Faculty Spotlight: Dr. Lawrence Chasin

Friday, September 23, 2022 - 18:15
Dr. Lawrence Chasin is pictured

Professor Larry Chasin recently retired after more than five decades of research and teaching in the Department of Biological Sciences. He has been a mentor to postdoctoral, graduate and undergraduate students and his research has contributed to the development of mammalian cell genetics as a powerful approach to pursue biological questions, especially those related to how RNA transcripts are spliced to create the messenger RNA used for the biosynthesis of proteins. Faculty Spotlight talked with Dr. Chasin about his pathway to molecular biology and his fifty-two years at Columbia.

Faculty Spotlight: How did you decide to become a scientific researcher, and why did you turn to biology, in particular?

I remember being curious early on about what stuff was made of and enjoyed tinkering with a chemistry set in my basement. I went on to major in chemistry as an undergraduate and studied the structure of a simple triangular molecule with seven atoms. I had never taken a course in biology—which I thought of as identifying trees by the shape of their leaves—but in my senior year a new assistant professor was offering a course called “Biochemistry” so I thought I should see if there was anything chemical about biology. This was 1961 and the first 3-dimensional structure of a protein, hemoglobin, had just been determined. To me, this protein was a gigantic  molecule with thousands of atoms, as compared to the small ones we studied in organic chemistry. Moreover, its structure could explain its function of capturing oxygen as we breathe. It seemed we might be able to understand how living things function based on chemistry. I was hooked.

Crossing paths with that teacher in 1961 certainly changed my future, turning me into a biologist rather than a chemist. A broader coincidence was that 1961was near the start of the molecular biology revolution; messenger RNA had just been discovered as the molecular link between genes and cell biochemisty. I feel lucky that I was able to make the right choice at the right time.

FS: How did you kick off your research at Columbia back in 1970? What questions did you pose and how did you approach them?

Life is driven through the action of thousands of proteins found in every cell, and many of these proteins are commonly found across cells, while many others are cell specific or temporal. The information for building each protein lies in each cell’s genes in the form of DNA, and each cell contains a complete set of these genes. It follows that in some cells a gene and its coded protein will be expressed yet in another it will not. As a graduate student, I was interested in how this regulation of gene expression works, studying a single cell organism, bacteria, as a simple model system. As I proceeded through postdoctoral studies, again a single encounter led to a major shift in my path. I came across a book by Ted Puck, a thin monograph entitled The Mammalian Cell as a Microorganism in which he proposed that many of the advantages of growing and working with cultured bacterial cells could be applied to organisms as large and complex as mammals by using their cells grown in Petri dishes. In particular, powerful genetic tools such as the effects of gene mutations on cell function could be carried out, just as they were in bacteria, by analyzing clones of mutant cells. In this way all the genes and proteins that were essential for a complex function could be discovered. I was immediately captivated by the idea of studying cultured  mammalian cells: if my goal was to understand how we humans function as living organisms, why not jump to human, or at least mammalian, cells and skip the bacterial middleman. I was fortunate to be able to join Ted Puck’s lab as a postdoc where I transitioned from doing experiments with bacterial cells to studying cells from a Chinese hamster (CHO cells).

I started at Columbia in 1970, at a time when Puck’s approach was viewed with skepticism. Mammalian cells were thought to be too complex. Rare mutants so useful for genetic analysis could not be isolated because cells from higher organisms were considered too unstable: variants would arise by a programmatic change from one kind of cell to another rather than by gene mutation. I therefore devoted the first few years of my research to disproving this pessimistic view. We, along with two other labs working independently, succeeded in showing that variant cells isolated in our labs were indeed gene mutants, validating the field that came to be called mammalian cell genetics.

By the late 1970s we began attacking the broad question that interested me: how does gene expression into proteins work in mammalian cells and how is it controlled? Taking a cue from successes using bacteria, my strategy was to focus on a single model gene in CHO cells and to isolate mutants that could no longer express it or expressed it at abnormally high levels. I basically followed this path for the next four decades.

For my model gene, I settled on the gene for a protein called DHFR, which was already known to be expressed at levels 100 times higher than normal in certain mutant CHO cells. By the early 1980’s we were able to isolate numerous CHO mutants that could no longer express DHFR, so‑­ called DHFR-cells. This ability enabled us to pursue our mutational analysis plan for many years. CHO DHFR- cells also turned out to be useful for the manufacture of therapeutic human proteins such as monoclonal antibodies.

FS: What were some of your most gratifying research accomplishments?

Unlike in bacteria, during gene expression in higher organisms DNA is first copied into long pre-messenger RNA molecules, from which dozens of smaller regions (exons) are then cut and spliced together to form the mature messenger RNAs that are translated into proteins, the machinery of a cell. A major class of the first 100 DHFR- mutants we isolated turned out to be deficient in pre-messenger RNA splicing. I realized that RNA splicing was an essential and intriguing step in gene expression and then devoted myself to its study.

I focused on the question of recognition of information: how does the cell recognize the splice sites that define what exons will end up in the messenger RNA? These were times of rapid technology development, especially in DNA sequencing and custom DNA synthesis. These technologies changed the way genetics was used as a tool in biology. We started out painfully accumulating 100 randomly located DHFR- mutants and measuring their splicing efficiency in each case. Today we can design and synthesize thousands of DHFR- genes and measure the degree of splicing exhibited by each in a single experiment. The analysis of such high throughput data required a degree of computational skills, which in turn stimulated the design of more and more powerful experiments. We did not completely abandon the creation and analysis of single mutations, but used that route to concoct simpler artificial exons of our own design (“designer exons”) to ask specific questions such as the effect on splicing of exon length and of the number of regions within the exon that promote activation or inhibition of splicing.

All of these experiments were a lot of work and also a lot of fun, and yielded useful information for understanding the splicing code, even if the code is not yet perfect. It has enabled us to predict the quantitative effect of mutation in human mutant genes associated with disease with enough accuracy to guide future therapies. In particular, our list of splicing scores assigned to all 4096 possible exon RNA regions six bases in length  are widely used for scoring the splicing performance of mutant exons in human genetic disease.

Our most recent high throughput mutational analysis suggested that exons are bound throughout their length by a panoply of specific proteins that can positively or negatively affect splicing, such that each exon may have a unique assortment of proteins at any given moment. Despite this complexity, it is likely that predictability will improve with more data.

FS: What is the most surprising thing you discovered during your scientific career?

There were two results that were both unexpected as well as important. In 1989 we noticed many of our first 100 DHFR- mutants produced only low levels of DHFR messenger RNA. It turned out that in all of these cases the mutation had produced a translational stop signal—a “nonsense” coding signal—in the messenger RNA sequence. We showed that this inability to translate into a full protein caused a more rapid degradation of the messenger RNA. Other researchers then showed this phenomenon to be general and it was dubbed NMD, for nonsense mediated decay. and was thought to function as a quality control.

The second surprise, described briefly above, came more recently, in 2018. We showed that a mutant’s ability to be spliced depended on its predicted ability to bind to one or more of a set of 90 known human RNA-binding proteins, whose affinity to RNA targets had been measured. The surprise was that 89 of the 90 RNA-binding proteins exhibited this effect for mutations at one site or another in the exon, even though there is only enough room for 5 or 10 such proteins to be bound to a messenger RNA molecule at any one time. Such promiscuity paints a picture of great heterogeneity in a messenger RNA population, such that no two fully bound molecules would be exactly alike. This was surprising, because most biomolecular interactions are thought to operate  with considerable specificity.  

FS: What has been most rewarding for you about teaching?

Teaching competes with research for your time but pushes you out of the narrow world of experimentation in rewarding ways. My favorite teaching experience was when I taught biochemistry to second year undergraduates in our Intro Bio course. I asked: what distinguishes living things from the rest of the world? The answer was chemistry. The emphasis was on this chemistry “making sense” as opposed to its memorization. I proceeded assuming the students had no background in biology whatsoever. I started with the properties of water and ended with why energy was essential for life and how it was extracted from sugar and breathing. With a class size of 400, most individual contact with students happened during office hours, where seeing an “aha” moment on a student’s face provided a unique kind of delight. But my main source of satisfaction was constantly honing my presentations, as well as my conviction that this was a good way to explain how life works.

Another kind of satisfaction comes from mentoring graduate students. The hours spent going over results and deciding what to do next leads to a kind of intellectual intimacy, with each learning how the other thinks. The satisfaction comes from realizing how this sharing of and arguing about ideas leads to better science. In the best cases, the teaching goes both ways.

FS: As someone who spent a lifetime doing science, how would you describe the main benefits of a career as a scientist?

I found being an academic researcher to be a great job. On the one hand, the work is hard, requiring a lot of time and bringing with it a certain amount of stress. On the other hand, to a large degree you do what you want to do—you ask the questions that interest you, dictated by your own curiosity and your ideas about how to answer them. In some ways, it is like an artist who starts with a blank canvas and decides what to put on it. That freedom to express yourself makes the hard work worth it. And of course, when you succeed in answering a good question and you share that answer by publishing, it provides the satisfaction of validating your efforts.

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