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Northwestern University Feinberg School of Medicine
Department of Biochemistry and Molecular Genetics

Recent Publications

  1. Fang J, Wang X  Opposing kinase signaling may underlie the inverse relationship between cancer and Alzheimer's disease.  J Proteomics  2026 Oct 15;331:105723. doi:10.1016/j.jprot.2026.105723
  2. Li L, Hernandez CC, Gimenez LE, Xu B, Dahir NS, Peisley A, Wu Z, Chen M, Serrato A, Wan R  et al.  Functional coupling between MC4R and Kir7.1 contributes to clozapine-induced weight gain in female mice.  Nat Commun  2026 Sep 03;17(1). pii:9139
  3. Zhang M, Mei H, Li Y, Xiao SY  Diversion-Associated Rectal Pathology in Patients With and Without Inflammatory Bowel Disease: A Rectum-Exclusive, Blinded Histologic Comparison and Practical Reporting Approach.  Am J Surg Pathol  2026 Aug 27;. doi:10.1097/PAS.0000000000002606
  4. Yu J, Ramirez MA, Wang YZ, Edassery S, Shramuk M, Yeom S, Li CJ, Joshi Y, Cheatham MA, Rutherford MA  et al.  Heat-shock pathway activation by TRC051384 protects spiral ganglion neurons from noise-induced hearing loss.  JCI Insight  2026 Aug 25;. pii:e203285
  5. Lowe DD, Shilatifard A  Transcriptional kinases drive gene expression network plasticity.  Mol Cell  2026 Aug 20;. pii:S1097-2765(26)00521-6
  6. Li L, Chao Z, Li J, Ma C, Zhang R, Zhang J, Luo J, Horne D, Wang Y, Hao X  et al.  Cofilin1-driven cytoskeletal remodeling modulates pan-cancer CD8+ T cell immunotherapy responses.  Cell Rep Med  2026 Aug 12;:102984. doi:10.1016/j.xcrm.2026.102984
  7. McNally EM, Puckelwartz MJ  The macromolecular native thick filament reveals pathogenic interfaces for hypertrophic cardiomyopathy.  Proc Natl Acad Sci U S A  2026 Aug 11;123(32):e2621061123. pii:e2621061123
  8. Lee G, Fitt AJ, Long AM, Vaught LA, DeBiasse D, Keeble AR, Kwon JM, Page PG, Daher MT, Hadhazy M  et al.  Excess muscle plasma membrane leak disrupts ECM content and shifts macrophage-mediated muscle repair.  JCI Insight  2026 Aug 10;11(15). pii:e205137
  9. Kanchustambham VL, Pla I, Xu T, Su P, Fisher NP, Hollas MAR, Markiv P, Agarwal U, Lysakowska M, Kafader JO  et al.  Proteoform Detection Across 17,000 Single Nuclei From Differentiating Skin Keratinocytes.  Mol Cell Proteomics  2026 Aug;25(8):101621. pii:101621
  10. Beauchamp EM, Jain A, Clutter M, Nahotko D, Lopez Fajardo E, Vagadia PP, Dunne SF, Mina A, Fischietti M, Oku CV  et al.  Development of a SIN1 Targeting Inhibitor as a Novel Therapeutic Approach for the Treatment of Malignancies.  Mol Cancer Ther  2026 Jul 02;25(7):1111-1129. doi:10.1158/1535-7163.MCT-25-0298
  11. Chang HR, Boull C, Cotton CH, Eichenfield DZ, García-Romero MT, Hawryluk EB, Lara-Corrales I, Oza VS, Wan J, Weiss M  et al.  Building consensus in pediatric dermatology research.  J Invest Dermatol  2026 Jul;146(7):1729-1732.e1. doi:10.1016/j.jid.2026.03.003
  12. Mazewski C, Perez RE, Vagadia PP, Kocherginsky M, Schiltz GE, Eckerdt F, Platanias LC  Potent Anti-Glioblastoma Effects of Next-Generation MNK Inhibitors.  Cancers (Basel)  2026 Jun 27;18(13). pii:2086
  13. Parast S, Das M, He Y, Wang S, Gold S, Howard B, Zeidner J, Philips C, Ben-Sahra I, Ramani V  et al.  Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome.  Proc Natl Acad Sci U S A  2026 Jun 23;123(25):e2607264123. pii:e2607264123
  14. Murmann AE, Ebadi M, Patel M, Ewe A, Barajas S, Xiao S, Ko MJ, Lee S, Cai W, Paudel B  et al.  Developing a pan cancer therapy based on DISE-inducing short RNAs.  Mol Ther Nucleic Acids  2026 Jun 16;37(2):102963. pii:102963
  15. Zhao Z, Shilatifard A  Enhancer and metabolic rewiring by KMT2C-COMPASS or KMT2D-COMPASS family loss in cancer creates druggable vulnerabilities.  Nat Rev Cancer  2026 Jun;26(6):437-451. doi:10.1038/s41568-026-00919-x
  16. Perez RE, Kellar KE, Hansaria N, Kocherginsky M, Fischietti M, Eckerdt F, Platanias LC  SLFN5 restrains type I interferon responses and promotes glioblastoma via its N-terminal Schlafen core domain.  Commun Biol  2026 May 27;9(1). pii:1128
  17. Soliman SHA, De Fabritiis S, Iwanaszko M, Lin LA, Das M, Gold S, Andersen GD, Chakrabarty RP, Chandel NS, Shilatifard A  Hypoxia-responsive interaction between P-TEFb, BHLHE40, and Tim8-Tim13 regulates hypoxic gene transcription.  Sci Adv  2026 May 22;12(21):eadz9295. pii:eadz9295
  18. Nahotko DA, Lee B, Lopez Fajardo E, Baran AH, Filip SK, Faull PA, Bartom ET, Kocherginsky M, Gao P, Miska J  et al.  Multi-omics analysis reveals LARP1 as a key integrator of translation and metabolism in AML.  Oncogenesis  2026 May 16;15(1). pii:37
  19. Gritsina G, Rath SK, Shi H, Chu Q, Xie W, Nguyen QTW, Senthil S, Myers TJ, Bilen MA, Fenton SE  et al.  AURKA inhibitor VIC-1911 induces mitotic defects and functional BRCAness, sensitizing prostate cancer to PARP inhibition.  JCI Insight  2026 May 08;11(9). pii:e196665
  20. Fisher NP, Kanchustambham VL, Tsui EL, Lock C, Xu T, McDowell HB, Pla I, Saunders DC, Kafader JO, Laronda MM  et al.  Probing Proteoform Heterogeneity From Single Human Oocytes.  Mol Cell Proteomics  2026 May;25(5):101566. pii:101566
  21. Du Z, Alasady MJ, Mendillo ML, Li L  Transcriptomic analysis of Rnq1 loss and prionization reveals alterations in translation pathways and energy metabolism.  Sci Rep  2026 Apr 02;16(1). pii:15778
  22. Su P, Hollas MAR, Pla I, Rubakhin S, Butun FA, Greer JB, Early BP, Fellers RT, Caldwell MA, Sweedler JV  et al.  Proteoform profiling of endogenous single cells from rat hippocampus at scale.  Nat Biotechnol  2026 Apr;44(4):563-567. doi:10.1038/s41587-025-02669-x
  23. Brea L, Shi H, Keo V, Huang J, Peng L, Chu Q, Xie W, Xie Y, Senthil S, Breneman MT  et al.  FOXA1 loss drives basal/squamous de-differentiation of prostate cancer and induces an immunosuppressive tumor microenvironment.  Nat Commun  2026 Mar 28;17(1). pii:4572
  24. Vidal-Cruchez O, Ben-Sahra I  The oncogenic control of nucleotide synthesis.  Oncogenesis  2026 Mar 26;15(1). pii:17
  25. Fischietti M, Zannikou M, Beauchamp EM, Saleiro D, Baran AH, Hryhorysak BN, Magaña JNG, Fajardo EL, Blyth GT, Castro BA  et al.  Schlafen 5 is an intracellular immune checkpoint and controls IFN responses in pancreatic ductal adenocarcinoma.  JCI Insight  2026 Mar 09;11(5). pii:e190031
  26. Smith RS, Mendillo ML  Heat shock transcription factors in development and disease.  Dis Model Mech  2026 Mar 01;19(3). pii:dmm052700
  27. Bodner J, Vadlamani P, Lee AS, Helmin KA, Liu Q, Pratasenia AE, Horst MMA, Ravisankar S, Khurana S, Mendillo ML  et al.  Human CRAMP1 specifically promotes the expression of histone H1 genes.  EMBO Rep  2026 Mar;27(5):1122-1145. doi:10.1038/s44319-026-00704-9
  28. Lee AS, Fisher NP, Marunde MR, Su P, Khan LF, Ezell RJ, Gillespie ZB, Graham B, Taylor HF, Onuoha UC  et al.  Direct Readout of Multivalent Chromatin Reader-Nucleosome Interactions by Nucleosome Mass Spectrometry.  ACS Cent Sci  2026 Feb 25;12(2):208-221. doi:10.1021/acscentsci.5c00736
  29. Chen YH, Collette JR, Sampat K, Yonchev ID, Hawkins CE, Ponne C, Rosencrance CD, Eagen KP  NSD3 stabilizes nuclear compartmentalization and promotes megabase-scale chromatin interactions.  bioRxiv  2026 Feb 10;. pii:2026.02.07.704091
  30. Vidal-Cruchez O, Ben-Sahra I  DHODH turns cytosolic, yet cells keep growing.  Nat Metab  2026 Feb;8(2):290-292. doi:10.1038/s42255-026-01466-3
  31. Xie W, Chu Q, Brea L, Zeng G, Wang Y, Lu X, Zheng M, Ley CR, Lei Z, Shi H  et al.  EZH2 PROTACs outperform catalytic inhibitors in prostate cancer by targeting a methylation-independent function of PRC2.  Oncogene  2026 Feb;45(5):636-649. doi:10.1038/s41388-025-03662-z
  32. Zheng B, Qiu R, Gold S, Iwanaszko M, Aoi Y, Howard BC, Das M, Shilatifard A  BRD2 bridges TFIID and MOF-H4K16ac-containing nucleosomes to promote transcriptional initiation.  Mol Cell  2026 Jan 22;86(2):273-288.e6. doi:10.1016/j.molcel.2025.12.010
  33. Sanchez A, Pla I, Huang CF, Kanchustambham VL, Hollas MAR, Greer JB, Ladner DP, Peterson KN, Fisher TD, Su T  et al.  SPAP: Soluble Human Plasma Proteoform Analysis via Acetonitrile Precipitation and Top-Down Mass Spectrometry.  J Am Soc Mass Spectrom  2026 Jan 07;37(1):188-199. doi:10.1021/jasms.5c00289
  34. Fisher TD, Compton PD, Robey MT, Fellers RT, Durbin KR, Kelleher NL  Automated Enzymatic Deglycosylation of Monoclonal Antibody with the SampleStream Platform.  J Am Soc Mass Spectrom  2026 Jan 07;37(1):336-340. doi:10.1021/jasms.5c00242
  35. Huang CF, Su T, Flozak AS, Gottardi CJ, Kelleher NL  Intact Mass Profiling Reveals Phospho-Proteoforms of the Catenins (85-110 kDa) Regulated by Actomyosin Contractility.  Angew Chem Int Ed Engl  2025 Dec 22;64(52):e18593. pii:e18593
  36. Parast S, Wang S, Iwanaszko M, He Y, Olgun DG, Gold S, Zeidner JM, Aoi Y, Howard BC, Thakur WR  et al.  Defective RNA processing and ELOA-mediated transcriptional elongation in reversible cellular senescence suggest aging by transcription.  Mol Cell  2025 Dec 18;85(24):4545-4561.e8. doi:10.1016/j.molcel.2025.11.021
  37. Srivastava S, Samaniego-Castruita D, Srivastava S, Khurana S, Rehman J, Shukla V, Ben-Sahra I, Foltz DR  Rate-limiting enzymes in nucleotide metabolism synchronize nucleotide biosynthesis and chromatin formation.  Mol Cell  2025 Dec 18;85(24):4510-4525.e8. doi:10.1016/j.molcel.2025.11.009
  38. Yu J, Ramirez MA, Wang YZ, Edassery S, Shramuk M, Cheatham MA, Rutherford MA, Welty LJ, Savas JN  Heat-shock pathway activation by TRC051384 protects spiral ganglion neurons from noise-induced hearing loss.  bioRxiv  2025 Dec 11;. pii:2025.12.08.693048
  39. Lu X, Peng L, Chu Q, Ye S, Liu M, Hussain M, Bilen MA, Harik LR, Melamed J, Zhao JC  et al.  Targeting p300 and CBP abolishes HOXB13-loss-induced lipogenesis and tumor metastasis.  JCI Insight  2025 Nov 24;10(22). pii:e195743
  40. Nengroo MA, Klein AT, Carr HS, Vidal-Cruchez O, Sahu U, McGrail DJ, Sahni N, Thompson NB, Faull PA, Gao P  et al.  Accumulation of succinate suppresses de novo purine synthesis through succinylation-mediated control of the mitochondrial folate cycle.  Mol Cell  2025 Nov 20;85(22):4215-4228.e9. doi:10.1016/j.molcel.2025.10.002
  41. Monroe TO, Puckelwartz MJ, Pesce LL, Kearns SD, Page P, Ibrahim N, Weber ZT, Ugwor EI, Nóbrega MA, Kannankeril P  et al.  A combined genomic arrhythmia propensity score delineates cumulative risk.  Cell Rep Med  2025 Nov 18;6(11):102455. pii:102455
  42. Guillen Magaña JN, Zannikou M, Baran A, Small S, Schieber M, Schipma MJ, Bartom ET, Kocherginsky M, Saleiro D, Beauchamp EM  et al.  Schlafen 12 Modulation and Targeting in Acute Myeloid Leukemia.  Cancer Res Commun  2025 Nov 01;5(11):2012-2024. doi:10.1158/2767-9764.CRC-25-0283
  43. Skinner KA, Fisher TD, Lee A, Su T, Forte E, Sanchez A, Caldwell MA, Kelleher NL  Next-generation protein sequencing and individual ion mass spectrometry enable complementary analysis of interleukin-6.  Anal Bioanal Chem  2025 Nov;417(28):6291-6299. doi:10.1007/s00216-025-06120-7
  44. Choi J, Gordon A, Eresen A, Zhang Z, Borhani A, Bagci U, Lewandowski R, Kim DH  Current applications of radiomics in the assessment of tumor microenvironment of hepatocellular carcinoma.  Abdom Radiol (NY)  2025 Oct;50(10):4661-4675. doi:10.1007/s00261-025-04916-w
  45. Lu X, Keo V, Cheng I, Xie W, Gritsina G, Wang J, Lu L, Shiau CK, He Y, Jin Q  et al.  NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling.  Nat Genet  2025 Aug;57(8):1966-1980. doi:10.1038/s41588-025-02265-4
  46. Wang X, Li Y, Lin Z, Pla I, Gajjela R, Mattamana BB, Joshi M, Liu Y, Wang H, Zun AB  et al.  Microtopography-induced changes in cell nucleus morphology enhance bone regeneration by modulating the cellular secretome.  Nat Commun  2025 Jul 11;16(1):6444. pii:6444
  47. Xu T, Su T, Soye BJD, Kandi S, Huang CF, Wilkins JT, Castellani RJ, Kafader JO, Patrie SM, Vassar R  et al.  The Proteoform Landscape of Tau from the Human Brain.  J Proteome Res  2025 Jun 06;24(6):2916-2925. doi:10.1021/acs.jproteome.5c00139
  48. Zhang M, Rodriguez A, Weir R, Hanmer J, Harrison JM, Edelen MO  Validity evidence for the Patient Reported Outcome Measurement Information System (PROMIS)® Cognitive Screener (PRO-CS) to detect risk for cognitive decline as part of the Medicare Annual Wellness Visit.  Adv Patient Rep Outcomes  2025 Jun;1(2). pii:100190
  49. Wang X, Grobe N, Franchin B, Levitsky J, Cravedi P, Kotanko P  Metabolomic and proteomic analyses of renal function after liver transplantation.  Front Transplant  2025;4:1572852. pii:1572852
  50. Ives AN, Jooß K, Melani RD, Fellers RT, Janetzko J, Kelleher NL  Capillary Zone Electrophoresis-Mass Spectrometry of Intact G Protein-Coupled Receptors Enables Proteoform Profiling.  Anal Chem  2025 Apr 08;97(13):7307-7316. doi:10.1021/acs.analchem.4c06994

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