First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Harini Iyer is first author on ‘ The Cl transporter ClC-7 is essential for phagocytic clearance by microglia’, published in JCS. Harini conducted the research described in this article while a Postdoctoral Scholar in William Talbot's lab at Beckman Center, Stanford, USA. She is now an Assistant Professor at Rice University, Houston, USA investigating lysosomal signaling in the neuroimmune system.

Harini Iyer

How would you explain the main findings of your paper in lay terms?

Lysosomes have traditionally been considered merely the waste disposal and recycling unit of the cell. In recent years, however, lysosomes have emerged as key signaling hubs that govern multiple aspects of cellular activity and function. Although all cells require lysosomes for effective degradation and recycling of debris, the functions of some cells of the immune system, particularly professional phagocytes (debris-clearing cells), such as macrophages and microglia, are intimately linked with the activity of lysosomes. Microglia, brain-resident immune cells, play essential roles in the formation and function of the central nervous system, and most brain disorders are accompanied by disruption of microglial activity. Thus, a deeper understanding of how microglia appropriately sense and respond to extracellular cues, and the extent to which the functions of microglia are dependent on lysosomal activity, is crucial for revealing causes behind the onset or progression of neurodegenerative disorders. In the present study, we employ a combination of genetics, cell biology, and live imaging to decipher the role of the lysosomal chloride channel ClC-7 in microglia. Mutations in clcn7, the gene that encodes ClC-7, lead to bone malformation and neurodegeneration; however, we lack a comprehensive understanding of the function of this protein in microglia. We found that microglia lacking ClC-7 can effectively take up extracellular debris but are unable to process the ingested material. In addition to defective clearance of cellular and neuronal debris, microglia in clcn7 mutants also show a diminished capacity to process the amyloid-β peptide 1–42, which might contribute to pathology in Alzheimer's disease. Thus, our research reveals a key mechanism that microglia and lysosomes use to respond appropriately to environmental cues and provides insight into how the vital process of debris clearance by microglia can fail in neurodegeneration.

Were there any specific challenges associated with this project? If so, how did you overcome them?

The primary challenge with this project had more to do with my professional life than the science or any techniques associated with the project. I entered the academic job market just as I initiated this project, and with the faculty job search process being a full-time job these days, it was incredibly difficult to find large enough chunks of time to make substantial progress with this project during my job application and interview phases. There was a brief period during which I had wrapped up my interviews, but had no job offers, and I poured myself into this project to fight the feelings of dejection. While many of the hypotheses I had laid out for this project failed, as with any other project, I am grateful that the story developed (even if in fits and spurts) and that it found a great home in Journal of Cell Science.

When doing the research, did you have a particular result or ‘eureka’ moment that has stuck with you?

Yes! In clcn7 mutants, microglia and embryonic macrophages appear normal but are unable to digest ingested debris. In zebrafish, we typically use transgenic lines to label different cell types, and our microglia transgene appeared normal in the mutants, which was initially quite disappointing. However, since mutations in clcn7 have been shown to result in neurodegeneration, I decided to look at a neuronal transgene in the mutants and give up on this project if I did not see a phenotype. Before I had finished imaging a handful of animals, I realized that some animals had clumps of the neuronal marker in the midbrain of the fish, showing a striking overlap with the regions where microglia are enriched. Although in live imaging experiments we perform all genotyping post-imaging, I could score the animals as mutants simply based on the expression of the neuronal marker (later confirmed by genotyping)! This observation led me to realize that in clcn7 mutants, although the microglia appear normal and can ingest neuronal debris, these cells are not able to process or degrade the ingested debris.

Why did you choose Journal of Cell Science for your paper?

Publishing in one of the journals associated with The Company of Biologists has been a career-long dream for me. We initially submitted my first first-author manuscript to Development, and I took the rejection from that journal particularly hard. However, even back then, the more naïve version of me understood the reasons behind the desk rejection. As I slowly – and unintentionally – transitioned from being a developmental biologist to a cell biologist during the course of my training, Journal of Cell Science became the obvious choice not only for my present research but also for many of the projects I envision for my future laboratory. My independent research program will focus on understanding lysosomal signalling in the neuroimmune system, and will thus be very much aligned with the research interests of Journal of Cell Science. We will continue to regard this journal as one of the top choices for publishing our future research.

Confocal microscopy image of a zebrafish midbrain. The image shows microglia (blue) and neurons (pink). Ingested neuronal debris can be observed inside microglia.

Confocal microscopy image of a zebrafish midbrain. The image shows microglia (blue) and neurons (pink). Ingested neuronal debris can be observed inside microglia.

Have you had any significant mentors who have helped you beyond supervision in the lab? How was their guidance special?

Absolutely! I am incredibly fortunate that at almost every stage of my career, I had people who took me under their wing, nurtured and guided me, celebrated my achievements with me, and most importantly, had my back during the tough times. After obtaining my master's degree, I began my research career as an Assistant Research Scientist at AstraZeneca. One of my earliest mentors was Dr Achyut Sinha, who led the Molecular Biology group for the AstraZeneca drug discovery program. He encouraged me to get out of my comfort zone and apply to PhD programs in the US. Honestly, I would not have even considered the possibility of pursuing a PhD or moving abroad to do so if he hadn't been quite pushy! Dr Sinha passed away shortly after I defended my PhD thesis, and it's one of my deepest regrets that he was not around to see me secure a faculty position. Second, I am honored and truly fortunate to call Dr Jie Chen one of my career-long mentors. Dr Chen was the Chair of the Department of Cell and Developmental Biology at the University of Illinois, where I received my PhD, and in short, she is an inspiration in every way. On top of being a brilliant scientist, she genuinely cares about her trainees, is an incredible mentor, advisor and leader, and has been my role model in more ways than one. There is no other way to say this: I would not be where I am without her. More recently, I have benefited hugely from the mentorship of Dr Irene Salinas. We met during my job interview at the University of New Mexico, and although I did not get an offer from the program, we felt an instant connection that is priceless. Both Dr Salinas's research and her tireless efforts toward enhancing diversity, equity and inclusion (DEI) in academia are an inspiration to many, including me.

What motivated you to pursue a career in science, and what have been the most interesting moments on the path that led you to where you are now?

In India, where I grew up, we typically choose our majors before admission into college, and my first scientific love was microbiology. My fascination with the world of invisible organisms led me to a brief foray into the pharmaceutical industry. Despite the many interesting aspects of the drug discovery program and being more than well-compensated, I decided that world was not for me, and I made the decision to pursue my PhD at the University of Illinois at Urbana-Champaign due to the strength of the microbiology program at this school. Through some combination of choice and circumstance, I ended up not doing a single microbiology rotation! I heard my graduate advisor, Phil Newmark, give a talk on planarians and fell in love with these flatworms with their astounding abilities of regeneration. Next, my love for regeneration drew me to zebrafish as the organism of choice for my postdoctoral training. I joined Will Talbot's lab intending to study remyelination, but once again, this early project did not work out for many reasons. I decided to pivot to studying microglia and neurodegeneration. I think you can see that my scientific career followed a non-traditional path, but I have come to embrace this circuitous route as a strength. Most importantly, I have learned that having a plan is good, and I always have one, but now I eagerly await the moment when the plan spectacularly fails – because the alternative that emerges is almost always more exciting and fulfilling.

Who are your role models in science? Why?

In the past few years, I have admired two scientists from afar (I have not met either one). The first of these is Randall Peterson at the University of Utah. I find the vast array of scientific questions and techniques that his lab adapts truly admirable. Equally importantly, Dr Peterson's commitment to ensuring the professional development of his postdoctoral trainees is obvious from the successful career trajectories of his postdocs. Another scientist I admire, who I have corresponded briefly with but have not met, is Dr Yamuna Krishnan. Dr Krishnan's lab has conducted some remarkable research on understanding the biology of lysosomes through a combination of tool development and investigation into novel biology of these critical organelles. Dr Krishnan is also a role model to me as an immigrant scientist who has overcome many challenges to be hugely successful in settings very different from her country of origin.

What's next for you?

I am currently an Assistant Professor in the Department of Biosciences at Rice University, so I am firmly entrenched in academia. Members of my lab will seek to decipher the complex interplay between the nervous and immune systems during development, homeostasis and neurodegeneration from the perspective of microglia, the sentinel immune cells of the brain. Our primary objective will be to understand the fundamental principles of microglia biology and the activation of lysosomal pathways in these critical glial cells. We will investigate microglia in their niche using zebrafish by exploiting the many experimental advantages of this vertebrate model organism, such as the accessibility to live imaging, the feasibility of large-scale CRISPR screens and the availability of transgenic tools to visualize microglia in vivo.

Tell us something interesting about yourself that wouldn't be on your CV

I recently had an opportunity to look at the CVs of two late-stage postdoctoral fellows. It was obvious to me that whereas one of these scientists had been given every advantage in life, the other scientist had undeniably overcome significant hurdles and detours to get to this stage in their career. One of my peeves is that if these two scientists went on the academic job market, the former candidate would be chosen over the latter by a majority – if not all – of the search committees. A CV, by definition, records career triumphs and accomplishments, and some of us are uncomfortable with discussing the many challenges we face in our lives and careers. I urge people, in committees or elsewhere, to look beyond the checklist of credentials, and focus more on traits such as grit, malleability and resilience, because I believe that everything interesting about a person is not in their CV.

Harini Iyer’s contact details: 6100 Main St. MS-140, Houston, TX 77005, USA.


W. S.
The Cl transporter ClC-7 is essential for phagocytic clearance by microglia
J. Cell Sci.