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Using postmortem formalin fixed paraffin-embedded tissues for molecular testing of sudden cardiac death: A cautionary tale of utility and limitations

Lin, Ying; Gryazeva, Tatyana; Wang, Dawei; Zhou, Bo; Um, Sung Yon; Eng, Lucy S; Ruiter, Kevin; Rojas, Lisa; Williams, Nori; Sampson, Barbara A; Tang, Yingying
For archived cases of previously young healthy individuals where cause of sudden death remains undetermined, formalin fixed paraffin-embedded tissues (FFPE) samples are often the only biological resource available for molecular testing. We aim to ascertain the validity of postmortem molecular analysis of 95 cardiac genes using the FFPE samples routinely processed in the offices of medical examiners - typical fixation time in formalin ranges from days to months. The study was conducted in the College of American Pathologists accredited Molecular Genetics Laboratory within the City of New York Office of Chief Medical Examiner. Twelve cases, with FFPE samples and corresponding non-formalin fixed samples (RNAlater-preserved tissues or bloodstain card), were chosen for testing results comparison. The methods of extracting DNA from FFPE samples using Covaris, Qiagen, and Promega products showed comparable results. The quality of the extracted DNA, the target-enriched DNA libraries of 95 cardiac genes using HaloPlex Target Enrichment system by Agilent Technologies, and sequencing results using Illumina Miseq instrument were evaluated. Compared to the sequencing results of the nonfixed samples, the FFPE samples were categorized into three groups: 1) Group 1 samples fixed in formalin 2-6 days, had greater than 55 % sequencing regions ≥30x and 94%-100% variant concordance. 2) Group 2 samples fixed in formalin for 8 days, showed intra-sample sequencing variations: the surface tissues showed 25%-27% extra variants (false positive) and 8.1%-9.7% missing variants (false negative), whereas the repeated core tissues showed reduced extra variants to 1.6 % and the false negative error was unchanged. 3) Group 3 samples fixed in formalin 29-136 days, had 2-55 % sequencing regions ≥30x, up to 52.2 % missed variants and up to 6.3 % extra variants. All reportable variants (pathogenic, likely pathogenic or variant of uncertain significance) identified in the nonfixed samples were also identified in FFPE, albeit three variants had low confidence variant calling. In summary, our study showed that postmortem molecular diagnostic testing using FFPE samples routinely processed by the medical examiners should be cautioned, as they are replete with false positive and negative results, particularly when sample fixation time is longer than 8 days. Saving non-formalin fixed samples for high fidelity molecular analysis is strongly encouraged.
PMID: 32155531
ISSN: 1872-6283
CID: 4348962

Molecular autopsy: using the discovery of a novel de novo pathogenic variant in the KCNH2 gene to inform healthcare of surviving family

Dong, Jingyun; Williams, Nori; Cerrone, Marina; Borck, Christopher; Wang, Dawei; Zhou, Bo; Eng, Lucy S; Subbotina, Ekaterina; Um, Sung Yon; Lin, Ying; Ruiter, Kevin; Rojas, Lisa; Coetzee, William A; Sampson, Barbara A; Tang, Yingying
Background/UNASSIGNED:pathogenic variant in a decedent. Methods/UNASSIGNED:Forensic investigation and molecular autopsy were performed on an 18-year-old female who died suddenly and unexpectedly. Co-segregation family study of the first-degree relatives and functional characterization of the variant were conducted. Findings/UNASSIGNED:arose de novo, which eliminated the need for exhaustive genome testing and annual cardiac follow-up for the parents and four siblings. Interpretation/UNASSIGNED:Molecular testing enables accurate determination of natural causes of death and precision care of the surviving family members in a time and cost-saving manner. We advocate for molecular autopsy being included under the healthcare coverage in US.
PMID: 30582040
ISSN: 2405-8440
CID: 3560052

Phenotypic variations in carriers of predicted protein-truncating genetic variants in MYBPC3: an autopsy-based case series

Williams, Nori; Marion, Robert; McDonald, Thomas V; Wang, Dawei; Zhou, Bo; Eng, Lucy S; Um, Sung Yon; Lin, Ying; Ruiter, Kevin; Rojas, Lisa; Sampson, Barbara A; Tang, Yingying
Our aim is to characterize predicted protein-truncating variants (PTVs) in MYBPC3, the gene most commonly associated with hypertrophic cardiomyopathy (HCM), found in a series of autopsied HCM cases after sudden unexpected cardiac death. All cases underwent death scene investigation, gross and microscopic autopsies, toxicological testing, a review of medical records, and a molecular analysis of 95 cardiac genes. We found four pathogenic PTVs in MYBPC3 among male decedents. All variants were previously submitted to ClinVar without phenotype details. Two PTVs were located in the cardiac-specific myosin S2-binding (M) motif at the N-terminus of the MYBPC3-encoded cMyBP-C protein, and two PTVs were in the non-cardiac-specific C-terminus of the protein. The carriers of two cardiac-specific M-motif PTVs died at age 38 years; their heart weight (HW, g) and body mass index (BMI, kg/m2) ratio were 34.90 (890/25.5) and 23.56 (980/41.6), respectively. In contrast, the carriers of two non-cardiac-specific C-terminal PTVs died at age 57 and 67 years, respectively; their HW and BMI ratio were 14.71 (450/30.6) and 13.98 (600/42.9), respectively. A detailed three-generation family study was conducted in one case. This study showed age-at-death variations among MYBPC3 PTVs carriers in adult males.
PMID: 30282064
ISSN: 1879-1336
CID: 3328102

Applying High-Resolution Variant Classification to Cardiac Arrhythmogenic Gene Testing in a Demographically Diverse Cohort of Sudden Unexplained Deaths

Lin, Ying; Williams, Nori; Wang, Dawei; Coetzee, William; Zhou, Bo; Eng, Lucy S; Um, Sung Yon; Bao, Ruijun; Devinsky, Orrin; McDonald, Thomas V; Sampson, Barbara A; Tang, Yingying
BACKGROUND:Genetic variant interpretation contributes to testing yield differences reported for sudden unexplained death. Adapting a high-resolution variant interpretation framework, which considers disease prevalence, reduced penetrance, genetic heterogeneity, and allelic contribution to determine the maximum tolerated allele count in gnomAD, we report an evaluation of cardiac channelopathy and cardiomyopathy genes in a large, demographically diverse sudden unexplained death cohort that underwent thorough investigation in the United States' largest medical examiner's office. METHODS AND RESULTS/RESULTS:The cohort has 296 decedents: 147 Blacks, 64 Hispanics, 49 Whites, 22 Asians, and 14 mixed ethnicities; 142 infants (1 to 11 months), 39 children (1 to 17 years), 74 young adults (18 to 34 years), and 41 adults (35 to 55 years). Eighty-nine cardiac disease genes were evaluated. Using a high-resolution variant interpretation workflow, we classified 17 variants as pathogenic or likely pathogenic (2 of which were incidental findings and excluded in testing yield analysis), 46 novel variants of uncertain significance, and 130 variants of uncertain significance. Nine pathogenic or likely pathogenic variants in ClinVar were reclassified to likely benign and excluded in testing yield analysis. The yields of positive cases by ethnicity and age were 21.4% in mixed ethnicities, 10.2% Whites, 4.5% Asians, 3.1% Hispanics, and 2% Blacks; 7.7% children, 7.3% in adults, 5.4% young adults, and 2.8% infants. The percentages of uncertain cases with variants of uncertain significance by ethnicity were 45.5% in Asians, 45.3% Hispanics, 44.20% Blacks, 36.7% Whites, and 14.3% in mixed ethnicities. CONCLUSIONS:High-resolution variant interpretation provides diagnostic accuracy and healthcare efficiency. Under-represented populations warrant greater inclusion in future studies.
PMID: 29247119
ISSN: 1942-3268
CID: 2892682

Whole Exome Sequencing Reveals Severe Thrombophilia in Acute Unprovoked Idiopathic Fatal Pulmonary Embolism

Halvorsen, Matt; Lin, Ying; Sampson, Barbara A; Wang, Dawei; Zhou, Bo; Eng, Lucy S; Um, Sung Yon; Devinsky, Orrin; Goldstein, David B; Tang, Yingying
BACKGROUND: Acute unprovoked idiopathic fatal pulmonary embolism (IFPE) causes sudden death without an identifiable thrombogenic risk. We aimed to investigate the underlying genomic risks of IFPE through whole exome sequencing (WES). METHODS: We reviewed 14years of consecutive out-of-hospital fatal pulmonary embolism records (n=1478) from the ethnically diverse population of New York City. We selected 68 qualifying IFPE cases for WES. We compared the WES data of IFPE cases to those of 9332 controls to determine if there is an excess of rare damaging variants in the genome using ethnicity-matched controls in collapsing analyses. FINDINGS: We found nine of the 68 decedents (13.2%) who died of IFPE had at least one pathogenic or likely pathogenic variant in one of the three anti-coagulant genes: SERPINC1 (Antithrombin III), PROC, and PROS1. The odds ratio of developing IFPE as a variant carrier for SERPINC1 is 144.2 (95% CI, 26.3-779.4; P=1.7x10-7), for PROC is 85.6 (95% CI, 13.0-448.9; P=2.0x10-5), and for PROS1 is 56.4 (95% CI, 5.3-351.1; P=0.001). The average age-at-death of anti-coagulant gene variant carriers is significantly younger than that of non-carriers (28.56years versus 38.02years; P=0.01). INTERPRETATION: This study showed the important role of severe thrombophilia due to natural anti-coagulant deficiency in IFPE. Evaluating severe thrombophilia in out-of-hospital fatal PE beyond IFPE is warranted.
PMID: 28174134
ISSN: 2352-3964
CID: 2437432

Input-specific maturation of synaptic dynamics of parvalbumin interneurons in primary visual cortex

Lu, Jiangteng; Tucciarone, Jason; Lin, Ying; Huang, Z Josh
Cortical networks consist of local recurrent circuits and long-range pathways from other brain areas. Parvalbumin-positive interneurons (PVNs) regulate the dynamic operation of local ensembles as well as the temporal precision of afferent signals. The synaptic recruitment of PVNs that support these circuit operations is not well-understood. Here we demonstrate that the synaptic dynamics of PVN recruitment in mouse visual cortex are customized according to input source with distinct maturation profiles. Whereas the long-range inputs to PVNs show strong short-term depression throughout postnatal maturation, local inputs from nearby pyramidal neurons progressively lose such depression. This enhanced local recruitment depends on PVN-mediated reciprocal inhibition and results from both pre- and postsynaptic mechanisms, including calcium-permeable AMPA receptors at PVN postsynaptic sites. Although short-term depression of long-range inputs is well-suited for afferent signal detection, the robust dynamics of local inputs may facilitate rapid and proportional PVN recruitment in regulating local circuit operations.
PMID: 25385583
ISSN: 1091-6490
CID: 5303432

Cardiac channelopathy testing in 274 ethnically diverse sudden unexplained deaths

Wang, Dawei; Shah, Krunal R; Um, Sung Yon; Eng, Lucy S; Zhou, Bo; Lin, Ying; Mitchell, Adele A; Nicaj, Leze; Prinz, Mechthild; McDonald, Thomas V; Sampson, Barbara A; Tang, Yingying
Sudden unexplained deaths (SUD) in apparently healthy individuals, for which the causes of deaths remained undetermined after comprehensive forensic investigations and autopsy, present vexing challenges to medical examiners and coroners. Cardiac channelopathies, a group of inheritable diseases that primarily affect heart rhythm by altering the cardiac conduction system, have been known as one of the likely causes of SUD. Adhering to the recommendations of including molecular diagnostics of cardiac channelopathies in SUD investigation, the Molecular Genetics Laboratory of the New York City (NYC) Office of Chief Medical Examiner (OCME) has been routinely testing for six major channelopathy genes (KCNQ1, KCNH2, SCN5A, KCNE1, KCNE2, and RyR2) since 2008. Presented here are the results of cardiac channelopathy testing in 274 well-characterized autopsy negative SUD cases, all with thorough medicolegal death investigation including complete autopsy by NYC OCME between 2008 and 2012. The cohort consisted of 141 infants (92.9% younger than six-month old) and 133 non-infants (78.2% were between 19 and 58 years old). Among the ethnically diverse cohort, African American infants had the highest risks of SUD, and African American non-infants died at significantly younger age (23.7 years old, mean age-at-death) than those of other ethnicities (30.3 years old, mean age-at-death). A total of 22 previously classified cardiac channelopathy-associated variants and 24 novel putative channelopathy-associated variants were detected among the infants (13.5%) and non-infants (19.5%). Most channelopathy-associated variants involved the SCN5A gene (68.4% in infants, 50% in non-infants). We believe this is the first study assessing the role of cardiac channelopathy genes in a large and demographically diverse SUD population drawn from a single urban medical examiner's office in the United States. Our study supports that molecular testing for cardiac channelopathy is a valuable tool in SUD investigations and provides helpful information to medical examiners/coroners seeking cause of death in SUD as well as potentially life-saving information to surviving family members.
PMID: 24631775
ISSN: 0379-0738
CID: 951052

A resource of cre driver lines for genetic targeting of GABAergic neurons in cerebral cortex

Taniguchi, Hiroki; He, Miao; Wu, Priscilla; Kim, Sangyong; Paik, Raehum; Sugino, Ken; Kvitsani, Duda; Fu, Yu; Lu, Jiangteng; Lin, Ying; Miyoshi, Goichi; Shima, Yasuyuki; Fishell, Gord; Nelson, Sacha B; Huang, Z Josh
A key obstacle to understanding neural circuits in the cerebral cortex is that of unraveling the diversity of GABAergic interneurons. This diversity poses general questions for neural circuit analysis: how are these interneuron cell types generated and assembled into stereotyped local circuits and how do they differentially contribute to circuit operations that underlie cortical functions ranging from perception to cognition? Using genetic engineering in mice, we have generated and characterized approximately 20 Cre and inducible CreER knockin driver lines that reliably target major classes and lineages of GABAergic neurons. More select populations are captured by intersection of Cre and Flp drivers. Genetic targeting allows reliable identification, monitoring, and manipulation of cortical GABAergic neurons, thereby enabling a systematic and comprehensive analysis from cell fate specification, migration, and connectivity, to their functions in network dynamics and behavior. As such, this approach will accelerate the study of GABAergic circuits throughout the mammalian brain
PMID: 21943598
ISSN: 1097-4199
CID: 138980

A silent synapse-based mechanism for cocaine-induced locomotor sensitization

Brown, Travis E; Lee, Brian R; Mu, Ping; Ferguson, Deveroux; Dietz, David; Ohnishi, Yoshinori N; Lin, Ying; Suska, Anna; Ishikawa, Masago; Huang, Yanhua H; Shen, Haowei; Kalivas, Peter W; Sorg, Barbara A; Zukin, R Suzanne; Nestler, Eric J; Dong, Yan; Schlüter, Oliver M
Locomotor sensitization is a common and robust behavioral alteration in rodents whereby following exposure to abused drugs such as cocaine, the animal becomes significantly more hyperactive in response to an acute drug challenge. Here, we further analyzed the role of cocaine-induced silent synapses in the nucleus accumbens (NAc) shell and their contribution to the development of locomotor sensitization. Using a combination of viral vector-mediated genetic manipulations, biochemistry, and electrophysiology in a locomotor sensitization paradigm with repeated, daily, noncontingent cocaine (15 mg/kg) injections, we show that dominant-negative cAMP-element binding protein (CREB) prevents cocaine-induced generation of silent synapses of young (30 d old) rats, whereas constitutively active CREB is sufficient to increase the number of NR2B-containing NMDA receptors (NMDARs) at synapses and to generate silent synapses. We further show that occupancy of CREB at the NR2B promoter increases and is causally related to the increase in synaptic NR2B levels. Blockade of NR2B-containing NMDARs by administration of the NR2B-selective antagonist Ro256981 directly into the NAc, under conditions that inhibit cocaine-induced silent synapses, prevents the development of cocaine-elicited locomotor sensitization. Our data are consistent with a cellular cascade whereby cocaine-induced activation of CREB promotes CREB-dependent transcription of NR2B and synaptic incorporation of NR2B-containing NMDARs, which generates new silent synapses within the NAc. We propose that cocaine-induced activation of CREB and generation of new silent synapses may serve as key cellular events mediating cocaine-induced locomotor sensitization. These findings provide a novel cellular mechanism that may contribute to cocaine-induced behavioral alterations.
PMID: 21632938
ISSN: 1529-2401
CID: 5303452

EphB controls NMDA receptor function and synaptic targeting in a subunit-specific manner

Nolt, Mark J; Lin, Ying; Hruska, Martin; Murphy, Jessica; Sheffler-Colins, Sean I; Kayser, Matthew S; Passer, Joel; Bennett, Michael V L; Zukin, R Suzanne; Dalva, Matthew B
Dynamic regulation of the localization and function of NMDA receptors (NMDARs) is critical for synaptic development and function. The composition and localization of NMDAR subunits at synapses are tightly regulated and can influence the ability of individual synapses to undergo long-lasting changes in response to stimuli. Here, we examine mechanisms by which EphB2, a receptor tyrosine kinase that binds and phosphorylates NMDARs, controls NMDAR subunit localization and function at synapses. We find that, in mature neurons, EphB2 expression levels regulate the amount of NMDARs at synapses, and EphB activation decreases Ca(2+)-dependent desensitization of NR2B-containing NMDARs. EphBs are required for enhanced localization of NR2B-containing NMDARs at synapses of mature neurons; triple EphB knock-out mice lacking EphB1-3 exhibit homeostatic upregulation of NMDAR surface expression and loss of proper targeting to synaptic sites. These findings demonstrate that, in the mature nervous system, EphBs are key regulators of the synaptic localization of NMDARs.
PMID: 21471370
ISSN: 1529-2401
CID: 5303442