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1. Asher, J. E., Lamb, J. A., Brocklebank, D., Cazier, J.-B., Maestrini, E., Addis, L., Sen, M., Baron-Cohen, S., & Monaco, A. P. (2009, February 5). A whole-genome scan and fine-mapping linkage study of auditory-visual synesthesia reveals evidence of linkage to chromosomes 2q24, 5q33, 6P12, and 12p12. The American Journal of Human Genetics. Retrieved January 20, 2022, from https://www.sciencedirect.com/science/article/pii/S0002929709000196

2. Brang, D., & Ramachandran, V. S. (2011, November). Survival of the synesthesia gene: Why do people hear colors and taste words? PLoS biology. Retrieved January 20, 2022, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222625/

3. Hubbard, E. M., & Ramachandran, V. S. (2005, November 2). Neurocognitive mechanisms of synesthesia. Neuron. Retrieved January 20, 2022, from https://www.sciencedirect.com/science/article/pii/S0896627305008354

4. Pultarova, T. (2018, March 5). Why can some people 'hear' colors? LiveScience. Retrieved January 20, 2022, from https://www.livescience.com/61930-synesthesia-hear-colors-genes.html

5. Tilot, A. K., Kucera, K. S., Vino, A., Asher, J. E., Baron-Cohen, S., & Fisher, S. E. (2018, March 20). Rare variants in axonogenesis genes connect three families with sound–color synesthesia. PNAS. Retrieved January 20, 2022, from https://www.pnas.org/content/115/12/3168

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Synesthesia is a neurological condition that affects 2-4% of the population in which multiple senses are essentially binded (Brang, Ramachandran, 2011). Sounds, letters, numbers, and words can trigger a certain taste, smell, or color in a synesthete. This condition has been studied by researchers, however it has been difficult to identify the foundation of the condition (Pultarova, 2018). Synesthesia does not affect all synesthetes the same as different senses can be binded, and different colors or sounds associated with letters or numbers. While synesthesia is defined as a neurological condition or phenomenon, it does not necessarily impact those it affects in a negative manner.  Many artists are affected by synesthesia, and synesthetes report increased creativity (Brang, Ramachandran, 2011).

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Research has shown that synesthesia is a familial trait, however patterns of inheritance have been difficult to recognize as the condition can skip generations and affects both men and women (Hubbard, Ramachandran, 2005). In order to further understand synesthesia and patterns of inheritance, studies have focused on families of synesthetes rather than just the synesthetes themselves. These studies have demonstrated that synesthesia is “genetically heterogeneous and unlikely to be explained by a single genetic locus” (Tilot et. al., 2018). There are at least sixty different forms of synesthesia, indicating the condition can be the result of  multiple genetic variations (Brang, Ramachandran, 2011). Studies have indicated that synesthesia is caused by “altered neural connectivity” and that “alterations in white matter that could indicate the existence of increased connectivity in the brains of synesthetes” (Asher et. al., 2009).

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DNA sequencing is used to study the genes of the participating synesthetes and family members. These genes are then compared in an attempt to identify which genes may be responsible for the expression of synesthesia, however the results have been inconclusive as thirty seven possible gene variations were identified (Pultarova, T. (2018, March 5). The conclusion that synesthesia is heterogeneous suggests the inheritance of gene mutations leading to synthesia can come from different points in the chromosome (Asher et. al. 2009).

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The biological effects of synesthesia are found in the connectivity and development of neurons. Axonogenesis is a process that aids in the development and connectivity of the brain. Axonogenesis was one of the biological themes found in the candidates of a study done on synesthesia. Altered brain connectivity is consistent in synesthetes, and is identified through the genes. (Pultarova, 2018). It was found that there were “a core set of six genes” related to axonogenesis, and that these genes are expressed during the development of the auditory and visual cortex of the brain. These genes may play a role in processes developing these regions of the brain (Tilot et. al., 2018). Another study proposed the idea that synesthesia is the result of “an excess of neural connections between associated modalities” (Brang, Ramachandran, 2011).

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The cause of synesthesia is still unknown, but studies have been able to identify similarities between synesthetes, allowing them to make conclusions about the neurological condition. Axonogenesis and brain connectivity are just some of the biological themes of the condition. DNA sequencing and understanding of the genes related to neural connections will provide more information on the cause, and as our understanding of genetics and the genome increases so will our understanding of synesthesia.

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(Image credit: Shutterstock)

About 4 percent of the people on Earth experience a mysterious phenomenon called synesthesia: They hear a sound and automatically see a color; or, they read a certain word, and a specific hue enters their mind's eye. The condition has long puzzled scientists, but a small new study may offer some clues.

The study, published today (March 5) in the journal Proceedings of the National Academy of Sciences, offers insight into what might be happening in the brains of people with synesthesia.

Previous "studies of brain function using magnetic resonance imaging confirm that synesthesia is a real biological phenomenon," said senior study author Simon Fisher, director of the Max Planck Institute for Psycholinguistics in the Netherlands. For example, when people with synesthesia "hear" color, brain scans show that there's activity in the parts of the brain linked to both sight and sound, he said. (Not all people with the condition "hear" sights, however; the condition can also link other senses.) [ 10 Things You Didn't Know About the Brain]

Indeed, the brains of people with synesthesia previously have been shown to be more connected across different regions than the brains of people whose senses are not cross-linked, Fisher told Live Science. The question, however, was what causes this different brain wiring, he said.

To answer that question, Fisher and his team looked to genetics.

Synesthesia frequently runs in families, so the researchers decided to look for genes that might be responsible for the development of the condition. They chose three families, in which multiple members across at least three generations had a specific type of synesthesia, the so-called sound-color synesthesia, meaning that hearing sounds evokes perceptions of colors. Typically, a specific sound or musical tone is consistently associated with a specific color for people who have this type of synesthesia. However, different members of a single family can see different colors when hearing the same sound, Fisher said.

The scientists used DNA sequencing to study the participants' genes, Fisher said. Then, to identify genes that might be responsible for the condition, the scientists compared the genes of family members with synesthesia to the genes of family members without it, he said.

But the findings didn't yield a straightforward result: "There was not a single gene that could explain synesthesia in all three families," Fisher said. Instead, "there were 37 candidate variants," or possible gene variations, he said.

Because the study included only a small number of people, there wasn't enough data to single out the specific genes, of the 37 possibilities, that played a role in synesthesia. So, instead, the scientists looked at the biological functions of each gene to see how it could be related to the development of the condition. "There were just a few biological themes that were significantly enriched across the candidate genes identified," Fisher said. "One of those was axonogenesis, a crucial process helping neurons get wired up to each other in the developing brain." Axonogenesis refers to the development of neurons.

This is consistent with prior findings of altered connectivity in brain scans of people with synesthesia, Fisher said. In other words, the genes identified in the study play a role in how the brain is wired, offering a potential explanation for why the brains of people with synesthesia appear to be wired differently.

The researchers are now looking for more volunteers to participate in their future studies, which, they hope, will help them better understand how variations of certain genes alter brain structure and function. Studying synesthesia could essentially provide a window into how human brains in general create sensory representations of the outside world, Fisher said.

Tereza is a London-based science and technology journalist, video producer and health blogger. Originally from Prague, the Czech Republic, she spent the first seven years of her career working as a reporter, script-writer and presenter for various TV programmes of the Czech national TV station. She later took a career break to pursue further education and added a Master in Science from the International Space University, France, to her Bachelor's degree in Journalism from Prague's Charles University. She is passionate about nutrition, meditation and psychology, and sustainability.

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(Image credit: Shutterstock) About 4 percent of the people on Earth experience a mysterious phenomenon called synesthesia: They hear a sound and automatically see a color; or, they read a certain word, and a specific hue enters their mind's eye. The condition has long puzzled scientists, but a small new study may offer some clues.

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Significance

Our physical senses are separated not only into distinct experiences but also into specialized regions within the cerebral cortex. Synesthesia is a neurological phenomenon that causes unusual links between sensory experiences, and its molecular basis is completely unknown. We demonstrate that three families who experience color when listening to sounds are connected by rare genetic variants affecting genes that contribute to axonogenesis, a process essential for neuronal connections within and across brain regions. Multiple genes with similar activity patterns during neural development fall within parts of the genome previously linked to the condition. Our results connect synesthetes' altered structural and functional connectivity to genes that support the development of those connections.

Abstract

Synesthesia is a rare nonpathological phenomenon where stimulation of one sense automatically provokes a secondary perception in another. Hypothesized to result from differences in cortical wiring during development, synesthetes show atypical structural and functional neural connectivity, but the underlying molecular mechanisms are unknown. The trait also appears to be more common among people with autism spectrum disorder and savant abilities. Previous linkage studies searching for shared loci of large effect size across multiple families have had limited success. To address the critical lack of candidate genes, we applied whole-exome sequencing to three families with sound-color (auditory-visual) synesthesia affecting multiple relatives across three or more generations. We identified rare genetic variants that fully cosegregate with synesthesia in each family, uncovering 37 genes of interest. Consistent with reports indicating genetic heterogeneity, no variants were shared across families. Gene ontology analyses highlighted six genes- COL4A1, ITGA2, MYO10, ROBO3, SLC9A6, and SLIT2 -associated with axonogenesis and expressed during early childhood when synesthetic associations are formed. These results are consistent with neuroimaging-based hypotheses about the role of hyperconnectivity in the etiology of synesthesia and offer a potential entry point into the neurobiology that organizes our sensory experiences.

Results

We used WES to identify genetic variants within coding parts of the genome for three multigenerational families with sound-color synesthesia ( Fig. 1). For each family, we obtained exome sequences from four or five verified synesthetes across three generations plus at least one nonsynesthetic family member. All cases in this study had sound-color synesthesia as confirmed using the established Test of Genuineness (SI Materials and Methods), although it is possible that some also experience additional, more common types of synesthesia (e.g., colored weekdays). The families were identified from the Cambridge Synesthesia Research Group database and were originally included in a 2009 study using microsatellite markers to look for evidence of genetic linkage across 43 families of varying sizes with forms of auditory-visual synesthesia ( 20). The families in the present study were chosen as the most feasible for studying with WES based on size, structure, and availability of suitable DNA samples.

Using nonparametric linkage analysis and assuming genetic heterogeneity, the authors of the 2009 study found three regions with suggestive linkage (5q33, 6p12, and 12p12) ( 23). Chromosome 2q24 showed significant linkage after gene-drop simulations (heterogeneity logarithm of the odds score, HLOD 3.02, P value 0.047) ( 20). An independent investigation of five other families with sequence-color synesthesia (color associations for sequences such as numbers or months) reported suggestive evidence for a locus on chromosome 16q, but this was supported by only two of the five families ( 19). These studies suggest that synesthesia involves considerable genetic heterogeneity, with different genetic factors contributing in different families.

Following the Genome Analysis Toolkit's best practices guidelines for calling DNA variants, we identified 11,597 variants across our three sound-color families after removing low-quality variants and those with low sequencing depth (family 2: 8,195; family 11: 9,202; and family 16: 8,074) ( 24). To elevate potentially causative variants, we applied filtration criteria based on our limited knowledge of synesthesia's genetic architecture and the prevalence of the sound-color variety (familial or sporadic). A 2006 study established that up to 4.4% of the UK population may experience at least one form of synesthesia, but the prevalence of sound-color synesthesia is not well studied ( 7, 23, 25). Estimates range from 1 in 500 unselected individuals in the United Kingdom (from the same prevalence study) to 41% of self-referred Dutch and German synesthetes ( 7, 25). Given the uncertainty in these estimates, we chose a relatively inclusive maximum minor allele frequency (MAF) of 0.01 for highlighting variants of potential interest. In total, there were 3,864 variants across the families that were rare enough to be considered further (family 2: 1,812; family 11: 2,727; family 16: 1,862; note that, prior to the further filtering described below, these included some partially overlapping variants across families).

Based on pedigree structures of the three families, we next retained variants that followed dominant inheritance with full penetrance ( Fig. 1A). Given the findings of prior genetic screens, we hypothesized that while familial sound-color synesthesia may be due to single variants within a particular family, such variants were unlikely to be shared across different families ( 20). To test this, we looked in our retained variants for rare, heterozygous mutations that perfectly segregated with synesthesia within each separate family. This yielded a total of 37 variants across 37 genes ( Table 1). No variants were shared across all synesthetes in all families, consistent with the hypothesis of genetic heterogeneity. A missense variant in RGS21 was detected in all synesthetes from family 16 but was found in only one synesthete from family 2. Further supporting genetic heterogeneity in synesthesia, no single gene contained a perfectly segregating variant in all three families. None of the 37 highlighted variants fell within the suggestive linkage peaks reported in prior studies ( 19, 20).

To further define shared mechanisms across the three families, we assessed whether there were enriched gene ontology terms within our set of putative candidate genes from WES. We excluded inferred electronic annotations, as these are considered less informative than manually curated entries. The ontology analysis identified significant enrichment for a narrow set of terms primarily related to neural development ( Table 2). Notably, six genes were associated with axonogenesis (GO:0007409) and cell migration (GO:0016477), biological categories with clear relevance to the hyperconnectivity account of synesthesia. These genes, SLIT2, MYO10, ROBO3, ITGA2, COL4A1, and SLC9A6 (marked by an asterisk in Table 1), span the three families and may point to particular processes that can be investigated at higher levels (e.g., hyperconnectivity).

Having identified variants in a core set of six candidate genes with potential functional relevance for neurobiological accounts of synesthesia etiology, we went on to study their expression in neural tissues. We used two complementary datasets, the Genotype-Tissue Expression project (GTEx) based on RNA-sequencing (RNAseq) and the microarray-based Allen Human Brain Atlas (ABA), to determine expression patterns of the candidates ( 26, 27). GTEx includes data from >100 postmortem human brains with RNA sampled from 13 sites, including the frontal cortex ( 26). Each of the six genes had detectable expression in these samples, with SLC9A6 and ITGA2 having the highest and lowest expression, respectively ( Table S1).

As protein levels are not always well correlated with RNA expression ( 28), we combined these findings with immunohistochemistry data from the Human Protein Atlas, which includes manually quantified protein expression from human cerebral cortical tissue of three adult donor brains (age range, 37-70 y) ( 29). The Atlas included results for each of the relevant proteins, except ROBO3. All five remaining proteins were observed in neuronal cells, albeit to varying degrees ( Table S1 shows ranges when multiple antibodies produced different results). Beyond neurons, multiple candidates showed staining in neuropil and endothelial cells, while only SLIT2 was observed at high levels in glia. These results support the GTEx RNAseq data, indicating that the six genes are active in adult brain tissue.

The GTEx and Human Protein Atlas resources lack data from several cortical regions with relevance for synesthesia studies, and the tissues were primarily collected from middle-aged adults. Thus, we next sought to determine if the highlighted genes are active in the auditory, visual, and parietal cortices and to examine their expression patterns during development. Reports vary on the neuroanatomical regions and activity patterns that may mediate synesthetic experiences; some support a role for the visual cortex, and others emphasize sensory integration in the parietal lobe ( 11, 14, 30). We used microarray data from six postmortem brains, sampled at ∼500 locations, with the data mapped to structural MRI scans (ABA), to visualize gene expression in a more fine-grained fashion ( 27). Despite the differing methodologies, expression values from the GTEx cortical samples were well correlated with frontal cortical data from the ABA (Pearson's, r = 0.95, P = 0.004). In the ABA, we found that each of the six genes was widely expressed across the brain ( Fig. 2A), including the auditory, visual, and parietal cortices.

Longitudinal studies show that synesthetic associations often form during primary school years, and axonogenesis primarily occurs from early fetal development through the first years of life, prompting us to examine expression of our candidate genes across human brain development ( 15). To do this, we used data from the Allen Institute's BrainSpan project, which includes human brain tissue from age 8 wk post conception to 40 y, sampling an average of 13 regions (range, 1-17) from one to three brains per time point, measured using RNAseq ( 31). Each of the six genes of interest has detectable expression in auditory, visual, and parietal cortices during fetal development and early childhood ( Fig. 2B). Finally, to determine whether the six candidates were preferentially expressed in any specific neural cell types, we used an RNAseq dataset of six cell types isolated from the mouse cortex with a series of antibody-based purification steps to ensure high cell-type specificity ( 32). The candidate genes were broadly expressed across the neural and glial transcriptomes, with relatively lower expression levels in microglia ( Fig. 2C).

Previous synesthesia genetics studies not only faced limitations of small family sizes but also were restricted by the use of lower-precision methods than those adopted here. We thus sought to determine whether the results of the current study might be relevant for those earlier reports. Coexpression patterns can reveal genes involved in similar neurodevelopmental processes, and so we tested whether genes coexpressed with the six candidates fell within the putative linkage peaks of prior studies, while acknowledging that most evidence from previous reports was at the suggestive level ( 33). The peaks reported by Asher et al. ( 20) were unlikely to be a result of linkage within the three families used in the present study, as we found no segregating variants within those regions ( Table 1). Thus, the peaks from 5q33, 6p12, 12p12, 2q24 (sound-color synesthesia) and 16q12.2-23.1 (sequence-color synesthesia) represent signals from other families. Using the six putative candidates as seed genes, we found 109 genes coexpressed at r > 0.7 during neural development ( 31). The complete set of coexpressed genes contained six located within a previously reported synesthesia linkage peak. However, a formal test of enrichment did not achieve statistical significance (Fisher's exact test, odds ratio = 2.069, P = 0.08). Mapping known protein-protein interactions from Reactome within this extended set yielded a network that was relatively sparse but included ITGA2 and COL4A1 as hubs within a subnetwork ( Fig. S3).

Finally, recent findings suggest that people with autism spectrum conditions (henceforth, "autism") and savant abilities are more likely to experience synesthesia, while synesthetes as a group show atypical sensory sensitivities similar to those seen in autism ( 34, 35). We thus hypothesized that genetic variants uncovered in synesthetic individuals without autism may show links to genetic pathways implicated in autism. The presence of comorbid neurological conditions (including autism) was an exclusion criterion when recruiting the families for this work ( 20). Three of the 37 variants that tracked with synesthesia status in our families are within genes found in the Simons Foundation AutDB catalog of autism-associated genes: FGA (family 16), HYDIN (family 2), and SLC9A6 (family 11) ( 36). However, the specific genetic variants seen in the synesthesia families ( Table 1) are not shared with the autism cases currently contained in AutDB. Also, the three genes did not represent a significant enrichment (Fisher's exact test, odds ratio = 2.01, P value = 0.20); thus the presence of these variants is not unusual, given the large number of genes associated with autism. Four of the 109 coexpressed genes were previously associated with autism ( Fig. S3), although, again, this did not represent significant enrichment (Fisher's exact test, odds ratio = 2.084, P = 0.13).

Discussion

Synesthesia represents the outer edges of natural variation in sensory perception. In this study, we identified rare genetic variants perfectly cosegregating with the trait in three unrelated multigenerational families with at least five people affected with sound-color synesthesia. A core set of six genes was related to axonogenesis, the process by which immature neurons send out their primary process to connect with other brain regions by following secreted guidance cues. Among other cortical sites, these genes were expressed throughout development in auditory and visual cortex, consistent with a potential role in developmental processes spanning both brain regions. Using a network approach, we uncovered six additional genes with similar neural expression patterns that fall within suggestive linkage regions originally identified in screens of larger numbers of families, which could be further investigated in follow-up studies ( 20).

Potentially supporting emerging data that synesthesia shares some phenotypic and mechanistic features with autism, the overrepresented ontologies fit with data from the autism neural transcriptome. A 2011 study of 17 autism cases and 19 controls generated a weighted coexpression network from microarray data from three brain regions ( 37). The set of genes most closely correlated with autism status was enriched for down-regulated genes related to neuronal projection. On the other hand, we did not see significant convergence between our synesthesia findings and published data on autism when examining specific genes or the rare mutations themselves. Thus, etiological overlaps might be most apparent at the level of biological processes rather than at the level of individual genetic loci. With further investigation in model systems, these candidate genes for synesthesia may provide molecular support for hyperconnectivity between brain regions as an underlying mechanism.

The segregating mutations in these three families did not fall within regions suggested in the 2009 linkage-mapping study of 43 families of varying size; it is very likely that the current families did not contribute to the suggestive signals highlighted in that prior investigation ( 20). Note that we did not filter our list of rare variants to select exceptionally damaging mutations, e.g., by using high CADD (Combined Annotation-Dependent Depletion) or haploinsufficiency scores ( 38). While such approaches are appropriate for neurodevelopmental disorders, synesthesia is not a disorder and is unlikely to reduce biological fitness, so we do not expect causative variants to be subject to negative selection. The six candidates also did not fall within linkage regions suggested by Tomson and colleagues; however, that previous study focused on a different form of synesthesia (sequence-color synesthesia), and the reported linkage evidence did not meet strict thresholds for significance ( 19). It is too early to tell whether different forms of synesthesia share underlying mechanisms (most recent studies have focused on grapheme-color synesthesia), although that is probable given that many synesthetes experience multiple varieties ( 7).

The top candidates we identified include the well-studied SLIT/ROBO chemoattractant system plus other genes with roles in shaping neuronal processes. In family 11, we identified rare segregating variants in SLIT2 and ROBO3, which regulate axon guidance through separate signaling pathways ( 39). Family 16 contained a variant in MYO10, which encodes an actin-based motor protein that acts in neurite growth cones ( 40). Although the MYO10 variant is synonymous, it results in a rare cysteine codon with no corresponding transfer RNA genes in humans ( 41). Such nonoptimal codon usage can reduce mRNA stability and slow ribosomal progression, disrupting translational regulation ( 41, 42). We observed a variant in ITGA2, encoding an integrin receptor subunit, which segregated with sound-color synesthesia in family 2. While studies of the functions of ITGA2 in neurodevelopment are sparse, it acts as a heterodimer with integrin β1 in embryonic retinal cells and has been observed in adult rat hippocampal mossy fiber tracks ( 43, 44). Integrin receptors on axon growth cones are a key mechanism by which developing neurons sense and respond to chemoattractants in the extracellular matrix ( 44). Furthermore, COL4A1 (family 11) encodes an alpha subunit of type IV collagen, which binds αβ integrin heterodimers to promote axonal growth and branching ( 45).

Synesthesia is a nonpathological anomaly of sensory integration, and our results suggest that rare genetic variants may shape the outcome of this developmental process within a normal range of experience. There are multiple ways that slight alterations in axonogenesis could lead to hyperconnectivity, such as incorrect length or localization, unusual branching, or subtle changes in morphology. The idiosyncratic sensory associations experienced by synesthetes expand and become more consistent during childhood ( 15). Thus, genetic variants increasing the likelihood of synesthesia may act in concert with early life experiences to form synesthetes' unique secondary mappings (such as C♯ appearing orange, or B♭ as a deep brown) ( 13). Are the mechanisms that create a synesthetic brain developmentally restricted or do they involve processes also relevant in adulthood? That the top candidates from this study are expressed throughout development and are not neuron-specific but are also seen in glia and epithelial cells leaves this question open. The broad expression of these genes in the developing and adult brain fits with the wider synesthesia phenotype, which includes enhanced memory performance as well as altered sensory sensitivity ( 34, 46).

Since studies of the genetic basis for synesthesia are in early stages, there were limitations to our approach and dataset. Only one prevalence study has asked about sound-color synesthesia, confirming its presence in 1 of 500 UK college students surveyed ( 7). This conflicts with a survey of Dutch and German synesthetes where a much higher percentage reported sound-color associations ( 25). We erred on the side of inclusivity when determining the MAF threshold to use here. Despite this, we note that most of the synesthesia-specific variants we report are rare, falling well below this cutoff. We further focused on variants that perfectly tracked with the phenotype in each family. The families in this study were the largest multiplex families for whom we could obtain sufficient DNA for WES and validation, but they are still relatively small for linkage-based approaches, and we were unable to narrow the segregating variants to a single site per family. Further family-based studies of sound-color synesthesia and other forms will help clarify the genetic architecture and the potential role of altered neuronal morphology.

Over 130 y after the first reports of familial synesthesia, these results provide a molecular starting point for studies addressing the origins of healthy variation in sensory integration. While cellular and animal models will likely prove illustrative, behavioral experiments to test cross-modal perception in animals may elude the field for some time. It remains to be seen if other forms of synesthesia will involve alterations in axon growth and guidance. This study focused on relatively rare genetic variation occurring in families with multiple generations of synesthetes; assessing potential roles of common variation represents an intriguing question for the future.

Materials and Methods

Three families with sound-color (auditory-visual) synesthesia, without a history of drug use or any neurological, ophthalmological, or psychiatric disorder, were identified from the Cambridge Synaesthesia Research Group database. Ethical approval was granted by the Human Biology Research Ethics Committee of the University of Cambridge (Ref: 2011.06). Informed consent was obtained from all participants. Variants in exome-sequencing data were called using the Genome Analysis Toolkit best practices pipeline ( 24). Gene ontology analyses were performed with gProfileR, and human gene-expression data were downloaded from GTEx, the Allen Human Brain Atlas, and the BrainSpan database, while mouse RNAseq data were accessed from Zhang et al. ( 26, 31, 32). The datasets generated during the current study are available upon request from The Language Archive (TLA: https://corpus1.mpi.nl/ds/asv/?0), a public data archive hosted by the Max Planck Institute for Psycholinguistics. An extended description of materials and methods appears in Supporting Information.

Acknowledgments

We thank the families from the Cambridge Synaesthesia Research Group Database for their contributions to this study; Allen Chan and Laura Murphy for assistance with resampling the families; Han Brunner, Joris Veltman, and Alex Hoischen for assistance with exome sequencing; and Anthony Monaco for his contribution to earlier phases of the genetic analysis for these families. Funding was provided by European Commission Grant H2020-MSCA-IF-2015 #704393 (to A.K.T.) and the Hertie Foundation through the Eric Kandel Young Neuroscientists Prize (to S.E.F.). K.S.K., A.V., A.K.T., and S.E.F. were supported by the Max Planck Society. The funders had no role in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript.

Footnotes

Author contributions: A.K.T., K.S.K., S.B.-C., and S.E.F. designed research; A.K.T., K.S.K., A.V., and J.E.A. performed research; A.K.T., K.S.K., A.V., and S.E.F. analyzed data; A.K.T. and S.E.F. wrote the paper; and J.E.A. and S.B.-C. collected synesthesia families.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission. E.M.H. is a guest editor invited by the Editorial Board.

Data deposition: The datasets generated during the current study are available upon request from The Language Archive (TLA: https://corpus1.mpi.nl/ds/asv/?0), a public data archive hosted by the Max Planck Institute for Psycholinguistics. The data are stored under the node IDs MPI1758324# and MPI1815362# and are accessible at https://hdl.handle.net/1839/[email protected] .

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1715492115/-/DCSupplemental.

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Rare variants in axonogenesis genes connect three families with sound-color synesthesia

# data[].attributes.attachment_link.description
Our physical senses are separated not only into distinct experiences but also into specialized regions within the cerebral cortex. Synesthesia is a neurological phenomenon that causes unusual links between sensory experiences, and its molecular basis is completely unknown.

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A Whole-Genome Scan and Fine-Mapping Linkage Study of Auditory-Visual Synesthesia Reveals Evidence of Linkage to Chromosomes 2q24, 5q33, 6p12, and 12p12

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Synesthesia, a neurological condition affecting between 0.05%-1% of the population, is characterized by anomalous sensory perception and associated al...

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Abstract

Synesthesia is a perceptual experience in which stimuli presented through one modality will spontaneously evoke sensations in an unrelated modality. The condition occurs from increased communication between sensory regions and is involuntary, automatic, and stable over time. While synesthesia can occur in response to drugs, sensory deprivation, or brain damage, research has largely focused on heritable variants comprising roughly 4% of the general population. Genetic research on synesthesia suggests the phenomenon is heterogeneous and polygenetic, yet it remains unclear whether synesthesia ever provided a selective advantage or is merely a byproduct of some other useful selected trait. Progress in uncovering the genetic basis of synesthesia will help us understand why synesthesia has been conserved in the population.

Introduction

Synesthesia is a condition present in 2%-4% of the population [1] in which a sensory stimulus presented to one modality elicits concurrent sensations in additional modalities [2]. Synesthesia can theoretically bind any two senses, but research has largely focused on two of the most common variants in which auditory tones and achromatic (colorless) numbers produce vivid and perceptually salient colors. The specificity of these evoked colors remains stable over time within any given individual [3], but the same tone or grapheme doesn't necessarily evoke the same color in different people. Synesthesia has been of interest to scientists for nearly 200 years [4], and while familial linkage analyses show a strong genetic component, the precise genes involved and reasons why synesthesia has been conserved in the population remain unsolved mysteries.

Neural Basis of Synesthesia

The neural substrate of synesthesia has been thoroughly studied in grapheme-color synesthesia (in which numbers and letters evoke colors) using both psychophysical tests and functional imaging. Several groups have demonstrated that simple achromatic graphemes activate both grapheme regions as well as color area V4 (a region of visual cortex that shows a stronger response to colors than to grayscale stimuli) in the brains of synesthetes, which is consistent with the view that synesthetic colors are sensory in nature (i.e., arise through a bottom-up processing stream) [5],[6] as opposed to being high-level cognitive associations, as has been proposed [7]. Predicting this finding of "cross-activation" between grapheme and color regions, Ramachandran and Hubbard [6] proposed that synesthesia results from an excess of neural connections between associated modalities, possibly due to decreased neural pruning between (typically adjacent) regions that are interconnected in the fetus. Consistent with this suggestion, a number of studies have demonstrated anatomical differences in the inferior temporal lobe near regions related to grapheme and color processing in synesthetes, including increased fractional anisotropy (reflecting increased white matter or coherence of white matter) [8],[9] and increased gray matter volume [9],[10]; increased connectivity has been found in other forms of synesthesia as well [11]. Furthermore, Brang and colleagues recently demonstrated that color area V4 becomes active as early as 110 ms after viewing achromatic letters and numbers, signifying that synesthetic colors follow a similar time-course in the brain as colors evoked from the retina [12]-[14].

Adding support to the sensory cross-activation hypothesis, Ramachandran and Hubbard [6],[15] demonstrated that synthetically induced colors can lead to perceptual texture segregation; recent results by Jamie Ward and colleagues [16] lend additional empirical evidence for this view. Ramachandran and Brang also noted [17] that the same number can take on multiple colors in some synesthetes (e.g., the numbers 7 and 8 in ) or even the visual appearance of textural qualities like metallic and smooth [18], further suggesting that synesthesia is a bottom-up sensory phenomenon. Nevertheless, top-down influences (e.g., attention, context, etc.) must also play a significant role in synesthesia as first shown by Ramachandran and Hubbard [15] using Navon figures; that is, if the subject sees a large 5 made up of small 2 s, the evoked color will change depending on whether the subject focuses on the local or global image (i.e., the "trees" or "forest"). How integration of these bottom-up and top-down processing streams occurs is still not known.

Heredity in Synesthesia

While a proven genetic basis for synesthesia remains elusive, the phenomenon tends to run in families, as ∼40% of synesthetes report a first-degree relative with the condition [3],[19]. Pedigree analyses of synesthesia suggest high transmissibility from parent to offspring (), yet in at least one confirmed instance, synesthesia is present in only one monozygotic twin [20]. At least 60 different forms of synesthesia have been documented (i.e., different combinations among the senses), reflecting the extreme heterogeneity of the condition, and one could easily assume that each type of synesthesia is caused by a unique gene or set of genes. However, the specific form of synesthesia an individual expresses can vary within families [19], suggesting the genetic undertones impose a predisposition to synesthesia but not its expression. Indeed, individuals with one type of synesthesia are much more likely to have another as well, an observation that was adduced by Ramachandran and Hubbard [15] as support for the idea that the defective pruning gene or genes confer a general propensity to linking unrelated sensations or even concepts. Further, while individual synesthetes often display multiple forms of the phenomenon, large-scale factor analyses suggest that some variants co-occur with greater frequency within a single individual, suggesting that some forms are more highly related (i.e., local "clustering" or "islands" of synesthesia types), which is suggestive of a common origin [21]. However, non-clustering forms still co-occur with greater frequency than predicted by prevalence rates in the general population [22], significantly impeding theories of single genetic markers and the notion of independence among different forms of the condition.

Previous studies examining the prevalence of synesthesia found a significant gender gap with a 6∶1 ratio of female synesthetes to males, leading to the suggestion that synesthesia was an X-linked condition [23]. However, prevalence studies conducted using random sampling have shown an even distribution of synesthesia among the genders, suggesting the discrepancy was based on methodological flaws and self-report biases in earlier studies. Subsequent research on the genetics of synesthesia has unfortunately not clarified which genes underlie the phenomenon. Examining the relationship between synesthesia-like hallucinogenic experiences and serotonin 2A receptor coding on chromosome 13, Brang and Ramachandran [24] suggest that synesthesia might occur from over-expression of this gene, producing higher receptor density. However, direct investigations using a whole-genome linkage scan [25] and a family-based linkage analysis [26] each localized distinct loci that overlapped neither with the region suggested by Brang and Ramachandran [24] nor with one another, suggesting either a lack of power from the derived sample sizes or that the phenomenon is largely polygenic. A polygenic origin is likely, as transmissibility is heterogenous and synesthetes often possess multiple forms, as mentioned above [15],[19]. In light of these conflicting results, research into the genetics underlying synesthesia remains in a nascent state and will require much larger sample sizes and variants of the condition to understand the underlying factors for transmission. Furthermore, evidence suggests that synesthesia may in fact be a graded phenomenon in the general population, creating the possibility that non-synesthetic relatives of synesthetes show endophenotypes of the condition, complicating the use of family linkage analyses.

Why Was the Gene Conserved?

Epiphenomenal

Before asking why a synesthesia gene might have been preserved through evolution, one first must consider the possibility that synesthesia may likely be merely epiphenomenal, and that the gene(s) involved may have served some totally unrelated purpose. It is also possible that the gene(s) may have been retained simply because they did not incur a great enough cost to be purged by selection, and could be an example of an evolutionary spandrel. Another possible explanation is that synesthesia simply represents the tail end of a normal distribution of cross-modality interactions present in the general population [15],[23]. Partial evidence supporting this idea comes as sensory deprivation and deafferentation (i.e., loss of sensory input through the destruction of sensory nerve fibers) can lead to synesthetic-like experiences. For example, after early visual deprivation due to retinitis pigmentosa, touch stimuli can produce visual phosphenes [27], and after loss of tactile sensation from a thalamic lesion, sounds can elicit touch sensations [28]. More remarkably, arm amputees experience touch in the phantom limb merely by watching another person's hand being touched [29]. Long-standing evidence has also demonstrated that hallucinogenic drugs can cause synesthesia-like experiences (for a review see [30]), suggesting the neural mechanism is present in all or many individuals but is merely suppressed. However, no research has yet established the relationship between these acquired forms to the genetic variant and whether the same neural mechanism is responsible for both.

Creativity and Metaphor

The question of whether the synesthesia gene(s) may have a "hidden agenda" like the sickle cell anemia gene has with malaria resistance, and whether that agenda may be "creativity and metaphor", was first raised by Ramachandran and Hubbard [15]. Subjectively, synesthetes report these experiences are largely positive and engender facilitative benefits for creative aspects of their lives. Studies have indeed confirmed the increased incidence of synesthesia among artists [31] and, relative to controls, synesthetes report spending more time engaged in creative activities [32]. However, the nature of the link between synesthesia and creativity (including metaphor) remains elusive given that synesthesia involves arbitrarily connecting two unrelated things (e.g., color and number), whereas there is a non-arbitrary conceptual connection between, say, Juliet and the sun (of Romeo and Juliet). One potential solution to this problem comes from realizing that any given word has only a finite set of associations (e.g., the sun is warm, nurturing, radiant, bright, etc.). The overlapping region among halos of associations between two words (e.g., Juliet and the sun; both are radiant, warm, and nurturing)-the basis of metaphor-exists in all of us but is larger and stronger in synesthesia as a result of the cross-activation gene; in this formulation synesthesia is not synonymous with metaphor, but only that the gene which produces synesthesia confers a propensity towards metaphor. While the link between synesthesia and creativity has received remarkable interest over the last decade, research has not yet directly demonstrated any causal relationship between the two and so the argument, at this point, remains seductive and compelling but not conclusive.

Sensory Processing and Cognitive Abilities

Recently, research has confirmed numerous cognitive and perceptual benefits that are associated with synesthesia, any of which could be argued to produce a stronger basis for selection. As extreme examples of these benefits, two well-characterized savants have demonstrated remarkable memory abilities based on their synesthesias: Daniel Tammet used his synesthesia to memorize pi to 22,514 digits and Luria [33] described an individual ("S") with a prodigious memory based largely on using synesthetic associations evoked by the items to be memorized. Such cases have led to the suggestion that synesthesia may exist as a foundation for savantism, and while Tammet and S are at the extreme end of the spectrum, synesthetes as a group also have demonstrated improved memories relative to controls, particularly for items related to their synesthetic experiences (e.g., memory for phone numbers is aided by number-color associations) [6],[15],[34],[35].

Outside the realm of memory research there is accumulating evidence of enhanced sensory processing in synesthesia as well. Specifically, grapheme-color synesthetes show enhanced detection of colors on a perceptually low-level visual test of parvocellular processing (K. Wagner, D. Brang, V. Ramachandran, K. Dobkins, unpublished data) paralleled by the finding of differences in early visual processes to simple colors using visual-evoked potentials [36] well before the time period in the brain in which synesthesia engages. Furthermore, number-color synesthetes are also more sensitive at discriminating very similar colors [37]. These early perceptual effects suggest that synesthesia is associated with increased processing of color information; however, it remains possible that these differences in color processing are not due to synesthesia itself but are merely caused by synesthetes' excessive experience with colors. Confirming these sensory enhancements in a different form of the condition, Banissy and colleagues demonstrated that mirror-touch synesthetes (individuals who experience tactile sensations on their own body while watching someone else being touched) possess increased tactile acuity [37]. Lastly, individuals who experience auditory sounds evoked by visual motion process rhythmic visual stimuli more accurately than controls and in a manner similar to how non-synesthetes process auditory information [38].

These demonstrations of enhanced processing of sensory information suggest a provocative evolutionary hypothesis for synesthesia: synesthetic experiences may serve as cognitive and perceptual anchors to aid in the detection, processing, and retention of critical stimuli in the world; in terms of memory benefits, these links are akin to a method of loci association. In addition to facilitating processes in individual sensory modalities, synesthetes also show increased communication between the senses unrelated to their synesthetic experiences, suggesting that benefits from synesthesia generalize to other modalities as well, supporting their ability to process multisensory information [39]. Furthermore, others have argued that synesthesia is the direct result of enhanced communication between the senses as a logical outgrowth of the cross-modality interactions present in all individuals [40]. Taken collectively, these data suggest that synesthesia may be associated with enhanced primary sensory processing as well as the integration between the senses. However, to fully understand this relationship, identification of the genetic component involved and evidence of selection on these genes will be required to determine whether synesthesia serves to enhance normal sensory processing.

Towards a Solution

Synesthesia is associated with a wide variety of conceptual and perceptual benefits, suggesting that the gene(s) involved may have been selected for because of a hidden agenda. Whether this is true, and if so, what that agenda may be, beyond specific enhanced cognitive and sensory benefits, remains to be explicated (For a further exploration of the remaining scientific questions, please see Box 1). The picture is complicated not only by the fact that there appear to be many degrees and many variants of the phenomenon (as there is in dyslexia, autism, etc.), but also by the extraordinary phenomenological experiences of some synesthetes (e.g., "5 is not only red but has a grainy texture to it"). But it is precisely because synesthesia seems to occupy that mysterious boundary zone between elementary sensations on the one hand and higher level abstractions (such as gender and personality, and even emotions; e.g., sandpaper evoking the sensation of jealousy [41]) on the other that the phenomenon intrigues us and provides an experimental lever for investigating high-level mental processes. Indeed, Ramachandran and Hubbard [15] pointed out that number personifications in synesthesia (e.g., 5 is male, 7 is female, etc.) may reflect an amplification of the universal human propensity to "binarize" the world to economize cognitive processing.

In summary, synesthesia is a highly heritable phenomenon that is associated with numerous benefits to cognitive processing, potentially underscoring a basis for why this condition has survived evolutionary pressures. Research into synesthesia is now passing its bicentennial anniversary in science, and understanding both the mechanisms underlying the phenomenon and the reasons for its selection are finally at a point in which synesthesia can inform our understanding of cognitive and perceptual processes in the general population. To appropriately understand this condition and its relation to normal cognition will require both technically and intellectually diverse contributions from all areas of biology. In sum, this research suggests that synesthesia, far from being a "fringe" phenomenon as formerly believed (or that it is purely "conceptual" or associative in nature), can give us vital clues toward understanding some of the physiological mechanisms underlying some of the most elusive yet cherished aspects of the human mind.

Footnotes

The authors have declared that no competing interests exist.

No specific funding was received for this article.

References

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Survival of the Synesthesia Gene: Why Do People Hear Colors and Taste Words?

# data[].attributes.attachment_link.description
Synesthesia is a perceptual experience in which stimuli presented through one modality will spontaneously evoke sensations in an unrelated modality. The condition occurs from increased communication between sensory regions and is involuntary, automatic, and stable over time.

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Summary

Synesthesia is a condition in which stimulation of one sensory modality causes unusual experiences in a second, unstimulated modality. Although long treated as a curiosity, recent research with a combination of phenomenological, behavioral, and neuroimaging methods has begun to identify the cognitive and neural basis of synesthesia. Here, we review this literature with an emphasis on grapheme-color synesthesia, in which viewing letters and numbers induces the perception of colors. We discuss both the substantial progress that has been made in the past fifteen years and some open questions. In particular, we focus on debates in the field relating to the neural basis of synesthesia, including the relationship between synesthesia and attention and the role of meaning in synesthetic colors. We propose that some, but probably not all, of these differences can be accounted for by differences in the synesthetes studied and discuss some methodological implications of these individual differences.

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# data[].attributes.attachment_link.description
Synesthesia is a condition in which stimulation of one sensory modality causes unusual experiences in a second, unstimulated modality. Although long treated as a curiosity, recent research with a combination of phenomenological, behavioral, and neuroimaging methods has begun to identify the cognitive and neural basis of synesthesia.