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Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.

Cell systems

Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M.
PMID: 27135913
Cell Syst. 2015 Sep 23;1(3):224-37. doi: 10.1016/j.cels.2015.08.012. Epub 2015 Sep 17.

Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify...

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Ori A, Toyama BH, Harris MS, et al. Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. Cell Syst. 2015;1(3):224-37doi: 10.1016/j.cels.2015.08.012.
Ori, A., Toyama, B. H., Harris, M. S., Bock, T., Iskar, M., Bork, P., Ingolia, N. T., Hetzer, M. W., & Beck, M. (2015). Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. Cell systems, 1(3), 224-37. https://doi.org/10.1016/j.cels.2015.08.012
Ori, Alessandro, et al. "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." Cell systems vol. 1,3 (2015): 224-37. doi: https://doi.org/10.1016/j.cels.2015.08.012
Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M. Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. Cell Syst. 2015 Sep 23;1(3):224-37. doi: 10.1016/j.cels.2015.08.012. Epub 2015 Sep 17. PMID: 27135913; PMCID: PMC4802414.
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Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation.

Nature communications

Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJ, Parylak SL, Paquola AC, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH.
PMID: 27295945
Nat Commun. 2016 Jun 14;7:12020. doi: 10.1038/ncomms12020.

No abstract available.

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Lacar B, Linker SB, Jaeger BN, et al. Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Nat Commun. 2016;7:12020doi: 10.1038/ncomms12020.
Lacar, B., Linker, S. B., Jaeger, B. N., Krishnaswami, S. R., Barron, J. J., Kelder, M. J., Parylak, S. L., Paquola, A. C., Venepally, P., Novotny, M., O'Connor, C., Fitzpatrick, C., Erwin, J. A., Hsu, J. Y., Husband, D., McConnell, M. J., Lasken, R., & Gage, F. H. (2016). Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Nature communications, 712020. https://doi.org/10.1038/ncomms12020
Lacar, Benjamin, et al. "Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation." Nature communications vol. 7 (2016): 12020. doi: https://doi.org/10.1038/ncomms12020
Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJ, Parylak SL, Paquola AC, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH. Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Nat Commun. 2016 Jun 14;7:12020. doi: 10.1038/ncomms12020. PMID: 27295945; PMCID: PMC4911670.
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A mechanism for the response of KRAS.

Molecular & cellular oncology

McFall T, Stites EC.
PMID: 32158916
Mol Cell Oncol. 2020 Jan 15;7(2):1701914. doi: 10.1080/23723556.2019.1701914. eCollection 2020.

Previous analysis of Phase 3 clinical trial data for colorectal cancer patients treated with cetuximab revealed that patients harboring a KRAS mutation did not benefit from treatment. This finding set the stage for one of the first examples of...

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McFall T, Stites EC. A mechanism for the response of KRAS. Mol Cell Oncol. 2020;7(2):1701914doi: 10.1080/23723556.2019.1701914.
McFall, T., & Stites, E. C. (2020). A mechanism for the response of KRAS. Molecular & cellular oncology, 7(2), 1701914. https://doi.org/10.1080/23723556.2019.1701914
McFall, Thomas, and Stites, Edward Cooper. "A mechanism for the response of KRAS." Molecular & cellular oncology vol. 7,2 (2020): 1701914. doi: https://doi.org/10.1080/23723556.2019.1701914
McFall T, Stites EC. A mechanism for the response of KRAS. Mol Cell Oncol. 2020 Jan 15;7(2):1701914. doi: 10.1080/23723556.2019.1701914. eCollection 2020. PMID: 32158916; PMCID: PMC7051129.
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Realizing the Clinical Potential of Computational Psychiatry: Report From the Banbury Center Meeting, February 2019.

Biological psychiatry

Browning M, Carter CS, Chatham C, Den Ouden H, Gillan CM, Baker JT, Chekroud AM, Cools R, Dayan P, Gold J, Goldstein RZ, Hartley CA, Kepecs A, Lawson RP, Mourao-Miranda J, Phillips ML, Pizzagalli DA, Powers A, Rindskopf D, Roiser JP, Schmack K, Schiller D, Sebold M, Stephan KE, Frank MJ, Huys Q, Paulus M.
PMID: 32113656
Biol Psychiatry. 2020 Jul 15;88(2):e5-e10. doi: 10.1016/j.biopsych.2019.12.026. Epub 2020 Feb 26.

No abstract available.

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Browning M, Carter CS, Chatham C, et al. Realizing the Clinical Potential of Computational Psychiatry: Report From the Banbury Center Meeting, February 2019. Biol Psychiatry. 2020;88(2):e5-e10doi: 10.1016/j.biopsych.2019.12.026.
Browning, M., Carter, C. S., Chatham, C., Den Ouden, H., Gillan, C. M., Baker, J. T., Chekroud, A. M., Cools, R., Dayan, P., Gold, J., Goldstein, R. Z., Hartley, C. A., Kepecs, A., Lawson, R. P., Mourao-Miranda, J., Phillips, M. L., Pizzagalli, D. A., Powers, A., Rindskopf, D., Roiser, J. P., Schmack, K., Schiller, D., Sebold, M., Stephan, K. E., Frank, M. J., Huys, Q., & Paulus, M. (2020). Realizing the Clinical Potential of Computational Psychiatry: Report From the Banbury Center Meeting, February 2019. Biological psychiatry, 88(2), e5-e10. https://doi.org/10.1016/j.biopsych.2019.12.026
Browning, Michael, et al. "Realizing the Clinical Potential of Computational Psychiatry: Report From the Banbury Center Meeting, February 2019." Biological psychiatry vol. 88,2 (2020): e5-e10. doi: https://doi.org/10.1016/j.biopsych.2019.12.026
Browning M, Carter CS, Chatham C, Den Ouden H, Gillan CM, Baker JT, Chekroud AM, Cools R, Dayan P, Gold J, Goldstein RZ, Hartley CA, Kepecs A, Lawson RP, Mourao-Miranda J, Phillips ML, Pizzagalli DA, Powers A, Rindskopf D, Roiser JP, Schmack K, Schiller D, Sebold M, Stephan KE, Frank MJ, Huys Q, Paulus M. Realizing the Clinical Potential of Computational Psychiatry: Report From the Banbury Center Meeting, February 2019. Biol Psychiatry. 2020 Jul 15;88(2):e5-e10. doi: 10.1016/j.biopsych.2019.12.026. Epub 2020 Feb 26. PMID: 32113656.
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Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment.

iScience

Sonntag T, Ostojić J, Vaughan JM, Moresco JJ, Yoon YS, Yates JR, Montminy M.
PMID: 30611118
iScience. 2019 Jan 25;11:134-145. doi: 10.1016/j.isci.2018.12.012. Epub 2018 Dec 19.

The second messenger 3',5'-cyclic adenosine monophosphate (cAMP) stimulates gene expression via the cAMP-regulated transcriptional coactivator (CRTC) family of cAMP response element-binding protein coactivators. In the basal state, CRTCs are phosphorylated by salt-inducible kinases (SIKs) and sequestered in the cytoplasm...

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Sonntag T, Ostojić J, Vaughan JM, et al. Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. iScience. 2018;11:134-145doi: 10.1016/j.isci.2018.12.012.
Sonntag, T., Ostojić, J., Vaughan, J. M., Moresco, J. J., Yoon, Y. S., Yates, J. R., & Montminy, M. (2019). Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. iScience, 11134-145. https://doi.org/10.1016/j.isci.2018.12.012
Sonntag, Tim, et al. "Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment." iScience vol. 11 (2019): 134-145. doi: https://doi.org/10.1016/j.isci.2018.12.012
Sonntag T, Ostojić J, Vaughan JM, Moresco JJ, Yoon YS, Yates JR, Montminy M. Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. iScience. 2019 Jan 25;11:134-145. doi: 10.1016/j.isci.2018.12.012. Epub 2018 Dec 19. PMID: 30611118; PMCID: PMC6317279.
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Sex- and age-dependent outcomes of 9-hour time-restricted feeding of a Western high-fat high-sucrose diet in C57BL/6J mice.

Cell reports

Chaix A, Deota S, Bhardwaj R, Lin T, Panda S.
PMID: 34407415
Cell Rep. 2021 Aug 17;36(7):109543. doi: 10.1016/j.celrep.2021.109543.

Time-restricted feeding (TRF) is a nutritional intervention wherein food intake is limited to a consistent 8- to 10-h daily window without changes in nutritional quality or quantity. TRF can prevent and treat diet-induced obesity (DIO) and associated metabolic disease...

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Chaix A, Deota S, Bhardwaj R, et al. Sex- and age-dependent outcomes of 9-hour time-restricted feeding of a Western high-fat high-sucrose diet in C57BL/6J mice. Cell Rep. 2021;36(7):109543doi: 10.1016/j.celrep.2021.109543.
Chaix, A., Deota, S., Bhardwaj, R., Lin, T., & Panda, S. (2021). Sex- and age-dependent outcomes of 9-hour time-restricted feeding of a Western high-fat high-sucrose diet in C57BL/6J mice. Cell reports, 36(7), 109543. https://doi.org/10.1016/j.celrep.2021.109543
Chaix, Amandine, et al. "Sex- and age-dependent outcomes of 9-hour time-restricted feeding of a Western high-fat high-sucrose diet in C57BL/6J mice." Cell reports vol. 36,7 (2021): 109543. doi: https://doi.org/10.1016/j.celrep.2021.109543
Chaix A, Deota S, Bhardwaj R, Lin T, Panda S. Sex- and age-dependent outcomes of 9-hour time-restricted feeding of a Western high-fat high-sucrose diet in C57BL/6J mice. Cell Rep. 2021 Aug 17;36(7):109543. doi: 10.1016/j.celrep.2021.109543. PMID: 34407415; PMCID: PMC8500107.
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Single-Cell Transcriptomics Reveals a Conserved Metaplasia Program in Pancreatic Injury.

Gastroenterology

Ma Z, Lytle NK, Chen B, Jyotsana N, Novak SW, Cho CJ, Caplan L, Ben-Levy O, Neininger AC, Burnette DT, Trinh VQ, Tan MCB, Patterson EA, Arrojo E Drigo R, Giraddi RR, Ramos C, Means AL, Matsumoto I, Manor U, Mills JC, Goldenring JR, Lau KS, Wahl GM, DelGiorno KE.
PMID: 34695382
Gastroenterology. 2021 Oct 23; doi: 10.1053/j.gastro.2021.10.027. Epub 2021 Oct 23.

BACKGROUND & AIMS: Acinar to ductal metaplasia (ADM) occurs in the pancreas in response to tissue injury and is a potential precursor for adenocarcinoma. The goal of these studies was to define the populations arising from ADM, the associated...

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Ma Z, Lytle NK, Chen B, et al. Single-Cell Transcriptomics Reveals a Conserved Metaplasia Program in Pancreatic Injury. Gastroenterology. 2021;doi: 10.1053/j.gastro.2021.10.027.
Ma, Z., Lytle, N. K., Chen, B., Jyotsana, N., Novak, S. W., Cho, C. J., Caplan, L., Ben-Levy, O., Neininger, A. C., Burnette, D. T., Trinh, V. Q., Tan, M. C. B., Patterson, E. A., Arrojo E Drigo, R., Giraddi, R. R., Ramos, C., Means, A. L., Matsumoto, I., Manor, U., Mills, J. C., Goldenring, J. R., Lau, K. S., Wahl, G. M., & DelGiorno, K. E. (2021). Single-Cell Transcriptomics Reveals a Conserved Metaplasia Program in Pancreatic Injury. Gastroenterology, . https://doi.org/10.1053/j.gastro.2021.10.027
Ma, Zhibo, et al. "Single-Cell Transcriptomics Reveals a Conserved Metaplasia Program in Pancreatic Injury." Gastroenterology vol. (2021). doi: https://doi.org/10.1053/j.gastro.2021.10.027
Ma Z, Lytle NK, Chen B, Jyotsana N, Novak SW, Cho CJ, Caplan L, Ben-Levy O, Neininger AC, Burnette DT, Trinh VQ, Tan MCB, Patterson EA, Arrojo E Drigo R, Giraddi RR, Ramos C, Means AL, Matsumoto I, Manor U, Mills JC, Goldenring JR, Lau KS, Wahl GM, DelGiorno KE. Single-Cell Transcriptomics Reveals a Conserved Metaplasia Program in Pancreatic Injury. Gastroenterology. 2021 Oct 23; doi: 10.1053/j.gastro.2021.10.027. Epub 2021 Oct 23. PMID: 34695382.
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Progressive alterations in amino acid and lipid metabolism correlate with peripheral neuropathy in .

Science advances

Lim EW, Handzlik MK, Trefts E, Gengatharan JM, Pondevida CM, Shaw RJ, Metallo CM.
PMID: 34652935
Sci Adv. 2021 Oct 15;7(42):eabj4077. doi: 10.1126/sciadv.abj4077. Epub 2021 Oct 15.

[Figure: see text].

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Lim EW, Handzlik MK, Trefts E, et al. Progressive alterations in amino acid and lipid metabolism correlate with peripheral neuropathy in . Sci Adv. 2021;7(42):eabj4077doi: 10.1126/sciadv.abj4077.
Lim, E. W., Handzlik, M. K., Trefts, E., Gengatharan, J. M., Pondevida, C. M., Shaw, R. J., & Metallo, C. M. (2021). Progressive alterations in amino acid and lipid metabolism correlate with peripheral neuropathy in . Science advances, 7(42), eabj4077. https://doi.org/10.1126/sciadv.abj4077
Lim, Esther W, et al. "Progressive alterations in amino acid and lipid metabolism correlate with peripheral neuropathy in ." Science advances vol. 7,42 (2021): eabj4077. doi: https://doi.org/10.1126/sciadv.abj4077
Lim EW, Handzlik MK, Trefts E, Gengatharan JM, Pondevida CM, Shaw RJ, Metallo CM. Progressive alterations in amino acid and lipid metabolism correlate with peripheral neuropathy in . Sci Adv. 2021 Oct 15;7(42):eabj4077. doi: 10.1126/sciadv.abj4077. Epub 2021 Oct 15. PMID: 34652935; PMCID: PMC8519573.
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Parallels Between the Antiviral State and the Irradiated State.

Journal of the National Cancer Institute

McGee HM, Marciscano AE, Campbell AM, Monjazeb AM, Kaech SM, Teijaro JR.
PMID: 33252657
J Natl Cancer Inst. 2021 Aug 02;113(8):969-979. doi: 10.1093/jnci/djaa190.

Improved understanding of host antiviral defense and antitumor immunity have elucidated molecular pathways important to both processes. During viral infection, RNA or DNA in the host cell serves as a danger signal that initiates the antiviral response. Recent studies...

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McGee HM, Marciscano AE, Campbell AM, et al. Parallels Between the Antiviral State and the Irradiated State. J Natl Cancer Inst. 2021;113(8):969-979doi: 10.1093/jnci/djaa190.
McGee, H. M., Marciscano, A. E., Campbell, A. M., Monjazeb, A. M., Kaech, S. M., & Teijaro, J. R. (2021). Parallels Between the Antiviral State and the Irradiated State. Journal of the National Cancer Institute, 113(8), 969-979. https://doi.org/10.1093/jnci/djaa190
McGee, Heather M, et al. "Parallels Between the Antiviral State and the Irradiated State." Journal of the National Cancer Institute vol. 113,8 (2021): 969-979. doi: https://doi.org/10.1093/jnci/djaa190
McGee HM, Marciscano AE, Campbell AM, Monjazeb AM, Kaech SM, Teijaro JR. Parallels Between the Antiviral State and the Irradiated State. J Natl Cancer Inst. 2021 Aug 02;113(8):969-979. doi: 10.1093/jnci/djaa190. PMID: 33252657; PMCID: PMC8502484.
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Chronic cortisol differentially impacts stem cell-derived astrocytes from major depressive disorder patients.

Translational psychiatry

Heard KJ, Shokhirev MN, Becronis C, Fredlender C, Zahid N, Le AT, Ji Y, Skime M, Nelson T, Hall-Flavin D, Weinshilboum R, Gage FH, Vadodaria KC.
PMID: 34848679
Transl Psychiatry. 2021 Nov 30;11(1):608. doi: 10.1038/s41398-021-01733-9.

Major depressive disorder (MDD) is a prevalent psychiatric disorder, and exposure to stress is a robust risk factor for MDD. Clinical data and rodent models have indicated the negative impact of chronic exposure to stress-induced hormones like cortisol on...

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Heard KJ, Shokhirev MN, Becronis C, et al. Chronic cortisol differentially impacts stem cell-derived astrocytes from major depressive disorder patients. Transl Psychiatry. 2021;11(1):608doi: 10.1038/s41398-021-01733-9.
Heard, K. J., Shokhirev, M. N., Becronis, C., Fredlender, C., Zahid, N., Le, A. T., Ji, Y., Skime, M., Nelson, T., Hall-Flavin, D., Weinshilboum, R., Gage, F. H., & Vadodaria, K. C. (2021). Chronic cortisol differentially impacts stem cell-derived astrocytes from major depressive disorder patients. Translational psychiatry, 11(1), 608. https://doi.org/10.1038/s41398-021-01733-9
Heard, Kelly J, et al. "Chronic cortisol differentially impacts stem cell-derived astrocytes from major depressive disorder patients." Translational psychiatry vol. 11,1 (2021): 608. doi: https://doi.org/10.1038/s41398-021-01733-9
Heard KJ, Shokhirev MN, Becronis C, Fredlender C, Zahid N, Le AT, Ji Y, Skime M, Nelson T, Hall-Flavin D, Weinshilboum R, Gage FH, Vadodaria KC. Chronic cortisol differentially impacts stem cell-derived astrocytes from major depressive disorder patients. Transl Psychiatry. 2021 Nov 30;11(1):608. doi: 10.1038/s41398-021-01733-9. PMID: 34848679; PMCID: PMC8632962.
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Bisphenol A derivatives act as novel coactivator-binding inhibitors for estrogen receptor β.

The Journal of biological chemistry

Iwamoto M, Masuya T, Hosose M, Tagawa K, Ishibashi T, Suyama K, Nose T, Yoshihara E, Downes M, Evans RM, Matsushima A.
PMID: 34499926
J Biol Chem. 2021 Nov;297(5):101173. doi: 10.1016/j.jbc.2021.101173. Epub 2021 Sep 06.

Bisphenol A and its derivatives are recognized as endocrine disruptors based on their complex effects on estrogen receptor (ER) signaling. While the effects of bisphenol derivatives on ERα have been thoroughly evaluated, how these chemicals affect ERβ signaling is...

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Iwamoto M, Masuya T, Hosose M, et al. Bisphenol A derivatives act as novel coactivator-binding inhibitors for estrogen receptor β. J Biol Chem. 2021;297(5):101173doi: 10.1016/j.jbc.2021.101173.
Iwamoto, M., Masuya, T., Hosose, M., Tagawa, K., Ishibashi, T., Suyama, K., Nose, T., Yoshihara, E., Downes, M., Evans, R. M., & Matsushima, A. (2021). Bisphenol A derivatives act as novel coactivator-binding inhibitors for estrogen receptor β. The Journal of biological chemistry, 297(5), 101173. https://doi.org/10.1016/j.jbc.2021.101173
Iwamoto, Masaki, et al. "Bisphenol A derivatives act as novel coactivator-binding inhibitors for estrogen receptor β." The Journal of biological chemistry vol. 297,5 (2021): 101173. doi: https://doi.org/10.1016/j.jbc.2021.101173
Iwamoto M, Masuya T, Hosose M, Tagawa K, Ishibashi T, Suyama K, Nose T, Yoshihara E, Downes M, Evans RM, Matsushima A. Bisphenol A derivatives act as novel coactivator-binding inhibitors for estrogen receptor β. J Biol Chem. 2021 Nov;297(5):101173. doi: 10.1016/j.jbc.2021.101173. Epub 2021 Sep 06. PMID: 34499926; PMCID: PMC8551653.
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Cotyledon-Generated Auxin Is Required for Shade-Induced Hypocotyl Growth in Brassica rapa.

Plant physiology

Procko C, Crenshaw CM, Ljung K, Noel JP, Chory J.
PMID: 24891610
Plant Physiol. 2014 Jul;165(3):1285-1301. doi: 10.1104/pp.114.241844. Epub 2014 Jun 02.

Plant architecture is optimized for the local light environment. In response to foliar shade or neighbor proximity (low red to far-red light), some plant species exhibit shade-avoiding phenotypes, including increased stem and hypocotyl growth, which increases the likelihood of...

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Procko C, Crenshaw CM, Ljung K, et al. Cotyledon-Generated Auxin Is Required for Shade-Induced Hypocotyl Growth in Brassica rapa. Plant Physiol. 2014;165(3):1285-1301doi: 10.1104/pp.114.241844.
Procko, C., Crenshaw, C. M., Ljung, K., Noel, J. P., & Chory, J. (2014). Cotyledon-Generated Auxin Is Required for Shade-Induced Hypocotyl Growth in Brassica rapa. Plant physiology, 165(3), 1285-1301. https://doi.org/10.1104/pp.114.241844
Procko, Carl, et al. "Cotyledon-Generated Auxin Is Required for Shade-Induced Hypocotyl Growth in Brassica rapa." Plant physiology vol. 165,3 (2014): 1285-1301. doi: https://doi.org/10.1104/pp.114.241844
Procko C, Crenshaw CM, Ljung K, Noel JP, Chory J. Cotyledon-Generated Auxin Is Required for Shade-Induced Hypocotyl Growth in Brassica rapa. Plant Physiol. 2014 Jul;165(3):1285-1301. doi: 10.1104/pp.114.241844. Epub 2014 Jun 02. PMID: 24891610; PMCID: PMC4081337.
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