I did it! Officially a PhD Candidate!

The past few weeks months have been the most stressful times of my academic career. On November 16th, I successfully defended my original proposal in front of my preliminary committee and officially became a PhD candidate!!! I was looking forward to this day all through the summer and fall. I submitted my written proposal a month before my oral defense date and received feedback from my committee about the experiments proposed and the validity of my hypothesis. I am extremely grateful for each and every one of my preliminary committee members for taking the time to review my proposal and for providing their valuable feedback and criticism. This entire process helped me grow as a scientist and helped me think and write critically. I am also grateful for my family and friends who took the time to review my proposal, attended my practice talks, and provided useful comments.

As mentioned in my previous post, our graduate program requires us to pick a topic outside our main research area and develop an NIH-style original proposal related to the chosen topic. I chose to study the role of Myeloid-Derived Suppressor Cells (MDSCs) in Type 1 Diabetes (T1D). MDSCs are a heterogeneous population of immune cells that suppress or down-regulate the effector T cell responses in various immune microenvironments. In tumor microenvironments, T cells help kill the tumor cells and prevent the tumor cells from growing. However, MDSCs suppress these T cells and prevent them from killing the tumor cells thereby causing the cancer cells to proliferate. An autoimmune microenvrionment is opposite to the tumor microenvironment. In T1D, the T cells become autoreactive i.e., the T cells start killing the innocent insulin-producing beta cells in the pancreas. This leads to reduced insulin production and increased glucose in the bloodstream in the body. Insulin is an important hormone that helps in the transfer of glucose molecules into the cells that can then serve as the energy source for the cells and tissues. The destruction of the pancreatic beta cells therefore leads to an imbalance in the glucose homeostasis in the body. In such a microenvironment, we require MDSCs to suppress the T cells and prevent them from destroying the beta cells in the pancreas. The first question to ask here is, are MDSCs induced during T1D? The answer is yes. It was shown in 2014 that T1D patients have an increased MDSC induction in their peripheral blood. As to the best of my knowledge, this is the ONLY study that focusses on the native (body’s own) MDSCs during T1D. However, not much is known about the MDSCs and the different subpopulations of these cells that exists that are responsible for interacting with T cells in the pancreas. MDSC subsets and their mechanism of action are dependent on the specific tissue or the site of inflammation. Understanding the role of MDSCs in T1D and the specific MDSC subsets involved in T1D lead to several questions. I chose to investigate a few in my proposal:

  1. If MDSCs are induced in T1D patients, why are they unable to suppress the T cell responses in the pancreas? i.e., Are MDSCs defective during T1D?
  2. What are the specific subsets of MDSCs induced during T1D that are specific to the pancreatic microenvironment? MDSCs are incredibly heterogeneous and can exhibit several phenotypic and molecular states. These subsets are unique to the local tissue microenvironment.
  3. What is an MDSC-specific immune regulatory molecule and its corresponding pathway implicated in T1D that may contribute to disease pathogenesis? 

Without going into the details of each question posed, I proposed several experiments and techniques ranging from single-cell RNA sequencing analysis of the MDSC populations in the pancreas to generating MDSC-specific conditional gene knockout experiments in mice to answer these key questions. There were a few flaws in my experiments that were brought up during the presentation and I tried to address them to the best of my ability by proposing alternative approaches. Overall, my committee members were impressed with the breadth of background knowledge and experiments presented. The most important factor was to develop a hypothesis-driven proposal with a solid premise to back my hypothesis. The presentation didn’t feel one-sided and eventually developed into a curiosity-driven discussion.

Transitioning from a PhD student to a PhD candidate is a backbreaking process. Perhaps it is meant to be this way. Even though I felt numb for a few hours after the conclusion of my presentation, I could feel the academic apocalypse building up in a cloud over my head already. Here’s hoping for more successes and vital experiences in the future!

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Grad school diaries: The preliminary exam

The past few weeks months have been terrifying, nerve-wracking, depressing, and scary. My friends and family have also been subjected to my constant irritable and grouchy behavior. I have been preparing for my preliminary examination and everything seems to be coming together (very) slowly. I have woken up to sweaty nightmares about missing deadlines, submitting a complete crap proposal to my committee, and being told that my “scientific caliber” is not up to the mark to pursue an academic career (gulp!)

The first week of November is officially my “prelim week” and I will continue to go through series of mini heart-attacks and one too many mood swings until then. What exactly is a preliminary examination, you ask? Well, also called as the “candidacy exam”, or “the OP” (short for the original proposal – mostly followed in life sciences, I think), it is an examination that PhD students are required to take (and pass) in order to officially become PhD candidates. Many schools and department do this differently, and I can only tell you what is done in my program. Here is a short excerpt about the exam from our handbook –

The purpose of the Preliminary Examination is to stimulate you to develop original research ideas and to assess your academic knowledge, preparation and ability to analyze and synthesize the literature on and surrounding your topic. In the written proposal, you are expected to provide the examination committee with adequate background and details to understand the current state of the chosen field of research and to evaluate your proposed experiments. The oral examination allows the committee the opportunity to test your knowledge of the chosen research project, your ability to formulate and address a few research questions to anticipate the types of results to be obtained, and to evaluate your understanding of its scientific foundation. The examination will not only assess the science involved in the proposal but also will evaluate the quality of the presentation and the writing.

Basically, we are required to come up with an original idea – a topic that is not our main thesis research, write a hypothesis-driven research proposal in the NIH Exploratory/Developmental Research Grant (NIH R21)-type format, and defend it in front of our prelim committee (which is different from our thesis committee and consists of new members). The proposal must be original and designed to advance the current state of knowledge in the chosen field. It cannot be based on our own (current or previous) research projects. Also, our advisor cannot critique the research proposal prior to submission of the proposal to the prelim committee. The whole process takes almost 8-9 months and I have briefly summarized the timeline of the process below –

March-April 2017: Brainstorming ideas for the topic; Reading, reading, and more reading. (My topic is about the role of myeloid-derived suppressor cells or MDSCs in mediating pancreatic beta-cell death in Type 1 Diabetes, which is an autoimmune disorder.)

May 2017: Topic approval by the program office.

June-August 2017: Literature review; Brainstorming ideas and key questions for experiments, techniques, aims, etc; Beginning to write… maybe…

August 2017: Prelim committee assigned; Serious writing and reviewing (rinse, repeat); More reading.

September 2017: First draft completion; Review by peers, friends, and colleagues; Schedule date and time for the oral defense with committee; MORE READING.

October 2017: Submission of written proposal to the program office and prelim committee (4 weeks prior to oral defense); Approval of proposal for oral defense (or, revise and resubmission of proposal aka “your proposal is indefensible at this stage and requires more work”); Practicing oral talk (aka “pre-prelim talk”).

November 2017: Defense! Drinking and crying (if pass); Drinking and crying (if fail); New sense of purpose in life.

A few weeks into this process (around May), the horror stories start – stories about seniors failing their defense and “Mastering out” (which is seen in a really bad light), stories about committee member issues, stories about inadequate writing, etc. I have heard one too many stories about people dealing with depression and constant stress during the period of writing and oral defense. There are tons of useful advice about what to do and what not to do during the process. Of course, the experience is unique and different for every student but it would certainly be easy if I could get on with it without constantly being traumatized by every little detail (like feeling guilty every minute that I’m not thinking about my OP or working on it).

However, a few things have indeed helped me so far:

  • Finding a studying/writing spot outside of work and my apartment. I have been working at WALC until wee hours of night these days. (WALC is the active learning center on campus and is always hustling and bustling with students.) Just being among other students and the white noise in the background seems to be a great environment to focus and get stuff done.
  • Biking to and from work every day (around 6.5 miles). My friend recently convinced me to buy a bike and I must say that it has helped me get around the campus faster and save a ton of time. Not to forget the kick of endorphins in the morning that helps me focus on my experiments in the lab and plan things more effectively through the day. I spend most of the mornings doing cell culture work (I get done with this the first thing in the morning in order to make time for meetings and other experiments through the day) and afternoons on tissue processing and protein work. This gives me sufficient time from evening until late night to work on my OP.
  • Eating regularly, but not fussing over cooking. Most of the time spent on cooking and cleaning can be replaced by quickly grabbing something to eat on the go. (I can hear my sister squeaming at this already!)
  • Talking Ranting to friends, especially colleagues about the OP, work, life, and everything in general to relieve all the stress. I am fortunate to be on the same boat as many folks who can relate to my situation and listen to my rambling.
  • Reading something completely un-related to my research or the OP over the weekends. I have read three books in the past few months (check out my reading list!).

Alright, I should probably get back to work now (this was some major procrastination and I am feeling guilty already). Perhaps I should talk about my topic in detail on the next post. Until then, I will try to keep calm and carry on.

Keystone Neuroinflammation 2017

Last month, I attended my first scientific research conference as a PhD student at the beautiful town of Keystone in Colorado. The Keystone Symposia on “Neuroinflammation: Concepts, Characteristics, Consequences” was a week-long meeting with around 300 participants focussed on the interaction between two complex systems – the Central Nervous System (CNS) and the Immune System. Being a relatively new area of investigation, the conference brought together neuroscientists and immunologists who’re working on unraveling the mysteries of the brain and the human body. A traditional immunologist entering this field will have to grasp the intricacies of the brain with respect to microglia, astrocytes, neural circuits, neurodevelopment, the blood brain barrier (BBB), electrophysiology, behavior, degeneration, and more. Similarly, a traditional neuroscientist new to the field is expected to be familiar with all the details of the immune system from the heterogeneous immune cell types to different markers, the complement system, cytokines and chemokines, and be able to define aging in the context of immune regulation. As for me, being new to both the disciplines, this was an exciting opportunity to discover bold ideas as well as revisit my research objectives from a fresh perspective. Not to forget how wonderful Keystone itself was and made me realize how much I love the mountains!

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Without going into much of the details, some highlights of the conference are summarized below.

Microglia – the good, the bad, and the ugly

As expected, microglia were a hot topic through the meeting. Being the only resident immune cells in the CNS, microglia make up around 10% of the total cells in the brain. Activated microglia exhibit self-renewal and proliferative capacity along with phagocytic capability by engulfing toxic misfoled proteins (such as the aggregated amyloid beta peptides in Alzheimer’s disease and the alpha syneucleins in Parkinson’s disease). These “good” microglia are therefore essential for the maintenance of brain homeostasis. But what happens when these macrophages go haywire and start chewing up healthy neural synapses and start making more pro-inflammatory cytokines than necessary? How do these “bad” microglia contribute to neuroinflammation and accelerate the neurodegenerative phenomena? More importantly, the M1/M2 phenotypic characterization of microglia that I have previously written about is now considered to be an obsolete concept. Currently, we know that these cells are much more complex than to exhibit two polarized states. Microglia are heterogeneous in that their microenvironment dictates their characterization and therefore can exhibit multiple phenotypes.

Secretome – Looking beyond the transcriptome

A common method to predict the cellular phenotype or function is to study the transcriptome profile of a group of cells (or a single cell) under different activation states. In his talk, Christopher Glass highlighted the differences between the transcriptomes of human microglia and mouse microglia, and stressed on the importance of working with microenvironment-dependent microglial gene expression data. His work also showed the major differences in the up-regulated vs down-regulated genes in human vs mouse genomes highlighting the drawbacks of utilizing mouse models for characterizing human microglial cell behavior. Hugh Perry, in his talk laid out the “secretome” profile (the cytokines and chemokines) of microglial cells in the brain. Dr. Perry described the journey of his lab’s work towards targeted immunomodulation in chronic neurodegeneration by using this data.

The BBB – Pushing the boundaries of neuroinflammation

Among many topics of discussion, an interesting area was the role of the BBB in influencing immune cell proliferation into the CNS under stress and injury. (Side note: Other interesting areas of discussion were – cool new tools being developed for drug discovery, the use of various animal models in studying neuroinflammation such as transgenic and wild type zebra fish, drosophila, induced pluripotent stem cells, humanized mouse models, and rats). Studying the BBB in the context of inflammation can lead to some interesting questions such as – “What are the differences in the markers expressed and cytokines produced by the infiltrating macrophages versus the resident microglial cells?“, “How can the resident microglia be characterized in the context of microglial functions such as phagocytosis?“, “How do the pericytes and the oligodendrocytes contribute to inflammation in different disease models?

It’s all about the microglial cross-talk with glia (astrocytes) and neurons

Recently, Ben Barres’ group showed that activated microglial cells induce the formation of toxic A1 astrocytes by releasing TNF-a, IL-1a, and C1q that causing neurotoxicity and the eventual degradation of neurons. This study was significant because it showed that the neural death occurs through astrocytes and not directly from microglia. The importance of the role of astrocytes in mediating neuroinflammation has increased since then. Of course, the entire process in itself is a cross-talk between various cells within a particular microenvironment. Hence, when we discovery and design drugs to target microglia, we should also consider the effects of the compounds on glia and neurons in vitro, before moving to the in vivo studies.

Is anti-inflammation and not pro-inflammation the culprit in Alzheimer’s disease?

Perhaps one of the most provocative talks of the conference was by David Hansen from Genentech who illuminated the role of Triggering Receptor Expressed On Myeloid Cells 2 (Trem2) and debunked the myth of pro-inflammatory cytokines in Alzheimer’s pathology (i.e., lot of inflammation causes Alzheimer’s). Dr. Hansen highlighted key genes that are evident in anti-inflammation and immune suppression to be up regulated in his studies pointing towards an alternative activation pathway for neuroinflammation. This is an example where looking into the secretome along with the transcriptome becomes crucial in characterizing the cells and their subtypes in the progression of the disease.

My poster – Combination drug repurposing for the synergistic effect of enhancing microglial phagocytosis and reducing neurotoxicity in Alzheimer’s disease 

I presented a poster on one of my ongoing projects on combination drug repurposing for Alzheimer’s disease. I am grateful for everyone who stopped by and for all the valuable feedback and comments that I received on my work. Many questions were aimed towards the computation wing of the project (that I don’t directly work on). Briefly, these compounds are identified by utilizing the interactome-based drug discovery pipeline (called CANDO) that maps the signatures derived from the interaction between all the proteins in the proteome and all the human approved compounds. The overlapping mechanisms or pathways between Alzheimer disease with other diseases such as diabetes, heart failure, inflammation, among others can be utilized to determine drug behavior and therefore utilized for predicting novel targets.

And finally – Colorado!

I cannot leave out Colorado in this conversation about Keystone Symposia. I have been living on the plain lands among endless corn fields for almost four years now. Being around snow-capped mountains was an absolute treat to the eye (and to the soul). During the afternoon break sessions, we drove to various locations such as the Loveland pass which is around 11,990 feet above sea level in the Rocky mountains and the riven run area.  Intense winds and long stretches of snow welcomed us after a beautiful drive up the Rocky’s. I’ll let the photos do rest of the talking. Overall, attending the Keystone conference at this time in my research career was a great decision. I now have a better understanding of the field and my own project. I should really thank my advisor since it was he who pushed this idea and gave me valuable insight and advice throughout.

Religion, science, and believing.

I don’t usually talk about my personal views on this blog. However, this topic is something that I have contemplated for a while now and think is fair to be open about. I am still learning and evaluating my outlook on approaching this subject. Below are some bits revolving around the themes of religion and personal belief systems that were hidden away in my drafts folder for a long time. I have decided to publish all of them together. I’m sure I’ll have more to say about this topic in the future, but here’s a start.

***

Recently, I had a conversation with a fellow grad student about religion and his personal beliefs. Most academics shy away from this discussion in a professional (and sometimes even in a personal) setting. It is considered uncommon or rude to talk about it and people keep it to themselves. It is often acknowledged that as scientists, “we do science for science’s sake”, or that “a person’s religious beliefs has no place in his/her scientific pursuits.” This is something that has always boggled my mind. As a biologist and an atheist, I have confidence in my work/study because the underlying laws of biological systems are established and follow a set of proven scientific principles. For example, when we design an antibacterial drug against a particular strain of resistent bacteria, we know for a fact that the bacteria has mutated (or evolved) and therefore the old drug doesn’t work anymore. Similarly, we use mouse, worm, and other animal models for testing compounds in vivo because we have evidence to prove that humans are genetically related to other animals through a common evolutionary ancestor. Therefore, we can study the effects of the drugs in other animals before testing them to humans. The empirical evidence that exists as the basis of our research is inherently acknowledged to be the underlying force that drives scientific research. Now, how can someone who does similar work in a laboratory setting have a completely contradictory viewpoint in his/her private life? How can someone believe in a book (or many books) that preaches blatant falsehoods about our understanding of the universe and at the same time come to work every day and do science with a conscious mind? For me, science is deeply woven into our personal lives. No, I cannot pretend that science does not affect my personal views about the world. Similarly, my conscious will never let me pretend like my personal views have no affect on my scientific work.

***

One of the most common arguments that I have come across during such discussion is that people often say “I don’t believe in *everything* that this book says. I only believe in a few things that are important for my moral framework.” This is complete BS and hypocritical. One cannot disregard a particular theory written in a book (for example, “the earth is 6000 years old”, or, “when humans die we come back as another life form on earth”), and at the same time believe in another theory written in the same book. One can’t pick and choose what you want to accept and reject from a book, and then claim the book to guide one’s moral framework.

And then there is an argument that science is not perfect and that not everything published in all of the scientific literature is true. This is absolutely correct. This is why science is constantly changing – because our understanding of the world is constantly changing. This is why scientific literature constantly undergoes modifications and updates to accommodate our latest understanding of the world and the universe.

This is not the same with religious texts. These texts were written hundreds and thousands of years ago and are obsolete in this day and age. These texts were written to accommodate the worldview of an ancient time period. They are not relevant to the 21st century and we certainly do not have to submit to these texts in order to live within a moral framework of society. As of 2017, we have discovered around 8.7 million species on earth and can estimate a hundred billion galaxies in the observable universe. We have achieved things that were once considered unfathomable by humankind. Why do we have to be stuck in the ancient past and live by some 12th century law in order to be considered as “good humans”? Of course, religious texts provide interesting insight into various philosophical questions that one can ponder over. However, they do very little to the understanding and practice of science in this day and age.

It is also often argued that we need religion to understand morality and differentiate between good and evil. Religion does not equal morality. One does not have to be a good human just to please an invisible supreme being or to go to heaven. Altruism and kindness can exist on their own.

***

Talking about scientists with personal religious beliefs, I remember a wonderful conversation between Richard Dawkins and Lawrence Krauss many years ago. I can’t help but bring up a part of their conversation while thinking about this topic –

Krauss: I’ve had people write to me and say “I’m a medical doctor and I don’t believe in evolution.”

Dawkins: That’s a disgrace. I’m not supposed to say that, especially in this country (referring to the US) because one’s private beliefs are supposed to be irrelevant. But I would walk out of a doctor’s office and not consult him anymore if I heard that he said that. Because what that doctor is saying is that he’s a scientific ignoramus and a fool.

Krauss: In fact, in that regard, it is interesting to me at the same time how people can hold beliefs which are incompatible with other beliefs they have. And in some sense, everyone is a scientist and they just don’t realize they are, and yet in the time of crisis, that’s when.. (breaks). The example I gave is when George Bush was president, he said intelligent design must be taught alongside evolution so the kids will know what the debate is all about. And it wasn’t a stupid statement at priori, it was ignorant because he didn’t realize that there’s no debate. And that’s fine. I don’t mean ignorant in a pejorative sense, I just mean he wasn’t aware.

Dawkins: Ignorance is no crime.. you just don’t want to consult a doctor who’s ignorant.

Krauss: What amazed me is that in the same administration, when the avian flu was going to be a problem and mutating to humans, president Bush said “We’ve got to find how long it takes before the avian flu will mutate into humans.” And what amazed me is that no one in the administration – not a single person said “It’s been designed to kill us, forget about it.”

Dawkins: That’s a very good point. This kind of split-brain business which you’ve been referring to, the most glaring example I know, is more in your field (referring to Theoretical Physics and Astrophysics) than mine. I was told by a professor of Astronomy at Oxford, about a colleague of his who’s an astronomer and an astrophysicist, who writes learned papers – mathematical papers, published in astronomical journals, assuming that the universe is 13.7 billion years old. But he privately believes that the universe is only 6000 years old. How can a man like that hold down a job in a university as an astrophysicist? And yet, we are told “Well, it’s his private beliefs, you mustn’t interfere with this man’s private beliefs as long as he writes competent papers in astronomical journals”.

Krauss: Well, I mean, as long as he doesn’t teach his private beliefs.

Dawkins: Well, let’s hypothetically suppose that he teaches absolutely correctly – that the universe is 13.7 billion years old. How could you want to take a class from a man who teaches one thing and believes in something that is so many orders of magnitude different?

***

About believing in science.

My advisor once pointed out not to use the word ‘believe’ when someone said “I believe that..” during a lab meeting presentation. Back then, I didn’t understand what was wrong in saying we “believed” in something. I now understand. As scientists, we evaluate something on the basis of observation, experiment, and evidence. The evidence is dependent on the observations made and experiments performed. Therefore, something is either likely or unlikely to occur. It is either more probable or less probable. We don’t have to believe in evolution or the big bang theory. We accept the evidence that supports them. Believing in evolution or not doesn’t make it true. The evidence for evolution suggests that it is true. Belief is not a part of rational enquiry. Belief relies on faith and not on evidence.

Does arginase mediate immune suppression in the brain?

This week I want to talk about an interesting enzyme: Arginase-I (Arg1) and its metabolic pathway in an immune microenvironment. Arg1 is a cytosolic protein that is involved in the urea cycle. Specifically, it catalyzes the hydrolysis of L-arginine to L-ornithine and urea. It has been shown that the expression of Arg1 by macrophages has an important role in tumor growth. Macrophages that are recruited into the tumor microenvironment (tumor associated macrophages) express high levels of Arg1 resulting in the depletion of arginine – an essential nutrient required for T cell metabolism. Cytotoxic T cells, therefore, can no longer function and inhibit the tumor cells from proliferating. Arg1 is implicated in several inflammatory diseases as well as in autoimmunity. Arg1 plays a significant role in mediating immune suppression and blocking its metabolism is a novel strategy in preventing tumor growth and other inflammation-related conditions.

T cell suppression by MDSC
Myeloid-Derived Suppressor Cell suppresses cytotoxic T cell function through Arg1 metabolism. (IFNγ, IL-4, and IL-13 are cytokines that induced MDSC activation)

One hypothesis is that the immune suppressive cells in other immune microenvironments in the body must be similar to the Myeloid-Derived Suppressor Cells (MDSCs) that induce T cell suppression in the cancer microenvironment. The question is, do such immunosuppressive cells express increased levels of Arg1 and act through the Arg1 metabolic pathway? Since I am interested in the brain and neurodegeneration, this hypothesis can be extended to the brain immune microenvironment. Microglial cells in the brain also upregulate Arg1 and are neuroprotective in nature (in a healthy brain). These cells are the resident macrophages of the central nervous system and function by phagocytosing cell debris and toxic misfolded proteins (that eventually form aggregates and lead to neuronal death as seen in Alzheimer’s disease) out of the brain environment. The question now is – do the microglial cells exhibit immunosuppressive behavior by altering their Arg1 metabolism?

Kan et al., 2015, recently showed that CD11c positive microglial cells are immunosuppressive in the CVN-AD mouse model and that immune suppression is caused due to the deprivation of arginine (increased levels of extracellular Arg1 causing decreased levels of total brain arginine). What isn’t explicitly mentioned in this study is that arginine is also the substrate for nitric oxide synthase (NOS) that makes nitric oxide (NO) in an alternate L-arginine metabolic pathway. L-arginine is a substrate for both Arg1 and NOS. The Arg1 pathway polarizes the macrophages to M2 phenotype and the NOS pathway polarizes the macrophages to the M1 phenotype (Rath et al., 2014). The current model of microglial activation in the CNS is limited to these two polarized states, where, the M1 microglia are neurotoxic and the M2 microglia are neuroprotective. Arg1 is upregulated in microglia in the healthy brain and aids in phagocytosis of misfolded proteins and other cell debris. The classical microglial activation is through the M2 phenotype wherein the induced nitric oxide synthase (iNOS) is upregulated thereby accelerating inflammation in the brain (neuroinflammation is one of the hallmark characteristics of several neurological diseases such as Alzheimer’s Parkinson’s, Multiple Sclerosis, Traumatic Brain Injury, etc).

M1 and M2 microglia
The current model of microglial activation is limited to the Arg1-mediated M1 and iNOS-mediated M2 polarized states.

So, if an immunosuppressive cell exists in the brain, is it possible that the immune suppression is regulated through the M2 activation and that M1 activation is absent? In other words, L-arginine is metabolized through the Arg1 pathway and not through the NOS pathway. Other questions to consider: MDSCs upregulate both Arg1 and iNOS – so how does that fit into the two-state polarization model? How does iNOS modulate MDSC activity? We know that increased NO expression by MDSCs increases T cell suppression in the tumor microenvironment. Currently, both Arg1 and iNOS inhibitors are being developed to block the immune suppressive activity of MDSCs in the cancer microenvironment. However, understanding immunosuppression in the brain is still a long way to go and the idea is not widely accepted within the neurobiology community (my understanding from the currently available literature or published studies). Investigating this mechanism in the brain will be useful in developing potential therapeutic strategies for treating neuroinflammation and neurodegeneration.

References:

  • Kan MJ, Lee JE, Wilson JG, et al. Arginine Deprivation and Immune Suppression in a Mouse Model of Alzheimer’s Disease. The Journal of Neuroscience. 2015;35(15):5969-5982. DOI:10.1523/JNEUROSCI.4668-14.2015.
  • Rath M, Müller I, et al. Metabolism via arginase or nitric oxide synthase: two competing arginine pathways in macrophages. Front. Immunol., 27 October 2014. DOI: https://doi.org/10.3389/fimmu.2014.00532

[Almost] one year milestone – my first advisory committee meeting

Advisory committee meetings are held once every year (or twice every year, if the student or the committee chooses to do so) to asses the progress of a grad student’s PhD thesis. The meeting involves a written report that is to be submitted to the committee a week prior to the meeting and an oral presentation on the D-Day. During the presentation, the validity of the research work is thoroughly discussed along with the future direction(s) of the project(s) being undertaken. The advisory committee meetings are extremely important for the successful advancement and completion of a thesis – it is where brutal yet honest feedback is conveyed. We as grad students are forced to think critically of our work and defend our hypotheses as well as our results.

My first advisory committee meeting was an intense two-hour long session on a rather dull Tuesday afternoon. As I explained the premise of my work and my goals for the next year, my committee members brought up important questions that I had not previously ever considered. All the members of my committee, including my advisor, were supportive and encouraging. I learned some valuable lessons from the entire experience and got some great feedback from everyone. Some interesting and important points highlighted in my feedback assessment were –

  • Think carefully about how to present data and set up an argument in my presentation.
  • Work on clearly identifying the premise that sets the stage for my hypotheses.
  • Be critical about my data.
  • Continue to read literature: more reading, and reading more critically.
  • Focus on developing more robust immunological assays to answer the questions in my aims.
  • Interact more with colleagues on campus and at other schools to learn and get insight into techniques and relevant assays (wrt understanding what works and what doesn’t).
  • Explaining the experiments in detail before delving into my results (every assay is unique and has a question to be answered).
  • Think about how I want to present the previous studies done in the field that are relevant to my questions.
  • My hypotheses should be provided with a context (what is the data in support or against my hypotheses?)

These were just some of the significant parts of the feedback that I received. Now it’s time to put these into action and definitely work on continuing to build on my project more confidently. More later.

Metabolic interplay

fimmu-08-00248-g001
Renner K et al. Front Immunol. (2017)

I recently came across this figure that shows the key metabolic processes that dictates an immune cell behavior and function. Biochemists and pharmacologists sometimes focus on one or two key pathways in a disease model and forget that proteins don’t function in isolation. Protein networks are complex pathways with many overlays. A drug designed to inhibit or activate a specific protein can also affect other proteins in the connected pathways. This figure is focussed on an immune cell (natural killer cell) and its interaction with a tumor cell. The interplay between the different metabolic pathways applies to all kinds of cells in the body.

This figure is also quite interesting to me because I have been studying the arginase-1 (Arg1) pathway in microglial cells and this gives me a brief overview of where my study lies in the spectrum of key cellular metabolic pathways. Arg1 is an enzyme that metabolizes L-arginine to L-ornithine and urea in the urea cycle. With the help of ornithine decarboxylase (ODC), L-ornithine further makes polyamines that are important (? – it depends) for cell growth and survival (? – it depends). I think it is quite interesting to see how Arg1 and ODC would dictate the phenotypes of the microglial cells in the brain. Microglia are the brain’s resident immune cells – they chew up all the toxic stuff and get rid of them (this is known as phagocytosis). We have always studied these cells based on their two active states (M1 or M2). There has been evidence in the recent years to show that these cells in fact may exhibit multiple activated states (not just M1 and M2). Just like many immune cells in the body that exhibit a heterogenous phenotype, microglia in the brain may be no different. I’m curious if Arg1 and ODC may be involved in regulating a similar mechanism in microglial cells during neurodegeneration..

Source: Renner K., Singer K., et al. Metabolic Hallmarks of Tumor and Immune Cells in the Tumor Microenvironment. Front Immunol. 2017; 8: 248.