Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment is often used to force the distribution of the intensity log ratios to have a median of zero for each slide. However, such global normalization approaches are not adequate in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. This article proposes normalization methods that are based on robust local regression and account for intensity and spatial dependence in dye biases for different types of cDNA microarray experiments. The selection of appropriate controls for normalization is discussed and a novel set of controls (microarray sample pool, MSP) is introduced to aid in intensity-dependent normalization. Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides.

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

BACKGROUND

Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve.

RESULTS

We introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods.

CONCLUSIONS

Slingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression.

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly, by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing demonstrated that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing revealed that ACE2 is expressed in support cells, stem cells, and perivascular cells, rather than in neurons. Immunostaining confirmed these results and revealed pervasive expression of ACE2 protein in dorsally-located olfactory epithelial sustentacular cells and olfactory bulb pericytes in the mouse. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.

Spatial segregation of odorant receptor expression in the mammalian olfactory epithelium

The signal elicited by the interaction of odorous ligands with receptors on olfactory sensory neurons must be decoded by the brain to determine which of the numerous receptors have been activated. We have examined the patterns of odorant receptor expression in the rat olfactory epithelium to determine whether the mammalian olfactory system employs spatial segregation of sensory input to encode the identity of an odorant stimulus. In situ hybridization experiments with probes for 11 different odorant receptors demonstrate that sensory neurons expressing distinct receptors are topologically segregated into a small number of broad, yet circumscribed, zones within the olfactory epithelium. Within a given zone, however, olfactory neurons expressing a specific receptor appear to be randomly distributed, rather than spatially localized. The complex mammalian olfactory system may therefore compartmentalize the epithelium into anatomically and functionally discrete units, such that each zone expresses only a subset of the entire receptor repertoire.

General anosmia caused by a targeted disruption of the mouse olfactory cyclic nucleotide-gated cation channel

Olfactory neurons transduce the binding of odorants into membrane depolarization. Two intracellular messengers, cyclic AMP (cAMP) and inositol trisphosphate (IP3), are thought to mediate this process, with cAMP generating responses to some odorants and IP3 mediating responses to others. cAMP causes membrane depolarization by activating a cation-selective cyclic nucleotide-gated (CNG) channel. We created a mutant "knockout" mouse lacking functional olfactory CNG channels to assess the roles of different second messenger pathways in olfactory transduction. Using an electrophysiological assay, we find that excitatory responses to both cAMP- and IP3-producing odorants are undetectable in knockout mice. Our results provide direct evidence that the CNG channel subserves excitatory olfactory signal transduction, and further suggest that cAMP is the sole second messenger mediating this process.

Functional genomic analysis of oligodendrocyte differentiation

To better understand the molecular mechanisms governing oligodendrocyte (OL) differentiation, we have used gene profiling to quantitatively analyze gene expression in synchronously differentiating OLs generated from pure oligodendrocyte precursor cells in vitro. By comparing gene expression in these OLs to OLs generated in vivo, we discovered that the program of OL differentiation can progress normally in the absence of heterologous cell-cell interactions. In addition, we found that OL differentiation was unexpectedly prolonged and occurred in at least two sequential stages, each characterized by changes in distinct complements of transcription factors and myelin proteins. By disrupting the normal dynamic expression patterns of transcription factors regulated during OL differentiation, we demonstrated that these sequential stages of gene expression can be independently controlled. We also uncovered several genes previously uncharacterized in OLs that encode transmembrane, secreted, and cytoskeletal proteins that are as highly upregulated as myelin genes during OL differentiation. Last, by comparing genomic loci associated with inherited increased risk of multiple sclerosis (MS) to genes regulated during OL differentiation, we identified several new positional candidate genes that may contribute to MS susceptibility. These findings reveal a previously unexpected complexity to OL differentiation and suggest that an intrinsic program governs successive phases of OL differentiation as these cells extend and align their processes, ensheathe, and ultimately myelinate axons.

Coding of olfactory information: topography of odorant receptor expression in the catfish olfactory epithelium

Discrimination among the vast array of odors requires that the brain discern which of the numerous odorant receptors have been activated. If individual olfactory neurons express only a subset of the odorant receptor repertoire, then the nature of a given odorant can be discerned by identifying which cells have been activated. We performed in situ hybridization experiments demonstrating that individual olfactory neurons express different complements of odorant receptors and are therefore functionally distinct. Thus, a topographic map, defining either the positions of specific neurons in the epithelium or the positions of their projections, may be employed to determine the quality of an olfactory stimulus. Neurons expressing specific receptors appear to be randomly distributed within the olfactory epithelium. These data are consistent with a model in which randomly dispersed olfactory neurons with common receptor specificities project to common glomeruli in the olfactory bulb.

The molecular basis for water taste in Drosophila

The detection of water and the regulation of water intake are essential for animals to maintain proper osmotic homeostasis. Drosophila and other insects have gustatory sensory neurons that mediate the recognition of external water sources, but little is known about the underlying molecular mechanism for water taste detection. Here we identify a member of the degenerin/epithelial sodium channel family, PPK28, as an osmosensitive ion channel that mediates the cellular and behavioural response to water. We use molecular, cellular, calcium imaging and electrophysiological approaches to show that ppk28 is expressed in water-sensing neurons, and that loss of ppk28 abolishes water sensitivity. Moreover, ectopic expression of ppk28 confers water sensitivity to bitter-sensing gustatory neurons in the fly and sensitivity to hypo-osmotic solutions when expressed in heterologous cells. These studies link an osmosensitive ion channel to water taste detection and drinking behaviour, providing the framework for examining the molecular basis for water detection in other animals.

A multimodal cell census and atlas of the mammalian primary motor cortex

Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

The family of genes encoding odorant receptors in the channel catfish

The anatomical and numerical simplicity of the fish olfactory system has led us to examine the family of olfactory receptors expressed in the catfish. We have identified a family of genes encoding seven transmembrane domain receptors that share considerable homology with the odorant receptors of the rat. The size of the catfish receptor repertoire appears to be far smaller than in mammals. Analysis of the nucleotide sequences suggests that these receptor genes have undergone positive Darwinian selection to generate enhanced diversity within the putative odorant-binding domains. Individual receptor clones anneal with 0.5%-2% of the olfactory neurons, suggesting that a single cell expresses only a small subset of distinct odorant receptors. Each cell, therefore, possesses a unique identity defined by the receptors it expresses. These data suggest that the brain may discriminate among odors by determining which neurons have been activated.

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1-3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.

Functional identification of a goldfish odorant receptor

The vertebrate olfactory system utilizes odorant receptors to receive and discriminate thousands of different chemical stimuli. An understanding of how these receptors encode information about an odorant's molecular structure requires a characterization of their ligand specificities. We employed an expression cloning strategy to identify a goldfish odorant receptor that is activated by amino acids-potent odorants for fish. Structure-activity analysis indicates that the receptor is preferentially tuned to recognize basic amino acids. The receptor is a member of a multigene family of G protein-coupled receptors, sharing sequence similarities with the calcium sensing, metabotropic glutamate, and V2R class of vomeronasal receptors. The ligand tuning properties of the goldfish amino acid odorant receptor provide information for unraveling the molecular mechanisms underlying olfactory coding.

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans.

Anosmia-A Clinical Review

Anosmia and hyposmia, the inability or decreased ability to smell, is estimated to afflict 3-20% of the population. Risk of olfactory dysfunction increases with old age and may also result from chronic sinonasal diseases, severe head trauma, and upper respiratory infections, or neurodegenerative diseases. These disorders impair the ability to sense warning odors in foods and the environment, as well as hinder the quality of life related to social interactions, eating, and feelings of well-being. This article reports and extends on a clinical update commencing at the 2016 Association for Chemoreception Sciences annual meeting. Included were reports from: a patient perspective on losing the sense of smell with information on Fifth Sense, a nonprofit advocacy organization for patients with olfactory disorders; an otolaryngologist's review of clinical evaluation, diagnosis, and management/treatment of anosmia; and researchers' review of recent advances in potential anosmia treatments from fundamental science, in animal, cellular, or genetic models. As limited evidence-based treatments exist for anosmia, dissemination of information on anosmia-related health risks is needed. This could include feasible and useful screening measures for olfactory dysfunction, appropriate clinical evaluation, and patient counseling to avoid harm as well as manage health and quality of life with anosmia.

The Sp1-related transcription factors sp5 and sp5-like act downstream of Wnt/beta-catenin signaling in mesoderm and neuroectoderm patterning

BACKGROUND

Wnt/beta-catenin signaling regulates many processes during vertebrate development, including patterning of the mesoderm along the dorso-ventral axis and patterning of the neuroectoderm along the anterior-posterior axis during gastrulation. However, relatively little is known about Wnt target genes mediating these effects.

RESULTS

Using zebrafish DNA microarrays, we have identified several new targets of Wnt/beta-catenin signaling, including sp5-like (sp5l, previously called spr2), a zinc-finger transcription factor of the Sp1 family. sp5-like is a direct target of Wnt/beta-catenin signaling and acts together with its paralog sp5 (previously called bts1) downstream of wnt8 in patterning of the mesoderm and neuroectoderm because (1) overexpression of sp5-like, like overexpression of wnt8, posteriorizes the neuroectoderm, (2) sp5-like morpholino-mediated knockdown, like wnt8 knockdown, causes anteriorization of the hindbrain, (3) combined knockdown of sp5 and sp5-like, like loss of wnt8, causes expansion of dorsal mesoderm, (4) sp5-like knockdown reduces the defects in mesoderm and neuroectoderm patterning caused by wnt8 overexpression, and (5) inhibition of sp5-like enhances the effects of hypomorphic loss of wnt8. Importantly, (6) overexpression of sp5-like is able to partially restore normal hindbrain patterning in wnt8 morphants.

CONCLUSIONS

sp5-like is a direct target of Wnt/beta-catenin signaling during gastrulation and, together with sp5, acts as a required mediator of the activities of wnt8 in patterning the mesoderm and neuroectoderm. We conclude that sp5 transcription factors mediate the downstream responses to Wnt/beta-catenin signaling in several developmental processes in zebrafish.

Formation of precise connections in the olfactory bulb occurs in the absence of odorant-evoked neuronal activity

Olfactory neurons expressing the same odorant receptor converge to a small number of glomeruli in the olfactory bulb. In turn, mitral and tufted cells receive and relay this information to higher cortical regions. In other sensory systems, correlated neuronal activity is thought to refine synaptic connections during development. We asked whether the pattern of connections between olfactory sensory axons and mitral cell dendrites is affected when odor-evoked signaling is eliminated in mice lacking functional olfactory cyclic nucleotide-gated (CNG) channels. We demonstrate that olfactory sensory axons converge normally in the CNG channel mutant background. We further show that the pruning of mitral cell dendrites, although slowed during development, is ultimately unperturbed in mutant animals. Thus, the olfactory CNG channel-and by inference correlated neural activity--is not required for generating synaptic specificity in the olfactory bulb.

Molecular cloning and single-channel properties of the cyclic nucleotide-gated channel from catfish olfactory neurons

We have cloned a functional cDNA encoding the cyclic nucleotide-gated channel selectively expressed in catfish olfactory sensory neurons. The cyclic nucleotide-gated channels share sequence and structural features with the family of voltage-gated ion channels. This homology is most evident in transmembrane region S4, the putative voltage sensor domain, and the H5 domain, thought to form the channel pore. We have characterized the single-channel properties of the cloned catfish channel and compared these properties with the channel in native catfish olfactory sensory neurons. The channel is activated equally well by cAMP and cGMP, shows only a slight voltage dependence of gating, and exhibits a pH- and voltage-dependent subconductance state similar to that observed for the voltage-gated L-type calcium channel.

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution

A detailed understanding of the paths that stem cells traverse to generate mature progeny is vital for elucidating the mechanisms governing cell fate decisions and tissue homeostasis. Adult stem cells maintain and regenerate multiple mature cell lineages in the olfactory epithelium. Here we integrate single-cell RNA sequencing and robust statistical analyses with in vivo lineage tracing to define a detailed map of the postnatal olfactory epithelium, revealing cell fate potentials and branchpoints in olfactory stem cell lineage trajectories. Olfactory stem cells produce support cells via direct fate conversion in the absence of cell division, and their multipotency at the population level reflects collective unipotent cell fate decisions by single stem cells. We further demonstrate that Wnt signaling regulates stem cell fate by promoting neuronal fate choices. This integrated approach reveals the mechanisms guiding olfactory lineage trajectories and provides a model for deconstructing similar hierarchies in other stem cell niches.

The odorant receptor repertoire of teleost fish

BACKGROUND

Vertebrate odorant receptors comprise three types of G protein-coupled receptors: the OR, V1R and V2R receptors. The OR superfamily contains over 1,000 genes in some mammalian species, representing the largest gene superfamily in the mammalian genome.

RESULTS

To facilitate an informed analysis of OR gene phylogeny, we identified the complete set of 143 OR genes in the zebrafish genome, as well as the OR repertoires in two pufferfish species, fugu (44 genes) and tetraodon (42 genes). Although the genomes analyzed here contain fewer genes than in mammalian species, the teleost OR genes can be grouped into a larger number of major clades, representing greater overall OR diversity in the fish.

CONCLUSION

Based on the phylogeny of fish and mammalian repertoires, we propose a model for OR gene evolution in which different ancestral OR genes or gene families were selectively lost or expanded in different vertebrate lineages. In addition, our calculations of the ratios of non-synonymous to synonymous codon substitutions among more recently expanding OR subgroups in zebrafish implicate residues that may be involved in odorant binding.

Tissue-specific expression of two mRNA species transcribed from a single vimentin gene

We have isolated chicken cDNA and genomic clones for the intermediate filament subunit vimentin and show that the gene for this protein, which exists in a single copy in the haploid chicken genome, is transcribed into two mature mRNA species with approximate lengths of 2.0 and 2.3 kb. We have found cell-specific regulation in the expression of these two mRNAs; whereas both mRNA species are present in muscle cells, fibroblasts, spinal cord and lens, erythroid cells from 10- and 15-day-old chicken embryos express predominantly the lower molecular weight RNA. The difference between these two mRNAs is due to different lengths of their 3' untranslated regions, suggesting that the cell-specific regulation of their expression occurs either by specific termination of transcription or by differential post-transcriptional processing of the 3' untranslated region. Additionally, a remarkable induction (40- to 50-fold) in the abundance of the vimentin mRNA is observed in erythroid cells as chicken development proceeds from 4 to 15 days, which suggests that the level of expression of vimentin during erythroid development is regulated at the transcriptional level.

The cell biology of smell

The olfactory system detects and discriminates myriad chemical structures across a wide range of concentrations. To meet this task, the system utilizes a large family of G protein–coupled receptors—the odorant receptors—which are the chemical sensors underlying the perception of smell. Interestingly, the odorant receptors are also involved in a number of developmental decisions, including the regulation of their own expression and the patterning of the olfactory sensory neurons' synaptic connections in the brain. This review will focus on the diverse roles of the odorant receptor in the function and development of the olfactory system.

Learned recognition of maternal signature odors mediates the first suckling episode in mice

BACKGROUND

Soon after birth, all mammals must initiate milk suckling to survive. In rodents, this innate behavior is critically dependent on uncharacterized maternally derived chemosensory ligands. Recently, the first pheromone sufficient to initiate suckling was isolated from the rabbit. Identification of the olfactory cues that trigger first suckling in the mouse would provide the means to determine the neural mechanisms that generate innate behavior.

RESULTS

Here we use behavioral analysis, metabolomics, and calcium imaging of primary sensory neurons and find no evidence of ligands with intrinsic bioactivity, such as pheromones, acting to promote first suckling in the mouse. Instead, we find that the initiation of suckling is dependent on variable blends of maternal "signature odors" that are learned and recognized prior to first suckling.

CONCLUSIONS

As observed with pheromone-mediated behavior, the response to signature odors releases innate behavior. However, this mechanism tolerates variability in both the signaling ligands and sensory neurons, which may maximize the probability that this first essential behavior is successfully initiated. These results suggest that mammalian species have evolved multiple strategies to ensure the onset of this critical behavior.

Asynchronous onset of odorant receptor expression in the developing zebrafish olfactory system

The functional identity of an olfactory neuron is determined in large part by the odorant receptors it expresses. As an approach toward understanding the events that underlie the specification of olfactory neurons, we have examined the patterns of odorant receptor gene expression in the developing zebrafish. Surprisingly, we find that the onset of specific odorant receptor expression occurs asynchronously in the developing olfactory placode. Our results suggest that odorant receptor expression is not strictly stochastic, but rather is governed by temporally regulated cues during development. Moreover, by restricting the number of receptor genes competent for transcription at different times of development, temporal waves of expression may provide a mechanism for simplifying the regulation of the large odorant receptor gene family.

Pathfinding of olfactory neuron axons to stereotyped glomerular targets revealed by dynamic imaging in living zebrafish embryos

In the vertebrate olfactory system, sensory neurons with common odorant specificities project to specific glomeruli in the olfactory bulb. How do olfactory sensory neurons find their glomerular targets? To address this question, we have visualized the genesis of the peripheral olfactory system in living zebrafish embryos. Dye labelings reveal that a primordial yet stereotyped map of glomeruli is apparent during embryogenesis. By labeling a small number of cells with an ectopically expressed green fluorescent protein reporter, we can observe the dynamic growth behaviors of individual olfactory neuron growth cones as they project to their glomeruli. We find that olfactory axons extend directly to their partner glomeruli, suggesting that these cells' growth cones rely upon pathfinding cues to reach their targets.