Qingqin Li - Academia.edu (original) (raw)

Papers by Qingqin Li

ABSTRACTObjectiveSuicide death is a highly preventable, yet growing, worldwide health crisis. To ... more ABSTRACTObjectiveSuicide death is a highly preventable, yet growing, worldwide health crisis. To date, there has been a lack of adequately powered genomic studies of suicide, with no sizeable suicide death cohorts available for study. To address this limitation, we conducted the first comprehensive genomic analysis of suicide death, using a previously unpublished suicide cohort.MethodsThe analysis sample consisted of 3,413 population-ascertained cases of European ancestry and 14,810 ancestrally matched controls. Analytical methods included principle components analysis for ancestral matching and adjusting for population stratification, linear mixed model genome-wide association testing (conditional on genetic relatedness matrix), gene and gene set enrichment testing, polygenic score analyses, as well as SNP heritability and genetic correlation estimation using LD score regression.ResultsGWAS identified two genome-wide significant loci (6 SNPs, p<5×10−8). Gene-based analyses impli...

BMC Psychiatry, 2019

Background: There is a growing body of literature highlighting the role that wearable and mobile ... more Background: There is a growing body of literature highlighting the role that wearable and mobile remote measurement technology (RMT) can play in measuring symptoms of major depressive disorder (MDD). Outcomes assessment typically relies on self-report, which can be biased by dysfunctional perceptions and current symptom severity. Predictors of depressive relapse include disrupted sleep, reduced sociability, physical activity, changes in mood, prosody and cognitive function, which are all amenable to measurement via RMT. This study aims to: 1) determine the usability, feasibility and acceptability of RMT; 2) improve and refine clinical outcome measurement using RMT to identify current clinical state; 3) determine whether RMT can provide information predictive of depressive relapse and other critical outcomes. Methods: RADAR-MDD is a multi-site prospective cohort study, aiming to recruit 600 participants with a history of depressive disorder across three sites: London, Amsterdam and Barcelona. Participants will be asked to wear a wristworn activity tracker and download several apps onto their smartphones. These apps will be used to either collect data passively from existing smartphone sensors, or to deliver questionnaires, cognitive tasks, and speech assessments. The wearable device, smartphone sensors and questionnaires will collect data for up to 2-years about participants' sleep, physical activity, stress, mood, sociability, speech patterns, and cognitive function. The primary outcome of interest is MDD relapse, defined via the Inventory of Depressive Symptomatology-Self-Report questionnaire (IDS-SR) and the World Health Organisation's self-reported Composite International Diagnostic Interview (CIDI-SF). Discussion: This study aims to provide insight into the early predictors of major depressive relapse, measured unobtrusively via RMT. If found to be acceptable to patients and other key stakeholders and able to provide clinically useful information predictive of future deterioration, RMT has potential to change the way in which depression and other long-term conditions are measured and managed.

Pharmacogenetics and Genomics, 2017

Objective Clinical response to the atypical antipsychotic paliperidone is known to vary among sch... more Objective Clinical response to the atypical antipsychotic paliperidone is known to vary among schizophrenic patients. We carried out a genome-wide association study to identify common genetic variants predictive of paliperidone efficacy. Methods We leveraged a collection of 1390 samples from individuals of European ancestry enrolled in 12 clinical studies investigating the efficacy of the extended-release tablet paliperidone ER (n 1 = 490) and the once-monthly injection paliperidone palmitate (n 2 = 550 and n 3 = 350). We carried out a genome-wide association study using a general linear model (GLM) analysis on three separate cohorts, followed by meta-analysis and using a mixed linear model analysis on all samples. The variations in response explained by each single nucleotide polymorphism (h 2 SNP) were estimated. Results No SNP passed genome-wide significance in the GLM-based analyses with suggestive signals from rs56240334 [P = 7.97 × 10 − 8 for change in the Clinical Global Impression Scale-Severity (CGI-S); P = 8.72 × 10 − 7 for change in the total Positive and Negative Syndrome Scale (PANSS)] in the intron of ADCK1. The mixed linear model-based association P-values for rs56240334 were consistent with the results from GLM-based analyses and the association with change in CGI-S (P = 4.26 × 10 − 8) reached genome-wide significance (i.e. P < 5 × 10 − 8). We also found suggestive evidence for a polygenic contribution toward paliperidone treatment response with estimates of heritability, h 2 SNP , ranging from 0.31 to 0.43 for change in the total PANSS score, the PANSS positive Marder factor score, and CGI-S. Conclusion Genetic variations in the ADCK1 gene may differentially predict paliperidone efficacy in schizophrenic patients. However, this finding should be replicated in additional samples. Pharmacogenetics and Genomics

Genomic copy number variants (CNVs) have been strongly implicated in the etiology of schizophreni... more Genomic copy number variants (CNVs) have been strongly implicated in the etiology of schizophrenia (SCZ). However, apart from a small number of risk variants, elucidation of the CNV contribution to risk has been difficult due to the rarity of risk alleles, all occurring in less than 1% of cases. We sought to address this obstacle through a collaborative effort in which we applied a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. We observed a global enrichment of CNV burden in cases (OR=1.11, P=5.7e-15), which persisted after excluding loci implicated in previous studies (OR=1.07, P=1.7e-6). CNV burden is also enriched for genes associated with synaptic function (OR = 1.68, P = 2.8e-11) and neurobehavioral phenotypes in mouse (OR = 1.18, P= 7.3e-5). We identified genome-wide significant support for eight loci, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.2, 15q13.3, distal 16p11.2, proximal 16p11.2 and 22q11.2. We find support at a suggestive level...

European Journal of Cancer Supplements, 2004

Pharmacogenomics, 2014

Based on previous pharmacogenetic findings, we investigated the possible association between SULT... more Based on previous pharmacogenetic findings, we investigated the possible association between SULT4A1-1 haplotype and antipsychotic treatment response. Using Mixed Model Repeated Measures, we tested the relationship between SULT4A1-1 status (+carrier, -noncarrier) and clinical improvement (in Positive and Negative Syndrome Scale total score) among European ancestry patients treated with paliperidone extended release (n=937), paliperidone palmitate (n=990), risperidone (n=507) and olanzapine (n=381) in 12 schizophrenia, two schizoaffective disorder and three bipolar I disorder trials. SULT4A1-1 haplotype was determined using tagging SNP rs763120. There was no significant difference between SULT4A1-1(+) and SULT4A1-1(-) patients for treatment response to paliperidone or olanzapine. SULT4A1-1(-) patients had better treatment response to risperidone in one schizophrenia trial, but not in another schizophrenia trial or bipolar mania trial. Across three psychiatric disorders (n=2815 patien...

Scientific Reports, 2013

We carried out a GWAS meta-analysis of combined mixed-ancestry schizophrenia, schizoaffective, an... more We carried out a GWAS meta-analysis of combined mixed-ancestry schizophrenia, schizoaffective, and bipolar cohorts that resulted in the identification of six genome-wide significant loci, including one novel locus at chr8q24.3, encompassing TSNARE1 (P 5 1.28 3 10 29). The analysis included a total of 13,394 cases and 34,676 controls. While the function of TSNARE1 remains unknown, bioinformatic predictions based on phylogenetic ancestry indicate it may have a vertebrate-specific function in intracellular protein transport and synaptic vesicle exocytosis.

Monitoring sleep and activity through wearable devices such as wrist-worn actigraphs has the pote... more Monitoring sleep and activity through wearable devices such as wrist-worn actigraphs has the potential for long-term measurement in the individual’s own environment. Long periods of data collection require a complex approach, including standardized pre-processing and data trimming, and robust algorithms to address non-wear and missing data. In this study, we used a data-driven approach to quality control, pre-processing and analysis of longitudinal actigraphy data collected over the course of 1 year in a sample of 95 participants. We implemented a data processing pipeline using open-source packages for longitudinal data thereby providing a framework for treating missing data patterns, non-wear scoring, sleep/wake scoring, and conducted a sensitivity analysis to demonstrate the impact of non-wear and missing data on the relationship between sleep variables and depressive symptoms. Compliance with actigraph wear decreased over time, with missing data proportion increasing from a mean ...

Frontiers in Psychiatry

Major depressive disorder (MDD) is an episodic condition with relapsing and remitting disease cou... more Major depressive disorder (MDD) is an episodic condition with relapsing and remitting disease course. Elucidating biomarkers that can predict future relapse in individuals responding to an antidepressant treatment holds the potential to identify those patients who are prone to illness recurrence. The current study explored relationships between relapse risk in recurrent MDD and circulating microRNAs (miRNAs) that participate in RNA silencing and post-transcriptional regulation of gene expression. Serum samples were acquired from individuals with a history of recurrent MDD who were followed longitudinally in the observational study, OBSERVEMDD0001 (ClinicalTrials.gov Identifier: NCT02489305). Circulating miRNA data were obtained in 63 participants who relapsed (“relapsers”) and 154 participants who did not relapse (“non-relapsers”) during follow-up. The miRNA was quantified using the ID3EAL™ miRNA Discovery Platform from MiRXES measuring 575 circulating miRNAs using a patented qPCR t...

Additional file 2: Supplemental Tables.

Additional file 1. Supplemental Figures S1–S4.

Alzheimer's & Dementia, 2021

Identifying biomarkers associated with Alzheimer’s disease (AD) progression may enable patient en... more Identifying biomarkers associated with Alzheimer’s disease (AD) progression may enable patient enrichment and improve clinical trial designs. Epigenome‐wide association studies (EWAS) have revealed correlations between DNA methylation level at cytosine‐phosphate‐guanine (CpG) sites and AD pathology in the brain or diagnosis in peripheral blood.

Brain, Behavior, & Immunity - Health, 2021

Background: Alzheimer's disease (AD) is associated with abnormal tau and amyloid-β accumulation i... more Background: Alzheimer's disease (AD) is associated with abnormal tau and amyloid-β accumulation in the brain, leading to neurofibrillary tangles, neuropil threads and extracellular amyloid-β plaques. Treatment is limited to symptom management, a disease-modifying therapy is not available. To advance search of therapy approaches, there is a continued need to identify targets for disease intervention both by confirming existing hypotheses and generating new hypotheses. Methods: We conducted a mRNA-seq study to identify genes associated with AD in post-mortem brain samples from the superior temporal gyrus (STG, n ¼ 76), and inferior frontal gyrus (IFG, n ¼ 65) brain regions. Differentially expressed genes (DEGs) were identified correcting for gender and surrogate variables to capture hidden variation not accounted for by pre-planned covariates. The results from this study were compared with the transcriptome studies from the Accelerated Medicine Partnership-Alzheimer's Disease (AMP-AD) initiative. Over-representation and gene set enrichment analysis (GSEA) was used to identify disease-associated pathways. Protein-protein interaction (PPI) and weighted gene co-expression network analysis (WGCNA) analyses were carried out and co-expressed gene modules and their hub genes were identified and associated with additional phenotypic traits of interest. Results: Several hundred mRNAs were differentially expressed between AD cases and cognitively normal controls in the STG, while no and few transcripts met the same criteria (adjusted p less than 0.05 and fold change greater than 1.2) in the IFG. The findings were consistent at the gene set level with two out of three cohorts from AMP-AD. PPI analysis suggested that the DEGs were enriched in protein-protein interactions than expected by random chance. Over-representation and GSEA analysis suggested genes playing roles in neuroinflammation, amyloid-β, autophagy and trafficking being important for the AD disease process. At the gene level, 10 genes from the STG that were consistently differentially expressed in this study and in the MSBB study (one of the three cohorts within the AMP-AD initiative) were enriched in microglial genes (TREM2, C3AR1, ITGAX, OLR1, CD74, and HLA-DRA), but also included genes with a broader cell type expression pattern such as CDK2AP1. Among the DEGs with supporting evidence from an independent study, CDK2AP1 (most abundantly expressed in astrocyte) was the transcript with strongest association with antemortem cognitive measure (last Mini-Mental State Examination score) and neurofibril tangle burden but also associated with amyloid plaque burden, while OLR1 was the transcript with strongest association with amyloid plaque burden. GSEA and over-representation analyses revealed gene sets related to immune processes including neutrophil degranulation, interleukin 10 signaling, and interferon gamma signaling, complement and coagulation cascades, phosphatidylinositol signaling system, phagosome and neurotransmitter receptors and postsynaptic signal transmission were enriched from this study and replicated in an independent study. Conclusion: This study identified differential gene sets, common with two out of three AMP-AD cohorts (ROSMAP and MSBB) and highlights microglia and astrocyte as the key cell-types with DGEs associated with AD clinical diagnosis, and/or antemortem cognitive measure as well as neuropathological indices. Future meta-analysis and causal inferential analysis will be helpful in pinpointing the most relevant pathways and genes to intervene.

Biological Psychiatry Global Open Science, 2021

Journal of Cell Science, 2001

The centrosome is responsible for nucleating microtubules and performing other cellular roles. To... more The centrosome is responsible for nucleating microtubules and performing other cellular roles. To define the organization of the centrosome more completely, a human anti-centrosome serum was used to screen a human cDNA library, and a cDNA encoding a >350 kDa centrosome protein was identified. Sequence analyses revealed that this novel centrosome protein contains two coiled-coil domains bounded by non-coiled regions. The N-terminal region of the protein, named pericentrin-B, shares 61% identity (75% similarity) with pericentrin, suggesting an evolutionary relationship between these proteins. Antibodies against pericentrin-B stain centrosomes at all stages of the cell cycle, and pericentrin-B remains associated with centrosomes following microtubule depolymerization. Immunodepletion of neither pericentrin-B nor PCM-1 from cellular extracts inhibited the ability of salt-stripped centrosomes to recover microtubule nucleation potential, demonstrating that neither protein plays a key r...

Nature Genetics, 2021

Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights in... more Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology Bipolar disorder is a heritable mental illness with complex etiology. We performed a genome-wide association study of 41,917 bipolar disorder cases and 371,549 controls of European ancestry, which identified 64 associated genomic loci. Bipolar disorder risk alleles were enriched in genes in synaptic signaling pathways and brain-expressed genes, particularly those with high specificity of expression in neurons of the prefrontal cortex and hippocampus. Significant signal enrichment was found in genes encoding targets of antipsychotics, calcium channel blockers, antiepileptics and anesthetics. Integrating expression quantitative trait locus data implicated 15 genes robustly linked to bipolar disorder via gene expression, encoding druggable targets such as HTR6, MCHR1, DCLK3 and FURIN. Analyses of bipolar disorder subtypes indicated high but imperfect genetic correlation between bipolar disorder type I and II and identified additional associated loci. Together, these results advance our understanding of the biological etiology of bipolar disorder, identify novel therapeutic leads and prioritize genes for functional follow-up studies.

Frontiers in Neuroscience, 2021

Alzheimer’s disease (AD), the leading form of dementia, is associated with abnormal tau and β-amy... more Alzheimer’s disease (AD), the leading form of dementia, is associated with abnormal tau and β-amyloid accumulation in the brain. We conducted a miRNA-seq study to identify miRNAs associated with AD in the post-mortem brain from the inferior frontal gyrus (IFG, n = 69) and superior temporal gyrus (STG, n = 81). Four and 64 miRNAs were differentially expressed (adjusted p-value < 0.05) in AD compared to cognitively normal controls in the IFG and STG, respectively. We observed down-regulation of several miRNAs that have previously been implicated in AD, including hsa-miR-212-5p and hsa-miR-132-5p, in AD samples across both brain regions, and up-regulation of hsa-miR-146a-5p, hsa-miR-501-3p, hsa-miR-34a-5p, and hsa-miR-454-3p in the STG. The differentially expressed miRNAs were previously implicated in the formation of amyloid-β plaques, the dysregulation of tau, and inflammation. We have also observed differential expressions for dozens of other miRNAs in the STG, including hsa-miR-...

Brain, Behavior, and Immunity, 2020

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Alzheimer's & Dementia, 2018

Discovery (ADSP + ADNI) 248 4551 2 0 ADSP (non-discovery) 5604 194 0 0 ADNI (non-discovery) 196 1... more Discovery (ADSP + ADNI) 248 4551 2 0 ADSP (non-discovery) 5604 194 0 0 ADNI (non-discovery) 196 130 0 0 WashU (familial) 1143 462 3 (2 related) 0 WashU (case-control) 1279 874 0 0 UCL (UK) 1221 488 0 0 UCL (Portugal) 143 0 3 0 UCLA 224 224 0 0 UCSF 250 492 0 0 ADGC 8779 7039 2 1 (Age 70, E3/E3) CHARGE 1391 8100 0 1 Nottingham 532 182 0 0 ADC 404 202 1* 0 Combined Validation 21,266 18,387 8 2 TOTAL (Discovery + Validation) 21,414 22,938 10 2