Upadhyaylab

Publications

2025

Mishra, R., and Upadhyay, A. (2025). An update on mammalian and non-mammalian animal models for biomarker development in neurodegenerative disorders. Cellular and Molecular Life Sciences 82, 147. DOI : https://doi.org/10.1007/s00018-025-05668-y

Karunakaran, D.K.P., Ley, M., Guo, J., Khatri, A., Sadleir, K., Popovic, J., Upadhyay, A.K., Savas, J., Procissi, D., and Atwal, J. (2025). The UNC5C T835M mutation associated with Alzheimer’s disease leads to neurodegeneration involving oxidative stress and hippocampal atrophy in aged mice. Molecular neurodegeneration 20, 65. DOI: https://doi.org/10.1186/s13024-025-00850-z. (IF: 15)

2024

Upadhyay, A., and Joshi, V. (2024). The Ubiquitin Tale: Current Strategies and Future Challenges. ACS Pharmacology & Translational Science 7, 2573-2587. DOI: https://doi.org/10.1021/acsptsci.4c00278

Upadhyay, A. (2024). Vesicular Transport and Amyloids: The Growing Relationship. Biologics 4, 376-389. DOI: https://doi.org/10.3390/biologics4040023

Rao, N.R., Upadhyay, A., and Savas, J.N. (2024). Derailed protein turnover in the aging mammalian brain. Molecular Systems Biology 20, 120-139. DOI: https://doi.org/10.1038/s44320-023-00009-2. (IF: 12)

Rao, N.R., DeGulis, O., Nomura, T., Lee, S., Hark, T.J., Dynes, J.C., Dexter, E.X., Dulewicz, M., Ge, J., and Upadhyay, A. (2024). Levetiracetam prevents Aβ42 production through SV2a-dependent modulation of App processing in Alzheimer's disease models. bioRxiv. DOI: https://doi.org/10.1101/2024.10.28.620698

Noor, L., Upadhyay, A., and Joshi, V. (2024). Role of T lymphocytes in glioma immune microenvironment: two sides of a coin. Biology 13, 846. DOI: https://doi.org/10.3390/biology13100846

2023

Upadhyay, A., Chhangani, D., Rao, N.R., Kofler, J., Vassar, R., Rincon-Limas, D.E., and Savas, J.N. (2023). Amyloid fibril proteomics of AD brains reveals modifiers of aggregation and toxicity. Molecular neurodegeneration 18, 61. DOI: https://doi.org/10.1186/s13024-023-00654-z. (IF: 15)

Singh, S., Joshi, V., and Upadhyay, A. (2023). Amyloids and brain cancer: molecular linkages and crossovers. Bioscience Reports 43, BSR20230489. DOI: https://doi.org/10.1042/BSR20230489

Anand, U., Dey, A., Chandel, A.K.S., Sanyal, R., Mishra, A., Pandey, D.K., De Falco, V., Upadhyay, A., Kandimalla, R., and Chaudhary, A. (2023). Cancer chemotherapy and beyond: Current status, drug candidates, associated risks and progress in targeted therapeutics. Genes & Diseases 10, 1367-1401. DOI: https://doi.org/10.1016/j.gendis.2022.02.007

2022

Upadhyay, A., Vassar, R.J., and Savas, J.N. (2022). Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain. JoVE (Journal of Visualized Experiments), e63816. DOI: https://doi.org/10.3791/63816

Upadhyay, A., Sundaria, N., Dhiman, R., Prajapati, V.K., Prasad, A., and Mishra, A. (2022). Complex inclusion bodies and defective proteome hubs in neurodegenerative disease: new clues, new challenges. The Neuroscientist 28, 271-282. DOI: https://doi.org/10.1177/1073858421989582

Amanullah, A., Upadhyay, A., Dhiman, R., Singh, S., Kumar, A., Ahirwar, D.K., Gutti, R.K., and Mishra, A. (2022). Development and Challenges of Diclofenac-Based Novel Therapeutics: Targeting Cancer and Complex Diseases. Cancers 14, 4385. DOI: https://doi.org/10.3390/cancers14184385

2021

Upadhyay, A., Siemer, A., Langen, R., Vassar, R.J., and Savas, J.N. (2021). A new biochemical method for ultra‐purification of amyloids from Alzheimer’s disease brain tissues. Alzheimer's & Dementia 17, e054185. DOI: https://doi.org/10.1002/alz.054185

Upadhyay, A., Amanullah, A., Joshi, V., Dhiman, R., Prajapati, V.K., Poluri, K.M., and Mishra, A. (2021). Ibuprofen-based advanced therapeutics: breaking the inflammatory link in cancer, neurodegeneration, and diseases. Drug Metabolism Reviews 53, 100-121. DOI: https://doi.org/10.1080/03602532.2021.1903488

Upadhyay, A. (2021). Natural compounds in the regulation of proteostatic pathways: An invincible artillery against stress, ageing, and diseases. Acta Pharmaceutica Sinica B 11, 2995-3014. DOI: https://doi.org/10.1016/j.apsb.2021.01.006. (IF: 14)

Upadhyay, A. (2021). Cancer: An unknown territory; rethinking before going ahead. Genes & Diseases 8, 655-661. DOI: https://doi.org/10.1016/j.gendis.2020.09.002

Sundaria, N., Upadhyay, A., Prasad, A., Prajapati, V.K., Poluri, K.M., and Mishra, A. (2021). Neurodegeneration & imperfect ageing: Technological limitations and challenges? Mechanisms of Ageing and Development 200, 111574. DOI: https://doi.org/10.1016/j.mad.2021.111574

Prusty, D., Gupta, N., Upadhyay, A., Dar, A., Naik, B., Kumar, N., and Prajapati, V.K. (2021). Asymptomatic malaria infection prevailing risks for human health and malaria elimination. Infection, Genetics and Evolution 93, 104987. DOI: https://doi.org/10.1016/j.meegid.2021.104987

Prasanna, P., and Upadhyay, A. (2021). Flavonoid-Based Nanomedicines in Alzheimer’s Disease Therapeutics: Promises Made, a Long Way To Go. ACS Pharmacology & Translational Science 4, 74-95. DOI: https://doi.org/10.1021/acsptsci.0c00224

Prasanna, P., and Upadhyay, A. (2021). Heat shock proteins as the druggable targets in leishmaniasis: promises and perils. Infection and immunity 89, 10-1128. DOI: https://doi.org/10.1128/IAI.00559-20

Prasanna, P., Rathee, S., Upadhyay, A., and Sulakshana, S. (2021). Nanotherapeutics in the treatment of acute respiratory distress syndrome. Life Sciences 276, 119428. DOI: https://doi.org/10.1016/j.lfs.2021.119428

Prasanna, P., Kumar, R., Singh, V.K., and Upadhyay, A. (2021). Cloning, purification, and homology modeling of Histone deacetylase in Leishmania donovani. Infection, Genetics and Evolution 89, 104738. DOI: https://doi.org/10.1016/j.meegid.2021.104738

Mishra, R., Joshi, V., Upadhyay, A., Amanullah, A., Dubey, A.R., Singh, S., Dubey, V.K., Poluri, K.M., Jana, N.R., and Mishra, A. (2021). LRSAM1 E3 ubiquitin ligase promotes proteasomal clearance of E6-AP protein. Cellular Signalling 77, 109836. DOI: https://doi.org/10.1016/j.cellsig.2020.109836

Jakhmola, S., Upadhyay, A., Jain, K., Mishra, A., and Jha, H.C. (2021). Herpesviruses and the hidden links to Multiple Sclerosis neuropathology. Journal of Neuroimmunology 358, 577636. DOI: https://doi.org/10.1016/j.jneuroim.2021.577636

Hark, T.J., Rao, N.R., Castillon, C., Basta, T., Smukowski, S., Bao, H., Upadhyay, A., Bomba-Warczak, E., Nomura, T., and O’Toole, E.T. (2021). Pulse-chase proteomics of the App knockin mouse models of Alzheimer’s disease reveals that synaptic dysfunction originates in presynaptic terminals. Cell systems 12, 141-158. DOI: https://doi.org/10.1016/j.cels.2020.11.007. (IF: 13)

2020

Joshi, V., Upadhyay, A., Prajapati, V.K., and Mishra, A. (2020). How autophagy can restore proteostasis defects in multiple diseases? Medicinal research reviews 40, 1385-1439. DOI: https://doi.org/10.1002/med.21662. (IF: 12)

Graykowski, D.R., Wang, Y.-Z., Upadhyay, A., and Savas, J.N. (2020). The dichotomous role of extracellular vesicles in the central nervous system. Iscience 23. DOI: https://doi.org/10.1016/j.isci.2020.101456

2019

Upadhyay, A. (2019). Structure of proteins: Evolution with unsolved mysteries. Progress in Biophysics and Molecular Biology. DOI: https://doi.org/10.1016/j.pbiomolbio.2019.04.007

Sherine, J., Upadhyay, A., Mishra, A., Kumar, D., Pal, S., and Harinipriya, S. (2019). Ag (I) and Au (III) Mercaptobenzothiazole complexes induced apoptotic cell death. Scientific Reports 9, 621. DOI: https://doi.org/10.1038/s41598-018-36801-6

Mishra, R., Upadhyay, A., Prajapati, V.K., Dhiman, R., Poluri, K.M., Jana, N.R., and Mishra, A. (2019). LRSAM1 E3 ubiquitin ligase: molecular neurobiological perspectives linked with brain diseases. Cellular and Molecular Life Sciences 76, 2093-2110. DOI: https://doi.org/10.1007/s00018-019-03055-y

Joshi, V., Mishra, R., Upadhyay, A., Amanullah, A., Poluri, K.M., Singh, S., Kumar, A., and Mishra, A. (2019). Polyphenolic flavonoid (Myricetin) upregulated proteasomal degradation mechanisms: Eliminates neurodegenerative proteins aggregation. Journal of cellular physiology 234, 20900-20914. DOI: https://doi.org/10.1002/jcp.28695

2018

Upadhyay, A., and Mishra, A. (2018). Amyloids of multiple species: are they helpful in survival? Biological Reviews 93, 1363-1386. DOI: https://doi.org/10.1111/brv.12399. (IF: 12)

Mishra, R., Upadhyay, A., Prajapati, V.K., and Mishra, A. (2018). Proteasome‐mediated proteostasis: Novel medicinal and pharmacological strategies for diseases. Medicinal research reviews 38, 1916-1973. DOI: 10.1002/med.21502. (IF:12)

Khan, E., Tawani, A., Mishra, S.K., Verma, A.K., Upadhyay, A., Kumar, M., Sandhir, R., Mishra, A., and Kumar, A. (2018). Myricetin reduces toxic level of CAG repeats RNA in Huntington’s disease (HD) and Spino cerebellar Ataxia (SCAs). ACS chemical biology 13, 180-188. DOI: https://doi.org/10.1021/acschembio.7b00699

Joshi, V., Mishra, R., Upadhyay, A., Amanullah, A., Poluri, K.M., Singh, S., Kumar, A., and Mishra, A. (2019). Polyphenolic flavonoid (Myricetin) upregulated proteasomal degradation mechanisms: Eliminates neurodegenerative proteins aggregation. Journal of cellular physiology 234, 20900-20914. DOI: https://doi.org/10.1002/jcp.28695

Awasthi, M., Upadhyay, A.K., Singh, S., Pandey, V.P., and Dwivedi, U.N. (2018). Terpenoids as promising therapeutic molecules against Alzheimer’s disease: amyloid beta-and acetylcholinesterase-directed pharmacokinetic and molecular docking analyses.

Molecular Simulation 44, 1-11. DOI: https://doi.org/10.1080/08927022.2017.1395265

Amanullah, A., Mishra, R., Upadhyay, A., Reddy, P.P., Das, R., and Mishra, A. (2018). Indomethacin elicits proteasomal dysfunctions develops apoptosis through mitochondrial abnormalities. Journal of cellular physiology 233, 1685-1699. DOI: https://doi.org/10.1002/jcp.26081

2017

Upadhyay, A., Joshi, V., Amanullah, A., Mishra, R., Arora, N., Prasad, A., and Mishra, A. (2017). E3 Ubiquitin Ligases Neurobiological Mechanisms: Development to Degeneration. Frontiers in Molecular Neuroscience 10, 151. DOI: https://doi.org/10.3389/fnmol.2017.00151

Upadhyay, A., Amanullah, A., Mishra, R., Kumar, A., and Mishra, A. (2017). Lanosterol Suppresses the Aggregation and Cytotoxicity of Misfolded Proteins Linked with Neurodegenerative Diseases. Molecular Neurobiology, 1-14. DOI: https://doi.org/10.1007/s12035-016-0377-2

Joshi, V., Upadhyay, A., Kumar, A., and Mishra, A. (2017). Gp78 E3 Ubiquitin Ligase: Essential Functions and Contributions in Proteostasis. Frontiers in Cellular Neuroscience 11, 259. DOI: https://doi.org/10.3389/fncel.2017.00259

Amanullah, A., Upadhyay, A., Joshi, V., Mishra, R., Jana, N.R., and Mishra, A. (2017). Progressing neurobiological strategies against proteostasis failure: Challenges in neurodegeneration. Progress in neurobiology 159, 1-38. DOI: https://doi.org/10.1016/j.pneurobio.2017.08.005. (IF: 12)

Amanullah, A., Upadhyay, A., Chhangani, D., Joshi, V., Mishra, R., Yamanaka, K., and Mishra, A. (2017). Proteasomal Dysfunction Induced By Diclofenac Engenders Apoptosis Through Mitochondrial Pathway. Journal of cellular biochemistry 118, 1014-1027. DOI: https://doi.org/10.1002/jcb.25666

2016

Upadhyay, A., Amanullah, A., Chhangani, D., Mishra, R., Prasad, A., and Mishra, A. (2016). Mahogunin ring finger-1 (MGRN1), a multifaceted ubiquitin ligase: recent unraveling of neurobiological mechanisms. Molecular neurobiology 53, 4484-4496. DOI: https://doi.org/10.1007/s12035-015-9379-8

Upadhyay, A., Amanullah, A., Chhangani, D., Joshi, V., Mishra, R., and Mishra, A. (2016). Ibuprofen induces mitochondrial-mediated apoptosis through proteasomal dysfunction. Molecular neurobiology 53, 6968-6981. DOI: https://doi.org/10.1007/s12035-015-9603-6

Joshi, V., Amanullah, A., Upadhyay, A., Mishra, R., Kumar, A., and Mishra, A. (2016). A decade of boon or burden: what has the CHIP ever done for cellular protein quality control mechanism implicated in neurodegeneration and aging? Frontiers in molecular neuroscience 9, 93. DOI: https://doi.org/10.3389/fnmol.2016.00093

Chhangani, D., Endo, F., Amanullah, A., Upadhyay, A., Watanabe, S., Mishra, R., Yamanaka, K., and Mishra, A. (2016). Mahogunin ring finger 1 confers cytoprotection against mutant SOD1 aggresomes and is defective in an ALS mouse model. Neurobiology of disease 86, 16-28. DOI: https://doi.org/10.1016/j.nbd.2015.11.017

2015

Upadhyay, A., Amanullah, A., Chhangani, D., Mishra, R., and Mishra, A. (2015). Selective multifaceted E3 ubiquitin ligases barricade extreme defense: Potential therapeutic targets for neurodegeneration and ageing. Ageing Research Reviews 24, 138-159. DOI: https://doi.org/10.1016/j.arr.2015.08.003. (IF: 12)

2014

Chhangani, D., Upadhyay, A., Amanullah, A., Joshi, V., and Mishra, A. (2014). Ubiquitin ligase ITCH recruitment suppresses the aggregation and cellular toxicity of cytoplasmic misfolded proteins. Scientific reports 4, 5077. DOI: https://doi.org/10.1038/srep05077

Chhangani, D., Nukina, N., Kurosawa, M., Amanullah, A., Joshi, V., Upadhyay, A., and Mishra, A. (2014). Mahogunin ring finger 1 suppresses misfolded polyglutamine aggregation and cytotoxicity. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease 1842, 1472-1484. DOI: https://doi.org/10.1016/j.bbadis.2014.04.014

Book Chapters:

  1. Soni, S., Tiwari, A.N., Singh, A., and Upadhyay, A. (2025). Visualizing and mapping cell death: Biochemical tools, techniques and assays.
    DOI: https://doi.org/10.1016/B978-0-443-34645-3.00004-2
  2. Upadhyay, A., and Joshi, V. (2024). Proteasome Activators and Ageing: Restoring Proteostasis Using Small Molecules. Biochemistry and Cell Biology of Ageing: Part V, Anti-Ageing Interventions, 21-41. DOI: https://doi.org/1007/978-3-031-66768-8_2
  3. Rathod, S., Aggarwal, V., Upadhyay, A., and Choudhari, R. (2022). Timing of the Major Metabolic Switches in Immune Cell Activation and Differentiation During Cancer Development. In Immuno-Oncology Crosstalk and Metabolism, (Springer), pp. 187-218. DOI: https://doi.org/10.1007/978-981-16-6226-3_7
  4. Aggarwal, V., Rathod, S., Vashishth, K., and Upadhyay, A. (2022). Immune Cell Metabolites as Fuel for Cancer Cells. In Immuno-Oncology Crosstalk and Metabolism, (Springer), pp. 153-186.
    DOI: https://doi.org/10.1007/978-981-16-6226-3_6
  5. Badhwar, R., and Upadhyay, A. (2020). Modulation of Cellular Protein Quality Control Pathways Using Small Natural Molecules. In Bioactive Natural products in Drug Discovery, (Springer Nature), pp. 609-641.
    DOI: https://doi.org/10.1007/978-981-15-1394-7_22
  6. Joshi, V., Upadhyay, A., Amanullah, A., Mishra, R., and Mishra, A. (2019). Predicting E3 Ubiquitin Ligases as Possible Promising Biomarkers for Brain Tumors. In Molecular Diagnostics in Cancer Patients, (Springer), pp. 43-72. https://doi.org/1007/978-981-13-5877-7_4
  7. Upadhyay, A., Amanullah, A., Joshi, V., Mishra, R., and Mishra, A. (2016). Molecular and Cellular Insights: Neuroinflammation and Amyotrophic Lateral Sclerosis. In Inflammation: the Common Link in Brain Pathologies, (Springer), pp. 209-230. https://doi.org/10.1007/978-981-10-1711-7_8