Dr Akshay Bhinge

Dr. Akshay Bhinge leads research aimed at unraveling the complexities of RNA dysregulation in neurodegenerative diseases, with a focus on motor neuron disease and frontotemporal dementia. His team takes a multidisciplinary approach, combining cutting-edge techniques including human induced pluripotent stem cells (iPSCs), high-throughput high-content phenotypic characterization, single-cell genomics and CRISPR screens. Together, his team is striving to uncover therapeutic pathways to halt or reverse the relentless neurodegeneration in these devastating conditions.

Biography

Dr. Akshay Bhinge began his medical journey with an M.B.B.S. degree from Grant Medical College in Mumbai, India, followed by a Master’s in Biomedical Engineering (M.Tech) from the Indian Institute of Technology, Mumbai. He then pursued a Ph.D. at the University of Texas at Austin, where he graduated in 2009. His doctoral research involved developing innovative genomic tools using next-generation sequencing to identify downstream targets of oncogenic transcription factors and microRNAs in both human primary and cancer cell lines.

In 2010, Dr. Bhinge moved to the Genome Institute of Singapore as a postdoctoral fellow, where he focused on modeling human neurodevelopment and neurodegeneration with pluripotent stem cells. By 2017, he joined the LSI as a Research Fellow, establishing his own research group. His current work centers on creating advanced human models of the nervous system to study neurodegenerative diseases, including motor neuron disease and frontotemporal dementia.

Qualifications

• Doctor of Philosophy (Ph.D.): Cell and Molecular Biology, University of Texas at Austin, Texas, USA
• Master of Technology (M.Tech.): Biomedical Engineering, Indian Institute of Technology-Bombay, India
• Bachelor of Medicine, Bachelor of Surgery (M.B.B.S.): Clinical Medicine and Surgery, Grant Medical College, JJ group of Hospitals, Mumbai, India

Bhinge Lab website

Research keywords

• induced Pluripotent Stem Cells (iPSC)
• Motor Neuron Disease (Amyotrophic lateral Sclerosis)
• Frontotemporal Dementia (FTD)
• Disease modelling in a dish
• Neurodegeneration
• 3D models of brain and spinal cord
• ChIP-sequencing
• Single cell RNA-sequencing
• Enhancers
• MicroRNAs
• RNA binding proteins
• Regulatory networks
• Bioinformatics

Selected Publications

Hawkins S, Mondaini A, Namboori SC, Nguyen GG, Yeo GW, Javed A, Bhinge A. (2024). ePRINT: exonuclease assisted mapping of protein-RNA interactions. Genome Biology volume 25, Article number: 140

Ganssauge J, Hawkins S, Namboori SC, Leung S, Mill J, Bhinge A. Rapid and Inducible Mislocalization of Endogenous TDP43 in a Novel Human Model of Amyotrophic Lateral Sclerosis. eLife, doi: https://elifesciences.org/reviewed-preprints/95062v1 (2024)

Sophie Hawkins, Seema C. Namboori, Ammarah Tariq, Catherine Blaker, Christine Flaxman, Nidhi S. Dey, Peter Henley, Andrew Randall, Alessandro Rosa, Lawrence W. Stanton, Akshay Bhinge. Upregulation of β-catenin due to loss of miR-139 contributes to motor neuron death in amyotrophic lateral sclerosis. Stem Cell Reports June 23, DOI:https://doi.org/10.1016/j.stemcr.2022.05.019 (2022)

Seema C. Namboori, Patricia Thomas, Ryan Ames, Sophie Hawkins, Lawrence O. Garrett, Craig R.G. Willis, Alessandro Rosa, Lawrence W. Stanton, Akshay Bhinge. Single-cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS iPSC-derived motor neurons. Stem Cell Reports November 11, DOI:https://doi.org/10.1016/j.stemcr.2021.10.010 (2021)

Wang J, Jenjaroenpun P, Bhinge A, Angarica VE, Del Sol A, Nookaew I, Kuznetsov VA, Stanton LW. Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons. Genome Research Nov;27(11):1783-1794.(2017)

*Bhinge, A., Namboori, S. C., Zhang, X., VanDongen, A. M. J., Stanton, L. W., Genetic Correction of SOD1 Mutant iPSCs Reveals ERK and JNK Activated AP1 as a Driver of Neurodegeneration in Amyotrophic Lateral Sclerosis. Stem Cell Reports 8, 856-869 (2017). (*co-corresponding author)

Bhinge, A., Namboori, S. C., Bithell, A., Soldati, C., Buckley, N. J., Stanton, L. W., MiR-375 is Essential for Human Spinal Motor Neuron Development and May Be Involved in Motor Neuron Degeneration. Stem Cells 34, 124-134 (2016).

Bhinge, A., Poschmann, J., Namboori, S. C., Tian, X., Jia Hui Loh, S., Traczyk, A., Prabhakar, S., Stanton, L. W., MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF-beta/BMP signaling. The EMBO Journal 33, 1271-1283 (2014).

*Polioudakis, D., *Bhinge, A. A., Killion, P. J., Lee, B. K., Abell, N. S., Iyer, V. R., A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes. Nucleic Acids Research 41, 2239-2254 (2013). (*co-first author)

Lee, B. K., Bhinge, A. A., Battenhouse, A., McDaniell, R. M., Liu, Z., Song, L., Ni, Y., Birney, E., Lieb, J. D., Furey, T. S. et al., Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Research 22, 9-24 (2012).

ENCODE Consortium Project, An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).

Lee, B. K., Bhinge, A. A., Iyer, V. R., Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis. Nucleic Acids Research 39, 3558-3573 (2011).

*Shivaswamy, S., *Bhinge, A., Zhao, Y., Jones, S., Hirst, M., Iyer, V. R., Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biology 6, e65 (2008). (*co-first author, Selected as a Faculty of 1000 (Biology) article.)

ENCODE Consortium Project, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007).

Bhinge, A. A., Kim, J., Euskirchen, G. M., Snyder, M., Iyer, V. R., Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Research 17, 910-916 (2007).

Kim, J., Bhinge, A. A., Morgan, X. C., Iyer, V. R., Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nature Methods 2, 47-53 (2005).

Selected Grants

• MRC Investigator grant, 2024-2027
• Alzheimer's Research UK grant, 2024-2026
• BRACE Dementia PhD studentship, 2023-2026
• MRC IAA grant, 2023-2024
• NC3R (Co-PI), 2023-2024 
• MRC New Investigator Research grant, 2020-2024
• Drug Target discovery grant, 2022
• Motor Neuron Disease Association and Open Innovation Platform grant, 2022
• BRACE Alzheimer's Research grant, 2021-2022 (Co-I)
• LSI Catalyst Fund 2021-2022
• Academy of Medical Science Springboard award, 2018-2022
• UEMS PhD studentship 2018-2022
• Royal Society research grant, 2018-2019

Bhinge Lab members

• Seema Namboori             (Lab manager & Postgraduate Researcher)
• Johanna Ganssauge        (LSI Ph.D. student)
• Pragati Thakur                 (Research Technician)
• Tania Atienzar                  (BRC Ph.D. student)
• Yiyun (Aileen) Zhang       (CSC Ph.D. student)
• Antonio Fusciardi            (BRACE Ph.D. student)
• Harshitha Chandrashekar (Bioinformatician)
• Jeong Yeol Lee               (Ph.D. student with Ben Housden)