Publications

Bibliography : https://www.ncbi.nlm.nih.gov/myncbi/1pQ3ocvtrdAk5/bibliography/public/

Peer-Reviewed Articles: 2022

Sturm G, Karan KR, Monzel AS, Santhanam B, Taivassalo T, Bris C, Ware SA, Cross M, Towheed A, Higgins-Chen A, McManus MJ, Cardenas A, Lin J, Epel ES, Rahman S, Vissing J, Grassi B, Levine M, Horvath S, Haller RG, Lenaers G, Wallace DC, St-Onge MP, Tavazoie S, Procaccio V, Kaufman BA, Seifert EL, Hirano M, Picard M. OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases. Commun Biol. 2023 Jan 12;6(1):22. doi: 10.1038/s42003-022-04303-x. PubMed PMID: 36635485; PubMed Central PMCID: PMC9837150.

Sturm G, Monzel AS, Karan KR, Michelson J, Ware SA, Cardenas A, Lin J, Bris C, Santhanam B, Murphy MP, Levine ME, Horvath S, Belsky DW, Wang S, Procaccio V, Kaufman BA, Hirano M, Picard M. A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations. Sci Data. 2022 Dec 3;9(1):751. doi: 10.1038/s41597-022-01852-y. PubMed PMID: 36463290; PubMed Central PMCID: PMC9719499.

Verma M, Francis L, Lizama BN, Callio J, Fricklas G, Wang KZQ, Kaufman BA, D'Aiuto L, Stolz DB, Watkins SC, Nimgaonkar VL, Soto-Gutierrez A, Goldstein A, Chu CT. iPSC-Derived Neurons from Patients with POLG Mutations Exhibit Decreased Mitochondrial Content and Dendrite Simplification. Am J Pathol. 2022 Nov 19;. doi: 10.1016/j.ajpath.2022.11.002. [Epub ahead of print] PubMed PMID: 36414085.

Carew NT, Schmidt HM, Yuan S, Galley JC, Hall R, Altmann HM, Hahn SA, Miller MP, Wood KC, Gabris B, Stapleton MC, Hartwick S, Fazzari M, Wu YL, Trebak M, Kaufman BA, McTiernan CF, Schopfer FJ, Navas P, Thibodeau PH, McNamara DM, Salama G, Straub AC. Loss of cardiomyocyte CYB5R3 impairs redox equilibrium and causes sudden cardiac death. J Clin Invest. 2022 Sep 15;132(18). doi: 10.1172/JCI147120. PubMed PMID: 36106636; PubMed Central PMCID: PMC9479700.

Tian G, Katchur SR, Jiang Y, Briand J, Schaber M, Kreatsoulas C, Schwartz B, Thrall S, Davis AM, Duvall S, Kaufman BA, Rumsey WL. Small molecule-mediated allosteric activation of the base excision repair enzyme 8-oxoguanine DNA glycosylase and its impact on mitochondrial function. Sci Rep. 2022 Aug 29;12(1):14685. doi: 10.1038/s41598-022-18878-2. PubMed PMID: 36038587; PubMed Central PMCID: PMC9424235.

Rutledge CA, Kaufman BA, Dezfulian C, Elmer J. Metformin protects against cardiac and renal damage in diabetic cardiac arrest patients. Resuscitation. 2022 May;174:42-46. doi: 10.1016/j.resuscitation.2022.03.017. Epub 2022 Mar 21. PubMed PMID: 35331801; PubMed Central PMCID: PMC9050929.

Sidarala V, Zhu J, Levi-D'Ancona E, Pearson GL, Reck EC, Walker EM, Kaufman BA, Soleimanpour SA. Mitofusin 1 and 2 regulation of mitochondrial DNA content is a critical determinant of glucose homeostasis. Nat Commun. 2022 Apr 29;13(1):2340. doi: 10.1038/s41467-022-29945-7. PubMed PMID: 35487893; PubMed Central PMCID: PMC9055072.

Nath S, Caron NS, May L, Gluscencova OB, Kolesar J, Brady L, Kaufman BA, Boulianne GL, Rodriguez AR, Tarnopolsky MA, Truant R. Functional characterization of variants of unknown significance in a spinocerebellar ataxia patient using an unsupervised machine learning pipeline. Hum Genome Var. 2022 Apr 14;9(1):10. doi: 10.1038/s41439-022-00188-8. PubMed PMID: 35422034; PubMed Central PMCID: PMC9010413.

Peer-Reviewed Articles: 2021

Dosunmu-Ogunbi A, Yuan S, Reynolds M, Giordano L, Sanker S, Sullivan M, Stolz DB, Kaufman BA, Wood KC, Zhang Y, Shiva S, Nouraie SM, Straub AC. SOD2 V16A Amplifies Vascular Dysfunction in Sickle Cell Patients by Curtailing Mitochondria Complex IV Activity. Blood. 2021 Dec 27;. doi: 10.1182/blood.2021013350. [Epub ahead of print] PubMed PMID: 34958669.

Giordano L, Gregory AD, Pérez Verdaguer M, Ware SA, Harvey H, DeVallance E, Brzoska T, Sundd P, Zhang Y, Sciurba FC, Shapiro SD, Kaufman BA. Extracellular Release of Mitochondrial DNA: Triggered by Cigarette Smoke and Detected in COPD. Cells. 2022 Jan 22;11(3). doi: 10.3390/cells11030369. PubMed PMID: 35159179; PubMed Central PMCID: PMC8834490.

Kanshana JS, Mattila PE, Ewing MC, Wood AN, Schoiswohl G, Meyer AC, Kowalski A, Rosenthal SL, Gingras S, Kaufman BA, Lu R, Weeks DE, McGarvey ST, Minster RL, Hawley NL, Kershaw EE. A murine model of the human CREBRFR457Q obesity-risk variant does not influence energy or glucose homeostasis in response to nutritional stress. PLoS One. 2021;16(9):e0251895. doi: 10.1371/journal.pone.0251895. eCollection 2021. PubMed PMID: 34520472; PubMed Central PMCID: PMC8439463.

Kaufman BA, Mora AL. IRGM1, a guardian of mitochondrial DAMP-mediated autoinflammation. Nat Immunol. 2021 Mar;22(3):272-273. doi: 10.1038/s41590-021-00877-6. PMID: 33547457.

Trumpff C, Michelson J, Lagranha CJ, Taleon V, Karan KR, Sturm G, Lindqvist D, Fernström J, Moser D, Kaufman BA, Picard M. Stress and circulating cell-free mitochondrial DNA: A systematic review of human studies, physiological considerations, and technical recommendations. Mitochondrion. 2021 Jul;59:225-245. doi: 10.1016/j.mito.2021.04.002. Epub 2021 Apr 9. PMID: 33839318.

Peer-Reviewed Articles: 2020

Edmunds LR, Xie B, Mills AM, Huckestein BR, Undamatla R, Murali A, Pangburn MM, Martin J, Sipula I, Kaufman BA, Scott I, Jurczak MJ. Liver-specific Prkn knockout mice are more susceptible to diet-induced hepatic steatosis and insulin resistance. Mol Metab. 2020 Nov;41:101051. doi: 10.1016/j.molmet.2020.101051. Epub 2020 Jul 10. PubMed PMID: 32653576; PubMed Central PMCID: PMC7399260.

Ware SA, Desai N, Lopez M, Leach D, Zhang Y, Giordano L, Nouraie M, Picard M, Kaufman BA. An automated, high throughput methodology optimized for quantitative cell-free mitochondrial and nuclear DNA isolation from plasma. J Biol Chem. 2020 Sep 8;. doi: 10.1074/jbc.RA120.015237. [Epub ahead of print] PubMed PMID: 32900851.

Cole LK, Mejia EM, Sparagna GC, Vandel M, Xiang B, Han X, Dedousis N, Kaufman BA, Dolinsky VW, Hatch GM. Cardiolipin deficiency elevates susceptibility to a lipotoxic hypertrophic cardiomyopathy. J Mol Cell Cardiol. 2020 Jul;144:24-34. doi: 10.1016/j.yjmcc.2020.05.001. Epub 2020 May 11. PubMed PMID: 32418915.

Karan KR, Trumpff C, McGill MA, Thomas JE, Sturm G, Lauriola V, Sloan RP, Rohleder N, Kaufman BA, Marsland AL, Picard M. Mitochondrial respiratory capacity modulates LPS-induced inflammatory signatures in human blood. Brain Behav Immun Health. 2020 May;5. doi: 10.1016/j.bbih.2020.100080. Epub 2020 May 6. PubMed PMID: 33073254; PubMed Central PMCID: PMC7561023.

Rutledge C, Cater G, McMahon B, Guo L, Nouraie SM, Wu Y, Villanueva F, Kaufman BA. Commercial 4-dimensional echocardiography for murine heart volumetric evaluation after myocardial infarction. Cardiovasc Ultrasound. 2020 Mar 12;18(1):9. doi: 10.1186/s12947-020-00191-5. PubMed PMID: 32164714; PubMed Central PMCID: PMC7068892.

Rutledge CA, Chiba T, Redding K, Dezfulian C, Sims-Lucas S, Kaufman BA. A novel ultrasound-guided mouse model of sudden cardiac arrest. PLoS One. 2020 Dec 4;15(12):e0237292. doi: 10.1371/journal.pone.0237292. PMID: 33275630; PMCID: PMC7717537.

Levy MA, Kerkhof J, Belmonte FR, Kaufman BA, Bhai P, Brady L, Bursztyn LLCD, Tarnopolsky M, Rupar T, Sadikovic B. Validation and clinical performance of a combined nuclear-mitochondrial next-generation sequencing and copy number variant analysis panel in a Canadian population. Am J Med Genet A. 2021 Feb;185(2):486-499. doi: 10.1002/ajmg.a.61998. Epub 2020 Dec 10. PMID: 33300680.

Peer-Reviewed Articles: 2019

McManus MJ, Picard M, Chen H-W, De Haas HJ, Potluri P, Leipzig J, Towheed A, Angelin A, Sengupta P, Morrow RM, Kaufman BA, Vermulst M, Narula J, Wallace DC. Mitochondrial DNA Variation Dictates Expressivity and Progression of Nuclear DNA Mutations Causing Cardiomyopathy. Cell Metab. 2019 Jan 8;29(1):78-90.e5. doi: 10.1016/j.cmet.2018.08.002. Epub 2018 Aug 30. PubMed PMID: 30174309; PubMed Central PMCID: PMC6717513.

De Jesus D, DeVallance E, Li Y, Falabella M, Guimaraes D, Shiva S, Kaufman BA, Gladwin MT, Pagano P. Nox1/Ref-1-Mediated Activation of CREB Promotes Gremlin1-Driven Endothelial Cell Proliferation & Migration. Redox Biol. 2019 Apr;22:101138. doi: 10.1016/j.redox.2019.101138. Epub 2019 Feb 8. PubMed PMID: 30802716; PubMed Central PMCID: PMC6395885.

Falabella M, Kolesar JE, C. Wallace C, de Jesus D, Sun L, Taguchi YV, Wang C, Wang T, Xiang IM, Alder JK, Maheshan R, Horne W, Turek-Herman J, Pagano PJ, St. Croix CM, Sondheimer N, Yatsunyk LA, Johnson FB, Kaufman BA. G-quadruplex dynamics contribute to regulation of mitochondrial gene expression. Sci Rep. 2019 Apr 3;9(1):5605. doi: 10.1038/s41598-019-41464-y. PubMed PMID: 30944353; PubMed Central PMCID: PMC6447596.

Trumpff C, Marsland* AL, Basualto-Alarcón C, Martin JL, Carroll JE, Sturm G, Vincent AE, Mosharova EV, Gu Z, Kaufman BA*, Picard M*. Acute Psychological Stress Increases Serum Circulating Cell-Free Mitochondrial DNA. Psychoneuroendocrinology. 2019 Aug;106:268-276. PMCID: PMC6589121. *co-corresponding authors.

Patil P, Falabella M, Saeed A, Lee D, Kaufman BA, Shiva S, St. Croix C, Van Houten B, Neidernhofer LJ, Robbins PD, Lee J, Gwendolyn S, Vo N. Oxidative stress-induced senescence markedly increases disc cell bioenergetics. Mech Ageing Dev. 2019 Apr 17;180:97-106. (PMCID pending).

Trumpff C, Marsland AL, Sloan RP, Kaufman BA, Picard M. Predictors of ccf-mtDNA Reactivity to Acute Psychological Stress Identified Using Machine Learning Classifiers: A Proof-of-Concept. Psychoneuroendocrinology. 2019 Sep;107:82-92. PMCID: PMC6637411

Belmonte FR, Dedousis N, Sipula I, Desai NA, Singhi AD, Chu Y, Zhang Y, Bannwarth S, Paquis-Flucklinger V, Harrington L, Shiva S, Jurczak MJ, O’Doherty RM, and Kaufman BA. Petite Integration Factor 1 (PIF1) helicase deficiency increases weight gain in Western diet-fed female mice without increased inflammatory markers or decreased glucose clearance. PLoS One. 2019;14(5):e0203101. PMCID: PMC6538152.

Bueno M, Zank D, Buendia-Roldán I, Fiedler K, Mays BG, Alvarez D, Sembrat J, Kimball B, Bullock JK, Martin JL, Nouraie M, Kaufman BA, Rojas M, Pardo A, Selman M and Mora AL. PINK1 attenuates mtDNA release in alveolar epithelial cells and TLR9 mediated profibrotic responses. PLoS One. 2019;14(6):e0218003. PMCID: PMC6553779.

Naeem MM, Maheshan R, Costford SR, Wahedi A, Trajkovski M, Plavec J, Yatsunyk LA, Ciesielski GL, Kaufman BA and Sondheimer N. G-Quadruplex Mediated Reduction of a Pathogenic Mitochondrial Heteroplasmy. Hum Mol Genet. 2019 Jul 1. (PMCID pending).

Chung KW, Dhillon P, Huang S, Sheng X, Shrestha R, Qiu C, Kaufman BA, Park J, Pei L, Baur J, Palmer M, Susztak K. Mitochondrial Damage and Activation of the STING Pathway Lead to Renal Inflammation and Fibrosis. Cell Metab. 2019 Oct 1;30(4):784-799.e5. doi: 10.1016/j.cmet.2019.08.003. Epub 2019 Aug 29. PubMed PMID: 31474566.

2018

Guha M, Srinivasan S, Raman P, Jiang Y, Kaufman BA, Taylor D, Dong D, Chakravarti R, Picard M, Carstens R, Kijima Y, Feldman M, Avadhani N. Aggressive Triple Negative Breast Cancers have unique molecular signature on the basis of mitochondrial genetic and functional defects. BBA – Molecular Basis of Disease 2018 Apr; 1864(4 Pt A):1060-71. PMCID: PMC6417497.

Guha M, Srinivasan S, Johnson FB, Ruthel G,Guja K, Garcia-Diaz M, Kaufman BA, Glineburg MR, Fang J-K, Nakagawa H, Basha J, Kundu T, Avadhani NG. hnRNPA2 mediated acetylation reduces telomere length in response to mitochondrial dysfunction. PLoS One 2018 Nov 14: 13(11): e0206897. PMCID: PMC6241121.

2017

Howlett EH, Jensen N, Belmonte F, Zafar F, Hu X, Kluss J, Schüle B, Kaufman BA, Greenamyre JT, and Sanders LH. LRRK2 G2019S-induced mitochondrial DNA damage is LRRK2 kinase dependent and inhibition restores mtDNA integrity in Parkinson’s disease. Human Molecular Genetics 2017 Nov 15;26(22):4340-4351. PMCID: PMC5886254.

Falabella M, Sun L, Barr J, Pena AZ, Kershaw EE, Gingras S, Goncharova EA, Kaufman BA. Single-step qPCR and dPCR detection of diverse CRISPR-Cas9 gene editing events in vivo. G3 2017 7(10):3533-3542. PMCID: PMC5633400.

2016

Bannwarth S, Berg-Alonso L, Augé G., Fragaki K, Kolesar JE, Lespinasse F, Lacas-Gervais, S, Burel-Vandenbos F, Villa E, Belmonte F, Michiels J-F, Ricci J-E, Gherardi R, Harrington L, Kaufman BA, Paquis-Flucklinger V. Inactivation of Pif1 helicase causes a mitochondrial myopathy in mice. Mitochondrion. 2016 Feb 23 30:126-137. PMCID: PMC5454384.

Belmonte FR, Martin JL, Frescura K, Damas J, Pereira F, Tarnopolsky MA, and Kaufman BA. Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions. Scientific Reports 2016 6:25186. PMCID: PMC4848546.

Guha M, Srinivasan S, Guja K, Mejia E, Garcia-Diaz M, Johnson FB, Ruthel G, Kaufman BA, Rappaport EF, Glineburg MR, Fang J-K, Szanto AK, Nakagawa H, Basha J, Kundu T, and Avadhani NG. HnRNPA2 is a novel histone acetyltransferase which mediates mitochondrial stress induced nuclear gene expression. Cell Discovery 2016 Dec 6;2:16045 PMCID: PMC5148442.

2015 and earlier

Kaufman BA*, Newman SM*, Hallberg RL, Slaughter CA, Perlman PS, and Butow RA. In organello formaldehyde crosslinking of proteins to mtDNA: Identification of bifunctional proteins. Proc Natl Acad Sci U S A. 2000 Jul 5;97(14): 7772-7. PMCID: PMC16620. *these authors contributed equally to this work.

Kaufman BA, Kolesar JE, Perlman PS, Butow RA. A function for the mitochondrial chaperonin Hsp60 in the structure and transmission of mitochondrial DNA nucleoids in Saccharomyces cerevisiae. J Cell Biol. 2003 Nov 10; 163(3): 457-61. PMCID: PMC2173642.

Leary SC, Kaufman BA, Pellecchia G, Guercin GH, Mattman A, Jaksch M, Shoubridge EA. Human SCO1 and SCO2 have independent, cooperative functions in copper delivery to cytochrome c oxidase. Hum Mol Genet. 2004 Sep 1;13(17): 1839-48. PMID: 15229189

Chen XJ, Wang X, Kaufman BA, Butow RA. Aconitase couples metabolic regulation to mitochondrial DNA maintenance. Science. 2005 Feb 4;307(5710): 714-7. PMID: 15692048.

Leary SC, Cobine PA, Kaufman BA, Guercin GH, Mattman A, Palaty J, Lockitch G, Winge DR, Rustin P, Horvath R, Shoubridge, EA. The human cytochrome c oxidase assembly factors SCO1 and SCO2 have regulatory roles in the maintenance of cellular copper homeostasis. Cell Metab. 2007 Jan;5(1): 9-20. PMID: 17189203.

Kaufman BA*, Durisic N*, Mativetsky JM, Costantino S, Hancock MA, Grutter P, Shoubridge EA. The mitochondrial transcription factor TFAM coordinates the assembly of multiple DNA molecules into nucleoid-like structures. Mol Biol Cell. 2007 Sep;18(9): 3225-36. PMCID: PMC1951767. *these authors contributed equally to this work.

Weraarpachai W, Antonicka H, Sasarman F, Seeger J, Schrank B, Kolesar JE, Lochmüller H, Chevrette M, Kaufman BA, Horvath R, Shoubridge EA. Mutation in TACO1, encoding a translational activator of COX I, results in cytochrome c oxidase deficiency and late-onset Leigh syndrome. Nat Genet. 2009 Jul;41(7): 833-7. PMID: 19503089

Soubannier V, Rippstein P, Kaufman BA, Shoubridge EA, McBride HM. Reconstitution of mitochondria derived vesicle formation demonstrates selective enrichment of oxidized cargo. PLoS one. 2012;7(12): e52830. PMCID: PMC3530470.

Mallilankaraman K, Cárdenas C, Doonan PJ, Chandramoorthy HC, Irrinki KM, Golenár T, Csordás G, Madireddi P, Yang J, Müller M, Miller R, Kolesar JE, Molgó J, Kaufman B, Hajnóczky G, Foskett JK, Madesh M. MCUR1 is an Essential Component of Mitochondrial Ca2+ Uptake that Regulates Cellular Metabolism. Nat Cell Biol. 2012 Dec;14(12):1336-43. PMCID: PMC3511605.

Kolesar JE, Wang CY, Taguchi YV, Chou SH, Kaufman BA. Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome. Nucleic Acids Res. 2013 Feb 1;41(4);e58. PMCID: PMC3575812.

Soleimanpour S, Gupta A, Bakay M, Ferrari AM, Groff DN, Fadista J, Spruce LA, Kushner JA, Groop L, Seeholzer SH, Kaufman BA, Hakonarson H, Stoffers DA. The diabetes susceptibility gene Clec16a regulates mitophagy. Cell. 2014 Jun 19;157(7):1577-90. PMCID: PMC4184276.

Dong D, Pereira F, Barrett SP, Kolesar JE, Cao K, Damas J , Yatsunyk LA, Johnson FB, Kaufman BA. Association of G-quadruplex forming sequences with human mtDNA deletion breakpoints. BMC Genomics. 2014 Aug 13;15:677. PMCID: PMC4153896.

Kolesar JE, Safdar A, Abadi A, MacNeil LG, Crane JD, Tarnopolsky MA, Kaufman BA. Defects in mitochondrial DNA replication and oxidative damage in muscle of mtDNA mutator mice. Free Radic Biol Med. 2014 Oct;75:241-51. PMID: 25106705

Shanmughapriya S, Rajan S, Hoffman NE, Zhang X, Guo S, Kolesar JE, Hines KJ, Ragheb J, Jog NR, Caricchio R, Baba Y, Zhou Y, Kaufman BA, Cheung JY, Kurosaki T, Gill DL, Madesh M. Ca2+ signals regulate mitochondrial metabolism by stimulating CREB-mediated expression of the mitochondrial Ca2+ uniporter gene MCU. Sci Signal. 2015 Mar 3;8(366):ra23. PMCID: PMC4722812.

Soleimanpour SA, Ferrari AM, Raum JC, Groff DN, Yang J, Kaufman BA, Stoffers DA. Diabetes susceptibility genes Pdx1 and Clec16a function in a pathway regulating mitophagy in β-cells. Diabetes. 2015 Jun 17. pii: db150376. PMCID: PMC4587637.

Non-Peer Reviewed Publications

Kolesar JE, Kaufman BA. Using Two-Dimensional Intact Mitochondrial DNA (mtDNA) Agarose Gel Electrophoresis (2D-IMAGE) to Detect Changes in Topology Associated with Mitochondrial Replication, Transcription, and Damage. Methods Mol Biol. 2020;2119:25-42. doi: 10.1007/978-1-0716-0323-9_3. PubMed PMID: 31989512

Other Peer Reviewed Publications

Kaufman BA, Newman SM, Perlman PS, and Butow RA. Crosslinking of proteins to mtDNA. Methods Mol Biol. 2002; 197:377-389. PMID: 12013811.

Campbell CT, Kolesar JE, and Kaufman BA. Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number. Invited review. Biochim Biophys Acta. 2012 Sep-Oct: 1819(9-10): 921-929. PMID: 22465614.

Kaufman BA, Liu C, and Soleimanpour S. Mitochondrial regulation of beta cell function: maintaining the momentum for insulin release. Mol Aspects Med. 2015 Apr:42:91-104. PMCID: PMC4404204.

Kaufman BA and Van Houten B. POLB: A new role of DNA polymerase beta in mitochondrial base excision repair. DNA Repair. 2017 60:A1-A5. PMCID: PMC5713914.

Kaufman BA, Picard M, and Sondheimer N. Mitochondrial DNA, nuclear context and the risk for carcinogenesis. Environ Mol Mutagen 2018 Jan 14. (PMCID pending).

Falabella M, Fernandex III RJ, Johnson FB, and Kaufman BA. Potential roles for G-quadruplexes in mitochondria. Curr Med Chem 2018 Feb 28. PMCID: PMC6113130.

Kang I, Chu CT, and Kaufman BA. The mitochondrial transcription factor TFAM in neurodegeneration: Emerging evidence and mechanisms. FEBS Lett 2018 Mar; 592(5):793-811. PMCID:PMC5851836.

Kolesar JE and Kaufman BA. Using two-dimensional intact mitochondrial DNA (mtDNA) agarose gel electrophoresis (2D-IMAGE) to detect changes in topology associated with mitochondrial replication, transcription and damage. Methods in Molecular Biology. Invited review (accepted).