Publications

Contributions from members of the Naba lab are in bold

#Equal contribution; *Co-corresponding authors

1. Samarasinghe KW, Kotlyar M, Vallet SD, Naba A, Jurisica I, Lisacek F, Ricard-Blum S. MatrixDB 2024: an expanded interaction dataset and a new network explorer interface. Nucleic Acids Research, 2025 Database Issue. [Full Text]

2. Petrov PB, Considine JM, Izzi, V, and Naba A. Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. Journal of Cell Science, 2023, 136 (17): jcs261255. [Full Text] 

3. Desert R, Chen W, Ge X, Viel R, Han H, Athavale D, Das S, Song Z, Lantvit D, Cano L, Naba A, Musso O, Nieto N. Hepatocellular carcinoma exhibiting intratumor fibrosis, expresses cancer-specific extracellular matrix remodeling and WNT/TGFb signatures, associated with poor outcome. Hepatology, 2023. [Full Text]

4. Shao X, Gomez CD, Kapoor N, Considine JM, Grams C, Gao Y, Naba A. MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. Nucleic Acids Research, 2023, gkac1009. [Full Text] 

5. Sapao P, Roberson E, Shi B, Shervin Assassi S, Skaug B, Lee F, Naba A, Perez White B, Cordova Fletes C, Tsou PS, Sawalha AH, Gudjonsson JE, Ma F, Verma P, Bhattacharyya D, Carns M, Strauss III JF, Sicard D, Tschumperlin D, Champer M, Campagnola P, Teves ME, and Varga J. Reduced SPAG17 expression in systemic sclerosis triggers myofibroblast transition and drives fibrosis. Journal of Investigative Dermatology, 2022. [Full Text]

6.  Mondal C, Larkin K, Gacha Garcia M, Adikes R, Di Martino JS, Chien C, Fraser M, Eni-aganga I, Agullo-Pascual E, Ozbek U, Naba A, Gaitas A, Fu T, Upadhyayula S, Betzig E, Martin B, Matus DQ, and Bravo-Cordero JJ. A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGFβ2 signaling. Cell Reports, 2022, 40(12):111358. [Full Text]

7. Tellman TV, Dede M, Aggarwal VA, Salmon DR, Naba A, and Farach-Carson MC. Systematic analysis of actively transcribed core matrisome genes across tissues and cell phenotypes. Matrix Biology, 2022, 111:95-107. [Full Text]

8. Di Martino J, Nobre AR, Mondal C, Taha IN, Farias E, Fertig E, Naba A, Aguirre-Ghiso J, and Bravo-Cordero JJ. A collagen-III-rich ECM niche regulates tumor dormancy. Nature Cancer, 2021, 3(1):90-107. [Full Text]

9. Renner C, Gomez CD, Visetsouk MR, Taha IN, Khan A, McGregor S, Weisman P, Naba A*, Masters KS*, Kreeger PK*. Multi-modal profiling of the extracellular matrix of human fallopian tubes and serous tubal intraepithelial carcinomas. Journal of Histochemistry and Cytochemistry, 2021, 70(2):151-168. [Full Text]

10. Yazdanpanah G, Jiang Y, Rabiee B, Omidi M, Rosenblatt MI, Shokuhfar T, Pan Y, Naba A*, Djalilian A*. Fabrication, Rheological and Compositional Characterization of Thermoresponsive Hydrogel from Cornea.Tissue Eng Part C Methods, 2021, 27(5):307-321. [Full Text]

11. Vallet SD, Davis MN, Barqué A, Thahab AH, Ricard-Blum S, and Naba A. Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome. Biochemical Journal, 2021, BCJ20200675. [Full Text]

12. Pokhilko A, Brezzo G, Handunnetthi L, Heilig R, Lennon R, Smith C, Allan SM, Granata A, Sinha S, Wang T, Markus HS, Naba A, Fischer R, Van Agtmael T, Horsburgh K, and Cader MZ. Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease. J Cereb Blood Flow Metab. 2021, 17:271678X211004307. [Full Text]

13. Holstein E, Dittmann A, Kääriäinen, Pesola V, Koivunen J, Pihlajaniemi T, Naba A, and Izzi V. The Burden of Post-Translational Modification (PTM)—Disrupting Mutations in the Tumor Matrisome. Cancers, 2021, 13(5): 1081. [Full Text]

14. Barqué A, Jan K, De La Fuente E, Nicholas CL, and Hynes RO*, and Naba A*. Knockout of the gene encoding the extracellular matrix protein Sned1 results in craniofacial malformations and early neonatal lethality. Developmental Dynamics, 2020, 250(2):274-294. [Full Text]

15. Izzi V, Davis MN, and Naba A. Pan-Cancer Analysis of the Genomic Alterations and Mutations of the Matrisome. Cancers, 2020, 12(8), 2046 [Full Text]

16. Hebert JA, Myers SA, Naba A, Abbruzzese G, Lamar JM, Carr SA, and Hynes RO. Proteomic profiling of the ECM of xenograft breast cancer metastases in different organs reveals distinct metastatic niches. Cancer Research, 2020, 80(7):1475-1485 [Full Text]

17. Davis MN, Horne-Badovinac S, and Naba A. In-silico definition of the Drosophila melanogaster matrisome. Matrix Biology Plus, 2019, 100015. [Full Text]

> Press coverage: https://www.chicagobiomedicalconsortium.org/news/success-stories/august-2-2019/

18. Shao X, Taha IN, Clauser KR, Gao YT*, Naba A*. MatrisomeDB: the ECM-protein knowledge database. Nucleic Acids Research, 2019, pii: gkz849. [Full Text]

19. Teuscher A, Jongsma E, Davis MN, Statzer C, Gebauer JM*, Naba A*, and Ewald CY*. In-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. Matrix Biology Plus, 2019, 100001. [Full Text]

20. Clerc O, Deniaud M, Vallet S.D, Naba A, Rivet A, Perez S, Thierry-Mieg N, and Ricard-Blum S*. MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. Nucleic Acid Research, 2018, pii: gky1035.  [Full Text]

21. Nauroy P, Hughes S, Naba A*, and Ruggiero F*. The in-silico zebrafish matrisome: A new tool to study extracellular matrix gene and protein functions. Matrix Biology, 2018, 65:5-13. [Full Text]

22. Naba A*#, Pearce OMT*#, Del Rosario A, Ma D, Ding H, Rajeeve V, Cutillas PR, Balkwill FR, and Hynes RO. Characterization of the extracellular matrix of normal and diseased tissues using proteomics. Journal of Proteome Research, 2017, 16(8):3083-3091. [Full Text]

23. Gocheva V, Naba A*, Bhutkar A, Guardia T, Miller KM, Li CM, Dayton TL, Sanchez-Rivera FJ, Kim-Kiselak C, Jailkhani N, Winslow MW, Del Rosario A, Hynes RO, and Jacks T*. Quantitative proteomics identify Tenascin-C as a promoter of lung cancer progression and contributor to a signature prognostic of patient survival. Proceedings of the National Academy of Sciences, 2017, 114(28):E5625-E5634. [Full Text]

> Read the MIT News coverage

24. Glavey S.V#, Naba A#, Manier S#, Clauser K.R, Tahri S, Park J, Reagan MR, Moschetta M, Mishima Y, Gambella M, Rocci A, Sacco A, O'Dwyer M.E, Asara JM, Palumbo A, Roccaro AM, Hynes RO, and Ghobrial IM. Proteomic characterization of human multiple myeloma bone marrow extracellular matrix. Leukemia, 2017, (11):2426-2434 [Full Text]

25. Ragelle H#, Naba A#, Larson BL, Zhou F, Prijic M, Whittaker CA, Del Rosario A, Langer R, Hynes RO, and Anderson DG. Comprehensive proteomic characterization of stem-cell-derived extracellular matrices. Biomaterials, 2017, 128:147-159. [Full Text]

26. Naba A*, Clauser KR, Mani DR, Carr SA, and Hynes RO*. Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression. Scientific Reports, 2017, 7:40495. [Full Text]

27. Carmona G#, Perera U#, Gillett C, Naba A, Law A.L, Sharma V.P, Wang J, Wyckoff J, Balsamo M, Mosis F, De Piano M, Monypenny J, Woodman N, McConnell R.E, Mouneimne G, Van Hemelrijck M, Cao Y, Condeelis J, Hynes RO, Gertler FB, and Krause M. Lamellipodin promotes invasive 3D cancer cell migration via regulated interactions with Ena/VASP and SCAR/WAVE. Oncogene, 2016, 35:5155-69. [Full Text]

28. Naba A*, Clauser KR, and Hynes RO. Enrichment of extracellular matrix proteins from tissues and digestion into peptides for mass spectrometry analysis. Journal of Visualized Experiments, 2015, 101:e53057. [Video][Full Text]

29. Naba A*, Clauser KR, Whittaker CA, Carr SA, Tanabe KK, and Hynes RO*. Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver. BMC Cancer, 2014, 14(1):518. [Full Text]

> Received the “Highly Accessed” designation by BMC Cancer

> Read the F1000 recommendation of this article.

30. Naba A*, Clauser KR, Lamar JM, Carr SA, and Hynes RO*. Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters. eLife, 2014, 3:e01308. [Full Text]

> Read the F1000 recommendation of this article.

> Read the MIT News coverage

31. Naba A#, Clauser KR#, Hoersch S, Liu H, Carr SA*, and Hynes RO.* The matrisome: in-silico definition and in-vivo characterization by proteomics of normal and tumor extracellular matrices. Molecular and Cellular Proteomics, 2012, 11(4):M111.014647. [Full Text]

> Read the F1000 recommendation of this article.

32. Mak H#, Naba A#, Varma S#, Meens J, Arpin M, SenGupta S, and Elliott BE. Ezrin phosphorylation on tyrosine 477 regulates invasion and metastasis of breast cancer cells. BMC Cancer, 2012, 12(1):82-95. [Full Text]

> Received the “Highly Accessed” designation by BMC Cancer

33. Zwaenepoel I#, Naba A#, da Cunha MML#, Del Maestro L, Formstecher E, Louvard D, and Arpin M. Ezrin regulates microvillus morphogenesis by promoting distinct activities of Eps8 proteins. Molecular Biology of the Cell, 2012, 23(6):1080-95. Cover [Full Text]

34. Kanda S, Naba A, and Miyata Y. Inhibition of endothelial cell chemotaxis toward FGF-2 by Gefitinib associates with downregulation of Fes activity. International Journal of Oncology, 2009, 35:1305-1312. [Full Text]

35. Monni R, Haddaoui L, Naba A, Arpin M, Mayeux P, and Moreau-Gachelin F. Ezrin is a target for oncogenic Kit mutants in murine erythroleukemia. Blood, 2008, 6:3163-3172. [Full Text]

36. Naba A, Reverdy C, Louvard D, and Arpin M. Spatial recruitment and activation of the Fes kinase by ezrin promotes HGF-induced cell scattering. EMBO Journal, 2008, 27:38-50. [Full Text]

1. Bains AK and Naba A. Proteomic insights into the extracellular matrix: a focus on proteoforms and their implications in health and disease. Expert Review of Proteomics, 2024. [Full text]

2. Naba A. Mechanisms of assembly and remodeling of the extracellular matrix. Nature Reviews Molecular Cell Biology, 2024  [Full Text]

3. Pally D and Naba A. Extracellular matrix dynamics: a key regulator of cell migration across length-scales and systems. Current Opinion in Cell Biology, 2024, 86:102309. [Full Text]

4. Jain S, Pei L, Spraggins JM, Börner K, Snyder MP, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, HuBMAP Consortium. Advances and perspectives for the Human BioMolecular Atlas Program (HuBMAP). Nature Cell Biology, 2023. [Full Text]

5. Naba A. 10 years of extracellular matrix proteomics: Accomplishments, challenges, and future perspectives. Molecular and Cellular Proteomics, 2023, 22(4):100528. [Full Text]

6. Apte SS and Naba A. Editorial Beyond the matrisome: New frontiers in ECM research. Matrix Biology, 2023, 115:133-138. [Full Text]

7. Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Rodriguez H, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, and Kelleher NL. New views of old proteins: clarifying the enigmatic proteome. Molecular and Cellular Proteomics, 2022, S1535-9476(22)00062-7. [Full Text]

8. Nerger BA, Jones TM, Rose KWJ, Barqué A, Weinbaum JS, Petrie RJ, Chang J, Vanhoutte D, Kendra LaDuca K, Hubmacher D*, Naba A*. The Matrix in Focus: New Directions in Extracellular Matrix Research from the 2021 ASMB Hybrid Meeting. Biology Open, 2022, 11 (1): bio059156. [Full Text]

9. Gebauer J.M and Naba A. The Matrisome of Model Organisms: From In-Silico Prediction to Big-Data Annotation. In: Extracellular Matrix Omics. Biology of Extracellular Matrix, 2020, vol 7: 17-42, Springer. [Full Text]

10. Naba A* and Ricard-Blum S*. The Extracellular Matrix Goes -Omics: Resources and Tools. In: Extracellular Matrix Omics. Biology of Extracellular Matrix, 2020, vol 7: 1-16, Springer. [Full Text]

11. Bingham GC, Lee F, Naba A, Barker TH. Spatial-omics: Novel Approaches to Probe Cell Heterogeneity and Extracellular Matrix Biology. Matrix Biology, 2020, pii: S0945-053X(20)30049-4. [Full Text]

12. Arteel GE* and Naba A*. The liver matrisome: looking beyond collagens. JHEP Reports, 2020, pii: S2589-5559(20)30049-5. [Full Text] 

13. Taha IN and Naba A. Exploring the extracellular matrix in health and disease using proteomics. Essays in Biochemistry, 2019, EBC20190001 [Full Text]

> Press coverage: https://www.chicagobiomedicalconsortium.org/news/success-stories/2019-09-12-ecm-in-health-and-disease/

14. Socovich AM and Naba A. The cancer matrisome: from comprehensive characterization to biomarker discovery. Seminars in Cell & Developmental Biology, 2018, pii: S1084-9521(17)30580-3. [Full Text]

15. Zhou Y, Horowitz JC, Naba A, Ambalavanan N, Atabai K, Balestrini J, Bitterman PB, Corley RA, Ding BS, Engler AJ, Hansen KC, Hagood JS, Kheradmand F, Lin QS, Neptune E, Niklason L, Ortiz LA, Parks WC, Tschumperlin DJ, White ES, Chapman HA, Thannickal VJ. Extracellular matrix in lung development, homeostasis and disease. Matrix Biology, 2018, pii: S0945-053X(17)30434-1. [Full Text]

16. Naba A*, Clauser K.R, Ding H, Whittaker C.A, Carr S.A, and Hynes R.O*. The extracellular matrix in the “omics” era. Matrix Biology, 2016, pii: S0945-053X(15)00121-3. [Full Text]

17. Naba A, Hoersch S, and Hynes R.O. Towards Definition of an ECM Parts List: an Advance on GO Categories. Matrix Biology, 2012, 31(7/8):371-372. [Full Text]

18. Hynes R.O and Naba A. Overview of the Matrisome – an Inventory of ECM Constituents and Functions. In Extracellular Matrix Biology (eds. R.O. Hynes and K.M. Yamada), Cold Spring Harbor Perspectives in Biology, 2012, 4(1):a004903. [Full Text]

> Read the review of the book "Extracellular Matrix Biology" by Dr. Charles Streuli in Development.

19. Arpin M, Chirivino D, Naba A, and Zwaenepoel I. Emerging role for ERM proteins in cell adhesion and migration. Cell Adhesion and Migration, 2011, 5:199-206. [Full Text]

1. Lamba R, Paguntalan AM, Petrov PB, Naba A*, Izzi V*. MatriCom: a scRNA-Seq data mining tool to infer ECM-ECM and cell-ECM communication systems. bioRxiv, 2024. https://www.biorxiv.org/content/10.1101/2024.12.10.627834v1

2. Pally D, Kapoor N, Naba A. The novel ECM protein SNED1 mediates cell adhesion via α5β1 integrin. bioRxiv 2024. https://doi.org/10.1101/2024.08.07.606706  

3. Lee F, Shao X, Gao Y*, and Naba A*. Time-lapsed proteomics reveals a role of the novel protein, SNED1, in modulating ECM composition and protein folding. bioRxiv, 2022. https://doi.org/10.1101/2022.01.13.476092

4. Reis MC, Lee F, Bedran-Russo AK*, and Naba A*. Proteomic pipeline to identify age-related compositional and structural changes of the human dentin extracellular matrix. bioRxiv, 2021. https://www.biorxiv.org/content/10.1101/2020.05.27.116624v3

Cancer-related extracellular matrix signatures and related methods and products. Hynes R.O, Naba A, Carr S.A, Clauser K.R, and Tanabe K.K. Issued December 27, 2016 under the U.S. Patent No. 9,526,800 (colorectal cancer). Divisional application issued July 17, 2018 under the U.S. Patent No. 10,024,860 (breast cancer).