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.

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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.

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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.

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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?

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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.

[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.

Two months in: Last day in cancer lab

Today marks the last day of my first laboratory rotation. I want to pen down a few things that I learned and experienced during my time in the cancer lab:

  • Starting fresh in a new field of research was challenging at first, but got interesting once the different pieces of the puzzle were pieced together along the way.
  • Understanding the nitty-gritty of the investigation entails failures, failures, failures, followed by lots of optimizations and practice. Patience and perseverance is the key.
  • Staying positive and motivated throughout the journey can go a long way. My mentor/ senior grad student in the lab is one of the most optimistic people I’ve met in recent times.
  • Almost always, grad students manage multiple projects at the same time. It is essential to have a main project (or two) and a few side projects to keep the lab active, and research moving forward.
  • Taking a computing course along with the Biochemistry course has kept my study diverse and helped me broaden my thought bubble. At the same time, it has contributed to an additional pressure of having to take exams and submit assignments frequently (which I don’t want to be doing a lot of at grad school).
  • I nearly broke my arm while working with the french press for cell lysis (it really is a workout in itself!)
  • Having flexible working hours in the lab was good, but there were days when I took this for granted and ended up being awfully lazy. I am still learning to implement a fixed schedule for the weekdays to increase my productivity through the week.
  • Caffeine addiction is a real thing. I now even have a brew preference to satisfy my taste buds and more importantly, my brain.

Orientation week: What do I want out of grad school?

The first week of grad school was intense and exhaustive with all kinds of information being tossed at us from all directions. We started off with a formal introduction to the school, the department, and all the resources available at our disposal like the libraries, mentors, health benefits, and so on. Besides all this, a main objective of the orientation week was to decide the first two labs that we are interested to rotate in. The process involved meeting with several professors, going on lab tours, meeting other grad students and evaluating if a lab was a good fit for us or not. Although I knew the direction of research I wanted to pursue, discovering so many options and learning about cool new research areas left me wondering if I really knew what I wanted to be doing for the next five years! Right now, I feel like a first grader starting school for the first time and constantly being exposed to many things I never knew existed.

Grad school 101 - What I don't know
Grad school 101 – What I don’t know

Being in a big umbrella program, there are ten different training groups to choose from. First year graduate students pick four labs within any of the groups to rotate in during their first year. This is very different from a departmental graduate program where a student can only rotate in labs within that respective department. After all the decisions and evaluations, I have chosen my first two labs for the semester and I am looking forward to be officially starting next week.

This process has made me question some decisions that I’ve taken in the last couple of years. “What do I want out of grad school?” seems to be the most significant one. Before beginning my journey, I knew that I wanted to train to be a good scientist, learn how to think, develop skills unique to my field, master techniques that will make me employable, learn how to learn, and be an overall well rounded researcher. Now I’m not sure if there is a definite answer to the question. It is something that I’d have to figure out on-the-go.

Life update: Starting my PhD journey!

A lot has happened over the past few months. After graduating with my Master’s degree in Biological Sciences and spending the entire summer traveling across Europe & India, today marked the beginning of my PhD journey! Dreaming and preparing of this day for a long time now, I felt a little overwhelmed, nervous and excited at the same time. It is a long way ahead from this point onwards and I look forward to sharing my academic (mis)adventures here, in the hope of finding some clarity and meaning to life, the universe and everything (a.k.a 42). So stay with me, I am not done yet!