FACS-Based Sequencing Approach to Evaluate Cell Type to Genotype Associations Using Cerebral Organoids.

Recent technological developments have led to widespread applications of large-scale transcriptomics-based sequencing methods to identify genotype-to-cell type associations. Here we describe a fluorescence-activated cell sorting (FACS)-based sequencing method to utilize CRISPR/Cas9 edited mosaic cerebral organoids to identify or validate genotype-to-cell type associations. Our approach is high-throughput and quantitative and uses internal controls to enable comparisons of the results across different antibody markers and experiments.

Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus 10398A>G.

Mitochondrial (MT) dysfunction has been associated with several neurodegenerative diseases including Alzheimer's disease (AD). While MT-copy number differences have been implicated in AD, the effect of MT heteroplasmy on AD has not been well characterized. Here, we analyzed over 1800 whole genome sequencing data from four AD cohorts in seven different tissue types to determine the extent of MT heteroplasmy present. While MT heteroplasmy was present throughout the entire MT genome for blood samples, we detected MT heteroplasmy only within the MT control region for brain samples. We observed that an MT variant 10398A>G (rs2853826) was significantly associated with overall MT heteroplasmy in brain tissue while also being linked with the largest number of distinct disease phenotypes of all annotated MT variants in MitoMap. Using gene-expression data from our brain samples, our modeling discovered several gene networks involved in mitochondrial respiratory chain and Complex I function associated with 10398A>G. The variant was also found to be an expression quantitative trait loci (eQTL) for the gene MT-ND3. We further characterized the effect of 10398A>G by phenotyping a population of lymphoblastoid cell-lines (LCLs) with and without the variant allele. Examination of RNA sequence data from these LCLs reveal that 10398A>G was an eQTL for MT-ND4. We also observed in LCLs that 10398A>G was significantly associated with overall MT heteroplasmy within the MT control region, confirming the initial findings observed in post-mortem brain tissue. These results provide novel evidence linking MT SNPs with MT heteroplasmy and open novel avenues for the investigation of pathomechanisms that are driven by this pleiotropic disease associated loci.

oFlowSeq: a quantitative approach to identify protein coding mutations affecting cell type enrichment using mosaic CRISPR-Cas9 edited cerebral organoids.

Cerebral organoids are comprised of diverse cell types found in the developing human brain, and can be leveraged in the identification of critical cell types perturbed by genetic risk variants in common, neuropsychiatric disorders. There is great interest in developing high-throughput technologies to associate genetic variants with cell types. Here, we describe a high-throughput, quantitative approach (oFlowSeq) by utilizing CRISPR-Cas9, FACS sorting, and next-generation sequencing. Using oFlowSeq, we found that deleterious mutations in autism-associated gene KCTD13 resulted in increased proportions of Nestin+ cells and decreased proportions of TRA-1-60+ cells within mosaic cerebral organoids. We further identified that a locus-wide CRISPR-Cas9 survey of another 18 genes in the 16p11.2 locus resulted in most genes with > 2% maximum editing efficiencies for short and long indels, suggesting a high feasibility for an unbiased, locus-wide experiment using oFlowSeq. Our approach presents a novel method to identify genotype-to-cell type imbalances in an unbiased, high-throughput, quantitative manner.

A simple and rapid method for enzymatic synthesis of CRISPR-Cas9 sgRNA libraries.

CRISPR-Cas9 sgRNA libraries have transformed functional genetic screening and have enabled several innovative methods that rely on simultaneously targeting numerous genetic loci. Such libraries could be used in a vast number of biological systems and in the development of new technologies, but library generation is hindered by the cost, time, and sequence data required for sgRNA library synthesis. Here, we describe a rapid enzymatic method for generating robust, variant-matched libraries from any source of cDNA in under 3 h. This method, which we have named SLALOM, utilizes a custom sgRNA scaffold sequence and a novel method for detaching oligonucleotides from solid supports by a strand displacing polymerase. With this method, we constructed libraries targeting the E. coli genome and the transcriptome of developing zebrafish hearts, demonstrating its ability to expand the reach of CRISPR technology and facilitate methods requiring custom libraries.

Recognition of microbial and mammalian phospholipid antigens by NKT cells with diverse TCRs.

CD1d-restricted natural killer T (NKT) cells include two major subgroups. The most widely studied are Vα14Jα18(+) invariant NKT (iNKT) cells that recognize the prototypical α-galactosylceramide antigen, whereas the other major group uses diverse T-cell receptor (TCR) α-and ß-chains, does not recognize α-galactosylceramide, and is referred to as diverse NKT (dNKT) cells. dNKT cells play important roles during infection and autoimmunity, but the antigens they recognize remain poorly understood. Here, we identified phosphatidylglycerol (PG), diphosphatidylglycerol (DPG, or cardiolipin), and phosphatidylinositol from Mycobacterium tuberculosis or Corynebacterium glutamicum as microbial antigens that stimulated various dNKT, but not iNKT, hybridomas. dNKT hybridomas showed distinct reactivities for diverse antigens. Stimulation of dNKT hybridomas by microbial PG was independent of Toll-like receptor-mediated signaling by antigen-presenting cells and required lipid uptake and/or processing. Furthermore, microbial PG bound to CD1d molecules and plate-bound PG/CD1d complexes stimulated dNKT hybridomas, indicating direct recognition by the dNKT cell TCR. Interestingly, despite structural differences in acyl chain composition between microbial and mammalian PG and DPG, lipids from both sources stimulated dNKT hybridomas, suggesting that presentation of microbial lipids and enhanced availability of stimulatory self-lipids may both contribute to dNKT cell activation during infection.

Innate and cytokine-driven signals, rather than microbial antigens, dominate in natural killer T cell activation during microbial infection.

Invariant natural killer T cells (iNKT cells) are critical for host defense against a variety of microbial pathogens. However, the central question of how iNKT cells are activated by microbes has not been fully explained. The example of adaptive MHC-restricted T cells, studies using synthetic pharmacological α-galactosylceramides, and the recent discovery of microbial iNKT cell ligands have all suggested that recognition of foreign lipid antigens is the main driver for iNKT cell activation during infection. However, when we compared the role of microbial antigens versus innate cytokine-driven mechanisms, we found that iNKT cell interferon-γ production after in vitro stimulation or infection with diverse bacteria overwhelmingly depended on toll-like receptor-driven IL-12. Importantly, activation of iNKT cells in vivo during infection with Sphingomonas yanoikuyae or Streptococcus pneumoniae, pathogens which are known to express iNKT cell antigens and which require iNKT cells for effective protection, also predominantly depended on IL-12. Constitutive expression of high levels of IL-12 receptor by iNKT cells enabled instant IL-12-induced STAT4 activation, demonstrating that among T cells, iNKT cells are uniquely equipped for immediate, cytokine-driven activation. These findings reveal that innate and cytokine-driven signals, rather than cognate microbial antigen, dominate in iNKT cell activation during microbial infections.

Gene variation of the transient receptor potential cation channel, subfamily M, members 6 (TRPM6) and 7 (TRPM7), and type 2 diabetes mellitus: a case-control study.

Transient receptor potential cation channel, subfamily M, members 6 (TRPM6) and 7 (TRPM7), have been implicated in inflammatory disorders including diabetes, a major source of morbidity and mortality in developing and Western society. We hypothesized that gene variation of TRPM6 and TRPM7 may play a role in type 2 diabetes mellitus (T2DM) Using a case-control population sample of the Boston metropolitan area (all whites, 455 controls and 467 cases), we assessed the relationship of 29 TRPM6 and 11 TRPM7 tag-single nucleotide polymorphisms (SNPs) with (1) several diabetes-related intermediate phenotypes (fasting insulin levels, fasting glucose levels, hemoglobin A1c, and homeostatic model assessment) and (2) the presence of T2DM. All SNPs examined were in Hardy-Weinberg equilibrium. Overall, genotype distributions were similar between cases and controls. Linear regression analysis, adjusted for potential risk factors/confounders, showed no evidence of an association of any SNPs tested with the aforementioned diabetes-related intermediate phenotypes after correcting for multiple testing. Marker-by-marker multivariable logistic regression analysis showed no evidence of an association of any SNPs tested with the presence of T2DM after correcting for multiple testing. Continued investigation using an entropy-blocker-defined haplotype-based approach showed similar null findings. If corroboration occurs in future large prospective investigations, then the present investigation further suggests that TRPM6 and TRPM7 gene variation may not be useful predictors for T2DM risk assessment.

Gene variation of the transient receptor potential cation channel, subfamily M, member 2 (TRPM2) and type 2 diabetes mellitus: A case-control study.

BACKGROUND: Disordered cellular calcium regulation has been implicated in the pathophysiology of diabetes through mechanisms that remain unresolved. The non-selective calcium channel, transient receptor potential cation channel, subfamily M, member 2 (TRPM2), has been recently reported to play a role in insulin secretion by pancreatic beta-cells. We hypothesized that gene variation of TRPM2 may play a role in the pathophysiology of type 2 diabetes mellitus (T2DM). METHODS: Using a case-control study from a community-based population sample of the Boston metropolitan area (all whites: 455 controls and 467 cases), we assessed the relationship of 9 TRPM2 tag-SNPs with (i) diabetes-related intermediate phenotypes and (ii) the presence of T2DM. RESULT: All SNPs examined were in Hardy-Weinberg equilibrium. Overall allele, genotype, and haplotype distributions were similar between cases and controls. Three TRPM2 variants (rs2838553, rs2838554 and rs4818917) were associated with homeostasis model assessment of beta-cell function (HOMA-%B), but not with HOMA-insulin resistance (HOMA-IR), fasting glucose levels nor hemoglobin A1c levels. Marker-by-marker logistic regression analysis, adjusted for potential risk factors, showed no evidence for an association of any of the tag-SNPs tested with T2DM. Further investigation using an entropy blocker-defined haplotype-based approach showed similar null findings. CONCLUSIONS: The present investigation found no evidence for an association of the variants tested with T2DM, although HOMA-%B was negatively associated with three TRPM2 variants (rs2838553, rs2838554 and rs4818917). More importantly, our present findings require replication/confirmation in future large-scale, prospective investigations.

Relative leukocyte telomere length and risk of incident ischemic stroke in men: a prospective, nested case-control approach.

Recent data have implicated telomere-length shortening as potential risk predictor for vascular diseases, including stroke. However, to date, prospective epidemiological data are scarce in relation to ischemic stroke risk. Using leukocyte DNA samples collected at baseline in a prospective cohort of 14,916 initially healthy American men, we examined the relationship of leukocyte telomere repeat copy number to single gene copy number (TSR), using a quantitative polymerase chain reaction protocol, amongst 259 white males who subsequently developed an ischemic stroke and amongst an equal number of age- and smoking-matched white males who remained free of reported vascular disease during follow up (controls). The observed TSRs were inversely correlated with age in the controls (p < 0.0001). However, the observed TSRs were similar between cases and controls (p = 0.92). In a multivariable adjusted analysis, no evidence was found for an association of the TSRs with ischemic stroke risk (odds ratio [OR] = 1.100, 95% confidence interval [CI], 0.506-2.392, p = 0.811). The present investigation has shown no evidence for an association of relative leukocyte telomere length with risk of incident ischemic stroke. More importantly, our present findings require replication/confirmation in future large, prospective studies.

Mean leukocyte telomere length shortening and type 2 diabetes mellitus: a case-control study.

Recent data have implicated leukocyte telomere length shortening as a potential risk predictor for type 2 diabetes mellitus (T2DM) and its associated phenotypes. However, to date, epidemiologic data are scarce. Using a case-control study from a community-based population sample of the Boston metropolitan area (all whites: 424 controls and 432 cases), we examined the relationship of mean leukocyte telomere repeat copy number to single gene copy number (TSR) and T2DM. Associations of log(e)-transformed TSR with age, race, sex, body mass index (BMI), current smoking status, fasting insulin levels, fasting glucose levels, and hemoglobin A1c (HbA1c) were examined by multivariable linear regression analysis. A logistic regression analysis was performed to evaluate the association of log(e)-transformed TSR with T2DM with or without adjustment for potential confounders. The log(e)-transformed TSR was significantly shorter in the white cases than the white controls (P=0.003). In a multivariable linear regression analysis, an inverse association of log(e)-transformed TSR with BMI was observed (P=0.04). Furthermore, in a multivariable logistic regression analysis, decreased log(e)-transformed TSR was significantly associated with T2DM (adjusted odds ratio=1.748; 95% confidence interval [CI]=1.015-3.012; P=0.044). In summary, the current investigation has shown an association of mean leukocyte telomere length shortening with T2DM in white subjects. If corroborated in other studies, our findings suggest the potential importance of telomere biology in T2DM.

Mean leukocyte telomere length and risk of incident colorectal carcinoma in women: a prospective, nested case-control study.

BACKGROUND: To date, no prospective epidemiological data are available, particularly in women, on mean leukocyte telomere length as a risk predictor. METHODS: Using leukocyte DNA samples collected at baseline in a prospective cohort of over 28,000 initially healthy women, we examined the relationship between mean leukocyte telomere repeat copy number to single gene copy number (TSR) in 134 incident cases of colorectal carcinoma (CRC), and 357 matched controls; all were Caucasian. RESULTS: The observed log(e)-transformed TSRs were similar between cases and controls (p=0.79). Using an adjusted analysis, we found no evidence for an association of the log(e)-TSRs with CRC risk [adjusted odds ratio (OR)=0.943, 95% confidence interval (CI)=0.647-1.376, p=0.762]. Stratified analysis by median follow-up time, or postmenopausal status also showed similar null findings. CONCLUSIONS: In concordance with our previous findings in Caucasian men, the present study in Caucasian women found no evidence for an association of mean leukocyte telomere length with risk of incident CRC, further suggesting that leukocyte telomere length may not be a useful indicator for risk assessment.

Mean telomere length and risk of incident colorectal carcinoma: a prospective, nested case-control approach.

Recent studies have shown telomere length shortening in colorectal carcinoma (CRC). However, to date, no prospective, epidemiologic data are available on examining mean leukocyte telomere length as a risk predictor. Using leukocyte DNA samples collected at baseline in a prospective cohort of 14,916 initially healthy American men, we examined the relationship of mean telomere repeat copy number to single gene copy number (T/S ratio), using a modified quantitative PCR protocol, among 191 incident CRC cases (all white males), matched to 306 controls by age, smoking status, and length of follow-up. An inverse correlation between T/S ratio and age was observed in our sample population (P = 0.038). However, the T/S ratios were similar between cases and controls (P = 0.650). Furthermore, in a multivariable adjusted analysis, we found no evidence for an association of the observed T/S ratios with CRC risk (adjusted odds ratio, 1.249; 95% confidence interval, 0.863-1.808; P = 0.238). In summary, the present investigation found no evidence for an association of leukocyte mean telomere length with risk of incident CRC and further suggests that leukocyte mean telomere length may not be a useful indicator for risk assessment.