeline involving two-sample Mendelian randomization (MR) (for proteins), summary-based MR (SMR) (for mRNA), and colocalization (for coding genes) to identify potential multi-omics biomarkers for CKD and combined the protein-protein interaction, Gene Ontology (GO), and single-cell annotation to explore the potential biological roles. The outcomes included CKD, extensive kidney function phenotypes, and different CKD clinical types (IgA nephropathy, chronic glomerulonephritis, chronic tubulointerstitial nephritis, membranous nephropathy, nephrotic syndrome, and diabetic nephropathy). RESULTS Leveraging pQTLs of 3032 proteins from 3 large-scale GWASs and corresponding blood- and tissue-specific eQTLs, we identified 32 proteins associated with CKD, which were validated across diverse CKD datasets, kidney function indicators, and clinical types. Notably, 12 proteins with prior MR support, including fibroblast growth factor 5 (FGF5), isopentenyl-diphosphate delta-isomerase 2 (IDI2), inhibin beta C chain (INHBC), butyrophilin subfamily 3 member A2 (BTN3A2), BTN3A3, uromodulin (UMOD), complement component 4A (C4a), C4b, centrosomal protein of 170 kDa (CEP170), serologically defined colon cancer antigen 8 (SDCCAG8), MHC class I polypeptide-related sequence B (MICB), and liver-expressed antimicrobial peptide 2 (LEAP2), were confirmed. To our knowledge, 20 novel causal proteins have not been previously reported. Five novel proteins, namely, GCKR (OR 1.17, 95% CI 1.10-1.24), IGFBP-5 (OR 0.43, 95% CI 0.29-0.62), sRAGE (OR 1.14, 95% CI 1.07-1.22), GNPTG (OR 0.90, 95% CI 0.86-0.95), and YOD1 (OR 1.39, 95% CI 1.18-1.64,) passed the MR, SMR, and colocalization analysis. The other 15 proteins were also candidate targets (GATM, AIF1L, DQA2, PFKFB2, NFATC1, activin AC, Apo A-IV, MFAP4, DJC10, C2CD2L, TCEA2, HLA-E, PLD3, AIF1, and GMPR1). These proteins interact with each other, and their coding genes were mainly enrichment in immunity-related pathways or presented specificity across tissues, kidney-related tissue cells, and kidney single cells. CONCLUSIONS Our integrated analysis of plasma proteome and transcriptome data identifies 32 potential therapeutic targets for CKD, kidney function, and specific CKD clinical types, offering potential targets for the development of novel immunotherapies, combination therapies, or targeted interventions.
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Affiliation(s)
- Shucheng Si
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Hongyan Liu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Lu Xu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Siyan Zhan
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China.
- Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
- Institute for Artificial Intelligence, Peking University, Beijing, 100871, China.
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176
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Yilmaz AY, Ruzicka E, Jankovic J. Leg stereotypy syndrome: phenomenological and quantitative analysis. J Neurol 2024:10.1007/s00415-024-12501-2. [PMID: 38898269 DOI: 10.1007/s00415-024-12501-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Leg stereotypy syndrome (LSS) is a very common, yet underrecognized condition. The pathophysiology of the condition is not well understood. OBJECTIVE To evaluate and describe the visual kinematic characteristics of the repetitive leg movements in individuals with LSS. METHODS In this study, we identified and videotaped individuals diagnosed with LSS at the Parkinson's Disease Center and Movement Disorders Clinic, Baylor College of Medicine, Houston, Texas between 2000 and 2023. Only patients with LSS and without any co-morbidities were included in the study. Their medical records were carefully reviewed, and the demographic and clinical data were entered into a database. Video recordings of the repetitive leg movements were then analyzed using TremAn software. RESULTS We identified 14 individuals with LSS who were videotaped at our center. The videos of the 5 cases were too brief and therefore not suitable for TremAn quantitative analysis. The remaining 9 individuals exhibited regular rhythmic oscillations of the legs. Among these, two individuals displayed rhythmic movements only in video segments where their legs were in crossed positions. The other 7 individuals had regular rhythmic oscillations, always with the toes resting on the floor with the heels raised. Frequency analysis showed values between 4.5 and 6.5 Hz, fairly consistent with a variance below 0.5 Hz in individual cases. The oscillation frequency changed from 5.7 Hz to 2.7 Hz while standing. CONCLUSION In this study, 6 of 9 individuals with LSS showed 4.5-6.5 Hz regular rhythmic leg movements. Studies involving a larger LSS population with additional electrophysiological evaluations are needed to obtain further insights into this common movement disorder.
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Affiliation(s)
- Abdullah Yasir Yilmaz
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, TX, 77030-4202, USA
| | - Evzen Ruzicka
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Joseph Jankovic
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, TX, 77030-4202, USA.
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Rosoff DB, Hamandi AM, Bell AS, Mavromatis LA, Park LM, Jung J, Wagner J, Lohoff FW. Major Psychiatric Disorders, Substance Use Behaviors, and Longevity. JAMA Psychiatry 2024:2820199. [PMID: 38888899 PMCID: PMC11195603 DOI: 10.1001/jamapsychiatry.2024.1429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/04/2024] [Indexed: 06/20/2024]
Abstract
Importance Observational studies suggest that major psychiatric disorders and substance use behaviors reduce longevity, making it difficult to disentangle their relationships with aging-related outcomes. Objective To evaluate the associations between the genetic liabilities for major psychiatric disorders, substance use behaviors (smoking and alcohol consumption), and longevity. Design, Settings, and Participants This 2-sample mendelian randomization (MR) study assessed associations between psychiatric disorders, substance use behaviors, and longevity using single-variable and multivariable models. Multiomics analyses were performed elucidating transcriptomic underpinnings of the MR associations and identifying potential proteomic therapeutic targets. This study sourced summary-level genome-wide association study (GWAS) data, gene expression, and proteomic data from cohorts of European ancestry. Analyses were performed from May 2022 to November 2023. Exposures Genetic susceptibility for major depression (n = 500 199), bipolar disorder (n = 413 466), schizophrenia (n = 127 906), problematic alcohol use (n = 435 563), weekly alcohol consumption (n = 666 978), and lifetime smoking index (n = 462 690). Main Outcomes and Measures The main outcome encompassed aspects of health span, lifespan, and exceptional longevity. Additional outcomes were epigenetic age acceleration (EAA) clocks. Results Findings from multivariable MR models simultaneously assessing psychiatric disorders and substance use behaviorsm suggest a negative association between smoking and longevity in cohorts of European ancestry (n = 709 709; 431 503 [60.8%] female; β, -0.33; 95% CI, -0.38 to -0.28; P = 4.59 × 10-34) and with increased EAA (n = 34 449; 18 017 [52.3%] female; eg, PhenoAge: β, 1.76; 95% CI, 0.72 to 2.79; P = 8.83 × 10-4). Transcriptomic imputation and colocalization identified 249 genes associated with smoking, including 36 novel genes not captured by the original smoking GWAS. Enriched pathways included chromatin remodeling and telomere assembly and maintenance. The transcriptome-wide signature of smoking was inversely associated with longevity, and estimates of individual smoking-associated genes, eg, XRCC3 and PRMT6, aligned with the smoking-longevity MR analyses, suggesting underlying transcriptomic mediators. Cis-instrument MR prioritized brain proteins associated with smoking behavior, including LY6H (β, 0.02; 95% CI, 0.01 to 0.03; P = 2.37 × 10-6) and RIT2 (β, 0.02; 95% CI, 0.01 to 0.03; P = 1.05 × 10-5), which had favorable adverse-effect profiles across 367 traits evaluated in phenome-wide MR. Conclusions The findings suggest that the genetic liability of smoking, but not of psychiatric disorders, is associated with longevity. Transcriptomic associations offer insights into smoking-related pathways, and identified proteomic targets may inform therapeutic development for smoking cessation strategies.
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Affiliation(s)
- Daniel B. Rosoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
- Radcliffe Department of Medicine, NIH-Oxford-Cambridge Scholars Program, University of Oxford, United Kingdom
| | - Ali M. Hamandi
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Andrew S. Bell
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Lucas A. Mavromatis
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Lauren M. Park
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Josephin Wagner
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Falk W. Lohoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
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178
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Lee JM, McLean ZL, Correia K, Shin JW, Lee S, Jang JH, Lee Y, Kim KH, Choi DE, Long JD, Lucente D, Seong IS, Pinto RM, Giordano JV, Mysore JS, Siciliano J, Elezi E, Ruliera J, Gillis T, Wheeler VC, MacDonald ME, Gusella JF, Gatseva A, Ciosi M, Lomeikaite V, Loay H, Monckton DG, Wills C, Massey TH, Jones L, Holmans P, Kwak S, Sampaio C, Orth M, Bernhard Landwehrmeyer G, Paulsen JS, Ray Dorsey E, Myers RH. Genetic modifiers of somatic expansion and clinical phenotypes in Huntington's disease reveal shared and tissue-specific effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597797. [PMID: 38948755 PMCID: PMC11212857 DOI: 10.1101/2024.06.10.597797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Huntington's disease (HD), due to expansion of a CAG repeat in HTT , is representative of a growing number of disorders involving somatically unstable short tandem repeats. We find that overlapping and distinct genetic modifiers of clinical landmarks and somatic expansion in blood DNA reveal an underlying complexity and cell-type specificity to the mismatch repair-related processes that influence disease timing. Differential capture of non-DNA-repair gene modifiers by multiple measures of cognitive and motor dysfunction argues additionally for cell-type specificity of pathogenic processes. Beyond trans modifiers, differential effects are also illustrated at HTT by a 5'-UTR variant that promotes somatic expansion in blood without influencing clinical HD, while, even after correcting for uninterrupted CAG length, a synonymous sequence change at the end of the CAG repeat dramatically hastens onset of motor signs without increasing somatic expansion. Our findings are directly relevant to therapeutic suppression of somatic expansion in HD and related disorders and provide a route to define the individual neuronal cell types that contribute to different HD clinical phenotypes.
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Lu X, Ni P, Suarez-Meade P, Ma Y, Forrest EN, Wang G, Wang Y, Quiñones-Hinojosa A, Gerstein M, Jiang YH. Transcriptional determinism and stochasticity contribute to the complexity of autism-associated SHANK family genes. Cell Rep 2024; 43:114376. [PMID: 38900637 DOI: 10.1016/j.celrep.2024.114376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/08/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Precision of transcription is critical because transcriptional dysregulation is disease causing. Traditional methods of transcriptional profiling are inadequate to elucidate the full spectrum of the transcriptome, particularly for longer and less abundant mRNAs. SHANK3 is one of the most common autism causative genes. Twenty-four Shank3-mutant animal lines have been developed for autism modeling. However, their preclinical validity has been questioned due to incomplete Shank3 transcript structure. We apply an integrative approach combining cDNA-capture and long-read sequencing to profile the SHANK3 transcriptome in humans and mice. We unexpectedly discover an extremely complex SHANK3 transcriptome. Specific SHANK3 transcripts are altered in Shank3-mutant mice and postmortem brain tissues from individuals with autism spectrum disorder. The enhanced SHANK3 transcriptome significantly improves the detection rate for potential deleterious variants from genomics studies of neuropsychiatric disorders. Our findings suggest that both deterministic and stochastic transcription of the genome is associated with SHANK family genes.
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Affiliation(s)
- Xiaona Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Yu Ma
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Emily Niemitz Forrest
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guilin Wang
- Keck Microarray Shared Resource, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA; Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT 06520, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA; Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA.
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Zhu X, Si J, Jia B, He X, Zhou D, Wang C, Qin J, Liu Z, Zhang L. Changes of soil carbon along precipitation gradients in three typical vegetation types in the Alxa desert region, China. CARBON BALANCE AND MANAGEMENT 2024; 19:19. [PMID: 38884686 PMCID: PMC11181535 DOI: 10.1186/s13021-024-00264-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024]
Abstract
The changes and influencing factors of soil inorganic carbon (SIC) and organic carbon (SOC) on precipitation gradients are crucial for predicting and evaluating carbon storage changes at the regional scale. However, people's understanding of the distribution characteristics of SOC and SIC reserves on regional precipitation gradients is insufficient, and the main environmental variables that affect SOC and SIC changes are also not well understood. Therefore, this study focuses on the Alxa region and selects five regions covered by three typical desert vegetation types, Zygophyllum xanthoxylon (ZX), Nitraria tangutorum (NT), and Reaumuria songarica (RS), along the climate transect where precipitation gradually increases. The study analyzes and discusses the variation characteristics of SOC and SIC under different vegetation and precipitation conditions. The results indicate that both SOC and SIC increase with the increase of precipitation, and the increase in SOC is greater with the increase of precipitation. The average SOC content in the 0-300cm profile is NT (4.13 g kg-1) > RS (3.61 g kg-1) > ZX (3.57 g kg-1); The average value of SIC content is: RS (5.78 g kg-1) > NT (5.11 g kg-1) > ZX (5.02 g kg-1). Overall, the multi-annual average precipitation (MAP) in the Alxa region is the most important environmental factor affecting SIC and SOC.
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Affiliation(s)
- Xinglin Zhu
- Key Laboratory of Eco-Hydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianhua Si
- Key Laboratory of Eco-Hydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.
| | - Bing Jia
- Key Laboratory of Eco-Hydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiaohui He
- Faculty of Resources and Environment, Baotou Teachers' College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Dongmeng Zhou
- Key Laboratory of Eco-Hydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunlin Wang
- Key Laboratory of Eco-Hydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Qin
- Key Laboratory of Eco-Hydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zijin Liu
- Key Laboratory of Eco-Hydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Zhang
- Alxa Left Banner Public Service Center, Alxa League, 750306, China
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Carraro C, Montgomery JV, Klimmt J, Paquet D, Schultze JL, Beyer MD. Tackling neurodegeneration in vitro with omics: a path towards new targets and drugs. Front Mol Neurosci 2024; 17:1414886. [PMID: 38952421 PMCID: PMC11215216 DOI: 10.3389/fnmol.2024.1414886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024] Open
Abstract
Drug discovery is a generally inefficient and capital-intensive process. For neurodegenerative diseases (NDDs), the development of novel therapeutics is particularly urgent considering the long list of late-stage drug candidate failures. Although our knowledge on the pathogenic mechanisms driving neurodegeneration is growing, additional efforts are required to achieve a better and ultimately complete understanding of the pathophysiological underpinnings of NDDs. Beyond the etiology of NDDs being heterogeneous and multifactorial, this process is further complicated by the fact that current experimental models only partially recapitulate the major phenotypes observed in humans. In such a scenario, multi-omic approaches have the potential to accelerate the identification of new or repurposed drugs against a multitude of the underlying mechanisms driving NDDs. One major advantage for the implementation of multi-omic approaches in the drug discovery process is that these overarching tools are able to disentangle disease states and model perturbations through the comprehensive characterization of distinct molecular layers (i.e., genome, transcriptome, proteome) up to a single-cell resolution. Because of recent advances increasing their affordability and scalability, the use of omics technologies to drive drug discovery is nascent, but rapidly expanding in the neuroscience field. Combined with increasingly advanced in vitro models, which particularly benefited from the introduction of human iPSCs, multi-omics are shaping a new paradigm in drug discovery for NDDs, from disease characterization to therapeutics prediction and experimental screening. In this review, we discuss examples, main advantages and open challenges in the use of multi-omic approaches for the in vitro discovery of targets and therapies against NDDs.
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Affiliation(s)
- Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jessica V. Montgomery
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
| | - Julien Klimmt
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn and West German Genome Center, Bonn, Germany
| | - Marc D. Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn and West German Genome Center, Bonn, Germany
- Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
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Karaglani M, Agorastos A, Panagopoulou M, Parlapani E, Athanasis P, Bitsios P, Tzitzikou K, Theodosiou T, Iliopoulos I, Bozikas VP, Chatzaki E. A novel blood-based epigenetic biosignature in first-episode schizophrenia patients through automated machine learning. Transl Psychiatry 2024; 14:257. [PMID: 38886359 PMCID: PMC11183091 DOI: 10.1038/s41398-024-02946-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Schizophrenia (SCZ) is a chronic, severe, and complex psychiatric disorder that affects all aspects of personal functioning. While SCZ has a very strong biological component, there are still no objective diagnostic tests. Lately, special attention has been given to epigenetic biomarkers in SCZ. In this study, we introduce a three-step, automated machine learning (AutoML)-based, data-driven, biomarker discovery pipeline approach, using genome-wide DNA methylation datasets and laboratory validation, to deliver a highly performing, blood-based epigenetic biosignature of diagnostic clinical value in SCZ. Publicly available blood methylomes from SCZ patients and healthy individuals were analyzed via AutoML, to identify SCZ-specific biomarkers. The methylation of the identified genes was then analyzed by targeted qMSP assays in blood gDNA of 30 first-episode drug-naïve SCZ patients and 30 healthy controls (CTRL). Finally, AutoML was used to produce an optimized disease-specific biosignature based on patient methylation data combined with demographics. AutoML identified a SCZ-specific set of novel gene methylation biomarkers including IGF2BP1, CENPI, and PSME4. Functional analysis investigated correlations with SCZ pathology. Methylation levels of IGF2BP1 and PSME4, but not CENPI were found to differ, IGF2BP1 being higher and PSME4 lower in the SCZ group as compared to the CTRL group. Additional AutoML classification analysis of our experimental patient data led to a five-feature biosignature including all three genes, as well as age and sex, that discriminated SCZ patients from healthy individuals [AUC 0.755 (0.636, 0.862) and average precision 0.758 (0.690, 0.825)]. In conclusion, this three-step pipeline enabled the discovery of three novel genes and an epigenetic biosignature bearing potential value as promising SCZ blood-based diagnostics.
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Affiliation(s)
- Makrina Karaglani
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece
- Institute of Agri-food and Life Sciences, University Research & Innovation Center, H.M.U.R.I.C., Hellenic Mediterranean University, GR-71003, Crete, Greece
| | - Agorastos Agorastos
- Institute of Agri-food and Life Sciences, University Research & Innovation Center, H.M.U.R.I.C., Hellenic Mediterranean University, GR-71003, Crete, Greece
- II. Department of Psychiatry, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, GR-56430, Thessaloniki, Greece
| | - Maria Panagopoulou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece
- Institute of Agri-food and Life Sciences, University Research & Innovation Center, H.M.U.R.I.C., Hellenic Mediterranean University, GR-71003, Crete, Greece
| | - Eleni Parlapani
- Ι. Department of Psychiatry, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, GR-56429, Thessaloniki, Greece
| | - Panagiotis Athanasis
- II. Department of Psychiatry, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, GR-56430, Thessaloniki, Greece
| | - Panagiotis Bitsios
- Department of Psychiatry and Behavioral Sciences, Faculty of Medicine, University of Crete, GR-71500, Heraklion, Greece
| | - Konstantina Tzitzikou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece
| | - Theodosis Theodosiou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece
- ABCureD P.C, GR-68131, Alexandroupolis, Greece
| | - Ioannis Iliopoulos
- Division of Basic Sciences, School of Medicine, University of Crete, GR-71003, Heraklion, Greece
| | - Vasilios-Panteleimon Bozikas
- II. Department of Psychiatry, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, GR-56430, Thessaloniki, Greece
| | - Ekaterini Chatzaki
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, GR-68132, Alexandroupolis, Greece.
- Institute of Agri-food and Life Sciences, University Research & Innovation Center, H.M.U.R.I.C., Hellenic Mediterranean University, GR-71003, Crete, Greece.
- ABCureD P.C, GR-68131, Alexandroupolis, Greece.
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 70013, Heraklion, Greece.
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Chien H, Chu YD, Hsu YP, Yeh CT, Lai MW, Chang ML, Lim SN, Chen CW, Lin WR. An SNP Marker Predicts Colorectal Cancer Outcomes with 5-Fluorouracil-Based Adjuvant Chemotherapy Post-Resection. Int J Mol Sci 2024; 25:6642. [PMID: 38928347 PMCID: PMC11203489 DOI: 10.3390/ijms25126642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/04/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Colorectal cancer (CRC) is a global health concern, necessitating adjuvant chemotherapy post-curative surgery to mitigate recurrence and enhance survival, particularly in intermediate-stage patients. However, existing therapeutic disparities highlight the need for biomarker-guided adjuvant chemotherapy to achieve better CRC inhibition. This study explores the molecular mechanisms underlying the inhibition of CRC through a genome-wide association study (GWAS) focused on 5-fluorouracil (5-FU)-based adjuvant therapy in intermediate-stage CRC patients, a domain previously unexplored. We retrospectively included 226 intermediate-stage CRC patients undergoing surgical resection followed by 5-FU-based adjuvant chemotherapy. The exploration cohort comprised 31 patients, and the validation cohort included 195 individuals. Genotyping was carried out using either Axiom Genome-Wide TWB 2.0 Array Plate-based or polymerase chain reaction-based methods on genomic DNA derived from collected tissue samples. Statistical analyses involved descriptive statistics, Kaplan-Meier analyses, and Cox proportional hazard analyses. From the GWAS, potential genetic predictors, GALNT14-rs62139523 and DNMBP-rs10786578 genotypes, of 5-FU-based adjuvant therapy following surgery in intermediate-stage CRC patients were identified. Validation in a larger cohort of 195 patients emphasized the predictive significance of GALNT14-rs62139523 genotypes, especially the "A/G" genotype, for improved overall and progression-free survival. This predictive association remained robust across various subgroups, with exceptions for specific demographic and clinical parameters such as age < 58 years old, CEA ≤ 2.5 ng/mL, tumor diameter > 44.0 mm, and tumor-free margin ≥ 50 mm. This study identifies that the GALNT14-rs62139523 "A/G" genotype modulates therapeutic outcomes, establishing it as a promising biomarker for predicting favorable responses to 5-FU-based adjuvant chemotherapy in intermediate-stage CRC patients, although further investigations are needed to detail these mechanisms.
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Affiliation(s)
- Hao Chien
- Department of Hepatology and Gastroenterology, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (H.C.); (C.-T.Y.); (M.-L.C.)
| | - Yu-De Chu
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (Y.-D.C.); (Y.-P.H.); (M.-W.L.)
| | - Yi-Ping Hsu
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (Y.-D.C.); (Y.-P.H.); (M.-W.L.)
| | - Chau-Ting Yeh
- Department of Hepatology and Gastroenterology, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (H.C.); (C.-T.Y.); (M.-L.C.)
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (Y.-D.C.); (Y.-P.H.); (M.-W.L.)
- Institute of Stem Cell and Translational Cancer Research, Linkou Chang Gung Memorial Hospital, Taoyuan 333323, Taiwan
| | - Ming-Wei Lai
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (Y.-D.C.); (Y.-P.H.); (M.-W.L.)
- Division of Pediatric Gastroenterology, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | - Ming-Ling Chang
- Department of Hepatology and Gastroenterology, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (H.C.); (C.-T.Y.); (M.-L.C.)
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (Y.-D.C.); (Y.-P.H.); (M.-W.L.)
| | - Siew-Na Lim
- Department of Neurology, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
| | - Chun-Wei Chen
- Department of Hepatology and Gastroenterology, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (H.C.); (C.-T.Y.); (M.-L.C.)
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (Y.-D.C.); (Y.-P.H.); (M.-W.L.)
| | - Wey-Ran Lin
- Department of Hepatology and Gastroenterology, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (H.C.); (C.-T.Y.); (M.-L.C.)
- Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan; (Y.-D.C.); (Y.-P.H.); (M.-W.L.)
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Li M, Shi P, Yang H, Liu S, Sun R, Li L, Zhao Z, Sun J. The immune cells have complex causal regulation effects on cancers. Int Immunopharmacol 2024; 134:112179. [PMID: 38710118 DOI: 10.1016/j.intimp.2024.112179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND There was a large body of evidence linking immune cells to cancer risk. However, the causal relationship between immune cells, cancer, and what genes play an important role is unclear. METHODS In this study, we performed comprehensive two-sample Mendelian randomization analysis (TSMR) to determine the causal relationship between immune cells and common cancers. We also performed Multimarker Analysis of Genomic Annotation (MAGMA) on immune cells causally associated with cancer to identify their relevant genes and used data summary-based MR (SMR) analysis to investigate the causal relationship between their gene expression, methylation, and cancer, and further used drug prediction and molecular docking to validate the medicinal value of the targets. Finally, reverse TSMR analysis was performed on cancer and immune cells to rule out reverse causality. RESULTS After FDR correction (PFDR < 0.05), the results showed that 2 immune cells were associated with lung cancer risk, and 1 immune cell was significantly associated with pancreatic cancer risk. The expression of OSBPL10, CHD4, SMDT1, PHETA2, and NAGA was positively and causally related to the risk of lung cancer by SMR analysis and HEIDI test. We also found that increased expression of ANP32E decreased the risk of pancreatic cancer and that the methylation level of OSBPL10, CHD4, SULF2, CENPM, and CYP2D6 had a causal association with lung cancer. The methylation level of FCGR3A was causally associated with pancreatic cancer. The results of molecular docking indicated a strong affinity between the drugs and proteins that possessed existing structural information. CONCLUSION This data-driven Mendelian randomization (MR) study demonstrates the causal role of immune cells in cancers. In addition, this study identifies candidate genes that may be potential anti-cancer drug targets.
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Affiliation(s)
- Mingzheng Li
- Department of Environmental and Occupational Health, School of Public Health, China Medical University, Shenyang 110122, China
| | - Peng Shi
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Huajie Yang
- Department of Environmental and Occupational Health, School of Public Health, China Medical University, Shenyang 110122, China
| | - Shuailing Liu
- Institute for International Health Professions Education and Research, China Medical University, Shenyang 110122, China; College of Health Management, China Medical University, Shenyang 110122, China
| | - Ruixi Sun
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Luoxin Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Zetong Zhao
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Jiaxing Sun
- Ultrasound Department, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China.
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185
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Xiao X, Hammond C, Salmeron BJ, Wang D, Gu H, Zhai T, Nguyen H, Lu H, Ross TJ, Yang Y. Brain Functional Connectome Defines a Transdiagnostic Dimension Shared by Cognitive Function and Psychopathology in Preadolescents. Biol Psychiatry 2024; 95:1081-1090. [PMID: 37769982 PMCID: PMC10963340 DOI: 10.1016/j.biopsych.2023.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/27/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Cognitive function and general psychopathology are two important classes of human behavior dimensions that are individually related to mental disorders across diagnostic categories. However, whether these two transdiagnostic dimensions are linked to common or distinct brain networks that convey resilience or risk for the development of psychiatric disorders remains unclear. METHODS The current study is a longitudinal investigation with 11,875 youths from the Adolescent Brain Cognitive Development (ABCD) Study at ages 9 to 10 years at the onset of the study. A machine learning approach based on canonical correlation analysis was used to identify latent dimensional associations of the resting-state functional connectome with multidomain behavioral assessments including cognitive functions and psychopathological measures. For the latent resting-state functional connectivity factor showing a robust behavioral association, its ability to predict psychiatric disorders was assessed using 2-year follow-up data, and its genetic association was evaluated using twin data from the same cohort. RESULTS A latent functional connectome pattern was identified that showed a strong and generalizable association with the multidomain behavioral assessments (5-fold cross-validation: ρ = 0.68-0.73 for the training set [n = 5096]; ρ = 0.56-0.58 for the test set [n = 1476]). This functional connectome pattern was highly heritable (h2 = 74.42%, 95% CI: 56.76%-85.42%), exhibited a dose-response relationship with the cumulative number of psychiatric disorders assessed concurrently and at 2 years post-magnetic resonance imaging scan, and predicted the transition of diagnosis across disorders over the 2-year follow-up period. CONCLUSIONS These findings provide preliminary evidence for a transdiagnostic connectome-based measure that underlies individual differences in the development of psychiatric disorders during early adolescence.
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Affiliation(s)
- Xiang Xiao
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland
| | - Christopher Hammond
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, Maryland
| | - Betty Jo Salmeron
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland
| | - Danni Wang
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland
| | - Hong Gu
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland
| | - Tianye Zhai
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland
| | - Hieu Nguyen
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland
| | - Hanbing Lu
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland
| | - Thomas J Ross
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland
| | - Yihong Yang
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland.
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186
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Chen F, Dong X, Yu Z, Zhang Y, Shi Y. The brain-heart axis: Integrative analysis of the shared genetic etiology between neuropsychiatric disorders and cardiovascular disease. J Affect Disord 2024; 355:147-156. [PMID: 38518856 DOI: 10.1016/j.jad.2024.03.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
BACKGROUND Multiple observational studies have reported substantial comorbidity between neuropsychiatric disorders and cardiovascular disease (CVD), but the underlying mechanisms remain largely unknown. METHODS Using GWAS summary datasets of 8 neuropsychiatric disorders and 6 cardiovascular diseases, an integrative analysis incorporating linkage-disequilibrium-score-regression (LDSC), Mendelian randomization (MR), functional mapping and annotation (FUMA), and functional enrichment analysis, was conducted to investigate shared genetic etiology of the brain-heart axis from the whole genome level, single-nucleotide polymorphism (SNP) level, gene level, and biological pathway level. RESULTS In LDSC analysis, 18 pairwise traits between neuropsychiatric disorders and CVD were identified with significant genetic overlaps, revealing extensive genome-wide genetic correlations. In bidirectional MR analysis, 19 pairwise traits were identified with significant causal relationships. Genetic liabilities to neuropsychiatric disorders, particularly attention-deficit hyperactivity disorder and major depressive disorder, conferred extensive significant causal effects on the risk of CVD, while hypertension seemed to be a risk factor for multiple neuropsychiatric disorders, with no significant heterogeneity or pleiotropy. In FUMA analysis, 13 shared independent significant SNPs and 887 overlapping protein-coding genes were detected between neuropsychiatric disorders and CVD. With GO and KEEG functional enrichment analysis, biological pathways of the brain-heart axis were highly concentrated in neurotransmitter synaptic transmission, lipid metabolism, aldosterone synthesis and secretion, glutathione metabolism, and MAPK signaling pathway. CONCLUSION Extensive genetic correlations and genetic overlaps between neuropsychiatric disorders and CVD were identified in this study, which might provide some new insights into the brain-heart axis and the therapeutic targets in clinical practice.
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Affiliation(s)
- Feifan Chen
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Chongqing 400014, China.
| | - Xinyu Dong
- Department of Neurosurgery, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing 400014, China.
| | - Zhiwei Yu
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Chongqing 400014, China.
| | - Yihan Zhang
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Chongqing 400014, China.
| | - Yuan Shi
- Department of Neonatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Chongqing 400014, China.
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187
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Thorpe HHA, Fontanillas P, Meredith JJ, Jennings MV, Cupertino RB, Pakala S, Elson SL, Khokhar JY, Davis LK, Johnson EC, Palmer AA, Sanchez-Roige S. Genome-wide association studies of lifetime and frequency cannabis use in 131,895 individuals. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.14.24308946. [PMID: 38947071 PMCID: PMC11213095 DOI: 10.1101/2024.06.14.24308946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cannabis is one of the most widely used drugs globally. Decriminalization of cannabis is further increasing cannabis consumption. We performed genome-wide association studies (GWASs) of lifetime (N=131,895) and frequency (N=73,374) of cannabis use. Lifetime cannabis use GWAS identified two loci, one near CADM2 (rs11922956, p=2.40E-11) and another near GRM3 (rs12673181, p=6.90E-09). Frequency of use GWAS identified one locus near CADM2 (rs4856591, p=8.10E-09; r2 =0.76 with rs11922956). Both traits were heritable and genetically correlated with previous GWASs of lifetime use and cannabis use disorder (CUD), as well as other substance use and cognitive traits. Polygenic scores (PGSs) for lifetime and frequency of cannabis use associated cannabis use phenotypes in AllofUs participants. Phenome-wide association study of lifetime cannabis use PGS in a hospital cohort replicated associations with substance use and mood disorders, and uncovered associations with celiac and infectious diseases. This work demonstrates the value of GWASs of CUD transition risk factors.
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Affiliation(s)
- Hayley H A Thorpe
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - John J Meredith
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Mariela V Jennings
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Renata B Cupertino
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Shreya Pakala
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | | | - Jibran Y Khokhar
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Lea K Davis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
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188
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Dwivedi SL, Heslop-Harrison P, Amas J, Ortiz R, Edwards D. Epistasis and pleiotropy-induced variation for plant breeding. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38875130 DOI: 10.1111/pbi.14405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
Abstract
Epistasis refers to nonallelic interaction between genes that cause bias in estimates of genetic parameters for a phenotype with interactions of two or more genes affecting the same trait. Partitioning of epistatic effects allows true estimation of the genetic parameters affecting phenotypes. Multigenic variation plays a central role in the evolution of complex characteristics, among which pleiotropy, where a single gene affects several phenotypic characters, has a large influence. While pleiotropic interactions provide functional specificity, they increase the challenge of gene discovery and functional analysis. Overcoming pleiotropy-based phenotypic trade-offs offers potential for assisting breeding for complex traits. Modelling higher order nonallelic epistatic interaction, pleiotropy and non-pleiotropy-induced variation, and genotype × environment interaction in genomic selection may provide new paths to increase the productivity and stress tolerance for next generation of crop cultivars. Advances in statistical models, software and algorithm developments, and genomic research have facilitated dissecting the nature and extent of pleiotropy and epistasis. We overview emerging approaches to exploit positive (and avoid negative) epistatic and pleiotropic interactions in a plant breeding context, including developing avenues of artificial intelligence, novel exploitation of large-scale genomics and phenomics data, and involvement of genes with minor effects to analyse epistatic interactions and pleiotropic quantitative trait loci, including missing heritability.
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Affiliation(s)
| | - Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, UK
| | - Junrey Amas
- Centre for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - David Edwards
- Centre for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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189
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Rogal J, Zamproni LN, Nikolakopoulou P, Ygberg S, Wedell A, Wredenberg A, Herland A. Human In Vitro Models of Neuroenergetics and Neurometabolic Disturbances: Current Advances and Clinical Perspectives. Stem Cells Transl Med 2024; 13:505-514. [PMID: 38588471 PMCID: PMC11165162 DOI: 10.1093/stcltm/szae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/23/2024] [Indexed: 04/10/2024] Open
Abstract
Neurological conditions conquer the world; they are the leading cause of disability and the second leading cause of death worldwide, and they appear all around the world in every age group, gender, nationality, and socioeconomic class. Despite the growing evidence of an immense impact of perturbations in neuroenergetics on overall brain function, only little is known about the underlying mechanisms. Especially human insights are sparse, owing to a shortage of physiologically relevant model systems. With this perspective, we aim to explore the key steps and considerations involved in developing an advanced human in vitro model for studying neuroenergetics. We discuss biological and technological strategies to meet the requirements of a predictive model, aiming at providing a guide and inspiration for future in vitro models of neuroenergetics.
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Affiliation(s)
- Julia Rogal
- Department of Neuroscience, Karolinska Institute, 17177 Stockholm, Sweden
- Division of Nanobiotechnology, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology at Science for Life Laboratory, 17165 Solna, Sweden
- Center for the Advancement of Integrated Medical and Engineering Sciences (AIMES), Karolinska Institute and KTH Royal Institute of Technology, 17177 Stockholm, Sweden
| | - Laura Nicoleti Zamproni
- Department of Neuroscience, Karolinska Institute, 17177 Stockholm, Sweden
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Polyxeni Nikolakopoulou
- Department of Neuroscience, Karolinska Institute, 17177 Stockholm, Sweden
- Center for the Advancement of Integrated Medical and Engineering Sciences (AIMES), Karolinska Institute and KTH Royal Institute of Technology, 17177 Stockholm, Sweden
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Sofia Ygberg
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 17177 Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
- Neuropediatric Unit, Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Anna Wedell
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 17177 Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, 17177 Stockholm, Sweden
| | - Anna Wredenberg
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 17177 Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Anna Herland
- Department of Neuroscience, Karolinska Institute, 17177 Stockholm, Sweden
- Division of Nanobiotechnology, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology at Science for Life Laboratory, 17165 Solna, Sweden
- Center for the Advancement of Integrated Medical and Engineering Sciences (AIMES), Karolinska Institute and KTH Royal Institute of Technology, 17177 Stockholm, Sweden
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Quinones-Valdez G, Amoah K, Xiao X. Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599101. [PMID: 38915585 PMCID: PMC11195283 DOI: 10.1101/2024.06.14.599101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Genetic regulation of alternative splicing constitutes an important link between genetic variation and disease. Nonetheless, RNA splicing is regulated by both cis-acting elements and trans-acting splicing factors. Determining splicing events that are directed primarily by the cis- or trans-acting mechanisms will greatly inform our understanding of the genetic basis of disease. Here, we show that long-read RNA-seq, combined with our new method isoLASER, enables a clear segregation of cis- and trans-directed splicing events for individual samples. The genetic linkage of splicing is largely individual-specific, in stark contrast to the tissue-specific pattern of splicing profiles. Analysis of long-read RNA-seq data from human and mouse revealed thousands of cis-directed splicing events susceptible to genetic regulation. We highlight such events in the HLA genes whose analysis was challenging with short-read data. We also highlight novel cis-directed splicing events in Alzheimer's disease-relevant genes such as MAPT and BIN1. Together, the clear demarcation of cis- and trans-directed splicing paves ways for future studies of the genetic basis of disease.
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Affiliation(s)
- Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kofi Amoah
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
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191
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Mato-Blanco X, Kim SK, Jourdon A, Ma S, Tebbenkamp AT, Liu F, Duque A, Vaccarino FM, Sestan N, Colantuoni C, Rakic P, Santpere G, Micali N. Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598925. [PMID: 38915580 PMCID: PMC11195173 DOI: 10.1101/2024.06.14.598925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development.
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Affiliation(s)
- Xoel Mato-Blanco
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Suel-Kee Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alexandre Jourdon
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Fuchen Liu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alvaro Duque
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Flora M. Vaccarino
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
- Departments of Psychiatry, Genetics and Comparative Medicine, Wu Tsai Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Carlo Colantuoni
- Depts. of Neurology, Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Pasko Rakic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gabriel Santpere
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Nicola Micali
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
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192
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Leone R, Zuglian C, Brambilla R, Morella I. Understanding copy number variations through their genes: a molecular view on 16p11.2 deletion and duplication syndromes. Front Pharmacol 2024; 15:1407865. [PMID: 38948459 PMCID: PMC11211608 DOI: 10.3389/fphar.2024.1407865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 07/02/2024] Open
Abstract
Neurodevelopmental disorders (NDDs) include a broad spectrum of pathological conditions that affect >4% of children worldwide, share common features and present a variegated genetic origin. They include clinically defined diseases, such as autism spectrum disorders (ASD), attention-deficit/hyperactivity disorder (ADHD), motor disorders such as Tics and Tourette's syndromes, but also much more heterogeneous conditions like intellectual disability (ID) and epilepsy. Schizophrenia (SCZ) has also recently been proposed to belong to NDDs. Relatively common causes of NDDs are copy number variations (CNVs), characterised by the gain or the loss of a portion of a chromosome. In this review, we focus on deletions and duplications at the 16p11.2 chromosomal region, associated with NDDs, ID, ASD but also epilepsy and SCZ. Some of the core phenotypes presented by human carriers could be recapitulated in animal and cellular models, which also highlighted prominent neurophysiological and signalling alterations underpinning 16p11.2 CNVs-associated phenotypes. In this review, we also provide an overview of the genes within the 16p11.2 locus, including those with partially known or unknown function as well as non-coding RNAs. A particularly interesting interplay was observed between MVP and MAPK3 in modulating some of the pathological phenotypes associated with the 16p11.2 deletion. Elucidating their role in intracellular signalling and their functional links will be a key step to devise novel therapeutic strategies for 16p11.2 CNVs-related syndromes.
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Affiliation(s)
- Roberta Leone
- Università di Pavia, Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Pavia, Italy
| | - Cecilia Zuglian
- Università di Pavia, Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Pavia, Italy
| | - Riccardo Brambilla
- Università di Pavia, Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Pavia, Italy
- Cardiff University, School of Biosciences, Neuroscience and Mental Health Innovation Institute, Cardiff, United Kingdom
| | - Ilaria Morella
- Cardiff University, School of Biosciences, Neuroscience and Mental Health Innovation Institute, Cardiff, United Kingdom
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193
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Wikarska A, Roszak K, Roszek K. Mesenchymal Stem Cells and Purinergic Signaling in Autism Spectrum Disorder: Bridging the Gap between Cell-Based Strategies and Neuro-Immune Modulation. Biomedicines 2024; 12:1310. [PMID: 38927517 PMCID: PMC11201695 DOI: 10.3390/biomedicines12061310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/26/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The prevalence of autism spectrum disorder (ASD) is still increasing, which means that this neurodevelopmental lifelong pathology requires special scientific attention and efforts focused on developing novel therapeutic approaches. It has become increasingly evident that neuroinflammation and dysregulation of neuro-immune cross-talk are specific hallmarks of ASD, offering the possibility to treat these disorders by factors modulating neuro-immunological interactions. Mesenchymal stem cell-based therapy has already been postulated as one of the therapeutic approaches for ASD; however, less is known about the molecular mechanisms of stem cell influence. One of the possibilities, although still underestimated, is the paracrine purinergic activity of MSCs, by which stem cells ameliorate inflammatory reactions. Modulation of adenosine signaling may help restore neurotransmitter balance, reduce neuroinflammation, and improve overall brain function in individuals with ASD. In our review article, we present a novel insight into purinergic signaling, including but not limited to the adenosinergic pathway and its role in neuroinflammation and neuro-immune cross-talk modulation. We anticipate that by achieving a greater understanding of the purinergic signaling contribution to ASD and related disorders, novel therapeutic strategies may be devised for patients with autism in the near future.
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Affiliation(s)
| | | | - Katarzyna Roszek
- Department of Biochemistry, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Lwowska 1, 87-100 Torun, Poland; (A.W.); (K.R.)
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194
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Meijsen J, Hu K, Krebs MD, Athanasiadis G, Washbrook S, Zetterberg R, Avelar E Silva RN, Shorter JR, Gådin JR, Bergstedt J, Howard DM, Ye W, Lu Y, Valdimarsdóttir UA, Ingason A, Helenius D, Plana-Ripoll O, McGrath JJ, Micali N, Andreassen OA, Werge TM, Fang F, Buil A. Quantifying the relative importance of genetics and environment on the comorbidity between mental and cardiometabolic disorders using 17 million Scandinavians. Nat Commun 2024; 15:5064. [PMID: 38871766 PMCID: PMC11176385 DOI: 10.1038/s41467-024-49507-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 06/07/2024] [Indexed: 06/15/2024] Open
Abstract
Mental disorders are leading causes of disability and premature death worldwide, partly due to high comorbidity with cardiometabolic disorders. Reasons for this comorbidity are still poorly understood. We leverage nation-wide health records and near-complete genealogies of Denmark and Sweden (n = 17 million) to reveal the genetic and environmental contributions underlying the observed comorbidity between six mental disorders and 15 cardiometabolic disorders. Genetic factors contributed about 50% to the comorbidity of schizophrenia, affective disorders, and autism spectrum disorder with cardiometabolic disorders, whereas the comorbidity of attention-deficit/hyperactivity disorder and anorexia with cardiometabolic disorders was mainly or fully driven by environmental factors. In this work we provide causal insight to guide clinical and scientific initiatives directed at achieving mechanistic understanding as well as preventing and alleviating the consequences of these disorders.
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Affiliation(s)
- Joeri Meijsen
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark.
| | - Kejia Hu
- Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Morten D Krebs
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
| | - Georgios Athanasiadis
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Sarah Washbrook
- Center for Eating and feeding Disorders research, Psychiatric Centre Ballerup, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Richard Zetterberg
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
| | - Raquel Nogueira Avelar E Silva
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
| | - John R Shorter
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Jesper R Gådin
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
| | - Jacob Bergstedt
- Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David M Howard
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yi Lu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Unnur A Valdimarsdóttir
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Centre of Public Health Sciences, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrés Ingason
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
| | - Dorte Helenius
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
| | - Oleguer Plana-Ripoll
- Department of Clinical Epidemiology, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
| | - John J McGrath
- Queensland Centre for Mental Health Research, Brisbane, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Nadia Micali
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
- Center for Eating and feeding Disorders research, Psychiatric Centre Ballerup, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ole A Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Thomas M Werge
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Fang Fang
- Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen University Hospital, Roskilde, Denmark.
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195
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Cameron D, Vinh NN, Prapaiwongs P, Perry EA, Walters JTR, Li M, O'Donovan MC, Bray NJ. Genetic Implication of Prenatal GABAergic and Cholinergic Neuron Development in Susceptibility to Schizophrenia. Schizophr Bull 2024:sbae083. [PMID: 38869145 DOI: 10.1093/schbul/sbae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
BACKGROUND The ganglionic eminences (GE) are fetal-specific structures that give rise to gamma-aminobutyric acid (GABA)- and acetylcholine-releasing neurons of the forebrain. Given the evidence for GABAergic, cholinergic, and neurodevelopmental disturbances in schizophrenia, we tested the potential involvement of GE neuron development in mediating genetic risk for the condition. STUDY DESIGN We combined data from a recent large-scale genome-wide association study of schizophrenia with single-cell RNA sequencing data from the human GE to test the enrichment of schizophrenia risk variation in genes with high expression specificity for developing GE cell populations. We additionally performed the single nuclei Assay for Transposase-Accessible Chromatin with Sequencing (snATAC-Seq) to map potential regulatory genomic regions operating in individual cell populations of the human GE, using these to test for enrichment of schizophrenia common genetic variant liability and to functionally annotate non-coding variants-associated with the disorder. STUDY RESULTS Schizophrenia common variant liability was enriched in genes with high expression specificity for developing neuron populations that are predicted to form dopamine D1 and D2 receptor-expressing GABAergic medium spiny neurons of the striatum, cortical somatostatin-positive GABAergic interneurons, calretinin-positive GABAergic neurons, and cholinergic neurons. Consistent with these findings, schizophrenia genetic risk was concentrated in predicted regulatory genomic sequence mapped in developing neuronal populations of the GE. CONCLUSIONS Our study implicates prenatal development of specific populations of GABAergic and cholinergic neurons in later susceptibility to schizophrenia, and provides a map of predicted regulatory genomic elements operating in cells of the GE.
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Affiliation(s)
- Darren Cameron
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - Ngoc-Nga Vinh
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - Parinda Prapaiwongs
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
| | - Elizabeth A Perry
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - James T R Walters
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - Meng Li
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | - Nicholas J Bray
- Division of Psychological Medicine and Clinical Neurosciences, Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
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196
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Zhang C, Yang Z, Li X, Zhao L, Guo W, Deng W, Wang Q, Hu X, Li M, Sham PC, Xiao X, Li T. Unraveling NEK4 as a Potential Drug Target in Schizophrenia and Bipolar I Disorder: A Proteomic and Genomic Approach. Schizophr Bull 2024:sbae094. [PMID: 38869147 DOI: 10.1093/schbul/sbae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
BACKGROUND AND HYPOTHESIS Investigating the shared brain protein and genetic components of schizophrenia (SCZ) and bipolar I disorder (BD-I) presents a unique opportunity to understand the underlying pathophysiological processes and pinpoint potential drug targets. STUDY DESIGN To identify overlapping susceptibility brain proteins in SCZ and BD-I, we carried out proteome-wide association studies (PWAS) and Mendelian Randomization (MR) by integrating human brain protein quantitative trait loci with large-scale genome-wide association studies for both disorders. We utilized transcriptome-wide association studies (TWAS) to determine the consistency of mRNA-protein dysregulation in both disorders. We applied pleiotropy-informed conditional false discovery rate (pleioFDR) analysis to identify common risk genetic loci for SCZ and BD-I. Additionally, we performed a cell-type-specific analysis in the human brain to detect risk genes notably enriched in distinct brain cell types. The impact of risk gene overexpression on dendritic arborization and axon length in neurons was also examined. STUDY RESULTS Our PWAS identified 42 proteins associated with SCZ and 14 with BD-I, among which NEK4, HARS2, SUGP1, and DUS2 were common to both conditions. TWAS and MR analysis verified the significant risk gene NEK4 for both SCZ and BD-I. PleioFDR analysis further supported genetic risk loci associated with NEK4 for both conditions. The cell-type specificity analysis revealed that NEK4 is expressed on the surface of glutamatergic neurons, and its overexpression enhances dendritic arborization and axon length in cultured primary neurons. CONCLUSIONS These findings underscore a shared genetic origin for SCZ and BD-I, offering novel insights for potential therapeutic target identification.
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Affiliation(s)
- Chengcheng Zhang
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Nanhu Brain-Computer Interface Institute, Hangzhou, China
| | - ZhiHui Yang
- Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaojing Li
- Department of Neurobiology, Affiliated Mental Health Center and Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liansheng Zhao
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wanjun Guo
- Department of Neurobiology, Affiliated Mental Health Center and Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Deng
- Department of Neurobiology, Affiliated Mental Health Center and Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiang Wang
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Xun Hu
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ming Li
- Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Pak Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for PanorOmic Sciences, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Xiao Xiao
- Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Tao Li
- Nanhu Brain-Computer Interface Institute, Hangzhou, China
- Department of Neurobiology, Affiliated Mental Health Center and Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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197
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Janoski JR, Aiello I, Lundberg CW, Finkielstein CV. Circadian clock gene polymorphisms implicated in human pathologies. Trends Genet 2024:S0168-9525(24)00110-0. [PMID: 38871615 DOI: 10.1016/j.tig.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
Circadian rhythms, ~24 h cycles of physiological and behavioral processes, can be synchronized by external signals (e.g., light) and persist even in their absence. Consequently, dysregulation of circadian rhythms adversely affects the well-being of the organism. This timekeeping system is generated and sustained by a genetically encoded endogenous mechanism composed of interlocking transcriptional/translational feedback loops that generate rhythmic expression of core clock genes. Genome-wide association studies (GWAS) and forward genetic studies show that SNPs in clock genes influence gene regulation and correlate with the risk of developing various conditions. We discuss genetic variations in core clock genes that are associated with various phenotypes, their implications for human health, and stress the need for thorough studies in this domain of circadian regulation.
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Affiliation(s)
- Jesse R Janoski
- Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Ignacio Aiello
- Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA
| | - Clayton W Lundberg
- Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA; Academy of Integrated Sciences, College of Science, Virginia Tech, Blacksburg, VA, USA
| | - Carla V Finkielstein
- Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA; Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA; Academy of Integrated Sciences, College of Science, Virginia Tech, Blacksburg, VA, USA.
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198
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Tiong KL, Luzhbin D, Yeang CH. Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data. BMC Bioinformatics 2024; 25:209. [PMID: 38867193 PMCID: PMC11167951 DOI: 10.1186/s12859-024-05825-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Single-cell RNA sequencing (sc-RNASeq) data illuminate transcriptomic heterogeneity but also possess a high level of noise, abundant missing entries and sometimes inadequate or no cell type annotations at all. Bulk-level gene expression data lack direct information of cell population composition but are more robust and complete and often better annotated. We propose a modeling framework to integrate bulk-level and single-cell RNASeq data to address the deficiencies and leverage the mutual strengths of each type of data and enable a more comprehensive inference of their transcriptomic heterogeneity. Contrary to the standard approaches of factorizing the bulk-level data with one algorithm and (for some methods) treating single-cell RNASeq data as references to decompose bulk-level data, we employed multiple deconvolution algorithms to factorize the bulk-level data, constructed the probabilistic graphical models of cell-level gene expressions from the decomposition outcomes, and compared the log-likelihood scores of these models in single-cell data. We term this framework backward deconvolution as inference operates from coarse-grained bulk-level data to fine-grained single-cell data. As the abundant missing entries in sc-RNASeq data have a significant effect on log-likelihood scores, we also developed a criterion for inclusion or exclusion of zero entries in log-likelihood score computation. RESULTS We selected nine deconvolution algorithms and validated backward deconvolution in five datasets. In the in-silico mixtures of mouse sc-RNASeq data, the log-likelihood scores of the deconvolution algorithms were strongly anticorrelated with their errors of mixture coefficients and cell type specific gene expression signatures. In the true bulk-level mouse data, the sample mixture coefficients were unknown but the log-likelihood scores were strongly correlated with accuracy rates of inferred cell types. In the data of autism spectrum disorder (ASD) and normal controls, we found that ASD brains possessed higher fractions of astrocytes and lower fractions of NRGN-expressing neurons than normal controls. In datasets of breast cancer and low-grade gliomas (LGG), we compared the log-likelihood scores of three simple hypotheses about the gene expression patterns of the cell types underlying the tumor subtypes. The model that tumors of each subtype were dominated by one cell type persistently outperformed an alternative model that each cell type had elevated expression in one gene group and tumors were mixtures of those cell types. Superiority of the former model is also supported by comparing the real breast cancer sc-RNASeq clusters with those generated by simulated sc-RNASeq data. CONCLUSIONS The results indicate that backward deconvolution serves as a sensible model selection tool for deconvolution algorithms and facilitates discerning hypotheses about cell type compositions underlying heterogeneous specimens such as tumors.
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Affiliation(s)
- Khong-Loon Tiong
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Dmytro Luzhbin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
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199
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Yu S, Lin Y, Yang Y, Jin X, Liao B, Lu D, Huang J. Shared genetic effect of kidney function on bipolar and major depressive disorders: a large-scale genome-wide cross-trait analysis. Hum Genomics 2024; 18:60. [PMID: 38858783 PMCID: PMC11165782 DOI: 10.1186/s40246-024-00627-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 05/27/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Epidemiological studies have revealed a significant association between impaired kidney function and certain mental disorders, particularly bipolar disorder (BIP) and major depressive disorder (MDD). However, the evidence regarding shared genetics and causality is limited due to residual confounding and reverse causation. METHODS In this study, we conducted a large-scale genome-wide cross-trait association study to investigate the genetic overlap between 5 kidney function biomarkers (eGFRcrea, eGFRcys, blood urea nitrogen (BUN), serum urate, and UACR) and 2 mental disorders (MDD, BIP). Summary-level data of European ancestry were extracted from UK Biobank, Chronic Kidney Disease Genetics Consortium, and Psychiatric Genomics Consortium. RESULTS Using LD score regression, we found moderate but significant genetic correlations between kidney function biomarker traits on BIP and MDD. Cross-trait meta-analysis identified 1 to 19 independent significant loci that were found shared among 10 pairs of 5 kidney function biomarkers traits and 2 mental disorders. Among them, 3 novel genes: SUFU, IBSP, and PTPRJ, were also identified in transcriptome-wide association study analysis (TWAS), most of which were observed in the nervous and digestive systems (FDR < 0.05). Pathway analysis showed the immune system could play a role between kidney function biomarkers and mental disorders. Bidirectional mendelian randomization analysis suggested a potential causal relationship of kidney function biomarkers on BIP and MDD. CONCLUSIONS In conclusion, the study demonstrated that both BIP and MDD shared genetic architecture with kidney function biomarkers, providing new insights into their genetic architectures and suggesting that larger GWASs are warranted.
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Affiliation(s)
- Simin Yu
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yifei Lin
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yong Yang
- Health Management Center, General Practice Medical Center, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Xi Jin
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Banghua Liao
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Donghao Lu
- Health Management Center, General Practice Medical Center, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
- Institute of Environmental Medicine, Karolinska Institutet, Nobels Väg 13, 17177, Stockholm, Sweden.
| | - Jin Huang
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
- Health Management Center, General Practice Medical Center, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
- Health Management Center, General Practice Medical Center and Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, People's Republic of China.
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200
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Hofstra BM, Kas MJH, Verbeek DS. Comprehensive analysis of genetic risk loci uncovers novel candidate genes and pathways in the comorbidity between depression and Alzheimer's disease. Transl Psychiatry 2024; 14:253. [PMID: 38862462 PMCID: PMC11166962 DOI: 10.1038/s41398-024-02968-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/10/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
There is growing evidence of a shared pathogenesis between Alzheimer's disease and depression. Therefore, we aimed to further investigate their shared disease mechanisms. We made use of publicly available brain-specific eQTL data and gene co-expression networks of previously reported genetic loci associated with these highly comorbid disorders. No direct genetic overlap was observed between Alzheimer's disease and depression in our dataset, but we did detect six shared brain-specific eQTL genes: SRA1, MICA, PCDHA7, PCDHA8, PCDHA10 and PCDHA13. Several pathways were identified as shared between Alzheimer's disease and depression by conducting clustering pathway analysis on hippocampal co-expressed genes; synaptic signaling and organization, myelination, development, and the immune system. This study highlights trans-synaptic signaling and synaptoimmunology in the hippocampus as main shared pathomechanisms of Alzheimer's disease and depression.
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Affiliation(s)
- Bente M Hofstra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Martien J H Kas
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
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