Publications in 2020

Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients.

Synthesis and Characterization of a Diazirine-Based Photolabel of the Nonanesthetic Fropofol

Synthesis and Characterization of a Diazirine-Based Photolabel of the Nonanesthetic Fropofol.  White ER, Leace DM, Bedell VM, Bhanu NV, Garcia BA, Dailey WP, Eckenhoff RG. ACS Chem Neurosci. 2020 Dec 23. doi: 10.1021/acschemneuro.0c00667.

Mechanistic insights into volatile anesthetic modulation of K2P channels

Mechanistic insights into volatile anesthetic modulation of K2P channels. Wague A, Joseph TT, Woll KA, Bu W, Vaidya KA, Bhanu NV, Garcia BA, Nimigean CM, Eckenhoff RG, Riegelhaupt PM. Elife. 2020 Dec 21;9:e59839. doi: 10.7554/eLife.59839. Online ahead of print.

H1 histones control the epigenetic landscape by local chromatin compaction

H1 histones control the epigenetic landscape by local chromatin compaction. Willcockson MA, Healton SE, Weiss CN, Bartholdy BA, Botbol Y, Mishra LN, Sidhwani DS, Wilson TJ, Pinto HB, Maron MI, Skalina KA, Toro LN, Zhao J, Lee CH, Hou H, Yusufova N, Meydan C, Osunsade A, David Y, Cesarman E, Melnick AM, Sidoli S, Garcia BA, Edelmann W, Macian F, Skoultchi AI. Nature. 2020 Dec 9. doi: 10.1038/s41586-020-3032-z. Online ahead of print.

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans

TET2 chemically modifies tRNAs and regulates tRNA fragment levels

H3K27M in Gliomas Causes a One-Step Decrease in H3K27 Methylation and Reduced Spreading within the Constraints of H3K36 Methylation

H3K27M in Gliomas Causes a One-Step Decrease in H3K27 Methylation and Reduced Spreading within the Constraints of H3K36 Methylation. Harutyunyan AS, Chen H, Lu T, Horth C, Nikbakht H, Krug B, Russo C, Bareke E, Marchione DM, Coradin M, Garcia BA, Jabado N, Majewski J. Cell Rep. 2020 Nov 17;33(7):108390.

Accelerating the field of epigenetic histone modification through mass spectrometry-based approaches

Accelerating the field of epigenetic histone modification through mass spectrometry-based approaches. Lu C, Coradin M, Porter EG, Garcia BA. Mol Cell Proteomics. 2020 Nov 17:mcp.R120.002257.

Epigenetic and transcriptional control of the epidermal growth factor receptor (EGFR) regulates the tumor immune microenvironment in pancreatic cancer

Epigenetic and transcriptional control of the epidermal growth factor receptor (EGFR) regulates the tumor immune microenvironment in pancreatic cancer. Li J, Yuan S, Norgard RJ, Yan F, Sun YH, Kim IK, Merrell AJ, Sela Y, Jiang Y, Bhanu NV, Garcia BA, Vonderheide RH, Blanco A, Stanger BZ. Cancer Discov. 2020 Nov 6:CD-20-0519.

Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression

Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression.  Jain SU, Khazaei S, Marchione DM, Lundgren SM, Wang X, Weinberg DN, Deshmukh S, Juretic N, Lu C, Allis CD, Garcia BA, Jabado N, Lewis PW. Proc Natl Acad Sci U S A. 2020 Oct 16:202006076.

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans.  Millan-Ariño L, Yuan ZF, Oomen ME, Brandenburg S, Chernobrovkin A, Salignon J, Körner L, Zubarev RA, Garcia BA, Riedel CG. Curr Protoc Protein Sci. 2020 Dec;102(1):e114.

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease.  Nativio R, Lan Y, Donahue G, Sidoli S, Berson A, Srinivasan AR, Shcherbakova O, Amlie-Wolf A, Nie J, Cui X, He C, Wang LS, Garcia BA, Trojanowski JQ, Bonini NM, Berger SL. Nat Genet. 2020 Oct;52(10):1024-1035.

SIRT1 is downregulated by autophagy in senescence and ageing

H3.3G34W promotes growth and impedes differentiation of osteoblast-like mesenchymal progenitors in Giant Cell Tumour of Bone

H3.3G34W promotes growth and impedes differentiation of osteoblast-like mesenchymal progenitors in Giant Cell Tumour of Bone. Khazaei S, De Jay N, Deshmukh S, Hendrikse LD, Jawhar W, Chen CC, Mikael LG, Faury D, Marchione DM, Lanoix J, Bonneil E, Ishii T, Jain SU, Rossokhata K, Sihota TS, Eveleigh R, Lisi V, Harutyunyan AS, Jung S, Karamchandani J, Dickson BC, Turcotte R, Wunder JS, Thibault P, Lewis PW, Garcia BA, Mack SC, Taylor MD, Garzia L, Kleinman CL, Jabado N. Cancer Discov. 2020 Sep 23:CD-20-0461. doi: 10.1158/2159-8290.CD-20-0461. Online ahead of print.

Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease

Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease.  Robinson AE, Binek A, Venkatraman V, Searle BC, Holewinski RJ, Rosenberger G, Parker SJ, Basisty N, Xie X, Lund PJ, Saxena G, Mato JM, Garcia BA, Schilling B, Lu SC, Van Eyk JE. J Proteome Res. 2020 Sep 23. doi: 10.1021/acs.jproteome.0c00685. Online ahead of print.

The catalytic domain of the histone methyltransferase NSD2/MMSET is required for the generation of B1 cells in mice

The catalytic domain of the histone methyltransferase NSD2/MMSET is required for the generation of B1 cells in mice.  Dobenecker MW, Marcello J, Becker A, Rudensky E, Bhanu NV, Carrol T, Garcia BA, Prinjha R, Yurchenko V, Tarakhovsky A. FEBS Lett. 2020 Aug 9. doi: 10.1002/1873-3468.13903. Online ahead of print.

The Viral Polymerase Complex Mediates the Interaction of Viral Ribonucleoprotein Complexes with Recycling Endosomes during Sendai Virus Assembly

The Viral Polymerase Complex Mediates the Interaction of Viral Ribonucleoprotein Complexes with Recycling Endosomes during Sendai Virus Assembly. Genoyer E, Kulej K, Hung CT, Thibault PA, Azarm K, Takimoto T, Garcia BA, Lee B, Lakdawala S, Weitzman MD, López CB. mBio. 2020 Aug 25;11(4):e02028-20. doi: 10.1128/mBio.02028-20.

Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers

Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers.  Hoshino A, Kim HS, Bojmar L, Gyan KE, Cioffi M, Hernandez J, Zambirinis CP, Rodrigues G, Molina H, Heissel S, Mark MT, Steiner L, Benito-Martin A, Lucotti S, Di Giannatale A, Offer K, Nakajima M, Williams C, Nogués L, Pelissier Vatter FA, Hashimoto A, Davies AE, Freitas D, Kenific CM, Ararso Y, Buehring W, Lauritzen P, Ogitani Y, Sugiura K, Takahashi N, Alečković M, Bailey KA, Jolissant JS, Wang H, Harris A, Schaeffer LM, García-Santos G, Posner Z, Balachandran VP, Khakoo Y, Raju GP, Scherz A, Sagi I, Scherz-Shouval R, Yarden Y, Oren M, Malladi M, Petriccione M, De Braganca KC, Donzelli M, Fischer C, Vitolano S, Wright GP, Ganshaw L, Marrano M, Ahmed A, DeStefano J, Danzer E, Roehrl MHA, Lacayo NJ, Vincent TC, Weiser MR, Brady MS, Meyers PA, Wexler LH, Ambati SR, Chou AJ, Slotkin EK, Modak S, Roberts SS, Basu EM, Diolaiti D, Krantz BA, Cardoso F, Simpson AL, Berger M, Rudin CM, Simeone DM, Jain M, Ghajar CM, Batra SK, Stanger BZ, Bui J, Brown KA, Rajasekhar VK, Healey JH, de Sousa M, Kramer K, Sheth S, Baisch J, Pascual V, Heaton TE, La Quaglia MP, Pisapia DJ, Schwartz R, Zhang H, Liu Y, Shukla A, Blavier L, DeClerck YA, LaBarge M, Bissell MJ, Caffrey TC, Grandgenett PM, Hollingsworth MA, Bromberg J, Costa-Silva B, Peinado H, Kang Y, Garcia BA, O’Reilly EM, Kelsen D, Trippett TM, Jones DR, Matei IR, Jarnagin WR, Lyden D. Cell. 2020 Aug 20;182(4):1044-1061.e18. doi: 10.1016/j.cell.2020.07.009. Epub 2020 Aug 13.

N6-methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis

Histone H3.3 phosphorylation amplifies stimulation-induced transcription

Histone H3.3 phosphorylation amplifies stimulation-induced transcription.  Armache A, Yang S, Martínez de Paz A, Robbins LE, Durmaz C, Cheong JQ, Ravishankar A, Daman AW, Ahimovic DJ, Klevorn T, Yue Y, Arslan T, Lin S, Panchenko T, Hrit J, Wang M, Thudium S, Garcia BA, Korb E, Armache KJ, Rothbart SB, Hake SB, Allis CD, Li H, Josefowicz SZ. Nature. 2020 Jul 22. doi: 10.1038/s41586-020-2533-0. Online ahead of print.

Plasma proteomic profiling suggests an association between antigen driven clonal B cell expansion and ME/CFS

Plasma proteomic profiling suggests an association between antigen driven clonal B cell expansion and ME/CFS.  Milivojevic M, Che X, Bateman L, Cheng A, Garcia BA, Hornig M, Huber M, Klimas NG, Lee B, Lee H, Levine S, Montoya JG, Peterson DL, Komaroff AL, Lipkin WI. PLoS One. 2020 Jul 21;15(7):e0236148.

Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing

Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing. Herrmann C, Dybas JM, Liddle JC, Price AM, Hayer KE, Lauman R, Purman CE, Charman M, Kim ET, Garcia BA, Weitzman MD. Nat Microbiol. 2020 Jul 13. doi: 10.1038/s41564-020-0750-9. Online ahead of print.

Histone Acetyltransferase MOF Blocks Acquisition of Quiescence in Ground-State ESCs through Activating Fatty Acid Oxidation

Histone Acetyltransferase MOF Blocks Acquisition of Quiescence in Ground-State ESCs through Activating Fatty Acid Oxidation.  Khoa LTP, Tsan YC, Mao F, Kremer DM, Sajjakulnukit P, Zhang L, Zhou B, Tong X, Bhanu NV, Choudhary C, Garcia BA, Yin L, Smith GD, Saunders TL, Bielas SL, Lyssiotis CA, Dou Y. Cell Stem Cell. 2020 Jun 24:S1934-5909(20)30272-1.

SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair

SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair. Rezazadeh S, Yang D, Biashad SA, Firsanov D, Takasugi M, Gilbert M, Tombline G, Bhanu NV, Garcia BA, Seluanov A, Gorbunova V. Aging (Albany NY). 2020 Jun 25;12.

Improvements on the quantitative analysis of Trypanosoma cruzi histone post translational modifications: Study of changes in epigenetic marks through the parasite’s metacyclogenesis and life cycle

Improvements on the quantitative analysis of Trypanosoma cruzi histone post translational modifications: Study of changes in epigenetic marks through the parasite’s metacyclogenesis and life cycle.  de Lima LP, Poubel SB, Yuan ZF, Rosón JN, de Luna Vitorino FN, Holetz FB, Garcia BA, da Cunha JPC. J Proteomics. 2020 May 29:103847. doi: 10.1016/j.jprot.2020.103847.

Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma

Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma. Michealraj KA, Kumar SA, Kim LJY, Cavalli FMG, Przelicki D, Wojcik JB, Delaidelli A, Bajic A, Saulnier O, MacLeod G, Vellanki RN, Vladoiu MC, Guilhamon P, Ong W, Lee JJY, Jiang Y, Holgado BL, Rasnitsyn A, Malik AA, Tsai R, Richman CM, Juraschka K, Haapasalo J, Wang EY, De Antonellis P, Suzuki H, Farooq H, Balin P, Kharas K, Van Ommeren R, Sirbu O, Rastan A, Krumholtz SL, Ly M, Ahmadi M, Deblois G, Srikanthan D, Luu B, Loukides J, Wu X, Garzia L, Ramaswamy V, Kanshin E, Sánchez-Osuna M, El-Hamamy I, Coutinho FJ, Prinos P, Singh S, Donovan LK, Daniels C, Schramek D, Tyers M, Weiss S, Stein LD, Lupien M, Wouters BG, Garcia BA, Arrowsmith CH, Sorensen PH, Angers S, Jabado N, Dirks PB, Mack SC, Agnihotri S, Rich JN, Taylor MD. Cell. 2020 May 20:S0092-8674(20)30553-5.

Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function

Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function. Ren W, Medeiros N, Warneford-Thomson R, Wulfridge P, Yan Q, Bian J, Sidoli S, Garcia BA, Skordalakes E, Joyce E, Bonasio R, Sarma K. Nat Commun. 2020 May 6;11(1):2219.

Human chimeric antigen receptor macrophages for cancer immunotherapy

Human chimeric antigen receptor macrophages for cancer immunotherapy. Klichinsky M, Ruella M, Shestova O, Lu XM, Best A, Zeeman M, Schmierer M, Gabrusiewicz K, Anderson NR, Petty NE, Cummins KD, Shen F, Shan X, Veliz K, Blouch K, Yashiro-Ohtani Y, Kenderian SS, Kim MY, O’Connor RS, Wallace SR, Kozlowski MS, Marchione DM, Shestov M, Garcia BA, June CH, Gill S. Nat Biotechnol. 2020 Mar 23. doi: 10.1038/s41587-020-0462-y. [Epub ahead of print]

Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High vs Low Content of Artemisinin

Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High vs Low Content of Artemisinin. Chen M, Yan T, Ji L, Yu D, Sidoli S, Yuan Z, Cai C, Chen J, Tang Y, Shen Q, Pan Q, Fu X, Xin K, Liao L, Garcia BA, Yan W, Tang K. Proteomics. 2020 May;20(10):e1900310.

Unraveling the RNA modification code with mass spectrometry

Unraveling the RNA modification code with mass spectrometry. Lauman R, Garcia BA. Mol Omics. 2020 Apr 14. doi: 10.1039/c8mo00247a. [Epub ahead of print]

Bacterial colonization reprograms the neonatal gut metabolome

Bacterial colonization reprograms the neonatal gut metabolome. Bittinger K, Zhao C, Li Y, Ford E, Friedman ES, Ni J, Kulkarni CV, Cai J, Tian Y, Liu Q, Patterson AD, Sarkar D, Chan SHJ, Maranas C, Saha-Shah A, Lund P, Garcia BA, Mattei LM, Gerber JS, Elovitz MA, Kelly A, DeRusso P, Kim D, Hofstaedter CE, Goulian M, Li H, Bushman FD, Zemel BS, Wu GD. Nat Microbiol. 2020 Apr 13. doi: 10.1038/s41564-020-0694-0. [Epub ahead of print]

Disruption of the Plasmodium falciparum life cycle through transcriptional reprogramming by inhibitors of Jumonji demethylases

Disruption of the Plasmodium falciparum life cycle through transcriptional reprogramming by inhibitors of Jumonji demethylases. Matthews KA, Senagbe KM, Notzel C, Gonzalez CA, Tong X, Rijo-Ferreira F, Natarajan BV, Miguel-Blanco C, Lafuente-Monasterio MJ, Garcia BA, Kafsack BF, Martinez ED. ACS Infect Dis. 2020 May 8;6(5):1058-1075.

Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment

Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment. Chan JC, Morgan CP, Adrian Leu N, Shetty A, Cisse YM, Nugent BM, Morrison KE, Jašarević E, Huang W, Kanyuch N, Rodgers AB, Bhanu NV, Berger DS, Garcia BA, Ament S, Kane M, Neill Epperson C, Bale TL. Nat Commun. 2020 Mar 20;11(1):1499.

Global regulation of the histone mark H3K36me2 underlies epithelial plasticity and metastatic progression

Global regulation of the histone mark H3K36me2 underlies epithelial plasticity and metastatic progression. Yuan S, Natesan R, Sanchez-Rivera FJ, Li J, Bhanu NV, Yamazoe T, Lin JH, Merrell AJ, Sela Y, Thomas SK, Jiang Y, Plesset JB, Miller EM, Shi J, Garcia BA, Lowe SW, Asangani IA, Stanger BZ. Cancer Discov. 2020 Jun;10(6):854-871.

Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins

Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins. Selamoglu N, Önder Ö, Öztürk Y, Khalfaoui-Hassani B, Blaby-Haas CE, Garcia BA, Koch HG, Daldal F. Metallomics. 2020 Apr 1;12(4):572-591.

Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy

Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy. Gehre M, Bunina D, Sidoli S, Lübke MJ, Diaz N, Trovato M, Garcia BA, Zaugg JB, Noh KM. Nat Genet. 2020 Mar;52(3):273-282.

Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis

Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis. Coradin M, Mendoza MR, Sidoli S, Alpert AJ, Lu C, Garcia BA. Methods. 2020 Feb 15. pii: S1046-2023(19)30173-2.

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry.

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Wein S, Andrews B, Sachsenberg T, Santos-Rosa H, Kohlbacher O, Kouzarides T, Garcia BA, Weisser H. Nat Commun. 2020 Feb 17;11(1):926.

HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics

HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics. Marchione DM, Ilieva I, Devins K, Sharpe D, Pappin DJ, Garcia BA, Wilson JP, Wojcik JB. J Proteome Res. 2020 Feb 7;19(2):973-983.

Quantitative live cell imaging reveals influenza virus manipulation of Rab11A transport through reduced dynein association

Quantitative live cell imaging reveals influenza virus manipulation of Rab11A transport through reduced dynein association. Bhagwat AR, Le Sage V, Nturibi E, Kulej K, Jones J, Guo M, Tae Kim E, Garcia BA, Weitzman MD, Shroff H, Lakdawala SS. Nat Commun. 2020 Jan 7;11(1):23.

Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance

Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance. Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D. Mol Cell. 2020 Jan 2;77(1):51-66.