Samuel Bakhoum: Publications

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Li J, Hubisz MJ, Earlie EM, Duran MA, Hong C, Varela AA, Lettera E, Deyell M, Tavora B, Havel JJ, Phyu SM, Amin AD, Budre K, Kamiya E, Cavallo JA, Garris C, Powell SN, Reis-Filho J, Wen H, Bettigole S, Khan AJ, Izar B, Parkes EE, Laughney AM*, Bakhoum SF* (2023) Cancer cell non-autonomous tumor progression from chromosomal instability. Nature, 620, 1080-1088.

Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BS, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau DA, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y*, Bakhoum SF* (2023) Epigenetic dysregulation from chromosomal transit in micronuclei. Nature, 619, 176-183.

Lin Y-F, Hu Q, Mazzagatti A, Valle-Inclan JE, Maurais EG, Dahiya R, Guyer A, Sanders JT, Engel JL, Nguyen G, Bronder D, Bakhoum SF, Cortés-Ciriano I, Peter Ly P (2023) Mitotic clustering of pulverized chromosomes from micronuclei. Nature. 618, 1041-1048.

Ho P, Melms JC, Rogava M, Frangieh CJ, Poźniak J, Shah SB, Walsh Z, Kyrysyuk O, Amin AD, Caprio L, Fullerton BT, Soni RK, Ager CR, Biermann J, Wang Y, Khosravi-Maharlooei M, Zanetti G, Mu M, Fatima H, Moore EK, Vasan N, Bakhoum SF, Reiner SL, Bernatchez C, Sykes M, Mace EM, Wucherpfennig KW, Schadendorf D, Bechter O, Shah P, Schwartz GK, Marine JC, Izar B (2023) The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity. Cancer Cell, 41, 1207-1221.

Shamseddine A, Patel SH, Chavez V, Moore ZR, Adnan M, Di Bona M, Li J, Dang CT, Ramanathan LV, Oeffinger KC, Liu JE, Steingart RM, Piersigilli A, Socci ND, Chan AT, Yu AF, Bakhoum SF, Schmitt AM (2023) Innate immune signaling drives late cardiac toxicity following DNA-damaging cancer therapies. Journal of Experimental Medicine, 220, e20220809,

Deyell M, Bakhoum SF (2023) Unjamming tumor cell invasion through cGAS-STING. Nature Materials. 22, 532-533.

Vázquez-García I, Uhlitz F, Ceglia N, Lim JLP, Wu M, Mohibullah N, Niyazov J, Ruiz AEB, Boehm KM, Bojilova V, Fong CJ, Funnell T, Grewal D, Havasov E, Leung S, Pasha A, Patel DM, Pourmaleki M, Rusk N, Shi H, Vanguri R, Williams MJ, Zhang AW, Broach V, Chi DS, Da Cruz Paula A, Gardner GJ, Kim SH, Lennon M, Long Roche K, Sonoda Y, Zivanovic O, Kundra R, Viale A, Derakhshan FN, Geneslaw L, Issa Bhaloo S, Maroldi A, Nunez R, Pareja F, Stylianou A, Vahdatinia M, Bykov Y, Grisham RN, Liu YL, Lakhman Y, Nikolovski I, Kelly D, Gao J, Schietinger A, Hollmann TJ, Bakhoum SF, Soslow RA, Ellenson LH, Abu-Rustum NR, Aghajanian C, Friedman CF, McPherson A, Weigelt B, Zamarin D, Shah SP (2022) Ovarian cancer mutational processes drive site-specific immune evasion. Nature, 612, 778-786.

Biermann J, Melms JC, Amin AD, Wang Y, Caprio LA, Karz A, Tagore S, Barrera I, Ibarra-Arellano MA, Andreatta M, Fullerton BT, Gretarsson KH, Sahu V, Mangipudy VS, Nguyen TTT, Nair A, Rogava M, Ho P, Koch PD, Banu M, Humala N, Mahajan A, Walsh ZH, Shah SB, Vaccaro DH, Caldwell B, Mu M, Wünnemann F, Chazotte M, Berhe S, Luoma AM, Driver J, Ingham M, Khan SA, Rapisuwon S, Slingluff CL Jr, Eigentler T, Röcken M, Carvajal R, Atkins MB, Davies MA, Agustinus A, Bakhoum SF, Azizi E, Siegelin M, Lu C, Carmona SJ, Hibshoosh H, Ribas A, Canoll P, Bruce JN, Bi WL, Agrawal P, Schapiro D, Hernando E, Macosko EZ, Chen F, Schwartz GK, Izar B (2022) Dissecting the treatment-naïve ecosystem of human melanoma brain metastasis. Cell, 185, 2591-2608.

Nguyen B, Fong C, Luthra A, Smith SA, DiNatale RG, Nandakumar S, Walch H, Chatila WK, Madupuri R, Kundra R, Bielski CM, Mastrogiacomo B, Donoghue MTA, Boire A, Chandarlapaty S, Ganesh K, Harding JJ, Iacobuzio-Donahue CA, Razavi P, Reznik E, Rudin CM, Zamarin D, Abida W, Abou-Alfa GK, Aghajanian C, Cercek A, Chi P, Feldman D, Ho AL, Iyer G, Janjigian YY, Morris M, Motzer RJ, O’Reilly EM, Postow MA, Raj NP, Riely GJ, Robson ME, Rosenberg JE, Safonov A, Shoushtari AN, Tap W, Teo MY, Varghese AM, Voss M, Yaeger R, Zauderer MG, Abu-Rustum N, Garcia-Aguilar J, Bochner B, Hakimi A, Jarnagin WR, Jones DR, Molena D, Morris L, Rios-Doria E, Russo P, Singer S, Strong VE, Chakravarty D, Ellenson LH, Gopalan A, Reis-Filho JS, Weigelt B, Ladanyi M, Gonen M, Shah SP, Massague J, Gao J, Zehir A, Berger MF, Solit DB, Bakhoum SF, Sanchez-Vega F, Schultz N (2022) Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients. Cell, 185, 563-575.

Bakhoum MF, Francis JH, Agustinus A, Earlie EM, Di Bona M, Abramson DH, Duran M, Masilionis I, Molina E, Shoushtari AN, Goldbaum MH, Mischel PS*, Bakhoum SF*, Laughney AM* (*co-corresponding authors) (2021) Loss of Polycomb Repressive Complex 1 Activity and chromosomal instability drive uveal melanoma progression. Nature Communications. 12, 5402,

Venkatesan S, Angelova M, Puttick C, Zhai H, Caswell DR, Lu WT, Dietzen M, Galanos P, Evangelou K, Bellelli R, Lim EL, Watkins TBK, Rowan A, Teixeira VH, Zhao Y, Chen H, Ngo B, Zalmas LP, Al Bakir M, Hobor S, Gronroos E, Pennycuick A, Nigro E, Campbell BB, Brown WL, Akarca AU, Marafioti T, Wu MY, Howell M, Boulton SJ, Bertoli C, Fenton TR, de Bruin RAM, Maya-Mendoza A, Santoni-Rugiu E, Hynds RE, Gorgoulis VG, Jamal-Hanjani M, McGranahan N, Harris RS, Janes SM, Bartkova J, Bakhoum SF*, Bartek J*, Kanu N*, Swanton C* (*Co-corresponding authors) (2021) Induction of APOBEC3 exacerbates DNA replication stress and chromosomal instability in early breast and lung cancer evolution. Cancer Discovery, ePub ahead of print.

Li J, Duran MA, Dhanota N, Chatila WK, Bettigole SE, Kwon J, Sriram RK, Humphries MP, Salto-Tellez M, James JA, Hanna MG, Melms JC, Vallabhaneni S, Litchfield K, Usaite I, Biswas D, Bareja R, Li HW, Martin ML, Dorsaint P, Cavallo JA, Li P, Pauli C, Gottesdiener L, DiPardo BJ, Hollmann TJ, Merghoub T, Wen HY, Reis-Filho JS, Riaz N, Su SM, Kalbasi A, Vasan N, Powell SN, Wolchok JD, Elemento O, Swanton C, Shoushtari AN, Parkes EE, Izar B, Bakhoum SF (2021) Metastasis and immune evasion from extracellular cGAMP hydrolysis. Cancer Discovery. 11, 1212-1227.

Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, Katsyv I, Rendeiro AF, Amin AD, Schapiro D, Frangieh CJ, Luoma AM, Filliol A, Fang Y, Ravichandran H, Clausi MG, Alba GA, Rogava M, Chen SW, Ho P, Montoro DT, Kornberg AE, Han AS, Bakhoum MF, Anandasabapathy N, Suárez-Fariñas M, Bakhoum SF, Bram Y, Borczuk A, Guo XV, Lefkowitch JH, Marboe C, Lagana SM, Del Portillo A, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B. (2021) A molecular single-cell lung atlas of lethal COVID-19. Nature, ePub ahead of print.

Xu Z, Verma A, Naveed U, Bakhoum SF, Khosravi P, Elemento O (2021) Deep learning predicts chromosomal instability from histopathology images. iScience. ePub ahead of print.

Vashi N and Bakhoum SF (2021) The evolution of STING signaling and its involvement in cancer. Trends in Biochemical Sciences. ePub ahead of print.

Watkins TBK, Lim EL, Petkovic M, Elizalde E, Birkbak NJ, Wilson GA, Moore DA, Grönroos E, Rowan A, Dewhurst SM, Demeulemeester J, Dentro SC, Horswell S, Au L, Haase K, Escudero M, Rosenthal R, Bakir MA, Xu H, Litchfield K, Lu WT, Mourikis TP, Dietzen M, Spain L, Cresswell GD, Biswas D, Lamy P, Nordentoft I, Harbst K, Castro-Giner F, Yates LR, Caramia F, Jaulin F, Vicier C, Tomlinson IP, Brastianos PK, Cho RJ, Bastian BC, Dyrskjøt L, Jönsson GB, Savas P, Loi S, Campbell PJ, Andre F, Luscombe NM, Steeghs N, Tjan-Heijnen VCG, Szallasi Z, Turajlic S, Jamal-Hanjani M, Van Loo P, Bakhoum SF, Schwarz RF, McGranahan N, Swanton C (2020) Pervasive Chromosomal Instability and Karyotype Order During Tumour Evolution. Nature. 587, 126-132.

Ngo B, Kim E, Osorio-Vasquez V, Doll S, Bustraan S, Liang RJ, Luengo A, Davidson SM, Ali A, Ferraro GB, Fischer GM, Eskandari R, Kang DS, Ni J, Plasger A, Rajasekhar VK, Kastenhuber ER, Bacha S, Sriram RK, Stein BD, Bakhoum SF, Snuderl M, Cotzia P, Healey JH, Mainolfi N, Suri V, Friedman A, Manfredi M, Sabatini DM, Jones DR, Yu M, Zhao JJ, Jain RK, Keshari KR, Davies MA, Vander Heiden MG, Hernando E, Mann M, Cantley LC, Pacold ME (2020) Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition. Cancer Discovery. 10, 1352-1373.

Cogan D and Bakhoum SF (2020) Re-awakening innate immune signaling: the development of highly potent ENPP1 inhibitors. Cell Chemical Biology: 27, 1327-1328.

Braunstein LZ, Gillespie EF, Hong L, Xu A, Bakhoum SF, Cuaron J, Mueller B, McCormick B, Cahlon O, Powell S, Khan AJ. (2020) Breast radiotherapy under COVID-19 pandemic resource constraints - approaches to defer or shorten treatment from a Comprehensive Cancer Center in the United States. Advances in Radiation Oncology: ePub ahead of print.

Bronder D and Bakhoum SF (2020) A CINful way to overcome addition: how chromosomal instability enables cancer to overcome its oncogene addiction. EMBO Molecular Medicine: 12, e12017.

Schonhoft JD, Zhao JL, Jendrisak A, Carbone EA, Barnett ES, Hullings MA, Gill A, Sutton R, Lee J, Dago AE, Landers M, Bakhoum SF, Wang Y, Gonen M, Dittamore R, Scher HI. (2020) Morphology-predicted large-scale transition number in circulating tumor cells identifies a chromosomal instability biomarker associated with poor outcome in castration-resistant prostate cancer. Cancer Research. 80, 4892-4903.

Kwon J, Bakhoum SF (2020) The cytosolic DNA sensing cGAS-STING pathway in cancer. Cancer Discovery. 10, 26-39.

Laughney AM, Hu J, Campbell NR, Bakhoum SF, Setty M, Lavallée VP, Xie Y, Masilionis I, Carr AJ, Kottapalli S, Allaj V, Mattar M, Rekhtman N, Xavier JB, Mazutis L, Poirier JT, Rudin CM, Pe’er D, Massagué J. (2020) Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Nature Medicine: 26, 259-269.

Bronder D and Bakhoum SF (2020) A CINful way to overcome addition: how chromosomal instability enables cancer to overcome its oncogene addiction. EMBO Molecular Medicine: 12, e12017.

Noble K, Owens J, Andre F, Bakhoum SF, Loi S, Reinhardt HC, Tuveson D, Swanton C (2020) Securing the future of the clinician-scientist. Nature Cancer: 1, 139-141.

Li J, Bakhoum SF. (2019) Expanding the role of STING in cellular homeostasis and transformation. Trends in Cancer: 5, 195-197.

Elizalde S, Laughney AM, Bakhoum SF (2018) A Markov chain for numerical chromosomal instability in clonally expanding populations. PLOS Computational Biology. 14:e1006447.

Bakhoum SF (corresponding author), Cantley LC (2018) The multifaceted role of chromosomal instability in cancer and its microenvironment. Cell: 174: 1347-1360

  • Cover Page Article
  • Faculty of 1000 selection
  • Highlighted in Science Translational Medicine, Cancer Discovery, and Nature Reviews Cancer
  • Highlighted by The Scientist Magazine April 1, 2018 by Jim Daley
  • Featured by Weill Cornell Medicine News Room and in the MSKCC Cancer Blog

Loh PR, Genovese G, Handsaker RE, Finucane HK, Reshef YA, Palamara PF, Birmann BM, Talkowski M, Bakhoum SF, McCarroll SA, Price AL (2018) An atlas of 8,342 mosaic structural variants reveals genetic drivers of clonal hematopoiesis. Nature: 559, 350-355.

Galluzzi L, Vanpouille-Box C, Bakhoum SF, Demaria S (2018) SnapShot: cGAS-STING signalling. Cell: 173, 276.

Bakhoum SF, Landau DA (2017) Cancer Evolution – no room for negative selection. Cell: 171, 987-989. 

Bakhoum SF (corresponding author), Kabeche L, Compton DA, Powell SN, Bastians H (2017) Mitotic DNA damage response: at the crossroads of structural and numerical cancer chromosome instabilities. Trends in Cancer:3, 225-234.

Bakhoum SF (corresponding author), Landau DA (2016) Chromosomal instability as a driver of tumor heterogeneity and evolution. Cold Spring Harbor Perspectives in Medicine: In press, doi: 10.1101/cshperspect.a029611.

Laughney AM, Elizalde S, Genovese G, Bakhoum SF (corresponding author) (2015) Dynamics of tumor heterogeneity derived from clonal karyotypic evolution. Cell Reports: 12, 809-820.

  • Cover Page Article

Bakhoum SF (corresponding author), Kabeche L, Wood MD, Laucius CD, Qu D, Laughney AM, Louie RJ, Phillips J, Chan DA, Petritsch C, Zaki BI, Murnane JP, Compton DA (2015) Numerical chromosomal instability mediates susceptibility to radiation treatment. Nature Communications: 6, 5990.

Genovese G, Kähler AK, Handsaker RE, Lindberg J, Rose SA, Bakhoum SF,Chambert K, Mick E, Neale BM, Fromer M, Purcell SM, Svantesson O, Landén M, Höglund M, Lehmann S, Gabriel SB, Moran J, Lander ES, Sullivan PF, Sklar P, Grönberg H, Hultman CM, McCarroll SA (2014) Clonal hematopoiesis and blood cancer risk in blood-derived DNA sequence. The New England Journal of Medicine: 371, 2477-2487.

  • Highlighted by Abkowitz JL (2014) Clone wars – the emergence of neoplastic blood-cell clones with aging. The New England Journal of Medicine 371, 2523-2525

Bakhoum SF* (corresponding author), Kabeche L*, Murnane JP, Zaki BI, Compton DA (2014) DNA damage response during mitosis induces whole chromosome missegregation. Cancer Discovery: 4, 1281-1289.

  • Highlighted by Jelluma N and Kops GJPL (2014) Collateral genome instability by DNA damage in mitosis. Cancer Discovery 4, 1256-1258

Zaki BI, Suriawinata A, Eastman A, Garner K, Bakhoum SF (corresponding author) (2014) Chromosomal instability portends superior response of rectal adenocarcinoma to chemoradiation therapy. Cancer: 120, 1733-1742.

Bakhoum SF, Silkworth WT, Nardi IK, Nicholson JM, Compton DA, Cimini D (2014) The mitotic origin of chromosomal instability. Current Biology: 24, R148-149.

Bekelis K, Desai A, Bakhoum SF, Missios S (2014) Spine surgery complication prediction: the National Surgical Quality Improvement Program (NSQIP) 2005-2010. The Spine Journal: 14, 1247-1255.

Bakhoum SF (corresponding author), Swanton C (2014) Chromosomal instability, aneuploidy, and cancer. Frontiers in Oncology: 4, 161.

Bekelis K, Bakhoum SF (co-first author), Desai A, Roberts D (2013) Outcome prediction in intracranial tumor surgery: the National Surgery Quality Improvement Program 2005-2010. Journal of Neurooncology: 113, 57-64.

Bekelis K, Bakhoum SF (co-first author), Desai A, Goodney P, Labropoulos N (2013) A risk factor-based predictive model of outcomes in carotid endarterectomy: the National Surgical Quality Improvement Program 2005-2010. Stroke: 44, 1085-1090.

Bakhoum SF (corresponding author), Compton DA (2012) Chromosomal instability and cancer: a complex relationship with therapeutic potential. The Journal of Clinical Investigation: 122, 1138-1143.

Bakhoum SF, Compton DA (2012) Kinetochores and disease: keeping microtubule dynamics in check! Current Opinion in Cell Biology: 24, 7704-7711.

Bakhoum SF (corresponding author), Danilova OV, Kaur P, Levy NB, Compton DA (2011) Chromosomal instability substantiates poor prognosis in patients with Diffuse Large B-Cell Lymphoma. Clinical Cancer Research: 17, 7704-7711.

  • Cover Page Article
  • Featured in Dartmouth Now “Samuel Bakhoum: exploring the intersection of science and medicine” by Joseph Blumberg. December 19, 2011

Manning AL, Bakhoum SF (co-first author), Maffini S, Correia-Melo C, Maiato H, Compton DA (2010) CLASP1, astrin, and Kif2b form a molecular switch that regulates kinetochore-microtubule dynamics to promote mitotic progression and fidelity. EMBO Journal: 29, 3531-3543.

  • Faculty of 1000 selection

Thompson SL, Bakhoum SF, Compton DA (2010) Mechanisms of chromosomal instability. Current Biology: 20, R285-R295.

Bakhoum SF, Thompson SL, Manning AL, Compton DA (2009) Genome stability is ensured by temporal control of kinetochore-microtubule dynamics.Nature Cell Biology: 11, 27-35.

  • Faculty of 1000 selection
  • Featured in the Dartmouth Medicine Magazine: “Manipulating proteins facilitates division” by Amos Esty. Sum 2009
  • Featured in Dartmouth College News: “Dartmouth Researchers identify a potential cancer target” Jan. 16th, 2009

Bakhoum SF, Genovese G, Compton DA (2009) Deviant kinetochore microtubule dynamics underlie chromosomal instability. Current Biology: 19, 1937-1942.

  • Faculty of 1000 selection
  • Featured by Khodjakov A and Rieder C (2009) Current Biology 19, R1032-1034

Bakhoum SF, Compton DA (2009) Cancer: CINful centrosomes. Current Biology: 19, R642-R645.

Kollu S, Bakhoum SF, Compton DA (2009) Interplay of microtubule dynamics and sliding during bipolar spindle formation in mammalian cells. Current Biology: 19, 2108-2113.

Manning AL, Ganem NJ, Bakhoum SF, Wagenbach M, Wordeman L, Compton DA (2007) The kinesin-13 proteins Kif2a, Kif2b, and Kif2c/MCAK have distinct roles during mitosis in human cells. Molecular Biology of the Cell: 18, 2970-2979.

  • Cover Page Article

Draper ND, Bakhoum SF, Haddrell AE, Agnes GR (2007) Ion-induced nucleation in solution: promotion of solute nucleation in charged levitated droplets. Journal of the American Chemical Society: 129, 11364-11377.

Bakhoum SF (2006) Bench-to-bedside solution to funding problems. Nature: 443, 7111.

Stirling PC, Bakhoum SF, Feigl AB, Leroux MR (2006) Convergent Evolution of Clamp-like binding sites in Diverse Chaperones. Nature Structural & Molecular Biology: 13, 865-870.

Bakhoum SF, Bogan MJ, Agnes GR (2005) Archiving and absolute quantitation of solutes separated by single charged droplet coulomb explosion. Analytical Chemistry: 77, 3461-3465.

Bakhoum SF, Agnes GR (2005) A Study of chemistry in droplets with net charge before and after coulomb explosion: Ion-induced nucleation in solution and implications for ion production in an electrospray. Analytical Chemistry: 77, 3189-3197.

Bogan MJ, Bakhoum SF, Agnes GR (2005) Promotion of a-cyano-4-hydroxycinnammic acid and peptide co-crystallization within levitated droplets with net charge. Journal of the American Society for Mass Spectrometry: 16, 254-262.

Opinion Articles and Editorials

Bakhoum SF (2010) Cultivating Collaboration. The Dartmouth Medicine Magazine: 34 (3), 25.

Bakhoum SF (2008) Graduate students meet ASCB council: Graduate student council, facebook group launched. American Society for Cell Biology Newsletter: 31 (4), 36.

Bakhoum SF (2009) Don’t speak in Greek to me. American Physician-Scientist Association Newsletter: 3 (3), 1.

 Bakhoum SF (2008) M.D.-Ph.D.–worth the investment? American Physician-Scientist Association Newsletter: 3 (2), 1.