kshitizlab

Publications

# Corresponding Authors, * Authors contributed equally

Google Scholar: https://scholar.google.com/citations?user=6JTbqZkAAAAJ&hl=en

 

  1. Du W, Novin A, Liu Y, Afzal J, Suhail Y, Gavin NR, Jorgensen J, Schmidt T, Morosky CM, Sanders M, Brewer M, Kshitiz (2024), Scar matrix drives Piezo1 mediated stromal inflammation leading to placenta accreta spectrum, Nature Communications, 8379.
  2. Suhail Y, Liu Y, Du W, Afzal J, Qiu X, Atiq A, Vera-Licona P, Agmon, E, Kshitiz (2024), Oscillatory hypoxia induced gene expression predicts low survival in human breast cancer patients, Molecular Carcinogenesis.
  3. Liu Y, Suhail Y, Novin A, Afzal J, Pant A, Kshitiz (2024), Lactate n breat cancer cells is associated with evasion of hypoxia-induced cell cycle arrest and adverse patient outcome, Human Cell 37, 768-781.
  4. Liu S, Liu Y, Qiu X, Suhail Y, Kshitiz (2024), Tissue-of-origin for cancers determine HIF-1 activation induced phenotypic heterogeneity, Molecular Carcinogenesis.
  5. Novin A, Wali K, Pant A, Liu S, Du W, Liu Y, Wang L, Xu M, Wang B, Suhail Y, Kshitiz (2024), Oscillatory Hypoxia can Induce Senescence of Adipose-derived Mesenchymal Stromal Cells Potentiating Invasive Transformation of Breast Epithelial Cells, Cancers 16(5), 969.
  6. Du W, Novin A, Liu Y, Afzal J, Liu S, Suhail Y, Kshitiz (2024), Oscillatory hypoxia induced gene expression predicts low survival in human breast cancer patients, Mechanobiology in Medicine 3, 100070-11.
  7. Dighe A, Maziarz J, Ibrahim-Hasin A, Gatenby RA, Kshitiz, Levchenko A, Wagner GP (2024), Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts, iScience 27(1), 108593.
  8. Afzal J, Kshitiz (2023), CRISPRing the hypertrophic cardiomyopathy: correcting one pathogenic variant at a time, Signal Transduction & Targeted Therapy, Nature Publications 116(254).
  9. Liu Y, Atiq A, Peterson A, Moody M, Novin A, Deymier AC, Afzal J, Kshitiz (2023), Metabolic Acidosis Results in Sexually Dimorphic Response in the Heart Tissue, Metabolites, 13(4), 549.
  10. Nikhil M, Suhail Y, Goyal R, Du W, Tanguay AP, Jay GD, Ghosh M, Kshitiz, Schmidt T (2022), Recombinant Human Proteoglycan 4 (rhPRG4) Downregulates TNFα-Stimulated NFκB Activity and FAT10 Expression in Human Corneal Epithelial Cells, International Journal of Molecular Sciences, 23(21), 12711.
  11. Afzal J*, Du W*, Novin A, Liu Y, Wagner G, Kshitiz (2022), Paracrine HB-EGF signaling reduce enhanced contractile and energetic state of activated decidual fibroblasts by rebalancing SRF-MRTF-TCF transcriptional axis, Frontiers in Cell & Development Biology, 10, 927631.
  12. Kshitiz±, Afzal J, Suhail Y, Chang H, Hubbi ME, Hamidzadeh A, Goyal R, Liu Y, Sun P, Dang CV±, Levchenko A± (2022), Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1a activity promoting proliferation of hypoxic cells, Cell Systems, Accepted. ± Corresponding authors. 
  13. Afzal J±, Liu Y, Du W*, Suhail Y*, Zong P, Feng J, Ajeti V, Sayyad WA, Nikolaus J, Yankova M, Deymier AC, Yue L, Kshitiz*, Cardiac ultrastructure inspired matrix induces advanced metabolic and functional maturation of differentiated human cardiomyocytes, Cell Reports, Accepted.
  14. Liu S, Suhail Y, Novin A, Perpetua L, Kshitiz (2022). Metastatic Transition of Pancreatic Ductal Cell Adenocarcinoma is Accompanied by the Emergence of Pro-Invasive Cancer-Associated Fibroblasts, Cancers, 14(9), 2197.
  15. Suhail Y, Maziarz J.D., Novin A, Dighe A, Afzal J, Wagner G, Kshitiz (2022). Tracing the cis-regulatory changes underlying the endometrial control of placental invasion, Proceedings of the National Academy of Sciences, 119(6).
  16. Wang L, Wang B, Gasek NS, Zhou Y, Zhou Y, Cohn RL, Martin DE, Zuo W, Flynn WF, Guo C, Jellison ER, Kin T, Prata LGPL, Palner AK, Li M, Inman CL, Barber LS, Al-Naggar IMA, Zhou Y, Du W, Kshitiz, Kuchel GA, Meves A, Tchknonia T, Kirkland JL, Robson P, Xu M (2022). Targeting p21Cip1 highly expressing cells in adipose tissue alleviates insulin resistance in obesity, Cell Metabolism, 34, 75-89.
  17. Wagner GP±, Kshitiz, Dighe A, Levchenko A (2021). The Coevolution of Placentation and Cancer, Annual Review of Animal Biosciences, 10, 259-279.
  18. Suhail Y, Afzal J, Kshitiz (2021). Evolved Resistance to Placental Invasion Secondarily Confers Increased Survival in Melanoma Patients, Journal of Clinical Medicine, 10(595).
  19. Suhail Y, Afzal J, Kshitiz (2021). Incorporating and addressing testing bias within estimates of epidemic dynamics for SARS-Cov-2, BMC Medical Research Methodology, 21(1).
  20. Novin A, Suhail Y, Ajeti V, Goyal R, Wali K, Seck A, Jackson A, Kshitiz (2021). Diversity in cancer invasion phenotypes indicates specific stroma regulated programs, Human Cell, 34(1), 111-121.
  21. Chiou G, Jui E, Rhea AC, Gorthi A, Miar S, Acosta FM, Perez C, Suhail Y, Kshitiz, Chen Y, Ong JL, Bizios R, Rathbone C, Guda T (2020). Scaffold Architecture and Matrix Strain Modulate Mesenchymal Cell and Microvascular Growth and Development in a Time Dependent Manner, Cellular and Molecular Bioengineering, 13, 507-526.
  22. Wagner G, Kshitiz, Levchenko A (2020). Comments on Boddy et al., 2020: Available data suggests positive relationship between placental invasion and malignancy, Evolution, Medicine, & Public Health, 1, 211-214.
  23. Suhail Y, Upadhyay M, Chhibber A, Kshitiz (2020). Machine Learning for the Diagnosis of Orthodontic Extractions: A Computational Analysis Using Ensemble Learning, Bioengineering, 7(2), 55.
  24. Gassaway BM, Cardone RL, Padyana AK, Petersen MC, Judd ET, Hayes S, Tong S, Barber KW, Apostolidi M, Abulizi A, Sheetz JB, Kshitiz, Aerni HR, Gross S, Kung C, Samuel VT, Shulman GI, Kibbey RG, Rinehart J (2019). Distinct Hepatic PKA and CDK Signaling Pathways Control Activity-Independent Pyruvate Kinase Phosphorylation and Hepatic Glucose Production, Cell Reports, 29(11), 3394-3404.
  25. Kshitiz±, Afzal J, Maziarz JD, Hamidzadeh A, Liang C, Erkenbrack EM, Ham H, Haeger, JD, Pfarrer C, Hoang T, Ott T, Spencer T, Pavlicev M, Antczak D, Levchenko A±, Wagner GP± (2019). The Evolution of Placental Invasion and Cancer Metastasis are Causally Linked, Nature Ecology and Evolution (Accepted). ±: Corresponding Authors
  26. Suhail Y, Cain MP, Vanaja K, Kurywchak PA, Levchekno A, Kalluri R, Kshitiz (2019). Systems Biology of Cancer Metastasis, Cell Systems, 9(2), 109-127.
  27. Kshitiz*±, Ellison DE*, Suhail Y*, Afzal J, Woo L, Kilic O, Spees J, Levchenko A± (2019).  Dynamic Secretome of Bone Marrow Derived Stromal Cells Reveals a Cardio-protective Biochemical Cocktail, Proceedings of the National Academy of Sciences, 116(28), 14374-83. ±: Corresponding Authors
  28. Park JS, Kim DH, Shah SR, Kim HN, Kshitiz, Kim P, Quinones-Hinojosa A, Levchenko A (2019). Switch-like enhancement of epithelial-mesenchymal transition by YAP through feedback regulation nof WT1 and Rho-family GTPases, Nature Communications, 2797.
  29. Kim DH, Ewald AJ, Park JS, Kshitiz, Kwark M, Gray RS, Su CY, Seo J, An SS, Levchenko A (2018), Biomechanical interplay between anisotropic re-organization of cell and the surrounding matrix underlies transition to invasive cancer spread, Scientific Reports, 14210.
  30. Ahn EH, Lee MB, SeoDJ, Lee J, Kim Y, Gupta K (2018). Sphigosine Induced Apoptosis and Down-regulation of MYCN in PAX3-FOXO1-positive Alveolar Rabdomyocarcoma Cells Irrespective of TP53 Mutation, Anticancer Research, 38(1), 71-76.
  31. Kshitiz, Afzal J, Chang H, Goyal R, Levchenko A (2015). Mechanics of Microenvironment as Instructive Cues Guiding Stem Cell Behavior, Current Stem Cell Biology, 2(1), 62-72.
  32. Kshitiz, Afzal J, Kim SY, Kim DH (2015). A nanotopography approach for studying the structure-function relationships of cells and tissues, Cell Adhesion & Migration, 9(4), 300-307.
  33. Kshitiz, Afzal J, Suhail Y, Ahn EH, Goyal R, Hubbi ME, Hussaini Q, Ellison DD, Goyal J, Nacev B, Kim DH, Lee JH, Frankel S, Gray K, Bankoti R, Chien AJ, Levchenko A (2015). Control of the interface between heterotypic cell populations reveals the mechanism of intercellular transfer of signaling proteins, Integrative Biology, 7, 364-372.
  34. Hubbi ME, Gilkes DM, Hu H, Kshitiz, Ahmed I, Semenza GL (2014). Cyclin-dependent kinases regulate lysosomal degradation of hypoxia-inducible factor 1-alpha to promote cell-cycle progression, Proceedings of the National Academy of Sciences, E3325-3334.
  35. Kshitiz, Afzal J, Kim DH, Levchenko A (2014). Mechanotransduction via p190RhoGAP regulates a switch between cardiomyogenic and endothelial lineages in adult cardiac progenitors, Stem Cells, 32(8): 1999 2007.
  36. Ahn EH*, Kim Y*, Kshitiz*, An SS, Afzal J, Lee S, Kwak M, Suh KY, Kim DH, Levchenko A (2014). Spatial control of adult stem cell fate using nanotopographic cues, Biomaterials, 35(8):2401-10. 
  37. Suhail Y*, Kshitiz*, Lee J, Walker M, Kim DH, Brennan MD, Bader JS, Levchenko A (2013). Modeling intercellular transfer of biomolecules through tunneling nanotubes, Bulletin of Mathematical Biology, 75(8):1400-16.
  38. Hubbi ME, Hu H, Kshitiz, Gilkes DM, Semenza GL (2013). Sirtuin-7 inhibits the activity of hypoxia-inducible factors, J. Biol. Chem., 288(29):20768-75.
  39. Hubbi ME, Hu Hongxia, Kshitiz, Ahmed I, Levchenko A, Semenza GL (2013). Chaperone-mediated autophagy targets HIF1a for lysosomal degradation, J. Biol. Chem., 288(15):10703-14.
  40. Hubbi ME*, Kshitiz*, Gilkes DM, Rey S, Wong CC, Luo W, Kim DH, Dang CV, Levchenko A, Semenza GL (2013). A non-transcriptional role for HIF-1a as a direct inhibitor of DNA replication, Science Signaling, 6(262), ra10. (cover article, also with a running commentary in Science).
  41. Berman SMC, Kshitiz, Wang CJ, Orukari I, Levchenko A, Bulte JWM (2013). Cell motility of neural stem cells is reduced after SPIO-labeling, which is mitigated after exocytosis, Magnetic Resonance in Medicine, 69(1), 255-262.
  42. Chaturvedi P, Gilkes DM, Wong CCL, Kshitiz, Luo W, Zhang H, Wei Hn Takano N, Schito L, Levchenko A, Semenza GL (2012), Hypoxia-inducible factor-dependent breast cancer-mesenchymal stem cell bidirectional signaling promotes metastasis, The Journal of Clinical Investigation, 123(1).
  43. Kshitiz*, Hubbi ME*, Ahn EH, Downey J, Kim DH, Rey S, Kundu A, Semenza GL, Abraham RM, Levchenko, A. (2012). Matrix rigidity coordinates the proliferation, differentiation, and morphogenesis of endothelial cells derived from cardiac progenitors, Science Signaling, 5(227):ra41. (cover article, also featured in Science)
  44. Bankoti R, Gupta K, Levchenko A, Stager S (2012). Marginal zone B cells regulate antigen-specific T cell responses during infection, The Journal of Immunology, 188(8), 3961-3971.
  45. Kim DH*, Kshitiz*, Smith R, Kim P, Marban E, Suh KY, Levchenko A, Nanopatterned Cardiac Cell Patches Promote Stem Cell Niche Formation and Myocardial Regeneration, Integrative Biology, 4(9):1019-33. (cover article)
  46. Kshitiz, Park JS, Kim P, Helen W, Engler AJ, Levchenko A, Kim DH. (2012). Control of stem cell fate and function by engineering physical microenvironment, Integrative Biology, 4:1008-1018.
  47. Kshitiz, Kim DH, Beebe D, Levchenko A. (2011). Micro- and nanoengineering for stem cell biology: the promise with a caution, Trends in Biotech, 29(8):399-408.
  48. Gupta K, Kim DH, Ellison D, Smith C, Levchenko A (2011). Using lab-on-chip technologies for stem cell biology, Stem Cells & Regenerative Medicine, Humana Press, 483-498.
  49. Gupta K, Kim DH, Ellison D, Smith C, Kundu A, Tuan J, Suh KY, Levchenko A. (2011). Lab-on- a-chip devices as an emerging platform for stem cell biology, Lab on a Chip, 10(16):2019-31.
  50. Rey S, Lee K, Wang CJ, Gupta K, Chen S, McMillan A, Bhise N, Levchenko A, Semenza GL. (2009). Synergistic effect of HIF-1alpha gene therapy and HIF-1-activated bone marrow-derived angiogenic cells in a mouse model of limb ischemia, Proc Natl Acad Sci USA. 106(48):20399-404.
  51. Niu X, Gupta K, Yang JT, Shamblott MJ, Levchenko A. (2009). Physical transfer of membrane and cytoplasmic components as a general mechanism of cell-cell communication, J Cell Sci., 122(Pt 5):600-610.
  52. Gupta K*, Sehgal V*, Levchenko A. (2008). A method for probabilistic mapping between protein structure and function taxonomies through cross training, BMC Structural Biology, 8:40.
  53. Gupta K, Thomas D, Vidya SV, Venkatesh KV, Ramakumar S. (2005).Detailed protein sequence alignment based on Spectral Similarity Score (SSS), BMC Bioinformatics, 6:105.