Nutrition facts, drug facts, and model facts: putting AI ethics into practice in gun violence research.

OBJECTIVE: Firearm injury research necessitates using data from often-exploited vulnerable populations of Black and Brown Americans. In order to reduce bias against protected attributes, this study provides a theoretical framework for establishing trust and transparency in the use of AI with the general population. METHODS: We propose a Model Facts template that is easily extendable and decomposes accuracy and demographics into standardized and minimally complex values. This framework allows general users to assess the validity and biases of a model without diving into technical model documentation. EXAMPLES: We apply the Model Facts template on 2 previously published models, a violence risk identification model and a suicide risk prediction model. We demonstrate the ease of accessing the appropriate information when the data are structured appropriately. DISCUSSION: The Model Facts template is limited in its current form to human based data and biases. Like nutrition facts, it will require educational programs for users to grasp its full utility. Human computer interaction experiments should be conducted to ensure model information is communicated accurately and in a manner that improves user decisions. CONCLUSION: The Model Facts label is the first framework dedicated to establishing trust with end users and general population consumers. Implementation of Model Facts into firearm injury research will provide public health practitioners and those impacted by firearm injury greater faith in the tools the research provides.

Identification and Connectomic Profiling of Concussion Using Bayesian Machine Learning.

Accurate early diagnosis of concussion is useful to prevent sequelae and improve neurocognitive outcomes. Early after head impact, concussion diagnosis may be doubtful in persons whose neurological, neuroradiological, and/or neurocognitive examinations are equivocal. Such individuals can benefit from novel accurate assessments that complement clinical diagnostics. We introduce a Bayesian machine learning classifier to identify concussion through cortico-cortical connectome mapping from magnetic resonance imaging in persons with quasi-normal cognition and without neuroradiological findings. Classifier features are generated from connectivity matrices specifying the mean fractional anisotropy of white matter connections linking brain structures. Each connection's saliency to classification was quantified by training individual classifier instantiations using a single feature type. The classifier was tested on a discovery sample of 92 healthy controls (HCs; 26 females, age µ ± σ: 39.8 ± 15.5 years) and 471 adult mTBI patients (158 females, age µ ± σ: 38.4 ± 5.9 years). Results were replicated in an independent validation sample of 256 HCs (149 females, age µ ± σ: 55.3 ± 12.1 years) and 126 patients with concussion (46 females, age µ ± σ: 39.0 ± 17.7 years). Classifier accuracy exceeds 99% in both samples, suggesting robust generalizability to new samples. Notably, 13 bilateral cortico-cortical connection pairs predict diagnostic status with accuracy exceeding 99% in both discovery and validation samples. Many such connection pairs are between prefrontal cortex structures, fronto-limbic and fronto-subcortical structures, and occipito-temporal structures in the ventral ("what") visual stream. This and related connectivity form a highly salient network of brain connections that is particularly vulnerable to concussion. Because these connections are important in mediating cognitive control, memory, and attention, our findings explain the high frequency of cognitive disturbances after concussion. Our classifier was trained and validated on concussed participants with cognitive profiles very similar to those of HCs. This suggests that the classifier can complement current diagnostics by providing independent information in clinical contexts where patients have quasi-normal cognition but where concussion diagnosis stands to benefit from additional evidence.

Current therapies and future prospective for locally aggressive mesenchymal tumors.

Locally aggressive mesenchymal tumors comprise a heterogeneous group of soft tissue and bone tumors with intermediate histology, incompletely understood biology, and highly variable natural history. Despite having a limited to absent ability to metastasize and excellent survival prognosis, locally aggressive mesenchymal tumors can be symptomatic, require prolonged and repeat treatments including surgery and chemotherapy, and can severely impact patients' quality of life. The management of locally aggressive tumors has evolved over the years with a focus on minimizing morbid treatments. Extensive oncologic surgeries and radiation are pillars of care for high grade sarcomas, however, play a more limited role in management of locally aggressive mesenchymal tumors, due to propensity for local recurrence despite resection, and the risk of transformation to a higher-grade entity following radiation. Patients should ideally be evaluated in specialized sarcoma centers that can coordinate complex multimodal decision-making, taking into consideration the individual patient's clinical presentation and history, as well as any available prognostic factors into customizing therapy. In this review, we aim to discuss the biology, clinical management, and future treatment frontiers for three representative locally aggressive mesenchymal tumors: desmoid-type fibromatosis (DF), tenosynovial giant cell tumor (TSGCT) and giant cell tumor of bone (GCTB). These entities challenge clinicians with their unpredictable behavior and responses to treatment, and still lack a well-defined standard of care despite recent progress with newly approved or promising experimental drugs.

Examination of Food Insecurity, Socio-Demographic, Psychosocial, and Physical Factors among Residents in Public Housing.

Objectives: Understanding associations between psychosocial and physical factors among those who experience food insecurity could help design effective food insecurity programs for improved cardiovascular health among low-income populations. We examined differences in psychosocial and physical factors between those who were food secure compared with food insecure among public housing residents. Methods: Data were from the baseline survey of a randomized controlled trial of a weight management intervention in Boston, Massachusetts from 2016-2017. Food insecurity and psychosocial and physical factors, including perceived stress, personal problems, social support, and physical symptoms, were measured via interviewer-administered screeners. Results: Mean age of the sample (N=102) was 46.5 years (SD=11.9). The majority were Hispanic (67%), female (88%), with ≤high school degree (62%). Nearly half were food insecure (48%). For psychosocial variables, those who were food insecure had higher ratings of perceived stress (adjusted mean difference 3.39, 95% CI:2.00,4.79), a higher number of personal problems (adjusted mean difference 1.85, 95% CI: 1.19, 2.51), and lower social support (adjusted mean difference -0.70, 95% CI:-1.30,-0.11) compared with those who were food secure. For physical variables, those who were food insecure had higher odds of reporting negative physical symptoms (aOR 4.92, 95% CI:1.84,13.16). Conclusion: Among this sample of public housing residents, food insecurity was associated with higher stress, more personal problems, higher experiences of physical symptoms, and lower social support.

Gut disease in systemic sclerosis - new approaches to common problems.

PURPOSE OF REVIEW: The goal of this manuscript is to discuss the new diagnostic and potential treatment options for gut disease in systemic sclerosis (SSc). The concepts of quantification of gut perfusion and motility is reviewed. The risks of empiric therapeutics and challenges of studying the microbiome in SSc is discussed. RECENT FINDINGS: There are diagnostics that can provide information on gut perfusion and function that are of value in SSc. Easily implemented diagnostic tests are critical to avoid complications of empiric therapy. The role of the microbiome and drugs that target dysmotility are areas of active research. SUMMARY: SSc-related gastrointestinal tract involvement can be heterogeneous in clinical presentation and disease course. Noninvasive gastrointestinal measurement techniques that quantify neural communications with microvasculature in SSc can potentially guide the proper addition and discontinuation of therapeutics. The role of the microbiome and the role of nitric oxide on gut function are important areas of research for understanding gut dysfunction in SSc.

Triple negative breast cancer development can be selectively suppressed by sustaining an elevated level of cellular cyclic AMP through simultaneously blocking its efflux and decomposition.

Triple negative breast cancer (TNBC) has the highest mortality among all breast cancer types and lack of targeted therapy is a key factor contributing to its high mortality rate. In this study, we show that 8-bromo-cAMP, a cyclic adenosine monophosphate (cAMP) analog at high concentration (> 1 mM) selectively suppresses TNBC cell growth. However, commonly-used cAMP-elevating agents such as adenylyl cyclase activator forskolin and pan phosphodiesterase inhibitor 3-isobutyl-1-methylxanthine (IBMX) are ineffective. Inability of cAMP elevating agents to inhibit TNBC cell growth is due to rapid diminution of cellular cAMP through efflux and decomposition. By performing bioinformatics analyses with publically available gene expression datasets from breast cancer patients/established breast cancer cell lines and further validating using specific inhibitors/siRNAs, we reveal that multidrug resistance-associated protein 1/4 (MRP1/4) mediate rapid cAMP efflux while members PDE4 subfamily facilitate cAMP decomposition. When cAMP clearance is prevented by specific inhibitors, forskolin blocks TNBC's in vitro cell growth by arresting cell cycle at G1/S phase. Importantly, cocktail of forskolin, MRP inhibitor probenecid and PDE4 inhibitor rolipram suppresses TNBC in vivo tumor development. This study suggests that a TNBC-targeted therapeutic strategy can be developed by sustaining an elevated level of cAMP through simultaneously blocking its efflux and decomposition.

3,5-Dihydroxybenzoic acid, a specific agonist for hydroxycarboxylic acid 1, inhibits lipolysis in adipocytes.

Niacin raises high-density lipoprotein and lowers low-density lipoprotein through the activation of the ß-hydroxybutyrate receptor hydroxycarboxylic acid 2 (HCA2) (aka GPR109a) but with an unwanted side effect of cutaneous flushing caused by vascular dilation because of the stimulation of HCA2 receptors in Langerhans cells in skin. HCA1 (aka GPR81), predominantly expressed in adipocytes, was recently identified as a receptor for lactate. Activation of HCA1 in adipocytes by lactate results in the inhibition of lipolysis, suggesting that agonists for HCA1 may be useful for the treatment of dyslipidemia. Lactate is a metabolite of glucose, suggesting that HCA1 may also be involved in the regulation of glucose metabolism. The low potency of lactate to activate HCA1, coupled with its fast turnover rate in vivo, render it an inadequate tool for studying the biological role of lactate/HCA1 in vivo. In this article, we demonstrate the identification of 3-hydroxybenzoic acid (3-HBA) as an agonist for both HCA2 and HCA1, whereas 3,5-dihydroxybenzoic acid (3,5-DHBA) is a specific agonist for only HCA1 (EC(50) ∼150 µM). 3,5-DHBA inhibits lipolysis in wild-type mouse adipocytes but not in HCA1-deficient adipocytes. Therefore, 3,5-DHBA is a useful tool for the in vivo study of HCA1 function and offers a base for further HCA1 agonist design. Because 3-HBA and 3,5-DHBA are polyphenolic acids found in many natural products, such as fruits, berries, and coffee, it is intriguing to speculate that other heretofore undiscovered natural substances may have therapeutic benefits.

Study of GPR81, the lactate receptor, from distant species identifies residues and motifs critical for GPR81 functions.

Receptors from distant species may have conserved functions despite significant differences in protein sequences. Whereas the noncritical residues are often changed in distant species, the amino acids critical in receptor functions are often conserved. Studying the conserved residues between receptors from distant species offers valuable information to probe the roles of residues in receptor function. We identified two zebrafish receptors (zGPR81-1 and zGPR81-2) that show approximately 60% identity to human GPR81, GPR109a, and GPR109b but respond only to l-lactate and not to the GPR109a ligands. Protein sequence comparison among zebrafish GPR81s, mammalian GPR81s, GPR109a, and GPR109b identified a common structure (six Cys residues at the extracellular domains that potentially form three disulfide bonds) in this subfamily of receptors. In addition, a number of residues conserved in all GPR81s but not in GPR109s have been identified. Furthermore, we identified a conserved motif, C165-E166-S167-F168, at the second extracellular loop of GPR81. Using site-directed mutagenesis, we showed that Arg71 at the transmembrane domain 2 is very critical for GPR81 function. In addition, we demonstrated that the C165-E166-S167-F168 motif at the second extracellular loop is critical for GPR81 function, and the conserved six Cys residues at the extracellular regions are necessary for GPR81 function. It is important to mention that for those residues important for GPR81 function, the corresponding residues or motifs in GPR109a are also critical for GPR109a function. These findings help us better understand the interaction between lactate and GPR81 and provide useful information for GPR81 ligand design.

Mutagenesis studies of neuropeptide S identify a suitable peptide tracer for neuropeptide S receptor binding studies and peptides selectively activating the I(107) variant of human neuropeptide S receptor.

Neuropeptide S and its receptor represent a novel neurotransmitter system mainly expressed in the brain. A single nucleotide polymorphism in the first extracellular loop (I107) increases the potency of neuropeptide S and has been identified for both the human neuropeptide S receptor short (A) and long (B) C-terminal forms. Preliminary human genetic studies link this polymorphism to asthma, panic disorders and altered sleep behavior. No polymorphism or splice variants have been reported for the rat neuropeptide S receptor, however it carries an isoleucine at position 107. To identify a suitable tracer for neuropeptide S receptor binding and investigate the role of specific amino acids within neuropeptide S we carried out mutagenesis of the peptide and assessed the ability of the mutations to stimulate calcium release in HEK293 cells expressing human neuropeptide S receptor variants (A, B, AI(107), BI(107)) and rat neuropeptide S receptor. Replacement of threonine at position 8 by arginine and methionine at position 10 by tyrosine resulted in a mutant peptide slightly more potent on all neuropeptide S receptor variants compared to neuropeptide S and more importantly the iodinated mutant peptide was found to be a suitable tracer for binding studies with improved signal to noise ratio and stability compared to [(125)I-Y(10)] neuropeptide S. Replacement of serine at position 1 of neuropeptide S peptide by arginine resulted in a complete loss of potency for the neuropeptide S receptor (long and short form) but not for the I(107) receptor variants (long and short) or rat neuropeptide S receptor.

Probing the functional domains of relaxin-3 and the creation of a selective antagonist for RXFP3/GPCR135 over relaxin receptor RXFP1/LGR7.

Both relaxin-3 and its receptor (RXFP3, also known as GPCR135) are predominantly expressed in brain regions known to play important roles in processing sensory signals. Recent studies have shown that relaxin-3 is involved in the regulation of stress and feeding behaviors. The mechanisms underlying the involvement of relaxin-3/RXFP3 in the regulation of stress, feeding, and other potential functions remain to be studied. Since relaxin-3 also activates the relaxin receptor (RXFP1, also known as LGR7), which is also expressed in the brain, selective RXFP3 agonists and antagonists are crucial for study of the physiological functions of relaxin-3 and RXFP3 in vivo. The finding that the B chain of relaxin-3 is an agonist for RXFP3 (albeit at low potency) but not RXFP1 suggests that the B chain of relaxin-3 plays a dominant role for RXFP3 binding and activation. Chimeric peptide studies using the B chain from relaxin-3 and the A chains from different members of the insulin and relaxin family have confirmed this hypothesis and led to the generation of R3/I5 (a chimeric peptide with relaxin-3 B chain and INSL5 A chain) as a selective agonist for RXFP3 over RXFP1. Truncation of the C-terminus of the B chain of R3/I5 results in a high-affinity antagonist, R3(BDelta23-27)R/I5, for RXFP3 over RXFP1. R3(BDelta23-27)R/I5 has pA2 values of 9.15 and 9.6 for human and rat RXFP3, respectively, but has no affinity or agonistic activity for the human and rat RXFP1. Ongoing and future in vivo studies using the selective agonist and antagonist for RXFP3 will shed light on the physiological role of the relaxin-3 system.

Lactate inhibits lipolysis in fat cells through activation of an orphan G-protein-coupled receptor, GPR81.

Lactic acid is a well known metabolic by-product of intense exercise, particularly under anaerobic conditions. Lactate is also a key source of energy and an important metabolic substrate, and it has also been hypothesized to be a signaling molecule directing metabolic activity. Here we show that GPR81, an orphan G-protein-coupled receptor highly expressed in fat, is in fact a sensor for lactate. Lactate activates GPR81 in its physiological concentration range of 1-20 mM and suppresses lipolysis in mouse, rat, and human adipocytes as well as in differentiated 3T3-L1 cells. Adipocytes from GPR81-deficient mice lack an antilipolytic response to lactate but are responsive to other antilipolytic agents. Lactate specifically induces internalization of GPR81 after receptor activation. Site-directed mutagenesis of GPR81 coupled with homology modeling demonstrates that classically conserved key residues in the transmembrane binding domains are responsible for interacting with lactate. Our results indicate that lactate suppresses lipolysis in adipose tissue through a direct activation of GPR81. GPR81 may thus be an attractive target for the treatment of dyslipidemia and other metabolic disorders.

Identification of the domains in RXFP4 (GPCR142) responsible for the high affinity binding and agonistic activity of INSL5 at RXFP4 compared to RXFP3 (GPCR135).

Relaxin-3 is a potent agonist for both G-protein coupled receptors (GPCR) RXFP3 (also known as GPCR135) and RXFP4 (also known as GPCR142) while insulin-like peptides 5 (INSL5) is a selective RXFP4 agonist. INSL5 is also a weak (low affinity) RXFP3 antagonist. RXFP3 and RXFP4 share about 50% homology. We have used gain-of-function (RXFP3 --> RXFP4) and loss-of-function (RXFP4 --> RXFP3) chimeras to identify the domains critical for the binding and activation induced by INSL5. Replacing extracellular loop (EL) 1 or EL3 of RXFP3 with the corresponding domains from RXFP4 does not change the RXFP3 pharmacological profile. Exchanging the N-terminus and EL2 of RXFP3 with these of RXFP4 results in a chimeric receptor (CR5) with a high affinity for INSL5. However, in contrast to native RXFP4, INSL5 does not elicit an agonist response from CR5. Conversely, replacing the N-terminus and EL2 of RXFP4 with counterparts from RXFP3 (CR15) results in a chimeric receptor for which relaxin-3 and INSL5 are high and low affinity agonists, respectively. Further mutagenesis studies indicate that transmembrane (TM) domains 2, 3 and 5 of RXFP4 are critical determinants of functional receptor activation by INSL5. Replacement of TM2, 3, and 5 of RXFP3 with equivalent domains from RXFP4 results in a chimeric receptor that can be activated by INSL5. These results suggest that the N-terminus and EL2 domains of RXFP3 and RXFP4 are involved in ligand binding while TM2, 3, and 5 are critical for receptor activation.

R3(BDelta23 27)R/I5 chimeric peptide, a selective antagonist for GPCR135 and GPCR142 over relaxin receptor LGR7: in vitro and in vivo characterization.

Both relaxin-3 and its receptor (GPCR135) are expressed predominantly in brain regions known to play important roles in processing sensory signals. Recent studies have shown that relaxin-3 is involved in the regulation of stress and feeding behaviors. The mechanisms underlying the involvement of relaxin-3/GPCR135 in the regulation of stress, feeding, and other potential functions remain to be studied. Because relaxin-3 also activates the relaxin receptor (LGR7), which is also expressed in the brain, selective GPCR135 agonists and antagonists are crucial to the study of the physiological functions of relaxin-3 and GPCR135 in vivo. Previously, we reported the creation of a selective GPCR135 agonist (a chimeric relaxin-3/INSL5 peptide designated R3/I5). In this report, we describe the creation of a high affinity antagonist for GPCR135 and GPCR142 over LGR7. This GPCR135 antagonist, R3(BDelta23-27)R/I5, consists of the relaxin-3 B-chain with a replacement of Gly23 to Arg, a truncation at the C terminus (Gly24-Trp27 deleted), and the A-chain of INSL5. In vitro pharmacological studies showed that R3(BDelta23-27)R/I5 binds to human GPCR135 (IC50=0.67 nM) and GPCR142 (IC50=2.29 nM) with high affinity and is a potent functional GPCR135 antagonist (pA2=9.15) but is not a human LGR7 ligand. Furthermore, R3(BDelta23-27)R/I5 had a similar binding profile at the rat GPCR135 receptor (IC50=0.25 nM, pA2=9.6) and lacked affinity for the rat LGR7 receptor. When administered to rats intracerebroventricularly, R3(BDelta23-27)R/I5 blocked food intake induced by the GPCR135 selective agonist R3/I5. Thus, R3(BDelta23-27)R/I5 should prove a useful tool for the further delineation of the functions of the relaxin-3/GPCR135 system.

G-protein-coupled receptor (GPCR)-142 does not contribute to relaxin-3 binding in the mouse brain: further support that relaxin-3 is the physiological ligand for GPCR135.

Relaxin-3 is a recently discovered member of the insulin/relaxin superfamily that has been shown to be the endogenous ligand for G-protein-coupled receptor (GPCR)135 (SALPR). In addition, relaxin-3 has demonstrated affinity and functional agonism for GPCR142 (GPR100) and LGR7 receptors in vitro. Recent evidence suggests GPCR142 is the insulin-like peptide 5 (INSL5) receptor and LGR7 is the actual relaxin receptor. We have recently described a chimeric R3/I5 peptide that selectively activates GPCR135 and GPCR142, but lacks affinity for LGR7. GPCR142 is a pseudogene in the rat, which allowed the use of [(125)I]-R3/I5 to show GPCR135-like binding sites in the rat central nervous system by autoradiography. However, mouse GPCR142 is a viable gene. In the present study we explore whether GPCR142 is expressed in the mouse brain and whether it is likely to contribute to or interfere with the pharmacological evaluation of relaxin-3 ligands. Competition binding studies confirmed mINSL5 and [(125)I]-mINSL5 bind to mGPCR142 with high affinity. However, no detectable specific [(125)I]-mINSL5 binding sites were detected throughout the mouse brain and unlabelled INSL5 did not displace [(125)I]-R3/I5 binding sites, indicating an absence of detectable GPCR142 binding sites. Consistent with these findings, neither GPCR142 nor INSL5 mRNA were detectable in mouse brain by in situ hybridization. Overall, the distribution of GPCR135 mRNA overlapped with the distribution of GPCR135 binding sites shown by autoradiography using [(125)I]-R3/I5. GPCR135 mRNA and GPCR135 receptor binding sites are most prominent in the mouse amygdala and hypothalamus. These data suggest that relaxin-3/GPCR135 is the receptor ligand pair with physiological relevance in mouse brain.

INSL5 is a high affinity specific agonist for GPCR142 (GPR100).

Insulin-like peptide 5 (INSL5) is a peptide that belongs to the relaxin/insulin family, and its receptor has not been identified. In this report, we demonstrate that INSL5 is a specific agonist for GPCR142. Human INSL5 displaces the binding of (125)I-relaxin-3 to GPCR142 with a high affinity (K(i) = 1.5 nM). In a saturation binding assay, (125)I-INSL5 binds GPCR142 with a K(d) value of 2.5 nM. In functional guanosine (gamma-thio)-triphosphate binding and cAMP accumulation assays, INSL5 potently activates GPCR142 with EC(50) values of 1.3 and 1.2 nM, respectively. In addition, INSL5 stimulates Ca(2+) mobilization in HEK293 cells expressing GPCR142 and G alpha(16). Overall, INSL5 behaves as an agonist for GPCR142 similar to relaxin-3. However, unlike relaxin-3, which is also a potent agonist for GPCR135 and LGR7, INSL5 does not activate either GPCR135 or LGR7. INSL5 inhibits (125)I-relaxin-3 binding to GPCR135 with a low potency (K(i) = 500 nM). A functional assay shows that INSL5 (1 microm) is a weak antagonist for GPCR135. In addition, INSL5 (up to 1 microm) shows no affinity or activity at LGR7 or LGR8 either in a binding assay or a bio-functional assay. Previously, we have demonstrated that GPCR142 mRNA is expressed in peripheral tissues, particularly in the colon. Here we show that INSL5 mRNA is expressed in many peripheral tissues, similar to GPCR142. The high affinity interaction between INSL5 and GPCR142 coupled with their co-evolution and partially overlapping tissue expression patterns strongly suggest that INSL5 is an endogenous ligand for GPCR142.

Characterization of heterogeneity in the molecular pathogenesis of lupus nephritis from transcriptional profiles of laser-captured glomeruli.

The molecular pathogenesis of focal/diffuse proliferative lupus glomerulonephritis was studied by cDNA microarray analysis of gene expression in glomeruli from clinical biopsies. Transcriptional phenotyping of glomeruli isolated by laser-capture microscopy revealed considerable kidney-to-kidney heterogeneity in increased transcript expression, resulting in four main gene clusters that identified the presence of B cells, several myelomonocytic lineages, fibroblast and epithelial cell proliferation, matrix alterations, and expression of type I IFN-inducible genes. Glomerulus-to-glomerulus variation within a kidney was less marked. The myeloid lineage transcripts, characteristic of those found in isolated activated macrophages and myeloid dendritic cells, were widely distributed in all biopsy samples. One major subgroup of the samples expressed fibrosis-related genes that correlated with pathological evidence of glomerulosclerosis; however, decreased expression of TGF-beta1 argued against its role in lupus renal fibrosis. Expression of type I IFN-inducible transcripts by a second subset of samples was associated with reduced expression of fibrosis-related genes and milder pathological features. This pattern of gene expression resembled that exhibited by activated NK cells. A large gene cluster with decreased expression found in all samples included ion channels and transcription factors, indicating a loss-of-function response to the glomerular injury.

Single-cell laser-capture microdissection and RNA amplification.

Generating gene-expression profiles from laser-captured cells requires the successful combination of laser-capture microdissection, RNA extraction, RNA amplification, and microarray analysis. To permit single-cell gene-expression profiling, the RNA amplification method has to be sufficiently powerful to bridge the gap between the amount of RNA available from a single cell to what is required by the microarray, a gap that spans 5 to 6 orders of magnitude. This chapter focuses on the amplification of RNA using a two-round T7 RNA amplification method. The protocols described are adapted for laser-captured material and have been used to generate gene expression profiles from single laser-captured cells.

Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity.

Laser capture microdissection in combination with microarrays allows for the expression analysis of thousands of genes in selected cells. Here we describe single-cell gene expression profiling of CA1 neurons in the rat hippocampus using a combination of laser capture, T7 RNA amplification, and cDNA microarray analysis. Subsequent cluster analysis of the microarray data identified two different cell types: pyramidal neurons and an interneuron. Cluster analysis also revealed differences among the pyramidal neurons, indicating that even a single cell type in vivo is not a homogeneous population of cells at the gene expression level. Microarray data were confirmed by quantitative RT-PCR and in situ hybridization. We also report on the reproducibility and sensitivity of this combination of methods. Single-cell gene expression profiling offers a powerful tool to tackle the complexity of the mammalian brain.