Dec 22, 2021 / Neuroscience

Investigating neurological disease at the single cell level: An interview with Dr. Manoj Kumar Jaiswal

Liz Lucero

For us, there’s nothing more exciting than finding out what’s coming next. What new finding will change our understanding of neurodegenerative disease development? Which recent discovery will provide a new approach for treating movement disorders? How will your latest project impact the future of neuroscience?

This year’s Society for Neuroscience (SfN) meeting—Neuroscience 2021—was filled with exciting new insights like these, giving us a chance to learn from not only leading minds in neuroscience but also new voices as they shared their latest findings. Even before the conference started, we had a feeling there was going to be some fascinating single cell and spatial discoveries on display (we were right!), which is why we decided to hold our own contest. We invited researchers who had submitted an abstract to SfN 2021 that featured 10x Genomics single cell or spatial data to enter, and we were anything but disappointed. Though there were many fascinating entries, based on our judging criteria—research creativity, scientific impact, and innovation—one entrant stood out.

The winner of the 10x Genomics 2021 SfN Abstract Contest and Drawing, Manoj Kumar Jaiswal, PhD, is an instructor in the Department of Psychiatry at the Icahn School of Medicine at Mount Sinai whose research focuses on understanding the cell-type-specific changes that characterize C9orf72-associated neurodegenerative disease. Previous studies have revealed that a repeat expansion mutation on C9orf72 is the most common genetic cause of two prevalent neurodegenerative diseases—amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (1). It is estimated that this mutation is responsible for 40% of familial ALS cases, 25% of familial FTD cases, and 88% of familial ALS/FTD cases (2). Using a multiomic approach that combines several methods, including single nuclei RNA sequencing, Dr. Jaiswal and his team are investigating the complex mechanisms and pathways involved in ALS and FTD. And the study he presented at SfN 2021 is the first to comprehensively characterize the molecular alterations in C9orf72-associated ALS and FTD at the single cell level.

Manoj Kumar Jaiswal, PhD, Instructor, Department of Psychiatry, Icahn School of Medicine at Mount Sinai
Manoj Kumar Jaiswal, PhD, Instructor, Department of Psychiatry, Icahn School of Medicine at Mount Sinai

On winning the contest, Dr. Jaiswal shared that he sees it not only as a recognition of his own work but of “all the important work of many folks in [his] lab.” He also feels the experience has made him a more visible member of the single cell multiomics research community, validating his research and encouraging him to “continue to research in new areas,” which is exciting given that, among other equally interesting findings, his most recent study yielded some unexpected results that hint towards a deeper understanding of dysregulation in ALS and FTD and, ultimately, the biological basis of these neurological diseases.

Read our Q&A with Dr. Jaiswal to find out more about his current research, potential next steps, and what it might mean for the future of neuroscience.

What is your research focus, and what led you to this topic? 

Precise dissection of the cell-type-specific pathophysiological alterations in C9orf72-associated neurodegenerative disease may help illuminate disease mechanisms. However, most molecular, genomic and epigenomic studies have used bulk brain specimens that represent mixed signals from diverse neuronal and glial cell types and, therefore, it is hard to delineate cell-type specificity. Using next-generation snRNA-seq, snATAC-seq, and HiPlex RNAScope, we identify transcriptomic and chromatin accessibility disruptions relevant to C9orf72 mutation in specific cell types.

My current research focuses on studying mechanisms and pathways involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) using next-generation sequencing (NGS; 10x Genomics multiomics), molecular biology, spatial transcriptomics, microscopy, and protein assays. Using high-resolution and high-throughput single-nucleus RNA sequencing (snRNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (snATAC-seq), along with epigenome (ChIP-Seq), and 3D genome (Hi-C) study in fluorescence-activated nuclei sorting (FANS)-sorted cell-type-specific populations of five major cell types (glutamatergic-neurons, GABAergic neurons, oligodendrocytes, astrocytes, and microglia), we started to uncover novel cell-type-specific alterations in the transcriptome and epigenome of human autopsy brain [samples] associated with C9orf72 ALS (C9-ALS) and C9-FTD.  These methods allow us to characterize the effect of genetic variation on the cellular architecture, and to shed light on the 1) complex pathophysiological mechanisms regulating gene expression in diseased cells, 2) cell-type-specific epigenetic impact on disease, and 3) 3D configuration of the diseased brain genome architecture.

My previous PhD research work emphasized the role of oxidative stress and selective vulnerability of motor neurons (MNs) and perturbed mitochondrial calcium homeostasis in ALS and its implications in MN-specific calcium dysregulation. The results of my studies provided, for the first time, the evidence of a critical role of Cu,Zn superoxide dismutase (SOD1), typical in familial ALS, in impairment of mitochondrial calcium handling and perturbation of Ca2+ homeostasis in SOD1G93A mice and cell culture models of ALS. My current work is a logical extension of my previous work on motor neuron diseases.

Can you give us a brief overview of the specific study you presented at SfN? 

In our work presented at Society for Neuroscience 2021, we profiled the cell-type-specific transcriptomes and epigenomes of two brain regions, the primary motor cortex (MCX) and medial prefrontal cortex (mPFC), using postmortem tissue samples from normal controls, and patients with C9orf72-ALS and C9orf72-FTD. We used snRNA-seq and snATAC-seq to identify transcriptomic and chromatin accessibility disruptions associated with C9ALS/FTD mutation in specific cell types. Our study represents the first comprehensive characterization of molecular alterations in C9orf72-associated ALS and FTD at the level of single brain cells.

What were some of the most interesting and/or surprising findings? 

We found that the transcriptome was most disrupted by both diseases in astrocytes and subtypes of excitatory neurons. Transcriptome alterations were accompanied by concordant changes of chromatin accessibility in the gene body or distal-linked enhancers of differentially expressed genes. We confirmed these findings in purified populations of the major brain nuclei obtained by FANS, as well as using protein level measurements for selected differentially expressed genes and at the mRNA level using RNAScope. Our unexpected finding of considerable Cc9-ALS/FTD-associated pathology in astrocytes and sub-types of excitatory neurons suggests novel biological pathways and genes that are dysregulated in these diseases.

How do you plan to follow-up this work? 

My future research plan aims to address the following unanswered questions:

  1. Because our snRNA-seq studies were limited only to C9-ALS/FTD cases in small cohorts, it is not known if the observed deficits limited to excitatory-neurons and astrocytic cells are specific for familial C9-ALS/FTD or also present in patients with sporadic ALS in bigger cohorts and, therefore, needs to be investigated further.
  2. snRNA-seq transcriptome and associated altered expression of activity-dependent genes (ADGs) is not mirrored by epigenetic changes in the predicted regulatory elements of these ADGs. The molecular underpinnings of these differences have not been investigated and is likely explained by a better understanding of cell-type-dependent brain epigenome landscapes of affected individuals; and
  3. snRNA-seq does not inform whether or not the identified gene expression changes at the transcriptome level translate into changes in the encoded proteins. In addition, the anatomical localization of the observed deficits cannot be inferred by this method. Therefore, I would like to continue my research in this direction to have a better insight into the biological basis of disease pathology.

What are the long-term goals of your research? 

Using multiomics studies combined with single cell RNASCope, my future research goal is to:

  1. Identify therapeutic targets for C9orf72 ALS/FTD, psychiatric diseases, and dementia.
  2. Delineate the molecular mechanism of novel therapeutic agents.
  3. Identify biomarkers for specific conditions and monitor therapeutic responses.

Existing therapies for ALS and FTD prolong survival by 2–3 months at best, with little effect on the quality of life. Progress has been slow due to an incomplete understanding of the biological basis of disease and the complexity of the human brain, which contains vast numbers of specialized cell types with diverse functions and intricate connections, I hope to integrate my knowledge of genomic medicine, molecular biology, and computation towards the search for new therapies and novel drugs that will be greatly beneficial to patients.


  1. Q Yang, B Jiao & L Shen, The development of C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia disorders. Front Genet. 11, 562758 (2020). doi: 10.3389/fgene.2020.562758
  2. M DeJesus-Hernandez et al., Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron. 72, 245–256 (2011). doi: 10.1016/j.neuron.2011.09.011