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Biology by Any Means Necessary: Vlad Denic in MCB

Biology by Any Means Necessary: Vlad Denic in MCB

Sometimes how you get where you’re going is as important as what you do when you get there. This is true of the proteins in our cells, whose movement and targeting have been the focus of Prof. Vladimir Denic’s career. But it may be equally true of Vlad himself, and the path he followed to arrive where he is today.

During his teen years, Vlad lived in four different countries. The first migration, though abrupt, did not even require him to cross the street: he went to bed in Yugoslavia and woke up in a newly independent Serbia. To avoid the vicissitudes of the ensuing war, he spent much of high school in rural Pennsylvania and San Francisco. From there, he crossed the Pacific, Equator, and International Date Line to the University of Auckland, where he studied biochemistry, learned to surf, and was bitten by a shark.

Perhaps to help make sense of the world whizzing by, he acquired a precocious appreciation for the value of theory-driven investigation. Perhaps out of necessity, he accumulated a great deal of practice at the art of starting over.

His undergraduate education was cut short by a summer internship at the University of California–San Francisco, from which he never returned to the antipodes. Fortunately, UCSF’s graduate program did not consider his lack of a Bachelor’s degree an obstacle to admission. There, he joined Jonathan Weissman’s laboratory, where he performed seminal work in lipid synthesis that laid the groundwork for his subsequent mastery of membrane biochemistry. After his long but ultimately successful thesis project and a short postdoc in the same lab, he made his way to Harvard’s Department of Molecular and Cell Biology, where he was awarded tenure in 2015.

These days, Vlad gives every indication of having arrived at the right place in the world. A year or so ago, he and his wife, Dr. Florencia Caro (currently a postdoc in the Department of Microbiology at HMS), moved into a beautiful house just off Somerville’s Davis Square. In September, they welcomed their first child, Milan, into the world. It is obvious to all who know them that the child will not want for love, a sense of humor, or the genetic determinants of intelligence.

Davis Square boasts an abundance of excellent coffee shops, which Vlad rarely patronizes because he is a master barista in his own right. Lucky guests are presented with perfect cappuccinos, pulled from a sleek chrome espresso machine with hissing valves and a mystifying abundance of analog controls; the process of making them fills him with a fussy, nerdy delight. Even more fortunate guests are treated to dinner prepared in the spacious and well-appointed kitchen. The cookbooks and appliances show signs of heavy use; in the kitchen, as in the lab, Vlad is an experimentalist, not a theoretician.

Well-caffeinated and well-fed, one notices the stacks of papers and books occupying the corners of many rooms. Flipping through any pile reveals interests both omnivorous and discerning: recent journal articles, well-thumbed copies of classic biochemistry papers, poems by Brodsky and Auden. The books careen from punishingly involved recipes for modern Californo-Hungarian cuisine to the collected works of Gogol and Borges. The selections distill and reflect Vlad’s personality; to know these works is to know him.

Vlad’s wardrobe, honed in San Francisco, is idiosyncratic yet self-consistent, implying the existence of a nearby hip neighborhood where everyone dresses that way. His manner is easy and relaxed, his sardonic wit tempered by a hint of coastal California twang. His temples are graying, but if Vlad will ever seem middle-aged, he has not yet.

“Vlad is the kind of colleague that we all fantasize that we are,” says Prof. Dan Kahne of his friend. “Smart and cool don’t normally go together. He seems to do it all without effort. We’re lucky to have him.”

His youthful, quirky personal style serves him well in the lecture hall, where for the past 4 years he has co-taught MCB 60. During this time, he has thought deeply about how best to introduce students to our field.

“The issue,” Vlad says, “is how do you get students interested in cell biology without relying on ‘data dumps’ via traditional lectures and textbook reading?” As an alternative, he experiments with interactive learning. “Rather than covering things systematically, I push students through discussions of experimental results to figure things out for themselves. Then they talk to each other, and that has power that I never have.”

Vlad also monitors students’ conceptual understanding, and uses this information to modify his tactics in subsequent class meetings. “The dream result would be something resembling an experimental arc within the class itself, or some combination of ‘Choose Your Own Adventure’ and neural network learning,” he continues, describing his vision of a dynamic course that could redesign itself in real time in response to the intellectual needs of the students.

His teaching experience also influences Vlad’s approach to communicating with colleagues. “You have to re-learn certain things that you thought you knew, but didn’t understand deeply enough to explain to young people. My ability to convey our lab’s research has gotten significantly better because it started to resemble the way I talk in class.” The process has not been entirely painless. “Before, I never appreciated how awful my slides were.”

Just as Vlad’s techniques for teaching and disseminating knowledge have evolved, research in the Denic laboratory has stretched, transmuted, and reinvented itself.

Initially, the lab extended Vlad’s postdoctoral work focused on tail-anchored (TA) proteins, which play critical roles in cellular functions from vesicle fusion to programmed cell death. TA proteins are inserted into the endoplasmic reticulum via the GET (Guided Entry of TA) pathway. Using genetic and biochemical approaches in budding yeast, the Denic lab answered key questions about how TA proteins are targeted. “Basically, it’s a bucket brigade,” Vlad explains. “The protein is grabbed and then handed off to a chain of proteins. The last pair of hands knows which membrane to go to, and is programmed to know when to let go of the bucket once it’s time.”

Although some details remain to be resolved, the lab’s work on the GET pathway is winding down. Why is it time to let go of the bucket? “Some of it is wanderlust,” he muses. “Maybe because of my own inclinations, maybe because of my training, I was exposed to the idea that there are a lot of things that might interest me over the course of my career. At some point you have to set sail for new lands.”

The first spot on the horizon was autophagy, another field in which Vlad could bring his expertise in membrane biochemistry to bear. The lab focuses on selective autophagy, which captures unwanted cellular components, such as damaged organelles or protein aggregates, within endomembrane compartments called autophagosomes. After sequestration, the cargo is destroyed.

Critical questions about this process remain unanswered: What types of organelle damage are detected by selective autophagy? Furthermore, how do the Atg factors make local decisions about individual organelles?

The Denic lab’s findings unify these overarching concepts. “We saw the core machinery being deployed at various places throughout the cell,” he explains, “but didn’t understand how it was regulated.” They found that autophagic receptors bound to damage signals on target organelles (or aggregates) activate nearby molecules of a regulatory kinase, ensuring that autophagosome formation and selective degradation only occur at the proper sites.

In this, Vlad glimpses an even broader principle: “The more you look at cell biology these days, the more you realize that the land to be discovered is regulatory land—that is, how do we explain specificity?” Accordingly, the lab is combining CRISPR/Cas9-based gene targeting with quantitative reporters to identify mammal-specific autophagy factors. “My sense is that this unexplored regulatory layer exists for many mammalian processes, but that a lot of the core cell biology is mediated by homologs of yeast proteins.”

Autophagy is critical for protecting essential cells such as neurons, which do not divide and therefore cannot eliminate cellular detritus by simple dilution. Unfortunately, the efficiency of selective autophagy decreases with aging, and the resultant buildup of protein aggregates may contribute to the pathogenesis of neurodegeneration.

Aging and aggregation are deeply connected to another major effort in the lab: revealing why protein aggregates accumulate in aged cells. “When organisms get older, they have a worsened ability to maintain proteostasis—making just enough protein that it can be folded, but not so much that there’s aggregation. We wanted to figure out why proteostasis collapses with aging.”

Early insight came from the observation that heat shock factor (HSF), a transcription factor that regulates chaperone genes, becomes less responsive to protein unfolding in old yeast cells. “Once we saw that HSF was not working properly, it led us in two directions: first, is reducing the function of this factor sufficient to cause proteostasis collapse? And second, why does it stop working when you get older?”

To address these questions, the lab developed an engineered system in yeast. “The major goal is to test, in this ‘toy’ system, the idea that proteostasis comes from HSF-mediated transcriptional regulation, and secondarily the tenet that proteostasis collapse is a hallmark of aging: If we engineer mutations in Hsf1 that alleviated its functional attenuation with age, would the mutants live longer?” On sabbatical in 2016 at Calico, a company dedicated to the biology of aging, Vlad used new microfluidics technologies to monitor proteostasis in single cells as they age; this method has since been deployed in his lab.

The ability to control age-related protein aggregation and extend cellular lifespan would be of major clinical importance. “It’s up for debate whether aging itself is largely the consequence of proteostasis collapse, and whether that represents a major ‘breaking point’ in aging,” he cautions. “But if you were able to make a cell very good at protein folding, I think that cell would be resistant to many neurodegenerative conditions.”

The diversity of his ongoing work has not diminished Vlad’s appetite for new challenges. “My favorite dream, I guess, is that we could just look at a cell and see something that makes you wonder, ‘How does that work?’ and then focus on that process. This is a goal we haven’t achieved yet: starting from observation, rather than dissecting something previously defined.”

To that end, the lab is adopting new methods, requiring the members to develop new skills. Invariably, the choice of experimental tools governed by the question of the moment. “We never say a priori, ‘this is a great solution in need of a problem.’” Pushing his large-rimmed glasses up the bridge of his nose in a patented gesture of self-deprecation, Vlad expands: “Our general strategy is still to fumble in the dark a little bit, but then take a ‘by any means necessary’ approach, and this sometimes means getting into new areas. Sometimes that’s the only way through.”

In MCB, Vlad has found a home where his dedication to risk-taking is not merely appreciated, but celebrated. “We are thrilled to have Vlad as a colleague because of his quirky smarts, scientific creativity, and wonderful camaraderie,” says Prof Venkatesh Murthy, chair of the department. “He has this expansive, roll-your-eyes wit that often brings laughs and groans, but there is always this deep and passionate scholarship underneath it all. I look forward to seeing him continue to enrich the world with his research and education.”

Vlad’s openness to new methods requires that the lab provide a safe environment for exploration, even if that means following the occasional blind alley—or ignoring the traffic signs. “I hope that the culture in the lab is such that people are free to do something that I would say is never going to work. Even if my intuition says no, they’re free to do it and show that I’m wrong.”

Such an approach can take time to bear fruit, but Vlad is content with that, having benefited from a mentor who encouraged his junior colleagues to find their paths at their own pace. “The biggest lesson I learned from Jonathan [Weissman] is a kind of unconditional patience. Different people need different amounts of time to hit their stride, and this is something you can try to facilitate.” His postdocs and students appreciate this patience, as well as his generosity of attention: “When you knock on the door, he will stop mid-keystroke to chat,” said Chris Shoemaker, a postdoc in the lab. “I don’t know how he does it.”

However long it may take, the rewards are clear to Vlad, both scientifically and in regard to personal development. Pressed to describe what makes him the proudest about his career in MCB, he says, “I think the biggest achievement is placing people. Seeing people transition to the next level—there’s nothing like seeing someone move on. It’s about creating an environment in the lab that allows people to go on and do interesting things on their own.”

He pauses to think, and then breaks into a generous grin and chuckles at his own words, perhaps because they are so precisely on the nose for a scholar of protein targeting: “The biggest achievement is getting people where they want to be.”

by Chris Patil

Vlad Denic faculty profile

Denic lab website