Introduction: Increasing evidence suggests a role for the gut microbiome in central nervous system disorders and specific role for the gut-brain axis in neurodegeneration. Bile acids (BA), products of cholesterol metabolism and clearance, are produced in the liver and are further metabolized by gut bacteria. They have major regulatory and signaling functions and seem dysregulated in Alzheimer disease (AD). Methods: Serum levels of 15 primary and secondary BAs and their conjugated forms were measured in 1,464 subjects including 370 cognitively normal older adults (CN), 284 with early mild cognitive impairment (MCI), 505 with late MCI, and 305 AD cases enrolled in the AD Neuroimaging Initiative. We assessed associations of BA profiles including selected ratios with diagnosis, cognition, and AD-related genetic variants, adjusting for cofounders and multiple testing. Results: In AD compared to CN, we observed significantly lower serum concentrations of a primary BA (cholic acid CA) and increased levels of the bacterially produced, secondary BA, deoxycholic acid (DCA), and its glycine and taurine conjugated forms. An increased ratio of DCA:CA, which reflects 7α-dehydroxylation of CA by gut bacteria, strongly associated with cognitive decline, a finding replicated in serum and brain samples in the Rush Religious Orders and Memory and Aging Project. Several genetic variants in immune response related genes implicated in AD showed associations with BA profiles. Conclusion: We report for the first time an association between altered BA profile, genetic variants implicated in AD and cognitive changes in disease using a large multicenter study. These findings warrant further investigation of gut dysbiosis and possible role of gut liver brain axis in the pathogenesis of AD.

44Across a large variety of Mendelian disorders, ~50-75% of patients do not receive a 45 genetic diagnosis by whole exome sequencing indicative of underlying disease-causing 46 variants in non-coding regions. In contrast, whole genome sequencing facilitates the 47 discovery of all genetic variants, but their sizeable number, coupled with a poor 48 understanding of the non-coding genome, makes their prioritization challenging. Here, we 49 demonstrate the power of transcriptome sequencing to provide a confirmed genetic 50 diagnosis for 10% (5 of 48) of undiagnosed mitochondrial disease patients and identify 51 strong candidate genes for patients remaining without diagnosis. We found a median of 1 52 aberrantly expressed gene, 5 aberrant splicing events, and 6 mono-allelically expressed 53 rare variants in patient-derived fibroblasts and established disease-causing roles for each 54 kind. Private exons often arose from sites that are weakly spliced in other individuals, 55providing an important clue for future variant prioritization. One such intronic exon-56 creating variant was found in three unrelated families in the complex I assembly factor 57 TIMMDC1, which we consequently established as a novel disease-associated gene. In 58 conclusion, our study expands the diagnostic tools for detecting non-exonic variants of 59Mendelian disorders and provides examples of intronic loss-of-function variants with 60 pathological relevance. 61Despite the revolutionizing impact of whole exome sequencing (WES) on the molecular 62 genetics of Mendelian disorders, ~50-75% of the patients do not receive a genetic diagnosis after 63 WES [1][2][3][4][5][6] . The disease-causing variants might be detected by WES but remain as variants of 64 unknown significance (VUS, Methods) or they are missed due to the inability to prioritize them. 65Many of these VUS are synonymous or non-coding variants that may affect RNA abundance or 66 isoform but cannot be prioritized due to the poor understanding of regulatory sequence to date 67 compared to coding sequence. Furthermore, WES covers only the 2% exonic regions of the 68 genome. Accordingly, it is mostly blind to regulatory variants in non-coding regions that could 69 affect RNA sequence and abundance. While the limitation of genome coverage is overcome by 70 whole genome sequencing (WGS), prioritization and interpretation of variants identified by 71 WGS is in turn limited by their amount [7][8][9] . 72With RNA sequencing (RNA-seq), limitations of the sole genetic information can be 73 complemented by directly probing variations in RNA abundance and in RNA sequence, 74 including allele-specific expression and splice isoforms. At least three extreme situations can be 75 directly interpreted to prioritize candidate disease-causing genes for a rare disorder. First, the 76 expression level of a gene can lie outside its physiological range. Genes with expression outside 77 their physical range can be identified as expression outliers, often using a stringent cutoff on 78 expression variat...

Detangling gene-disease connections Many diseases are at least partially due to genetic causes that are not always understood or targetable with specific treatments. To provide insight into the biology of various human diseases as well as potential leads for therapeutic development, Pietzner et al . undertook detailed, genome-wide proteogenomic mapping. The authors analyzed thousands of connections between potential disease-associated mutations, specific proteins, and medical conditions, thereby providing a detailed map for use by future researchers. They also supplied some examples in which they applied their approach to medical contexts as varied as connective tissue disorders, gallstones, and COVID-19 infections, sometimes even identifying single genes that play roles in multiple clinical scenarios. —YN

In cross-platform analyses of 174 metabolites we identify 499 associations (p<4.9×10 -10 ) characterized by pleiotropy, allelic heterogeneity, large and non-linear effects, and enrichment for nonsynonymous variation. We identify a signal at GLP2R (p.Asp470Asn) shared between higher citrulline levels, body mass index, fasting glucose-dependent insulinotropic peptide and type 2 diabetes, with beta-arrestin signalling as the underlying mechanism. Genetically-higher serine levels are shown to reduce the likelihood (by 95%) and predict development of macular telangiectasia type 2, a rare degenerative retinal disease. Integration of genomic and small molecule data across platforms enables discovery of regulators of human metabolism and translation into clinical insights. M.P. was supported by a fellowship from the German Research Foundation (DFG PI 1446/2-1). C.O. was founded by an early career fellowship at Homerton College, University of Cambridge. L. B. L. W.