The widespread presence of Mayer waves in brainstem sympathetic-related and non-sympathetic-related cells would seem to betray a general tendency of neurons to oscillate at this frequency. We have thus presented an extensive and, hopefully cohesive, discourse evaluating, and evolving the interpretive consideration of, evidence seeking to illumine our understanding of origins of, and insight into mechanisms contributing to, the genesis of Mayer waves. We have predicated our arguments and conjectures in the substance and matter of empirical data, though we have occasionally waxed philosophical beyond these traditional confines in suggesting interpretations exceeding these limits. We believe our synthesis and interpretation of the relevant literature will fruitfully inspire future studies from the perspective of a more intimate appreciation and conceptualization of network mechanisms generating oscillatory variability in neuronal and neural outputs. Our evaluation of Mayer waves informs a novel set of disciplines we term quantum neurophysics extendable to describing subatomic reality. Beyond informing our appreciation of mechanisms generating sympathetic oscillations, Mayer waves may constitute an intrinsic property of neurons extant throughout the cerebrum, brainstem, and spinal cord or reflect an emergent property of interactions between arteriogenic and neuronal oscillations.Mayer waves may synchronize overlapping propriobulbar interneuronal microcircuits constituting the respiratory rhythm and pattern generator, sympathetic oscillators, and cardiac vagal preganglionic neurons. Initially described by Sir Sigmund Mayer in the year 1876 in the arterial pressure waveform of anesthetized rabbits, authors have since extensively observed these oscillations in recordings of hemodynamic variables, including arterial pressure waveform, peripheral resistance, and blood flow. Authors would later reveal the presence of these oscillations in sympathetic neural efferent discharge and brainstem and spinal zones corresponding with sympathetic oscillators. Mayer wave central tendency proves highly consistent within, though the specific frequency band varies extensively across, species. Striking resemblance of the Mayer wave central tendency to the species-specific baroreflex resonant frequency has led the majority of investigators to comfortably presume, and generate computational models premised upon, a baroreflex origin of these oscillations. Empirical interrogation of this conjecture has generated variable results and derivative interpretations. Sinoaortic denervation and effector sympathectomy variably reduces or abolishes spectral power contained within the Mayer wave frequency band. Refractorines of Mayer wave generation to barodeafferentation lends credence to the hypothesis these waves are chiefly generated by brainstem propriobulbar and spinal cord propriospinal interneuronal microcircuit oscillators and likely modulated by the baroreflex. The presence of these waves in unitary discharge of medullary lateral tegmental field and rostral ventrolateral medullary neurons (contemporaneously exhibiting fast sympathetic rhythms [2–6 and 10 Hz bands]) in spectral variability in vagotomized pentobarbital-anesthetized and unanesthetized midcollicular  decerebrate cats supports genesis of Mayer waves by supraspinal sympathetic microcircuit oscillators. Persistence of these waves following high cervical transection in vagotomized unanesthetized midcollicular decerebrate cats would seem to suggest  Vasomotor waves were initially recorded by Stephan en masse retro-arterially transmitted to hemodynamic variables. Magnitude of dynamic arterial blood pressure oscillations were relatively attenuated in the presence of low mean integrated arterial pressure, significant irregularity of the cardiac interval or breathing cycle period, or by intravenous administration of hemoglobin.Several decades successive to the initial characterization of very low frequency oscillations of dynamic arterial blood pressure magnitude and splenic volume by Wagner in 1849 and Henle in 1852 and less than a decade successive to the discovery of respirophasic oscillations of dynamic arterial blood pressure magnitude by Traube (1865) and Hemorrhage-induced emergence of Mayer waves in dynamic arterial pressure magnitude exhibiting marked amplitude may be generated by mechano-unloading of baroreceptors and ensuant disinhibition of supraspinal sympathetic-related microcircuit oscillators residing within the medullary lateral tegmental field and rostral ventrolateral medulla RVLM; , hydrogeInvestigators have provided data suggesting Mayer waves may be generated via dynamic interactions occurring amongst sympathetic-related propriobulbar interneuronal microcircuit oscillators residing within the confines of the brainstem , 1996, s2) enhanced spectral power of very low frequency oscillations in cerebral blood flow volume and mean arterial blood pressure in otherwise healthy subjects  via mechanotransductive propagation through the neural interstitium see . These wAutochthonously generated neural oscillations insufficiently explain emergent genesis of Mayer waves. The majority of investigators concur oscillations of arteriolar diameter  may be conveyed to neurons constituting the sympathetic-related microcircuit oscillators and conveyed to sympathetic neural efferent discharge and hemodynamic oscillations incipiently generate Mayer waves . Intersp1 and T2 sympathetic preganglionic neuronal somata in Nembutal-anesthetized and unanesthetized midcollicularly decerebrated cats, though misinterpreted their data to indicate these oscillations represent Mayer waves. Analogous to our observations, these arterial pressure oscillations exhibited a central frequency significantly less than the central tendency of Mayer waves in cats (∼0.1 Hz), more closely approximated to the frequency of vasogenic autorhythmicity (∼0.03 Hz)  cf., .Vasogenic autorhthmicity and multiplicative pseudo-harmonics thereof may consequently emergently generate analogous oscillations propagating through the perivascular fluid compartment and neural interstitium to neural elements to generate corresponding fluctuations of the somatodendritic membrane, axon hillock, axonal membrane, and neurosynaptic machinery see . MechanoArteriogenic neuronal oscillations deflecting somatodendritic and axonal neuronal membranes may generate nano-oscillatory or micro-oscillatory variability of electrotonically-propagated graded somatodendritic and axonal potentials, by conferring an oscillatory perturbation upon somatodendritic space and time constants cf., , 1952a,b(VGNa+) reflecting the sum of activation †act, inactivation (†inact), and deinactivation (†deinact) time constants:. †VGNa +)((τ)oscillates according to the frequency of oscillations of arteriolar diameter, γ and a subtended amplitude modifiable by the Yaşargilian modulus operator, Д expressing the visco-elastic properties of the neural interstitium, ΛVGNa +)((τ) = Д[†VGNa +)(]sin(2πγτ) + [†(VGNa +)]. Oscillations of voltage-gated sodium channel activation, inactivation, and deinactivation time values, traditionally believed to be invariant, in turn, generate oscillations of maximal neuronal spiking frequency, ψ(τ)max according to. Arteriogenic oscillations propagating through somatodendritic and axonal membranes amplify decomposable nested spectral power through vibrations of cytoskeletal elements, generating powerful oscillations of membrane ion channels and their activation and inactivation kinetics, through vibratory oscillations of covalent bonds and molecular orbitals linking amino acid residues. We accordingly suggest oscillations of the ball-and-chain-like string of amino acid residues inactivatingly gating the voltage-gated sodium channel specifically generates oscillatory perturbations contributing quite powerfully to emergently generating oscillations of action potential discharge by neurons. Arteriogenic neuronal oscillations may generate micro-oscillatory variability of distinct conductances perpendicularly traversing the membrane via hydrophilic channel pores, in effect generating oscillations of dynamic current traversing the neurolemmal phopspholipid bilayer and frequency of action potentials propagating from axon hillock to axon terminal. Current, voltage, and membrane conductances vary interdependently and time-dependently. The presence of distinct isoforms of membrane ion channels belonging within the same family  subjectable to differential modulation by neurolemmal oscillations may constitute a biomolecular substrate by which out-of-phase summation of the oscillations may generate integer pseudo-harmonics of conveyed oscillatory frequency . Let us consider the activation-inactivation-deinactivation cycle time of the voltage gated sodium channel, † efforts . These cC) current  using amperes(A), voltage using volts (V), resistance  using Ohms (Ω), resistivity  using Ohms per meter (Ω/m), magnetic force ) using Tesla, mass using grams or kilograms, force using Newtons or kilograms multiplied by meters divided by seconds squared (kgm/s2), velocity  using meters per second (m/s), acceleration  using meters per seconds squared (m/s2), momentum  using kilograms multiplied by meters divided by seconds (kgm/s), frequency  using Hertz (Hz), period  using inverse seconds (s−1), wavelength  using meters, (m) distance  using meters (m), time  using seconds (s), and energy  using Joules (J). Any of these entities may be expressed as a scalar value, vector, set of vectors, vector field, or set of vector fields. Authors have classically used the dendritic length constant to represent the length along the neurolemmal membrane of the somatodendritic compartment an electrical potential will travel prior to decaying to nil may be represented by the dendritic length constant. This value may be more appropriately termed the somatodendritic length constant,λ . The equation asserts the distance an electrotonically propagated potential, ƛ will travel prior to decaying to zero is constant. We may alternatively express the somatodendritic length constant, ƛ in terms of the square root of the arithmetic ratio of the product of the neuronal radius, r, and the neuronal membrane resistivity,ρm to the scalar double of the intraneuronal cytoplasmic resistivity,ρi:The equation expresses the somatodendritic length constant, ƛ in terms of the square root of the arithmetic ratio of the membrane resistance, σρm represents neuronal membrane resistivity, and ρi represents the intraneuronal cytoplasmic resistivity  + μ where α represents wave amplitude, Arteriolar oscillations constituting the vasogenic autorhythmicity  generatetime variant somatodendritic space function, yielding a time variant somatodendritic space value, Γ ƛ represents the classically derived somatodendritic space constant and central tendency of the oscillations, γ represents the frequency of the vasogenic autorhythmicity. The amplitude of the oscillations varies according to the product of the viscoelasticity Yaşargilian modulus operator, Y and the somatodendritic space value central tendency ƛ. The Yaşargilian modulus operator reflects biophysical mechanotransduction properties of the neural interstitium. AlternativelyWhere Γ(τ) is the We fix the wave with an amplitude ƛ of at time zero. We substitute for ƛ to generate the time variant somatodendritic space value accordingly:We have accordingly generated a continuous monovariate function expressible in two-dimensional Euclidean Cartesian space yielding a time variant somatodendritic space value. Alternatively:The rate of change of the somatodendritic space value with respect to time may be expressed as the first order derivative of the monovariate somatodendritic space function with γ stabilized as a constant:cos(2πγτ)represents the first order derivative of the termsin(2πγτ). Alternatively:Where 2πγThe somatodendritic space function, Γ(τ) may accordingly be expressed simply as the improper integral of the first order derivative of the somatodendritic space function with respect to time, τ:Alternatively:o we may express the somatodendritic space function accordingly:Alternatively, presuming negligible extracellular matrix resistance, σAlternatively:The first order derivative expressing rate of change of the monovariate somatodendritic space function may be expressed accordingly:Alternatively:The somatodendritic space function,Γ(τ) assuming conditions of negligible extracellular matrix resistance, may alternatively be expressed as the integral of the first order derivative of the somatodendritic space wave function:Alternatively:The somatodendritic space function, Γ(τ) may alternatively be expressed in terms of the neurolemmal membrane and intraneuronal cytoplasmic resistivities:Alternatively:We generate the first order derivative of the somatodendritic space function in terms of neuronal membrane and intraneuronal cytoplasmic resistivities accordingly:Alternatively:The somatodendritic space wave function, Γ(τ) may thus alternatively be represented as the integral of the first order derivative of the somatodendritic space wave function:Alternatively:A sinusoidal wave oscillating in Euclidean Cartesian coordinate space  about the horizontal τ axis of zero takes the form, Ŧ(τ) = asin(bτ) + m where a represents wave amplitude, time variant somatodendritic time function, yielding a time variant somatodendritic time value, Ŧ(τ), τ represents the classic somatodendritic time constant and central tendency of the oscillations, γ represents the frequency of the arteriolar oscillations. Oscillatory amplitude varies according with the product of the viscoelasticity Yaşargilian modulus operator, and the somatodendritic time value central tendency τ. The Yaşargilian modulus operator reflects biophysical mechanotransduction properties of the neural interstitium. Alternatively:Where Ŧ(τ) expresses the We fix the wave with an amplitude of τ at τ = 0. We substitute for τ to generate the time variant somatodendritic time value accordingly:We have thus generated a continuous monovariate function expressible in two-dimensional Euclidean Cartesian space yielding a time variant somatodendritic time value. Alternatively:Rate of change of the somatodendritic time value with respect to time may be expressed as the first order derivative of the monovariate somatodendritic with γ stabilized constant:Alternatively:cos(2πγτ) represents the first order derivative of the term sin(2πγτ). The somatodendritic time value function, Ŧ(τ) may accordingly be expressed simply as the line integral of the first order derivative of the somatodendritic time wave function with respect to time,τ:Where 2πγAlternatively:The somatodendritic time value function, Ŧ(τ) may alternatively be expressed in terms of the neurolemmal membrane and intraneuronal cytoplasmic resistivities:Alternatively:We derive the first order derivative of the somatodendritic time function in terms of the neuronal membrane and intraneuronal cytoplasmic resistivities accordingly:Alternatively:The somatodendritic time function, Ŧ(τ) may thus alternatively be represented as the line integral of the first order derivative of the somatodendritic time function:Alternatively:The somatodendritic time function Ŧ(τ), may alternatively be expressed in terms of neurolemmal membrane resistivity:Alternatively:We derive the first order derivative of the somatodendritic time function in terms of neuronal membrane and intraneuronal cytoplasmic resistivities accordingly:Alternatively:The somatodendritic time function, Ŧ(τ) may alternatively be represented as the line integral of the first order derivative of the somatodendritic time function:Alternatively:spinal sympathetic microcircuit oscillators generate these waves (Mayer waves may synchronize overlapping propriobulbar interneuronal microcircuits constituting the respiratory rhythm and pattern generator, sympathetic oscillators, and cardiac vagal preganglionic neurons . Initialse waves . The widse waves .Sir Sigmund Mayer described oscillations of arterial pressure magnitude in anesthetized rabbits exhibiting a lesser frequency compared with respirophasic variations of blood pressure described a few years earlier by Traube in 1865 and Hering in 1869. The origins of Mayer waves remain a mystery. The works of Guyton, Harris, and Andersson in the 1950’s suggested baroreflex or chemoreflex mechanisms may chiefly generate of these oscillations. Authors would later demonstrate spectral power reduction, though persistence, of Mayer waves following sinoaortic denervation or pharmacological ganglionic antagonism, in most experiments, indicating supraspinal and/or spinal microcircuits oscillators may generate this rhythmic activity. Zones which may chiefly generate these oscillations include the medullary lateral tegmental field and RVLM, though our impression lead us to deduce these oscillations may constitute a rhythm expressed by most neurons. Persistence of these dynamic oscillations following cervicomedullary transection, indicates the myelic propriospinal interneuronal circuits may be independently capable of generating Mayer wave-like oscillations. Mayer waves generated intra-neuraxially propagate throughout propriospinal interneurons constituting brainstem and spinal cord microcircuits oscillators and are conveyed via sympathetic nerves to sympathetically innervated arterioles, becoming manifest in dynamic arterial pressure magnitude, peripheral resistance, and blood flow. We propose autochthonous arteriogenic oscillations propagating throughout the neural interstitium generate oscillations of neuronal membranes and neuronal biophysical properties leading to oscillations of electrotonically propagated graded somatodendritic and axonal potentials and neuronal spiking frequency. Out-of-phase summation of arteriogenic very low frequency oscillations may generate integer pseudo-harmonic Mayer waves. We have extended the formalism to characterize the novel subdisciplines of dynamic and quantum neurophysics and describe the behavior of entitities constituting invisible reality. In the words of Emeritus Professor Dr. V. Marchenko, “Everything is Waves.”All datasets generated for this study are included in the article/supplementary material.All studies were in accordance with Karolinska Institutet, Stockholm, and Linköping ethical committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.MG and GG: conception and design, acquisition of data, analysis and interpretation of data, drafting the article and critically revising for intellectual content, and approval of the final version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Understanding gene regulation is important but difficult. Elucidating tissue-specific gene regulation mechanism is even more challenging and requires gene co-expression network assembled from protein–protein interaction, transcription factor and gene binding, and post-transcriptional regulation  information. The miRNA binding affinity could therefore be changed by SNP(s) located at the 3′ untranslated regions (3′UTR) of the target messenger RNA (mRNA) which miRNA(s) interacts with. Genome-wide association study (GWAS) has reported significant numbers of loci hosting SNPs associated with many traits. The goal of this study is to pinpoint GWAS functional variants located in 3′UTRs and elucidate if the genes harboring these variants along with their targeting miRNAs are associated with genetic traits relevant to certain tissues.By applying MIGWAS, CoCoNet, ANNOVAR, and DAVID bioinformatics software and utilizing the gene expression database (e.g. GTEx data) to study GWAS summary statistics for 43 traits from 28 GWAS studies, we have identified a list of miRNAs and targeted genes harboring 3′UTR variants, which could contribute to trait-relevant tissue over miRNA-target gene network.SFMBT2, ZC3HAV1, and UGT3A1) targeted by miRNAs for PBC trait and its tissue association network. After employing Gene Ontology (GO) analysis for PBC trait, we have also identified a very important miRNA targeted gene over miRNA-target gene network, PFKL, which encodes the liver subunit of an enzyme.Our result demonstrated that strong association between traits and tissues exists, and in particular, the Primary Biliary Cirrhosis (PBC) trait has the most significant p-value for all 180 tissues among all 43 traits used for this study. We reported SNPs located in 3′UTR regions of genes  of genes harbor variants can often change the binding affinity of targeting miRNAs playing important roles in protein translation degree. Our study has shown that GWAS variants could play important roles on miRNA-target gene networks by contributing the association between traits and tissues. Our analysis expands our knowledge on trait-relevant tissue network and paves way for future human disease studies. A microRNA (miRNA), a noncoding RNA which contains about 22 nucleotides, plays a significant role on the regulation of gene expression. By binding to the 3′ untranslated regions (3′UTR) of the target messenger RNA (mRNA), which transfers the genetic information from DNA to the ribosome for protein synthesis in RNA polymerase, miRNA suppresses the translation of the targeting mRNA and/or can activate gene expression under certain conditions . Due to Single nucleotide polymorphism or SNP is a change or mutation at a single position in a DNA sequence. The development of human diseases is also affected by SNP(s) on the basis of the observation that SNPs can cause synonymous and non-synonymous changes which affects amino acid sequence or protein function . HoweverPTEN is known to be regulated by miRNAs through competing endogenous RNA networks [In many cancers, the gene networks , 5. SuchGenome-wide association studies (GWAS) has identified and analyzed millions of genetic risk variants which trigger the development of complex diseases , and it Composite likelihood-based Covariance regression Network model (CoConet) is a network method for identification of trait-relevant tissues or cell types by incorporating tissue-specific gene co-expression networks . CoCoNetANNOVAR  is an efThe goal of our study is to identify causative SNPs which could change the binding affinity of miRNAs and genes, which could contribute to trait-tissue relevance over miRNA-target gene network.We obtained summary statistics in the form of marginal z-scores for 43 traits from 28 GWAS studies . These sWe employed MIGWAS , CoCoNet6  and identified biologically relevant tissues. In particular, we identified that 94 out of 180 tissues have significant  association with at least two traits and that 11 traits have significant association with more than 10 tissues  for the PBC trait. We used CoCoNet to calculate the association between traits and tissues in terms of log likelihood Fig. .Fig. 5LiWe examined the PBC trait showing the smallest association p-value reported by MIGWAS to see if there are any SNPs located in 3′UTR regions of genes targeted by miRNAs. To do so, we took the SNP list for the PBC trait and converted them to ANNOVAR variant annotated input format with ANNOVAR package. We obtained 9,890 annotated variants (5279 genes) exclusively located in 3′UTR region of these genes . This gene encodes the liver (L) subunit of an enzyme that catalyzes the conversion of d-fructose 6-phosphate to d -fructose 1,6-bisphosphate, which is a key step in glucose metabolism (glycolysis) [Gene Ontology (GO) analysis on 55 miRNA targeted genes harboring 3′UTR variants with significant tissue-trait association for PBC trait only showed that colysis) .The list of genes and their GO terms identified as the top cluster by DAVID is shown in Table hsa-mir-590 with target relationship of PTEN. Some enrichment analysis results are reported in Table We have also conducted a GO analysis for 22 genes targeted by In our study, we used several cutting-edge bioinformatics tools  to dissecting SNPs reported for 43 traits from GWAS. The MIGWAS reported miRNA enrichment over target gene network for most (31) of traits. The CoCoNet was adopted to analyze the PBC trait for its significant tissue association over gene co-expression network. The ANNOVAR tool was employed to annotate 3′UTR variants class harbored by a list of miRNA target genes associated with Primary Biliary Cirrhosis (PBC) traits.Although it may seem like the tools are interrelated and are three separate experiments, they are indeed connected. We first applied the tool MIGWAS to 43 traits and identified significant biologically relevant tissues. When the p-value association between traits and all tissues were calculated by using MIGWAS for 43 GWAS, we found that the PBC trait had the most significant p-value for all tissues. The CoCoNet experiment then utilized some of the results produced by MIGWAS to provide an output. Specifically, for the retrieved PBC trait result from the MIGWAS experiment, we used CoCoNet to analyze the tissues association over gene co-expression network. Again, we used the PBC trait result reported by MIGWAS in another tool: ANNOVAR. We analyzed the PBC trait for SNPs in 3′UTR regions by converting the SNP list into ANNOVAR variant annotated input, and we retrieved 5279 genes located in 3′UTR regions. We then crossed the 55 genes from MIGWAS with the 5279 genes from ANNOVAR and found 13 genes in common. The experiments might seem unrelated, but the results from MIGWAS analyzed by both CoCoNet and ANNOVAR shows that the 3 tools are indeed connected and are not interrelated.CTLA4, a gene which has an impact on the risk of PBC [PTEN is associated with 9 traits  out of Total 12 traits  do not have MIGWAS association results reported in the analysis. It seems that liver tissue does not appear to have the smallest likelihood with PBC based on the total genes in human genome. We also ran CoCoNet with the targeted gene set of miRNAs enriched over the target network for PBC trait only to calculate loglikelihood, and the result stays the same.PFKL has the highest RPKM  in kidney samples in the RNA-seq which was performed from 4 human individuals in order to determine tissue-specificity of all protein-coding genes [The transcript expression of ng genes .PFKL contains a transcript variant ATP-dependent 6-phosphofructokinase, liver type isoform a which represents the longer transcript and encodes the shorter isoform (a). The CD-Search shows the protein classification of this transcript variant, which is Eukaryotic_PFK domain-containing protein, and finds a specific hit, Eukaryotic_PFK, which shows a high confidence association between the query sequence and a domain model. Phosphofructokinase (PFK) is a key regulatory enzyme that that phosphorylates fructose 6-phosphate in glycolysis. It belongs to the PFK family, evolving from the bacterial PFKs by gene duplication and fusion events and then exhibiting complex behavior. PFK family also includes ATP-dependent phosphofructokinases  and pyrophosphate (PPi)-dependent phosphofructokinases . In addition, protein sequences of Opisthokonta are in the multiple sequence alignment in the Eukaryotic_PFK [otic_PFK .UGT3A, SYNGR, ASAP3, CD80, GXYLT1, IFNAR, KLHL22, POU2AF1, SFMBT2, SIRPB1, SIRPG, ZC3HAV1 and ZNF585B which are in common in the gene list applied from MIGWAS and ANNOVAR.We found 13 genes, ASAP3 encodes a member of a subfamily of ADP-ribosylation factor(Arf) GTPase-activating proteins that its expression level affects cell proliferation and migration, and it called up-related in liver cancer 1 [DDEFL1 (cloned ASAP3) is unregulated in hepatocellular carcinoma (HCC) through microarray analysis. The studies [DDEFL1 had increased expression and had overexpression which increased colony formation in NIH3T3 cells and human hepatoma cell lines [cancer 1 . DDEFL1  studies  showed tll lines .UGT3A1, liver samples have the second highest RPKM among 27 different tissues [In the transcript expression of  tissues .SFMBT2 are polycomb group proteins that bind to methylated lysins in histone tails. The formation of transcription-resistant higher-order chromatin structures at target genes are induced by it so that this gene can repress transcription [SFMBT2 was cloned and designated as KIAA1617 by Nagase et al. [SFMBT2 interacted with the YY1 (600013) transcription when SFMBT2 was expressed from the paternal allele in mouse blastocysts and in mouse embryonic tissues early in development, and later during mouse embryonic development [cription . SFMBT2 e et al. , who obte et al. . Kuzmin e et al.  reportedelopment .ZC3HAV1 encodes a zinc finger protein that can prevent replication certain viruses and inhibit viral gene expression by targeting and eliminating viral mRNAs in the cytoplasm [ZC3HAV1 and called it ZAP in their analysis of gene expressed in human fetal liver [ytoplasm . Yu et aytoplasm  identifial liver . Northeral liver  showed tal liver .Our study tried to understand GWAS data through identifying candidate miRNA-gene pairs over miRNA-target gene network. Using several cutting-edge bioinformatical tools and databases and adopting visualization, we assessed trait-tissue relevance based on tissue-specific gene co-expression information including protein–protein interaction and transcription factor binding evidence. We annotated 3′UTR variants harbored by genes targeted by miRNAs expressed in tissues significantly associated with PBC trait. Our study provides evidence that the association between tissues and traits could be affected by the 3′UTR variants of genes which change binding affinity of targeting miRNAs. The analysis emphasizes the influence of variants on genetic traits and miRNA-targeting gene networks, and thus could contribute to additional studies and detections on human diseases. We think our study provided a valuable approach for elucidating 3′UTR variants which could contribute to genetic traits with tissue relevance in the context of miRNA influential human diseases.Additional file 1: Table S1. Details of the summary statistics of 43 traits from 29 GWAS studies.Additional file 2: Table S2. Tissue association result from MIGWAS.Additional file 3: Table S3. Gene-miRNA target pairs identified by MIGWAS for each trait.Additional file 4: Table S4. Identified 9890 annotated variants exclusively located in 3′UTR region of 5279 genes.Additional file 5: Table S5. Identified SNPs for ten genes with ClinVar variant information.Additional file 6: Table S6. Genes and GO terms in the top cluster for 55 genes with significant tissue and PBC trait association identified by DAVID.Additional file 7: Table S7. Genes and GO terms in the top cluster for hsa-mir-590 with target relationship of PTEN.


IL8 rs4073 any A carriers, compared to TT carriers, were associated with worse progression-free survival (PFS)  and TBK1 rs7486100 TT carriers, compared to any A carriers, were associated with worse PFS in KRAS wild-type (wt) patients , replicating previous findings. Machine learning identified novel associations in genes encoding the inflammasome protein NLRP1 and the ER protein Sarcalumenin (SRL). A negative association between PFS and carriers of any A at NLRP1 rs12150220 and AA for SRL rs13334970 in APD KRAS wild-type patients , which validated in two independent clinical cohorts involving BVZ, MAVERICC and TRIBE. Our findings highlight a key role for inflammation and ER signalling underpinning BVZ + chemotherapy responsiveness.Chemotherapy combined with the angiogenesis inhibitor bevacizumab (BVZ) is approved as a first-line treatment in metastatic colorectal cancer (mCRC). Limited clinical benefit underpins the need for improved understanding of resistance mechanisms and the elucidation of novel predictive biomarkers. We assessed germline single-nucleotide polymorphisms (SNPs) in 180 mCRC patients (Angiopredict [APD] cohort) treated with combined BVZ + chemotherapy and investigated previously reported predictive SNPs. We further employed a machine learning approach to identify novel associations. In the APD cohort  Almost half of patients diagnosed with CRC develop metastatic disease (mCRC). Outcomes of mCRC have improved with introduction of targeted agents such as monoclonal antibodies directed at the epidermal growth factor receptor (EGFR) and the vascular endothelial growth factor (VEGF). Current treatments for mCRC includes 5-fluorouracil-based treatment regimens , with the addition of monoclonal antibodies against EGFR  or VEGF (bevacizumab (BVZ), either as first, second, or third line therapy. Results from phase III clinical trials have demonstrated that the addition of BVZ to cytotoxic chemotherapy improves response rate as well as prolongs PFS and overall survival (OS) of mCRC patients3. Nevertheless, only a subset of patients respond and overall clinical benefit is limited. Moreover, BVZ therapy is associated with a significant side effect profile including hypertension, renal toxicity, bleeding, wound-healing complications, gastrointestinal perforations, and thromboembolic events4.Colorectal cancer (CRC) is the third most commonly diagnosed cancer in both men and women and is associated with high mortality and morbidity5. Hypothesizing that genetically stable endothelial cells or stromal cells play an essential role in anti-VEGF responsiveness, we and others14 have assessed single-nucleotide polymorphisms (SNPs) in several candidate genes for their association with clinical responses. However validation of identified SNPs in independent cohorts often proved to be difficult. For example, among ten previously identified candidate SNPs15, association with treatment outcome could be validated in a larger mCRC cohort only for one SNP in VEGFR2 rs125057589, with C variants for VEGFR2 rs12505758 being associated with shorter PFS and OS. Another predictive SNP that was replicated in several cohorts was rs4073 in the IL8 promoter. Presence of the minor allele A in rs4073 correlates with increased IL-8 production after stimulation of whole blood with lipopolysaccharide16, and was associated with poor response to BVZ11. More recently, it has been reported that AA carriers for rs8602 on MKNK1, a gene that upregulates angiogenic factors, had worse PFS in KRAS wt patients13, and AA carriers for rs4588 on GC, a vitamin D-binding protein, had shorter OS14 in two independent cohorts of patients treated with BVZ + chemotherapy.Resistance to bevacizumab has been linked to several signaling pathways, such as VEGF -associated alterations in angiogenesis, non-VEGF compensatory mechanisms of blood vessel formation, and stromal cell interactions19. The patient characteristics of the APD cohort are given in Table VEGFA rs833061; VEGFR1 rs9513070, rs7993418, rs9582036; VEGFR2 rs1531289, rs2305948; rs11133360; IL8 rs4073; CCL2 rs4586; TBK1 rs7486100) for their association with BVZ + chemotherapy responsiveness, and have identified novel associations using machine learning (ML). ML has emerged as a powerful computational tool which utilizes a variety of analytical algorithms to iteratively learn from data points. It has been successfully employed to investigate complex genomic and proteomic data sets to identify prognostic signatures21. In the present study, we have employed repeated cross-validated Cox penalized regression as a ML approach to select SNPs as candidate biomarkers to predict therapy outcome, and validated novel identified SNPs in two independent clinical cohorts.Notwithstanding these studies, identifying and validating predictive biomarkers for BVZ remains an urgent clinical need. To this end we have performed exome sequencing to assess germline SNPs in a retrospective cohort of 180 mCRC patients treated with BVZ + chemotherapy regimens as part of the ANGIOPREDICT (APD) studyA number of SNP candidates have been proposed for association with response to BVZ + chemotherapy. We selected SNPs based on their biological plausibility, or replication in more than one study Table  and for VEGFR2/KDR rs11133360 C/T, TT carriers had improved OS  in APD, partially in line with our earlier study that any T at this locus was associated with improved PFS in mCRC, renal cell carcinoma and breast cancer patients treated with BVZ (22 and references therein). VEGFR2/KDR rs2305948 C/T mutant carriers, harbouring a Val273Ile substitution that reduces binding of VEGF-A to VEGFR223, did not associate with outcome in APD. Gerger et al.12 reported that this polymorphism showed an association in Asian, but did not associate with outcome in Caucasian patients. VEGFR1/FLT1 rs9582036 and rs7993418 and VEGFA rs833061 did not replicate in APD, while rs9513070 showed a same-sense association with OS as in11 without reaching significance, Table For IL8 rs4073 T/A showed a significant association with PFS in APD: any A carriers for this SNP had worse PFS than TT carriers, , in line with previously reported results in CRC24 and ovarian cancer25. Furthermore, TT carriers for TBK1 rs7486100 A/T, regulatory of tumor-associated macrophages, associated with worse PFS  and OS  in KRAS wt patients from APD, partially in line with results in26, where any T was associated with worse PFS in KRAS wt mCRC patients.Interestingly, two inflammatory genes showed significant associations: CD133/PROM1 rs2286455 were associated to better OS  than any T carriers in APD, partially replicating the results from27, where CD133 rs2286455 CC concomitant with CD133 rs3130 CC where among the favourable allele combinations for PFS in mCRC patients treated with BVZ + chemotherapy.CC carriers of VEGFA rs699946 and rs6999476, VEGFR2/KDR rs125057589, CXCR2 rs223005425, MKNK1 rs860213, GC rs458814 and CD133 rs313027, were in regions not covered by our exome sequencing or not detected in our cohort.Other polymorphisms which were associated with outcome in other BVZ studies, such as CYP4F3 related) departed from Hardy-Weinberg equilibrium and thus was eliminated from the analysis. The remaining 47 SNPs and their characteristics  are given in the Suppl. Table Next, we extended our study in order to identify predictive SNPs across all exomes by machine learning, Fig. . To curbKRAS mutant and wt patients, and like the majority of patients in APD (98%), were treated with first-line BVZ plus chemotherapy. All SNPs were in Hardy-Weinberg equilibrium in both validation cohorts, while genotype frequency was significantly different from the APD cohort in MAVERICC for 7 and in TRIBE for 9 SNPs, , carriers of 2 copies of the rare allele T had significantly better PFS than carriers of any A in both APD  and MAVERICC . Survival plots are shown in Suppl. Fig. S2. Carrying TT at this location reduced the hazard of relapse by ~50% in APD and ~60% in MAVERICC. In further exploratory analyses, we investigated the associations in the KRAS wt versus KRAS mutant patients in the three cohorts. We noticed that the association was conserved in the KRAS wt patients in both APD and MAVERICC , of which the immediate two downstream SNPs are also missense  and the next four SNPs are intron variants . All of these SNPs were highly correlated and co-inherited with rs12150220 . One of the missense variants, rs11651270 (Suppl. Table 28 and polymorphism phenotyping (PolyPhen)29. rs12150220 is predicted deleterious by SIFT and benign by PolyPhen, while the other two mutations are predicted as tolerated by both algorithms. While in this context rs12150220 is likely the causal variant, the association of rs12150220 with PFS could well result from LD with another causal variant.An association between PFS and genotype was also shown for six consecutive downstream SNPs all mapping to SRL , carriers of homozygous rare allele A at this location had shorter PFS than carriers of at least one allele G in both APD  and MAVERICC , see Suppl. Fig. p = 0.003), but comparable for KRAS wt patients (p = 0.34). We thus assessed the same association in the KRAS wt patients. While the association maintained significance for APD and MAVERICC in the KRAS wt patients, any G and AA behaved similarly in TRIBE , Suppl. Table SRL rs13334970 AA carriers have increased risk of relapse compared to any G carriers in KRAS wt mCRC patients.For rs13334970, mapping to 2+-binding glycoprotein, which facilitates Ca2+ sequestration in the sarcoplasmic reticulum30. Together with rs13334970, another 11 SNPs were annotated to SRL, of which one 355 base pairs (bp) downstream (intronic variant rs13334805) was both co-inherited (D’ = 0.99) and highly correlated (r = 0.99) with rs13334970. This suggested that rs13334805 may represent a substitution marker for rs13334970 and that the haplotype involving these 2 SNPs may be causative for the observed association.Sarcalumenin is a CaSTPB rs229592 A/G, the negative association between KRAS wt rs229592 GG carriers and PFS  validated in the TRIBE cohort , however the GG numbers were low in both APD (seven) and TRIBE (three) KRAS wt cohorts, Suppl. Table For NLRP1 rs12150220 and SRL rs13334970 in the overall patient cohort and, based on the above data, specifically in the KRAS wt patients. Figure NLRP1 rs12150220 did significantly better  regardless of their SRL rs13334970 allele, while NLRP1 rs12150220 any A and SRL rs13334970 AA carriers had significantly worse PFS , with all other combinations as baseline (concomitant NLRP1 rs12150220 any A and SRL rs13334970 any G). Suppl. Fig. NLRP1 rs12150220 TT carriers,  and worse outcome for NLRP1 rs12150220 any A and SRL rs13334970 AA carriers, , but not for the overall patients in TRIBE, . As expected from the above exploratory analysis, this association validated in both MAVERICC KRAS wt  and TRIBE KRAS wt , Fig. NLRP1 rs12150220 any A/SRL rs13334970 AA genotype, we also conducted an analysis of the combined datasets , Fig. p < 10–4), Suppl. Table KRAS wt patients, the NLRP1 rs12150220 any A / SRL rs13334970 AA carriers showed a remarkably shorter PFS than the other two genotype combinations with better outcomes  and also shorter OS .We finally looked at the combination of BE, Fig. . In the VEGFR2/KDR rs11133360 and CD133/PROM1 rs2286455, and for two SNPs in pro-inflammatory genes: IL8  and TBK1 . Of note, IL8 rs4073 represents one of the few SNPs that have been replicated in more than one metastatic colon cancer study. IL8, besides showing angiogenic activity, is a major mediator of the inflammatory response. IL8 rs4073 A carriers, which associate with worse outcomes, exhibited significantly higher baseline IL8 serum levels in a cohort of KRAS mutant mCRC patients24. TBK1 (NF-κB-Activating Kinase) plays an essential role in regulating inflammatory responses, as it associates with TRAF3 and TANK to activate NF-κB and phosphorylates interferon regulatory factors (IRFs). This activity allows nuclear translocation of the IRFs leading to transcriptional activation of pro-inflammatory and antiviral genes including IFNA and IFNB. Hence differences in inflammatory signaling in the tumour microenvironment appears to play a prominent role in responses to BVZ plus chemotherapy, as recently also identified by next generation sequencing and immunoprofiling analyses of metastatic CRC tumors31.In this study we have investigated previously discovered SNPs associated with BVZ-responsiveness, and used a machine-learning approach to select new candidate germline SNPs. We have used the germline SNP data of 180 mCRC patients treated with BVZ plus chemotherapy, obtained with exome sequencing in the APD project, to replicate SNPs that have been proposed as candidate biomarkers for response to BVZ plus chemotherapy in other studies. Of 11 variants assessed, we could replicate statistically significant same-sense association between the SNP and treatment response (PFS or OS) for NLRP1 rs12150220 and SRL rs13334970, were validated in the MAVERICC cohort for the overall patient cohort, one of which also encoding for a pro-inflammatory gene (NLRP1). These associations were conserved in the KRAS wt patients in both APD and MAVERICC, but partially lost (NLRP1 rs12150220) in the MAVERICC KRAS mutant patients. Interestingly, when combining the effects of these two SNPs, we found a negative association between PFS and NLRP1 rs12150220 any A and SRL rs13334970 AA concomitant bearers that validated in both MAVERICC and TRIBE cohorts for KRAS wt patients, and in the combined cohorts. While the polymorphism SRL rs13334970 has a statistically different distribution of genotypes in TRIBE compared to APD for the overall patients , the two cohorts are actually comparable for the KRAS wt patients only, for this same polymorphism, . Therefore, our finding that the combination of NLRP1 rs12150220 and SRL rs13334970 only validated in the TRIBE KRAS wt patients , patients with KRAS mutant tumors had less benefit from BVZ than KRAS wt patients in TRIBE32, which may also explain our findings. Although NLRP1 rs12150220 and SRL rs13334970 did not associate with survival in the chemotherapy-only-treated mCRC patients of the APD cohort, the small number of patients (n = 16) warrants further validation in a larger chemotherapy-only treated group.Of the 34 novel SNPs selected by ML from the APD cohort which were assessed for validation in two independent cohorts, two SNPs, NLRP1 is a missense variant at amino acid 155 (His to Leu) of NLRP1 (NLR Family Pyrin Domain Containing 1). This protein mediates inflammasome activity in response to damage-associated signals through activation of Caspase-1, playing a key role in innate immunity and inflammation. Following activation, NLRP1 can directly interact with Caspase-1 to form a functional inflammasome, a molecular complex that participates at maturation and release of cytokines including interleukin-1β33. NLRP1 also collaborates with Apoptotic Peptidase Activating Factor 1 (APAF1) to induce caspase activation and apoptosis in intact cells34, suggesting interaction between host defence and apoptosis machinery, presumably allowing for coordination of cell death and host defence33. Interestingly, among the SNPs that were outlined as strongly associated with PFS by our ML approach, rs7104785 mapped to PIDD (p53-induced protein with a death domain). PIDD activates Caspases-2, -3 and -7 and is structurally similar to NLRP1 C terminus in that an LRR (leucine-rich repeats) and a CARD (caspase activation and recruitment domain), flank the site of proteolysis35. However, the association between this variant and PFS (data not shown) could not be replicated in the two validation cohorts.rs12150220 on SRL , a Ca2+-binding glycoprotein, which facilitates Ca2+ sequestration in the sarcoplasmic reticulum30, a subcompartment of Endoplasmic Reticulum (ER)36. ER is the major site of calcium storage and protein folding. Misfolded protein aggregates trigger ER stress, known to produce pro-inflammatory signals, and to activate stress signalling and apoptosis37. Interestingly, senescent SRL knock-out mice exhibited increased ER stress38 suggesting SRL has a role in ER stress signalling. SRL rs13334970 is coinherited and highly correlated with another intronic variant SRL rs13334805. Intronic variants can affect the phenotype in many ways, for example by disrupting intron transcription regulatory motifs, inclusion of pseudo-exons or else competition with natural splice sites, possibly leading to altered SRL protein levels or function39.The second new germline SNP emerging from this study, rs13334970, maps to NLRP1 rs12150220 and SRL rs13334970, the associations for the other 32 SNPs, that were tested in the two validation cohorts, could not be replicated. However, one key difference that may preclude a direct comparison of the cohorts is the chemotherapy backbone. While the treatment was homogeneous across the present TRIBE and MAVERICC subgroups (FOLFIRI + BVZ), most patients in APD had an oxaliplatin-based chemotherapy backbone. Differences also exist within TRIBE and MAVERICC regarding tumor location (in MAVERICC more patients had their primary tumour on the right side) and number of metastases (MAVERICC had less patients with 2 or more metastases). Furthermore in MAVERICC, most patients did not have their primary tumour resected, Table 40, and allelic frequencies of polymorphisms may differ between ethnic groups and influence clinical effects12. Despite the differences across the three subgroups, it is noteworthy that PFS associations for the SRL and NRLP1 combination were consistent across the KRAS wt patients in all three cohorts. We have limited our feature selection approach to a manageable number of plausibly associated SNPs, of but it is not excluded that other clinically relevant variants could be detected and validated using less stringent selection criteria.A limitation to our findings is that, apart from NLRP1 rs12150220 and SRL rs13334970, our findings nevertheless highlight the importance of germline variations in genes encoding for pro-inflammatory proteins and ER proteins in responses of mCRC to BVZ + chemotherapy. Further validation of these SNPs, including using a larger chemotherapy-only group, may be warranted to convincingly demonstrate the predictive vs. prognostic potential of the identified SNP combination. Specifically, this study indicates that KRAS wt patients bearing the less favourable combination for the two SNPs discussed (AA for SRL rs13334970 and any A for NLRP1 rs12150220) should not be considered for first-line treatment with chemotherapy plus BVZ, they should rather receive chemotherapy plus an anti-EGFR for example (subject to further research), while KRAS wt patients carrying TT for the inflammasome-related gene NLRP1 rs12150220 could benefit from first-line chemotherapy plus BVZ. Our study also highlights the interest of ML approaches in identifying novel genomic biomarkers of drug responsiveness and the importance of clinical validation of genetic variation findings.Our study is limited by the fact that only a relative small cohort of chemotherapy-only treated patients were included in the Angiopredict study, which prevents from concluding on the predictive vs prognosic value of the signature. Through validation of previously identified SNPs, and identification of novel SNPs on 17 and a multi-center subgroup of patients selected from the CAIRO2 trial41. A total of 180 patients were treated with BVZ + chemotherapy and 16 patients - with chemotherapy-only.Patients with advanced  CRC receiving chemotherapy alone or in combination with BVZ  between July 2004 and April 2012 were included in this analysis. The data were retrospectively collected by reviewing patient records within four different European cohorts (Table http://www.fmwv.nl and www.federa.org) and the Commissie Regelgeving in Onderzoek (COREON), in close cooperation with BBMRI-NL and patient organisations.Informed consent was obtained from each patient and the study was carried out in accordance with the relevant guidelines and regulations effective for the 3 participating study centers. Specifically, ethical review and approval of health-related research studies which are not clinical trials of medicinal products for human use as defined in SI 190/2004 was undertaken by the Research Ethics Committee of Beaumont Hospital, RCSI Hospital Group in Ireland. The study was approved by the Medical Ethics Commission of the Faculty of Medicine in Mannheim, Heidelberg University in Germany. The collection, storage, and use of archival tissue and patient data were performed in compliance with the Code for Proper Secondary Use of Human Tissue in The Netherlands (2011), developed by the standing committee of the FEDERA  and wt patients. The second validation cohort consisted of 215 mCRC patients treated with first-line FOLFIRI + BVZ from the open-label, phase 3, randomized TRIBE study32, comprising both KRAS mutant  and wt patients. In both validation cohorts, genomic DNA was extracted from blood samples using the QIAmp DNA easy kit  and then genotyped through the OncoArray.Germline mutations have been determined using the OncoArray, a customized array manufactured by Illumina  including approximately 530 K SNP markersGermline SNPs in APD were analysed by exome-sequencing of normal tissue from 196 patients. We designed a custom exome capture kit, which in addition to the regular exome also captured promoter regions and 5′ or 3′UTRs from a number of key angiogenic factors, covering ~14 K additional SNPs. We performed whole-exome sequencing using the Nimblegen SeqCapV3 exome capture kit (Roche Sequencing Inc.) applied to the Illumina HiSeq2000 sequencing platform (in a 2 × 100 bp paired-end run).45. Picard (v1.43) was used to remove PCR duplicates, resulting in an average coverage per sample of 37 ± 25X. The Genome Analysis Tool Kit (GATK v3.3)46 was used for local realignment around insertions and deletions and base recalibration. After this quality assessment, mapped germ-line sequencing data were available for 196 patients and an initial number of 441.440 germline SNPs were called. Common germline SNPs were selected using the following criteria: (1) The SNP had to be present in at least 10% and less than 100% of all the patients. (2) The SNP had to be present in at least 5% of the European individuals of the 1000 genomes project. (3) The position of the SNP had to be covered in at least 90% of the patients. 4) The SNP was annotated with a unique gene using Variant Effect Predictor (VEP) 8.147. 74.648 final SNPs responding to the aforementioned criteria remained in the analysis. In the validation cohorts, SNPs that were not covered in at least 80% samples were excluded from analysis.In APD, on average 40 ± 20 million reads per sample were generated. The raw sequencing reads were mapped to the human reference genome (NCBI37/hg19) using Burrows-Wheeler Aligner (BWA v0.5.8a)49 and Elastic Net50, which combines the L2 regularization (used in ridge regression) and L1 regularization (used in LASSO). Both Lasso and Elastic Net are efficient methods to perform variable selection in high-dimensional data settings with relatively few observations50, as the case is here. The Elastic Net algorithm depends on a parameter α comprised between 0 and 1. The number of selected variables (SNPs here) increases when α is close 0, decreases as α approaches 1 and LASSO is performed when α = 1. The value of α was set to 0.5 for this study.To select candidate SNPs from 74.648 featuring SNPs, a machine learning (ML) approach based on cross-validated Cox penalized regression was applied, with PFS as outcome variable. Two penalized regression algorithms were used: LASSOglmnet. Each three-fold cv Cox regression repeat selects a list of SNPs that result in a minimum mean cross-validated error. The cv method of penalized regression performed repetitively on smaller fractions of the dataset selects the features that are correlated to the outcome (PFS) without over-fitting to our specific sample set. For LASSO, where fewer variables per repeat are selected (on average 21 germline SNPs), variables selected in more than 250 of 1000 cv repeat models were reported at the end of the process. Elastic Net tends to select considerably more variables: in our case (α = 0.5), on average 184 variables were selected per cv repeat. Therefore, to limit the selected variables to the most correlated over the entire dataset, only variables selected in 700 or more cv repeat models were aggregated and reported at the end of the process,  Cox LASSO and Elastic Net regression respectively were repeated on 1000 random subsets of 90% of the samples, using the Bioconductor R package PFS was the primary end-point of the analysis and was defined as the time from start of treatment (chemotherapy + BVZ or chemotherapy-only) to relapse (progressive disease) or death from any cause, whichever occurred first. Patients stopping BVZ therapy due to other reasons than progression or death were censored at date of treatment stop. OS was defined as time from start of BVZ to death from any cause.st vs grouped 2nd and higher), chemotherapy backbone administered together with BVZ ] for the retrospective APD cohort. For the patients in the validation cohort MAVERICC, Cox models were adjusted for age, ECOG performance status, number of metastases, and resection of the primary tumor. For the patients in the validation cohort TRIBE, Cox models were adjusted for age, sex, ECOG performance status, primary tumour site, resection of the primary tumour, liver limited disease, adjuvant chemotherapy, BRAF status, and RAS status. For each of the candidate SNPs, HR and CI were generated using codominant, dominant and recessive models for the discovery and validation cohorts, respectively. The Wald p-values  presented for Cox models correspond to the significance of the Wald test across the three genotype groups  or the two genotype groups for the dominant and recessive models. For each HR specifically, the order of significance of the HR being different from 1 is also given, representing the probability p that the estimated Cox model coefficient could be zero. The order of magnitude of p is given by asterisks in the tables. The threshold for all p-values was set to 0.05.Cox proportional hazards regression analysis (Cox models) were used to correlate each SNP selected by ML with PFS and estimate genotype-specific hazard ratios (HR) and 95% confidence intervals (CI), adjusting for the available covariates  cohort, our study highlights the importance of inflammatory signaling in the tumor microenvironment in the clinical response of metastatic colorectal cancer patients to the angiogenesis inhibitor bevacizumab. From a methodological perspective, our study highlights the significance and demonstrates the limitations of machine learning approaches for the identification of novel genomic biomarkers of therapy responsiveness. From a clinical perspective, our study identifies a novel combination of two germline SNPs that are associated with unfavorable responses to bevacizumab plus chemotherapy, a finding that was validated in two independent clinical cohorts for Supplementary Information .Supplementary Table S1.


Loeys-Dietz syndrome (LDS) is a systemic connective tissue disease (CTD) associated with a predisposition for intestinal inflammation, food allergy, and failure to thrive, often necessitating nutritional supplementation via gastrostomy tube. Poor wound healing has also been observed in in some patients with CTD, potentially increasing the risk of surgical interventions. We undertook to determine the safety and efficacy of gastrostomy tube placement in this population.We performed a retrospective cohort study of 10 LDS patients who had a total of 12 gastrostomy tubes placed.No procedural complications occurred, although one patient developed buried bumper syndrome in the near post-procedural time period and one patient had a small abscess at a surgical stitch. Most patients exhibited improvements in growth, with a median immediate improvement in BMI Z-score of 0.2 per month following the institution of gastrostomy tube feedings. Those with uncontrolled inflammation due to inflammatory bowel disease or eosinophilic gastrointestinal disease showed the least benefit and in some cases failed to demonstrate significant weight gain despite nutritional supplementation.Gastrostomy tube placement  is a generally safe and a reasonable therapeutic option for patients with LDS despite their underlying CTD. TGFBR1) and transforming growth factor β receptor II (TGFBR2) genes  [Over 200 disorders have been identified that affect the connective tissue, including a number of genetic disorders that result from single gene mutations. First described in 2005, Loeys–Dietz syndrome (LDS) is an autosomal-dominant connective tissue disorder most commonly caused by mutations in the transforming growth factor β receptor I TGFBR and tranctively) , 4.Infants and children with LDS frequently present with failure to thrive. The cause is likely multifactorial and may include the impact of repeated surgical interventions and hospitalizations, increased baseline caloric expenditures in patients with inadequately treated asthma and eczema, and unrecognized food allergies and/or intestinal inflammation that result in both increased expenditures and decreased nutrient absorption. Indeed, LDS patients with concomitant food allergy have significantly lower BMI than both normal and children with LDS who do not have food allergy . AdditioThis study was approved by the University’s institutional review board. We performed a retrospective cohort study of all patients with a genetically confirmed diagnosis of LDS Types 1 and 2 seen at our institution through December 12, 2017.The records of 182 Type 1 and 2 LDS patients were evaluated. Eleven (6%) have undergone gastrostomy tube placement as part of their clinical care. Original records regarding gastrostomy tube placement were not available for one patient who has been excluded from further discussion. Patient characteristics are listed in Table BMI Z-score based on CDC growth chart (or weight/length Z-score based on WHO growth chart for patients less than 2 years old) was calculated at a physician visit just prior to placement, and again at a physician visit after placement, but at least 2 months post-placement , and are shown in Fig. After a median follow-up of 6.2 years (considering only follow-up after the second gastrostomy tube placement for the two patients who received two tubes), all patients had improvement in their BMI Z score over the time period they were receiving feeds through the gastrostomy tube, except for the two patients with IBD. Overall, the BMI Z-score improved a median of 0.2 per year (range − 1.3 – 7.7) for this time period. 60% (7/12) of gastrostomy tube placements resulted in an increase in BMI Z-score in the short term post-operative period. Long-term, 70% (7/10) had improvement in their BMI Z-score.Evaluation of postoperative complications included infection, bleeding, perforation, or other complication. No procedural complications occurred during the endoscopic or surgical placement of the tubes. Patient 5 had a small abscess at a surgical suture 1 week post placement of her first gastrostomy tube, treated by incision and drainage. Patient 7 had buried bumper syndrome diagnosed 3 weeks after placement. Buried bumper occurs when pressure from the internal bumper leads to migration of the bumper out of the lumen and into the gastric wall along the tract  but has Gastrostomy tubes are known to be an effective means to supplement nutrition in children unable to sustain adequate growth via oral intake alone. However, the safety of this procedure in children with an underlying connective tissue disease is not known. Here, we report on the outcome of the placement of 12 gastrostomy tubes in 10 patients with Loeys-Dietz syndrome (LDS), an autosomal dominant connective tissue disease caused by mutations in genes in the TGFβ signaling pathway. LDS is a multisystem disorder associated with an increased propensity for allergic disease, EGID and IBD (both ulcerative colitis and crohns). We have previously demonstrated that the BMI Z-score of patients with LDS are significantly below 0; furthermore, the BMI Z-score of those with comorbid allergic or intestinal disease are significantly below those without these comorbidities . As a reAmong patients who were receiving feeds through their gastrostomy tube, the median BMI (or weight/length for patients less than 2 years old) Z score increased 0.2 per month of gastrostomy tube feedings in the immediate post-procedural time period. The three patients who used their gastrostomy tube but did not have improvement in their BMI Z-score all had ongoing intestinal inflammation (either IBD or EGID), emphasizing that while gastrostomy tubes can provide effective nutritional support, control of underlying inflammatory disease is essential. Long term, all patients using their gastrostomy tube had an increase in their BMI Z-score excepting those with IBD. The selection of formula used post-gastrostomy tube placement should take into account the increased incidence of food allergy and EGID in this population.Given the data presented here, gastrostomy tubes can be placed in this population safely. Physicians can recommend placement of a gastrostomy tubes in an LDS patient when clinically indicated.


VP1, due to the high occurrence of BKPyV-associated diseases in transplant patients and their clinical implications. Here BKTyper is presented, a free online genotyper for BKPyV, based on a VP1 genotyping and a novel algorithm for NCCR block identification. VP1 genotyping is based on a modified implementation of the BK typing and grouping regions (BKTGR) algorithm, providing a maximum-likelihood phylogenetic tree using a custom internal BKPyV database. Novel NCCR block identification relies on a minimum of 12-bp motif recognition and a novel sorting algorithm. A graphical representation of the OPQRS block organization is provided.Human BK polyomavirus (BKPyV) prevalence has been increasing due to the introduction of more potent immunosuppressive agents in transplant recipients, and its clinical interest. BKPyV has been linked mostly to polyomavirus-associated hemorrhagic cystitis, in allogenic hematopoietic stem cell transplant, and polyomavirus-associated nephropathy in kidney transplant patients. BKPyV is a circular double-stranded DNA virus that encodes for seven proteins, of which Viral Protein 1 (VP1), the major structural protein, has been extensively used for genotyping. BKPyV also contains the noncoding control region (NCCR), configured by five repeat blocks (OPQRS) known to be highly repetitive and diverse, and linked to viral infectivity and replication. BKPyV genetic diversity has been mainly studied based on the NCCR and  Human polyomavirus 1, was first described in 1971 by Gardner and collaborators . (v) NCCR blocks are not coding and are only functional in short transcriptional binding sites, therefore, high diversity between input sequences is expected. (vi) Terminal regions of a block with low similarity with the references may be excluded from the block. (vii) NCCR blocks may be missing. Subsequently, alignments must allow for zero or more hits of each NCCR fragment per query, accounting for diverse order and minimum alignment size and nucleotide identity. Minimum alignment size has been delimited to 12 exact nucleotides, meaning that at least 12 exact nucleotides are needed between the query sequence and the NCCR archive block sequences in order to progress the classification. This parameter has been manually fine-tuned in order to ensure a low false-positive rate and a high sensitivity for fragmented blocks. Minimum identity between a putative block in the query sequence and a given block from the NCCR archive sequences has been set to 75%, 5% more stringent than previous estimates [0]. (v) NBKTyper includes a visual inspection of NCCR block structure as well as a short list of conserved transcriptional binding sites that can be found as exact matches from Moens et al. see  33]..33].Validation of NCCR BKTyper has been carried out with the 3 most used reference genomes  and the 10 available sequences reported by Carr et al. . BKTyperDifferent block identification has been reported between authors, articles, or reports. This lack of concordance may have occurred (i) due to alternative viral passage history , SJH16A (OPQPQRS), SJH16B (OPQRS), SHJ18A (OPQPQRS), SHJ18C (OPQP), SHJ85A (OPQPQRS), SHJ85B (OPQRS), MAN10B (OPQRS) and MAN11B (OPQRS) have their NCCR architecture correctly predicted by BKTyper, as can be observed in VP1 typing alone. Complete results are available as Supplementary Information VP1 groups, mostly represented by archetypical NCCR structure and VP1 groups I and IV.BKTyper has been used to genotype all available full-length genomes for BKPyV listed as genome neighbors from NIH NCBI resource. Out of 318 genomes (accession numbers in Supplementary Information VP1 and NCCR for BKPyV. It has shown to be sensible enough to detect inconsistencies in previous literature and perfect to summarize genotyping information in the range of hundreds of sequences in a few minutes. BKTyper will allow researchers and clinicians to obtain BKPyV typing in a fast and reliable manner, bolstering its research and clinical forecasting during routine screenings.BKTyper provides a free, automated, and reproducible alternative to manual genotyping of


Social adversity can impact immune function and is associated with increased morbidity and mortality. Many of these immune-related changes resemble the effects of the natural aging process. To date, little is known about the effects of social adversity on the immune system change across the lifetime. Here, we investigated how aging and social adversity  impact immune cell proportions. We performed flow cytometry on peripheral whole blood from a population of free-ranging rhesus macaques to quantify changes on immune cell proportions across the lifespan (n=99) and across different social statuses (n=53). Overall, we found that high adversity recapitulated the effects of aging. We found significant shared decreases in CD3+/CD4+ T cell proportions and corresponding increases in CD3+/CD8+ T cell proportions between individuals of older ages and low social status. These findings suggest that social adversity has similar effects to aging on T cell proportions, possibly affecting the T cell component of the immune response. In contrast, CD3+/CD4+/CD25+ T regulatory cell proportions increased with age, which is typical of normal aging. Contrary to our expectations, these cells were less abundant in low status individuals, indicating some overall regulatory immune deficits specific to lower status individuals. CD3+/CD8+/CD25+ T regulatory cells, which contribute to self-tolerance, were higher in high status individuals, suggesting that overall primary immune regulatory cells can be affected by social adversity and impair the regulation of inflammation. We provide evidence that social adversity alters immune cell proportions, implicating it in the development of inflammatory and/or aging-related diseases.


Studies of compensatory plasticity in early deaf (ED) individuals have mainly focused on unisensory processing, and on spatial rather than temporal coding. However, precise discrimination of the temporal relationship between stimuli is imperative for successful perception of and interaction with the complex, multimodal environment. Although the properties of cross-modal temporal processing have been extensively studied in neurotypical populations, remarkably little is known about how the loss of one sense impacts the integrity of temporal interactions among the remaining senses. To understand how auditory deprivation affects multisensory temporal interactions, ED and age-matched normal hearing (NH) controls performed a visual-tactile temporal order judgment task in which visual and tactile stimuli were separated by varying stimulus onset asynchronies (SOAs) and subjects had to discern the leading stimulus. Participants performed the task while EEG data were recorded. Group averaged event-related potential waveforms were compared between groups in occipital and fronto-central electrodes. Despite similar temporal order sensitivities and performance accuracy, ED had larger visual P100 amplitudes for all SOA levels and larger tactile N140 amplitudes for the shortest asynchronous (± 30 ms) and synchronous SOA levels. The enhanced signal strength reflected in these components from ED adults are discussed in terms of compensatory recruitment of cortical areas for visual-tactile processing. In addition, ED adults had similar tactile P200 amplitudes as NH but longer P200 latencies suggesting reduced efficiency in later processing of tactile information. Overall, these results suggest that greater responses by ED for early processing of visual and tactile signals are likely critical for maintained performance in visual-tactile temporal order discrimination. Natural timing discrepancies between multiple sensory signals inherently relay the source(s) and degree of congruency between those signals. Throughout development, with normal exposure to multisensory events, the brain develops an intrinsic strategy to compensate for the inherent differences in propagation and processing speeds of multimodal information allowing for coherent percepts  was induced via an auditory signal prior to either the synchronous or asynchronous presentation of the two visual cues. Participants demonstrated a clear perceptual bias toward the visual signal from the cued location as being presented first, regardless of simultaneous presentation and any latency differences in early visual evoked components  suggesting that such a perception is not driven by increased visual processing speed . HoweverAuditory input does appear to play a particularly important role in creating refined resolution for temporal processing. The Auditory Scaffolding Hypothesis suggests that early auditory experience provides a necessary framework, or scaffold, to develop sensitivity to temporal information, including serial order, since these properties are fundamental to sound . In earlAlternatively, some studies don’t show any deficits in visual or tactile temporal processing abilities of ED individuals and suggest that compensatory mechanisms lead to recruitment of auditory areas by intact modalities enabling normal or even enhanced perceptual abilities. For instance, tactual discrimination thresholds, estimated using stimuli ranging from 2 and 300 Hz, and tactile temporal order discrimination thresholds, estimated from a task discriminating which of two vibrotactile stimuli was presented first, did not significantly differ between ED and NH . SimilarThe conflicting results outlined above were found while assessing unisensory temporal processing abilities, however, as temporal discrepancies between signals significantly affects integrative processes, alterations in multisensory temporal processing are expected in ED adults. The extent of facilitation from audio-tactile simultaneous presentation compared to unimodal presentation was examined in both congenitally deaf cochlear implant (CI) users and late deaf CI users (age of onset 7 years or later) by comparing reaction times for a bimodal stimulus to reaction times for unimodal stimuli . While bAnother study that supports the notion of absent early auditory experience modifying multisensory processing and degraded visual influence over somatosensation showed that ED adults had increased susceptibility to a tactile induced double flash illusion compared to NH . In addiPresumably, for multisensory interactions in this auditory-to-tactile direction to occur  modulates the processing of a subsequent stimulus from a different modality , effects of early auditory deprivation on the multisensory integration process can be better understood. As precise integration relies on efficient decoding of temporal information between signals, what is the consequence of auditory deprivation on cross-modal influence of temporally disparate signals? Using a visual-tactile temporal order judgment task, this project investigated how information from one modality  affected the processing of temporally disparate lagging signals from the opposite modality  in ED compared to NH. In line with previously reported findings, we would expect reduced influence by leading visual stimuli on tactile processing in ED compared to NH but similar influence on visual processing by leading tactile cues for both groups . When a 12 early deaf with bilateral, severe to profound hearing loss . The 50 ms tactile stimulus of 50 Hz was generated using the PiezoTac tactor device . To approximate the same central location as the visual stimulus, the tactile stimulus was always presented to the tip of the participant’s right index finger positioned directly below the center of the display.Throughout each experimental block, a white fixation cross was presented in the center of the screen on a gray background. During each trial, a visual and tactile stimulus were presented at varying stimulus onset asynchronies (SOAs) where negative SOAs represent tactile-leading conditions and positive SOAs represent visual-leading conditions. Based on pilot data, 7 SOAs were chosen so that 2 were outside of the average TBW (± 250 ms), 2 were within the average TBW (± 30 ms), 2 were at the limit of the average TBW (± 100 ms), and the final SOA of 0 ms was a simultaneous, control condition. Each SOA was repeated 60 times, in a randomized order, for a total of 420 trials separated into 3 experimental blocks.After the visual-tactile pair was presented, participants were asked to make a temporal order judgment (TOJ) about the 2 signals by pressing “1” on the keyboard for a flash first response and “2” for a touch first response using their non-dominant left hand. To reduce muscle artifacts into the cortical signal, participants waited to enter their response until 800 ms after the second stimulus presentation, indicated when the fixation turned green. Trials were separated by a variable interval between 1000 – 1300 ms.Accuracy of temporal order judgments were quantified for all asynchronous conditions. For each individual, the average correct response was calculated for each asynchronous SOA level tested and individual proportions were averaged together across participants within both the NH and ED groups. Individual’s proportion of ‘visual first’ responses were also plotted as a function of SOA value and fit with a cumulative gaussian function. The mean and the standard deviation were estimated from the cumulative distribution as estimates of sensitivity or just noticeable difference (JND) and perceived synchrony or point of subjective equality (PSE), respectively . The JNDParticipants performed the visual-tactile TOJ task while EEG data were continuously recorded from a 128 channel BioSemi Active 2 system . In addition to the standard 10–20 electrode locations, this system included intermediate positions. Default electrode labels were renamed to approximate the more conventional 10–20 system see . 4 additFirst, EEG data were bandpass filtered from 0.1 to 40 Hz with a second order, non-causal Butterworth filter and re-referenced to the common average reference. Channels were identified for rejection using the TrimOutlier plugin (v.0.17) based on a threshold of ±200 μV. Across participants, an average of 2.8 (± 4.24) channels were rejected and spherically interpolated. Next, epochs of 1200 ms, beginning 200 ms before trial onset , were extracted from continuous data. Epochs corrupted by artifacts were identified following visual inspection and an average of 9.00 (± 7.78) trials (<2.2%) were rejected across participants. Blink and eye movement artifacts were corrected in the epoched data using Independent Component Analysis (ICA). Event related potentials (ERPs) were calculated for each individual as the average of all epochs within each experimental condition. ERPs were baseline corrected relative to the mean amplitude of the pre-trial interval of 200 ms. ERPs were then averaged across participants within the NH and the ED groups.To quantify the electrophysiological dynamics of processing a sensory stimulus preceded by a stimulus from a different modality, amplitudes and latencies were extracted for the lagging stimulus of the asynchronous experimental conditions for each participant. Amplitudes were defined as the maxima peak within a pre-defined time window while latencies were estimated as the time to peak onset within the time window. Specifically, amplitudes and latencies of early (P100) visual components were estimated in the 120 – 180 ms window post visual onset, based on To quantify topographic differences between groups for each SOA level and component, an index known as the global dissimilarity measure (DISS)  was compt-tests with a Bonferroni corrected alpha value of 0.0167 (0.05/3) were used to examine differences between ED and NH groups during the 0 ms SOA condition in tactile N140 and tactile P200 components within FC and in the visual P100 component in occipital ROI. Independent t-tests were also used to compare PSE and JND values between groups as well as for an a priori comparison of components evoked during synchronous presentation of visual-tactile stimuli.As ROIs had unequal number of channels, separate mixed ANOVAs were calculated for each region of interest using the between factor of group (NH vs ED) and the within factor of SOA (7 levels). Due to multiple ANOVAs to investigate differences in both amplitude and latency of visual P100 in occipital, tactile N140 in FC and tactile P200 in FC, the critical alpha level used to determine statistically significant effects will be 0.0167 (0.05/3). As processing of simultaneous visual-tactile events was an additional aspect of investigation, separate independent a priori defined significance level of 0.05, they were deemed significant.Non-parametric permutation tests were used to quantify the significance of estimated DISS values for each component at the respective SOA levels. Following the commonly used topographic ANOVA (TANOVA) method , individAll statistical analysis was performed in R statistical software.p < 0.001, p2n = 0.55] on performance accuracy. Although ED and NH groups did not perform differently overall , there was a significant interaction between group and SOA . However, follow up t-tests that compared group accuracy performance at each SOA level using a corrected p value of 0.0083 showed that ED did not perform significantly different from NH at any SOA (uncorrected ps ≥0.047). Average psychometric functions from both groups are displayed in the right panel of t-tests also revealed that ED and NH groups did not differ in their sensitivity (JND)  or point of subjective equality (PSE)  for the visual-tactile TOJ task.Initially, we quantified the proportion of correct responses for each asynchronous SOA condition within each group (a priori independent t-tests with Bonferroni correction (0.05/3 = 0.017) compared the amplitudes and latencies of tactile N140 and P200 in FC ROI and the visual P100 component within the occipital ROI. Amplitudes of the tactile N140 component were significantly larger in ED compared to NH in FC ROI  while amplitudes of the tactile P200 component were comparable between the two groups  (see p = 0.28] or tactile P200 components  in FC ROI. In occipital ROI, ED adults had a significantly larger amplitude for the visual P100 component   = 15.62, p < 0.001, p2n = 0.42]. However, these were qualified by a significant interaction . Follow up pair-wise comparisons with Bonferroni corrected alpha value of 0.007 (0.05/7) were performed for each SOA to determine which conditions had amplitude differences between ED and NH. For the synchronous and smallest SOA levels (±30), ED had significantly larger tactile N140 amplitudes than NH . However, there was no group difference at ±100 or ±250 SOAs .Group averaged ERPs are shown in p = 0.93], there was an effect of SOA  and a significant interaction . To explore this interaction post hoc, separate t-tests were performed for each SOA level. Only at −250 and −100 SOAs did ED have significantly shorter latencies than NH ; there was no latency difference between groups at the other 5 SOA levels .While there was no group difference in tactile N140 latencies  nor a significant interaction between group and SOA . However, there was a significant effect of SOA  (see p’s < 0.002). Further, the +100 SOA had a significantly smaller amplitude than the +250, −30 and −250 SOAs  but not than the +30 or −100 SOAs (p > 0.28). P200 amplitudes did not significantly differ between +30 and +250 (p = 1.0)  = 1.13, p < 0.05, p2n = 0.18]. In addition, there was a significant effect of SOA  but no significant interaction. Bonferroni corrected pairwise comparisons revealed that the latency in the + 250 SOA was significantly longer than +30, −100 and −250 SOAs . No other comparisons were significant (corrected p’s > 0.06).ED adults had significantly longer tactile P200 latencies than NH . While there was no significant interaction , SOA level did significantly affect visual P100 amplitudes . Post hoc comparisons with Bonferroni correction revealed that the visual P100 amplitude induced by the synchronous condition (0 ms) was significantly larger than ± 100 and ± 250 SOAs  but not ±30 SOAs (corrected p’s ≥ 0.30). As expected, amplitudes did not differ between the three visual-leading tactile conditions (+SOAs) (corrected p’s > 0.19). However, the visual P100 amplitude was significantly larger for the −30 SOA than both −100 and −250 ms SOAs .Next, we quantified the influence of tactile information on the processing of subsequent visual signals, within occipital ROI, presented at variable delays. While we were more interested in how the tactile stimulus may affect subsequent processing of the visual stimulus, p = 0.57] nor was there a significant interaction . However, there was a significant effect of SOA  with follow up pairwise comparisons using Bonferroni correction revealing that the latency in the −30 SOA condition was significantly shorter than the synchronous  and −100 SOA  but not −250 SOA (corrected p = 0.26) nor any of the positive, visual-leading SOAs (corrected p > 0.09).There was no significant difference between visual P100 latencies estimated from occipital region for ED and NH groups  can be There was no significant difference between ED and NH adults in behavioral performance accuracy, visual-tactile temporal order discrimination sensitivity or perceived visual-tactile synchrony. When the visuo-tactile pair was simultaneous, the ED group had larger amplitudes for early visual (P100)  and early tactile (N140) (in FC electrodes) components. When the two signals were temporally offset from each other, ED had larger amplitudes of the early N140 tactile component within FC ROI for the smallest SOA conditions (± 30 ms) while ED had larger visual P100 amplitudes in occipital ROI across SOA conditions. In addition, ED showed shorter latencies of the tactile N140 component for −250 and −100 SOAs while they demonstrated significantly longer latencies for tactile P200 component across SOA levels. Finally, regardless of group, there was a similar dependence on SOA level for amplitude modulation within all ROIs examined.The absence of any group differences in behavioral measures was somewhat surprising given prior studies that have shown impaired unisensory temporal order sensitivities  and reduDespite comparable temporal order perceptual abilities, differences in amplitudes for both visual and tactile components between ED and NH during simultaneous visual-tactile stimulation reveals altered sensory processing due to auditory deprivation. There was a greater amplitude of the visual P100 component in occipital region of ED for the synchronous condition. This finding may be indicative of increased cortical resources dedicated to processing visual information or altered visual processing at early stages in ED. Heightened visual P100 amplitudes in ED measured during a visual detection task predicted reaction times suggesting enhanced unisensory processing in ED . Larger Early processing of the tactile stimulus showed alterations in FC ROI of ED with greater tactile N140 amplitudes at the shortest SOAs tested . Increased responsiveness in somatosensory electrodes is in line with a previous study that suggested increased cortical excitability in ED for somatosensation , perhapsAs multisensory integration is thought to occur in early stages of sensory processing within traditionally unisensory areas  as well ED adults also had significantly larger amplitudes of the early visual P100 component, regardless of SOA, within occipital ROI. This is likely consequent of cross-modal reorganization dynamics and the resulting increased influence of the tactile modality on visual as a result of early auditory deprivation . Indeed,Compensatory mechanisms, such as increased cortical activation, may be largely driven by the haptic modality which is consistent with modality appropriateness, a hypothesis proposing that the sensory modality with greater resolution for the task at hand exerts greater influence in the subsequent processing and perception of the multisensory event. As the tactile modality has a heightened temporal resolution compared to the visual domain , the tacOne common finding for both groups was the amplitude modulation of tactile components dependent on the SOA. For tactile-leading visual conditions within occipital ROI, the amplitude of the early P100 component was largest for 30 ms condition compared to 100 ms and 250 ms SOA conditions. In a similar study, early sensory processing components of the lagging stimulus in an audio-visual pair showed reduced amplitudes in older versus young adults at the large SOA (270 ms) but not small SOA (70 ms) . In conjResults presented from this study showcase some alterations to processing visual-tactile stimuli between ED and NH participants. ED adults had larger amplitudes for early visual and tactile processing components estimated from the simultaneous visual-tactile condition suggesting increased cognitive resources for multisensory processing after early auditory deprivation. In addition, ED adults had larger tactile N140 components within FC electrodes at the shortest SOAs (± 30 ms). These findings along with the broader activation patterns observed on the scalp topographies of ED during the early time window post-tactile onset suggest compensatory mechanisms and potential recruitment of auditory areas by ED to process tactile information but not enhanced temporal processing. Future studies probing additional visual-tactile tasks  would further determine if cortical processing differences in ED, as reported in our study, are common across global visual-tactile processing or specific to temporal processing. Finally, ED adults also had larger visual P100 components estimated from occipital electrodes for all SOA conditions likely due to cross-modal reorganization of tactile inputs onto visual areas as well as modality appropriateness of the tactile system for temporal processing tasks.The de-identified raw data supporting the conclusions of this article will be made available by the authors upon request.The studies involving human participants were reviewed and approved by Institutional Review Board at the University of Nevada, Reno. The participants provided their written informed consent to participate in this study.AS and FJ designed the experiment and interpreted the data. AS and KC acquired the data and conducted statistical analysis. AS wrote the manuscript. FJ critically evaluated the manuscript. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.