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Eisert"],"software":["Not available"],"tissue":["Colon"],"sample_protocol":["Cells were lysed with 2% SDS, 150mM NaCl, 50mM Tris, pH 8.5 in the presence of PhosSTOP protease inhibitor and EDTA-free complete protease inhibitor (Sigma, PHOSS-RO and COEDDTAF-RO, respectively) and homogenized using QIAshredders.  Cysteines were reduced by adding DTT to a final concentration of 5mM for 1 h at 37° C.  After the samples were cooled to room temperature ammonium bicarbonate was added to achieve 50mM and iodoacetamide was added to a final concentration of 20mM for 25 min at room temperature in the dark.  The reactions were quenched with 50mM DTT.  Protein was precipitated using Methanol/Chloroform precipitation. Protein pellets were resuspended in 100µl 200mM EPPS pH 8.5 with 8M urea for 30min at 37° C with vortexing every 10 min.  300 µl EPPS buffer and 8 µl acetonitrile (ACN) was added to the samples followed by 3.5 µl of 2mg/mL LysC (Wako, #129-02541) for 3 hrs with shaking at 37° C.  The urea was diluted to 0.8 M with 0.6 mL 200mM EPPS pH 8.5 and 12 µl ACN.  Trypsin (Promega, #V5117) was added to the 18 samples, which were incubated overnight with shaking at 37° C.  Approximately 2µg of digested protein from each sample were individually desalted using STAGE tips and the missed cleavage rate was analyzed by LC-MS/MS to confirm less than 10% missed cleavage rate. For whole cell proteomics, 70ug of digested protein from each sample was diluted to a final volume of 100µl using EPPS buffer and 30µl of LC-MS grade ACN were added.  Each sample was labeled with TMTpro (Thermo Scientific, # A52045) for 1hr and labeling efficiency was assessed by pooling 2µl of each sample and, which was analyzed by an LC-SPS-MS3.  Once labeling was above 95%, the TMT reactions were quenched with 7µl of 10% hydroxylamine for 15 min at room temperature then acidified with LC-MS grade formic acid (FA).  Samples were pooled to achieve 1:1 ratios of TMT signal for all 18 samples.  The multiplex was dried by speed vacuum and desalted using a C18 sep-pak (Waters, #WAT020805).  The desalted multiplex was fractionated by reversed-phased alkaline fractionation on an Agilent 1260 with a C18 column.  The multiplex fractions were collected in a 96-well plate using a 65-minute gradient of 16-57%B (Buffer A: 10mM ammonium bicarbonate pH 8 with 5% acetonitrile, Buffer B: 90% acetonitrile with 10% 10M ammonium bicarbonate pH 8).  The 96 fractions were pooled into 24 fractions and desalted by STAGE tip.  Samples were dried and resuspended in 1% aqueous FA with 3% acetonitrile. The remaining digests were desalted with C18 Sep-Pak cartridges (Waters, #WAT020805).  Briefly, the digests were acidified using FA and trifluoroacetic acid (TFA).  The cartridges were pre-conditioned with 6 column volumes each of methanol, ACN, and 1% FA with 0.1% TFA.  The samples were loaded slowly onto the cartridges and washed with 6 column volumes of 1% FA, eluted with 5 column volumes of 80% ACN with 20% of aqueous 1% FA, and dried.  Phosphopeptides from each sample were individually enriched using the High Select™ Phosphopeptide Enrichment Kit (Thermo Scientific, #A32992) and the eluted phosphopeptides were acidified with neat FA, dried, and desalted by Sep-Pak (Waters, WAT054955) as described above.  The phosphopeptides were resuspended in 100 µl 200mM EPPS pH 8 buffer and 30µl acetonitrile then labeled with TMTpro, quenched, and pooled as previously described.  The resulting multiplex was desalted with a 500 mg Sep-Pak and fractionated also as described above except using a gradient of 5-44% B over 65 minutes.  The 24 fractions were resuspended in 1% FA with 0.1% TFA and desalted by STAGE tip then resuspended in aqueous 1% FA. Samples were analyzed on a Thermo Fisher Orbitrap Eclipse with a Vanquish Neo nano UHPLC and a FAIMS pro Interface as indicated.  Peptides were injected onto an EASY-Spray™ PepMap™ Neo UHPLC column (ES75500PN) with a 0.250 nL/min flow rate and a 4 hr gradient (Buffer A: 0.1%FA in water and Buffer B: 0.1%FA in 90% acetonitrile, 10% water).  Data was collected using an SPS-MS3 method.  MS1 scans were collected on the Orbitrap using 120k resolution over an m/z range of 400-1600 with the AGC target set to standard and injection time set to auto.  Charge states between 2-6 were needed for sequencing and the dynamic exclusion was set to 45 seconds.  After quadrupole isolation, MS2 was performed in the ion trap with CID fragmentation and the MZ window was set to 400-1600.  In the case of phosphoproteomics, CID with mulistage activation was used and the neutral mass loss was set to 97.9763.  SPS-MS3 TMT quantification was performed in the Orbitrap with a scan range of 100-500 m/z and a maximum injection time of 200 ms.  In the case of whole cell proteomics, real time search (RTS) with the human reference proteome downloaded from Uniprot on January 1, 2024.  Additionally, FAIMS was used for whole cell proteomics with the CVs set to -45, -55, and -70V.  FAIMS and RTS were not used for phosphoproteomics."],"repository":["Pride"],"labhead":["A. Sloan Devlin"],"instrument_platform":[""],"labhead_affiliation":["Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Boston, MA, United States"],"submission_type":["COMPLETE"],"publication":["41811452 Powell CE, McSween AM, Dohnalová L, Kim CH, Eisert RJ, Sun ZJ, Seo HS, Marquardt V, Dhe-Paganon S, Thaiss CA, Devlin AS. Gut microbiome-produced bile acid metabolite lengthens the circadian period in host intestinal cells. Proc Natl Acad Sci U S A. 2026 123(11):e2506313123 10.1073/pnas.2506313123"],"submitter_affiliation":["Harvard Medical School"],"labhead_mail":["sloan_devlin@g.harvard.edu"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"disease":["Colon Cancer"],"submitter_keywords":["Phosphoproteomics","Ht-29 cells","Circadian rhythm","Lithocholic acid","Microbiome"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD060420"],"quantification_method":[""],"modification":[""],"data_protocol":["Data was analyzed using GFY Core licensed through Harvard University.  First, Raw files were converted to mzXML for processing.  The data was searched using the reference proteome downloaded on January 27, 2025, which was modified to include common contaminants and reversed sequences as decoys.  The spectra were searched using COMET to determine identification scores (Xcorr, ΔCn, and precursor mass error), which were used for target-decoy hits.  The precursor mass tolerance was set to 20 ppm with a 0.9 fragment tolerance and a maximum of 2 missed cleavage sites.  Oxidized methionine was set as a variable modification (+15.9949 Da) and phosphorylated Ser, Thr, and Tyr (+79.9663 Da) when applicable.  Cysteine alkylation was set as a static modification (+57.0214 Da). N-terminal and lysine TMTpro-labeling were also set as static modifications (+304.2071 Da).  Peptides were filtered to achieve an FDR of <1% using linear discriminant analysis with a target decoy strategy and further filtered to obtain a protein FDR of 1%.  Phosphopeptide localization confidence was measured using the Ascore method with Ascore values set to ≥ 13.  For TMT quantification, only peptides with a total signal of >200 and an isolation specificity of at least 0.7 were used.  Columns were normalized by total protein to account for different protein loading in each channel.  All raw and processed data were submitted to PRIDE archive."],"omics_type":["Proteomics"],"species":["Homo Sapiens (human)"],"submitter_mail":["robyn_eisert@hms.harvard.edu"],"submitter_country":["United States"],"doi":["10.6019/PXD060420"],"pubmed_abstract":["Host circadian signaling, feeding, and the gut microbiome are tightly interconnected. Changes in the gut microbial community can affect the expression of core clock genes, but the specific metabolites and molecular mechanisms that mediate this relationship remain largely unknown. Here, we sought to identify gut microbial metabolites that impact circadian signaling. Through a phenotypic screen of a focused library of gut microbial metabolites, we identified a bile acid metabolite, lithocholic acid (LCA), as a circadian modulator. LCA lengthened the circadian period of core clock gene <i>hPer2</i> transcription in a dose-responsive manner in human colonic cells. We found evidence that LCA modulates the casein kinase 1 δ/ε (CK1δ/ε)-protein phosphatase 1 (PP1) feedback loop and stabilizes core clock protein cryptochrome 2 (CRY2). Furthermore, we showed that LCA feeding alters circadian transcription in mouse distal ileum and colon. Taken together, our work identifies LCA as a molecular link between host circadian biology and the microbiome. Because bile acids are secreted in response to feeding, our work provides potential mechanistic insight into the molecular nature of the food-entrainable oscillator (FEO) by which peripheral clocks adapt to the timing of food intake. Given the association between circadian rhythm, feeding, and metabolic disease, our insights may offer an avenue for modulating host health."],"pubmed_title":["Gut microbiome-produced bile acid metabolite lengthens the circadian period in host intestinal cells."],"pubmed_authors":["Powell Chelsea E CE, McSween Alana M AM, Dohnalová Lenka L, Kim Cecilia H CH, Eisert Robyn J RJ, Sun Zhen-Yu J ZJ, Seo Hyuk-Soo HS, Marquardt Vincent V, Dhe-Paganon Sirano S, Thaiss Christoph A CA, Devlin A Sloan AS"],"additional_accession":[]},"is_claimable":false,"name":"Gut Microbially Produced Bile Acid Metabolite Lengthens Circadian Period in Host Intestinal Cells","description":"Although it has been shown that host health, circadian signaling, and the microbiome are tightly connected, the mechanistic links remain unclear. We identified a bile acid metabolite, lithocholic acid (LCA), as a circadian modulator by screening a focused library of gut microbial metabolites. Out of the larger class of compounds, LCA, and to a lesser extent isoLCA, uniquely lengthened the circadian period of hPer2 transcription in a dose-responsive manner in human colonic cells. LCA modulated the casein kinase 1 / (CK1/)-protein phosphatase 1 (PP1) feedback loop and stabilized core clock protein cryptochrome 2 (CRY2). Furthermore, we showed that LCA feeding alters circadian transcription in mouse colons. Thus, our work identifies LCA as an endogenous molecular link between host circadian biology and the microbiome, providing a new avenue to examine host 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