Placement: Promote to Homepage
Chris Kaiser | School of Science
May 22, 2018
This story was originally published on the MIT School of Science.
The rise of the information age in the second half of the 20th century was spurred on by two related but distinct scientific and technological revolutions. The first, of course, was the digital revolution, which emerged with the development of the mathematics necessary for computation and data storage based entirely on a binary code. The second revolution came about from the discovery that information encoded in the molecular sequence of DNA carries the instructions for the working parts of a cell and thus is the blueprint of life. The field of molecular biology emerged as the study of how genetic information is transmitted from one generation to another and is read out to form functional cellular components and regulatory circuits.
The foundational science of molecular biology has led to methods for reading and writing biological information and to alter genomes by design. The capability to reprogram living organisms to do useful things forms the basis of the biotechnology industry.
No single institution has had a greater impact in accelerating the revolution in molecular biology and biotechnology than MIT. The origins of this revolution is woven deeply into the history of the Department of Biology.
MIT’s revolutionary foundation
In the late 1950s, MIT’s administration began a deliberate and concerted effort to recruit molecular biologists even before this nascent research area was recognized as a distinct field that would transform all of biology. The decision was made to hire faculty who were interested in studying biology by uncovering relationships between molecular structure and function and understanding the biochemical basis of genetic information and the transmission of genetic traits.
At the University of Wisconsin, Gobind Khorana celebrates his 1968 Nobel Prize in Physiology or Medicine awarded for his contributions to elucidation of the genetic code. Even at this celebration, he was already looking forward to the next experiments. Here, he explains the strategy for enzymatic gene synthesis using diagrams of hybridizing strands. Photo: Tom RajBhandary.
One such seminal hire was Alex Rich, the William Thompson Sedgwick Professor of Biophysics, who came to MIT in 1958. Rich contributed to the discovery of how single strands of DNA and RNA molecules can find and match complementary sequences. This process, called nucleic acid hybridization, remains one of the fundamental methods for reading out the identity of nucleic acid molecules. In addition to foundational research into hybridization, Rich also elucidated the three-dimensional structure of the transfer RNA molecule that functions in reading the genetic code.
A second enormously influential hire was Salvador Luria who moved from the University of Illinois to MIT in 1959. Luria was a leader in the study of bacteriophages — viruses that infect bacterial cells. Much in the same way that early quantum physicists used the hydrogen atom to establish a theory for quantum structure of atoms, the first molecular geneticists used the bacteriophage as a simple genetic system to reveal the rules for fundamental genetic processes such as replication, recombination, and mutation.
By the 1960s, the understanding of fundamental genetic mechanisms developed by Luria and others had merged with the work of structural biologists such as Rich to give the outline of how genetic information was stored, copied, and read.
The reading of genetic information takes place in two steps. In the first step, known as transcription, genetic information encoded in DNA is used as a template to make a copy in the form of a single-stranded messenger RNA. In the second step, the information contained within the messenger RNA is translated into a protein sequence at the site of protein synthesis — the ribosome. Transfer RNA molecules serve as the key adaptor molecules that allow translation of messenger RNA sequences into the amino acid sequences of proteins. Each transfer RNA carries a triplet of nucleotides that pairs with and thus “reads” a specific three-nucleotide sequence along the messenger RNA. At its other end, the transfer RNA carries a particular amino acid that is added in its place in the sequence of the elongating protein chain.
Khorana cracks the code
Before Har Gobind Khorana arrived in Cambridge, Massachusetts in 1970, he worked with the great nucleotide chemist, Alexander Todd at the University of Cambridge in the United Kingdom. Khorana was in the lab at the time that chemists were working out structure of the nucleotide building blocks of DNA and RNA. When Khorana started his own lab, first at University of British Columbia and then at University of Wisconsin, his work was devoted to using synthetic chemistry to make biologically important molecules and ever more complicated polynucleotide structures.
Khorana made one of the most consequential advances in molecular biology by using a hybrid approach that employed organic chemistry to synthesize short sequence of a few nucleotides followed by the use of a copying enzyme to generate long DNA molecules with many repeating copies of the short sequence. Khorana’s molecules with a repeating sequence were the keys to cracking the genetic code. A few years earlier, the complex process of translation was reconstituted in the test tube and was dependent on messenger RNA added from the outside. By using synthetic messenger RNAs to instruct the synthesis of proteins by the ribosome, Khorana’s group was able to work out rules for how specific sequences of three nucleotides in RNA are translated into the 20 possible amino acids. We now know that all forms of life use the same genetic code to read the information written in DNA. For his contributions to understanding the code, Khorana shared the 1968 Nobel Prize for Physiology or Medicine.
Synthesizing genes
As work on the code was nearing completion, Khorana began thinking about how to synthesize long polynucleotide molecules of even greater complexity. He had his eye on what could be considered a moonshot challenge in nucleic acid synthesis: to synthesize a functional gene.
Before an artificial gene could be synthesized, it was necessary, of course, to know the DNA sequence of the desired gene. In the mid-1960s, the ability to directly determine the DNA sequence of a protein-coding gene was still about a decade away; however, the DNA sequence of an RNA-coding gene could be deduced directly from the RNA sequence. The first complete sequence of a natural gene-encoded RNA molecule — the transfer RNA for the amino acid alanine — was determined by Robert Holley in 1965. In that year, Khorana began to organize his lab to synthesize the double-stranded DNA that would code for alanine transfer RNA. Although Khorana knew that this monumental task would require a combined and concerted effort of perhaps a decade of work, he expressed utter clarity and confidence in the purpose and significance of this endeavor.
In a review letter for the Biochemical Journal in 1968, he wrote: We would like to know, for example, what the initiation and termination signals for RNA polymerase are, what kind of sequences are recognized by repressors, by host modification and host restrictive enzymes, and by enzymes involved in genetic recombination, and so on. For these studies, ultimately what is required is the ability to synthesize long chains of DNA with specific non-repeating sequences. With this should come the ability to ‘manipulate’ DNA for different types of studies.
This description pretty well summarizes the work of a major segment of molecular biology for the next 50 years.
Copying of genetic information in DNA into RNA.Transcription is catalyzed by the enzyme RNA polymerase (not shown). This diagram shows that if the sequence of the RNA transcript is known, as was the case for alanine transfer RNA, the DNA sequence of the corresponding gene for the transfer RNA can be deduced from the rules of base pairing. This and figure below from he published lecture notes of Professor Salvador Luria who taught general biology (7.01) at MIT for many years. Credit: MIT Press, 1975, “36 Lectures in Biology.”
In theory, the DNA for alanine transfer RNA could be formed by synthesizing each complementary strand separately and then using hybridization to form a complete double-stranded helix. This approach would require synthesis of DNA strands that were 77 nucleotides long; however, at the time the upper limit for synthesis, even in Khorana’s laboratory, was about 20. The plan as originally conceived was to take advantage of the ability of DNA polymerase to synthesize DNA from a template. The idea was to synthesize oligo-nucleotides that partly overlapped and then to use DNA polymerase to complete a fully double-stranded DNA molecule. Khorana’s team started the synthesis of the gene for alanine transfer RNA in this way and showed that basic strategy of using chemical synthesis followed by synthesis by polymerase would work. But when the DNA ligase enzyme was discovered, it became more practical to chemically synthesize many short overlapping segments and stitch them together with ligase. In this manner, the synthesis of alanine transfer RNA gene was completed in 1970.
The first synthetic gene was in itself a monumental landmark in the progression of molecular biology; but like any successful moonshot, the technological innovations developed along the way may have had the furthest-reaching impact.
Knock-on effects
Marvin Caruthers joined Khorana part of the team synthesizing the alanine transfer RNA in 1966 and then came with him to MIT. Caruthers then went to the University of Colorado at Boulder, where he began his own research program developing methods for reliable automated synthesis of short DNA molecules, or oligonucleotides. He decided to carry out nucleotide synthesis on a solid support, which would greatly simplify and speed up the separation of the growing oligo-nucleotide chain away from precursor molecules as the process stepped through the reaction cycle for the addition of each base in the sequence.
Khorana had the vision and leadership to convince a team to follow him to an unknown place, and he had the supreme confidence that he would know what to do once he got there.
A second key innovation was Caruther’s development of nucleotide precursors that could be stored for long periods and then readily activated immediately before use. The so called “phosphoramidite method” for DNA synthesis was automated and its use enables scientists who are not expert organic chemists to synthesize their own oligonucleotides. The ready availability of oligonucleotide primers has driven the expansion of methods for reading DNA by sequencing and the copying and modification of DNA sequences at will. These technologies are analogous to the fundamental output and input devices of a digital computer but for the manipulation of biological information encoded in DNA.
The development of the by polymerase chain reaction (PCR) is another key technological advance that stemmed from Khorana’s work. PCR employs the same basic elements proposed by Khorana for the synthesis of the alanine transfer RNA gene; hybridization of synthetic oligonucleotides to a target DNA followed by synthesis with DNA polymerase to produce double-stranded DNA of defined sequence. The key innovation as proposed by Kary Mullis when he came up with the idea for PCR was to use the same synthetic oligonucleotides to conduct many cycles of hybridization and synthesis. Because of the doubling that results from each round of replication, 20 cycles would give a million-fold amplification allowing a specific sequence to be produced from an extremely complex mixture such as a whole genome.
Twelve years before the invention of PCR, Khorana’s group showed that oligonucleotides defining the ends of the completed transfer RNA gene segment could be used to carry out rounds of hybridization and DNA synthesis with polymerase to make more of the desired DNA product without any additional labor in chemical synthesis of DNA. This raises the question of whether Khorana, who was a visionary, foresaw the possible application of his method for the amplification of sequences from whole genomes. It is worth pointing out that at the time Khorana’s group was contemplating enzymatic amplification, their synthetic gene was one of the only DNA sequences that was known and therefore a basic ingredient of the PCR method — knowledge of enough of an interesting target sequence to design the oligonucleotide primers for its amplification — was not available to them. Years later, when PCR patents were under litigation, the question of prior art arose; but Khorana refrained from comment, having moved on to the study of the light-sensing protein rhodopsin.
Visions for the next revolution
At a memorial service for Khorana held at MIT in 2012, many stories were told about his intellectual independence and visionary leadership in basic research that had far-reaching implications.
How a suppressor transfer RNA works. A stop codon introduced in the middle of a gene will cause premature termination of the protein chain. A suppressor transfer RNA has been altered so that it can read past a stop mutation suppress its effect. This provides a definitive genetic demonstration for functionality of a suppressor transfer RNA gene. Credit: MIT Press, 1975, “36 Lectures in Biology.”
As the synthesis of alanine transfer RNA gene was well underway, Khorana initiated a project reaching for an even bigger prize — a synthetic gene that could be shown to carry out its biological function in the context of a living cell. The candidate, known as a suppressor transfer RNA, was a recently sequenced transfer RNA that had the ability to read past a stop mutation introduced in the middle of a gene, thereby suppressing the effect of the mutation and allowing ribosomes to read the RNA and produce the protein. The idea that Khorana laid out for the team was to synthesize the suppressor transfer RNA and then introduce the synthetic gene into a suitable bacterial host designed to test its ability to suppress a stop mutation.
At that time, now standard methods for gene cloning and expression did not exist. As the planning moved forward, the team synthesizing the suppressor transfer RNA began to envision more and more elaborate schemes to get a functional suppressor transfer RNA gene into cells. As Caruthers related the story, Khorana listened quietly to the brainstorming for a bit and then said, “Let’s first synthesize the gene. By that time, we will know how to express it.” Khorana was right; and by the time the synthetic suppressor gene was complete, methods were available for introducing the gene into cells.
Like the great explorers Frances Drake and Ernest Shackleton who were my heroes growing up, Khorana had the vision and leadership to convince a team to follow him to an unknown place, and he had the supreme confidence that he would know what to do once he got there.
Transformational scientific and technological revolutions, like those initiated by Khorana, Luria, and Rich, are of keen interest because they help us understand the sparks of genius and originality that we should be looking for when we hire new faculty and illustrate the kinds of research projects in our institutions and companies that might lead to fundamental advances in preparation for the next scientific revolution.
Chris Kaiser is the Amgen Inc. Professor of Biology and the former head of the MIT Department of Biology.
Biologist honored for his work developing yeast as a model organism for genetic studies.
Anne Trafton | MIT News Office
May 16, 2018
Gerald Fink, an MIT biologist and former director of the Whitehead Institute, has been named the recipient of the 2018-2019 James R. Killian Jr. Faculty Achievement Award.
Fink, the Margaret and Herman Sokol Professor in Biomedical Research and American Cancer Society Professor of Genetics, was honored for his work in the development of baker’s yeast, Saccharomyces cerevisiae. Fink’s work transformed yeast into the leading model for studying the genetics of eukaryotes, organisms whose cells contain nuclei.
“Professor Fink is among the very few scientists who can be singularly credited with fundamentally changing the way we approach biological problems. He has made numerous seminal contributions to understanding the fundamentals of all nucleated life on the planet, significantly advancing our knowledge of many cellular processes critical to life systems and human diseases,” according to the award citation, which was read at the May 16 faculty meeting by Michael Strano, the chair of the Killian Award selection committee and the Carbon P. Dubbs Professor of Chemical Engineering at MIT.
Established in 1971 to honor MIT’s 10th president, James Killian, the Killian Award recognizes extraordinary professional achievements by an MIT faculty member. “From understanding how cells are formed and function, to understanding cancer and developing insights into aging, his research has proved critical to modern day science,” the award committee wrote of Fink.
Fink, who was inspired to go into science partly by the Soviet Union’s launch of the Sputnik satellite in 1957, began studying yeast while working toward his PhD at Yale University in the 1960s.
“I studied yeast as a graduate student, when it was an extremely unpopular organism,” Fink recalls. “In fact, I was cautioned by my thesis advisor not to tackle it because it was an intractable system.”
Despite that warning, Fink dove into studies of yeast metabolism — in particular, the mechanism that yeast uses to regulate amino acid biosynthesis. At the time, yeast engineering was impeded because there was no way to insert a gene into yeast cells. Then, in 1976, Fink developed a way to insert any DNA into yeast cells, thus allowing researchers to study gene functions in eukaryotic cells in a way that was previously impossible.
“That technology dramatically changed everything, because it made it possible to insert a gene from any organism into yeast,” Fink says.
Fink’s advance allowed scientists to manipulate the yeast genome at will, turning the organism into a cell factory. This technology enabled the current large-scale production of vaccines, drugs (including insulin), and biofuels in yeast.
Fink, who joined the MIT faculty in 1982, currently studies the fungus Candida albicans — which can cause thrush, yeast infections, and severe blood infections — in hopes of developing new antifungal drugs. His lab recently discovered how this human pathogen switches back and forth from its usual yeast form to an invasive filamentous form.
Fink taught genetics to MIT undergraduates and graduate students for many years, and as director of the Whitehead Institute from 1990 to 2001 oversaw the Whitehead’s contribution to the Human Genome Project.
“The Human Genome Project would not have happened here at MIT if it had not been for the unique structure of the Whitehead Institute, which was able to move quickly,” Fink says. “We committed resources and space from the Whitehead to propel the project forward.”
In 2003, the Whitehead/MIT Center for Genome Research became the cornerstone of the newly launched Broad Institute. “MIT’s premier place in the world of biological research is due in no small part to Professor Fink’s selfless, tireless, and generally unheralded work in creating and nurturing these institutions,” reads the award citation.
In 2003, Fink chaired the National Academy of Sciences Committee on Research Standards and Practices to Prevent the Destructive Application of Biotechnology, which provided the nation with guidance on how to deal with the threat of bioterrorism without jeopardizing scientific progress.
Fink has received many other honors, including the National Academy of Sciences Award in Molecular Biology, the George W. Beadle Award from the Genetics Society of America, and the Gruber International Prize in Genetics. He has served as president of both the American Association for the Advancement of Science and the Genetics Society of America, and he is an elected member or fellow of the National Academy of Sciences, the American Academy of Arts and Sciences, the Institute of Medicine, and the American Philosophical Society.
Linc Sonenshein and Rich Losick
May 15, 2018
When the two of us, who were classmates and dorm mates at Princeton, came to MIT in 1965, we were joined by two other Princeton classmates, Mike Newlon (also a dorm mate) and Charlie Emerson. As a result, our Princeton class produced four of the 20 students who formed the entering class of 1965 of the MIT Biology Graduate Program. (The class was originally meant to include 21 students, but one of the accepted students, the recent Nobel Prize recipient Michael Rosbash, decided to spend a year at the Pasteur Institute before joining the MIT program.) Initially, we roomed together with Mike in Porter Square with a fourth member of our class, Ray White. As PhD students, we worked in the labs of Phillip Robbins (Rich), Salvador Luria (Linc and Mike), and Maury Fox (Ray); Charlie moved to UCSD to finish his degree. Back then the Luria and Robbins labs were located in Buildings 56 and 16. (Why does MIT use numbers rather than names for their buildings?) The department consisted of semi-independent sub-departments of Biochemistry, Microbiology, and Biophysics. All of us eventually became faculty members at various universities: Rich at Harvard, Linc at Tufts Medical School, Mike at Rutgers, Ray at UMass, Utah, and UCSF, and Charlie at UMass Medical School.
At Princeton, Rich had done thesis research in the lab of Charles Gilvarg, studying the synthesis of lysine oligopeptides in E. coli; Mike and Linc worked in the lab of Donald Helinski on the genetics of colicin synthesis. Our backgrounds in microbiology research served as inducements to continue studying microbes at MIT and throughout our careers. Indeed, Linc’s PhD thesis research with Luria on the bacterium Bacillus subtilis and its ability to produce spores sparked a collaboration with Rich that greatly influenced both their subsequent careers. Yet another lifelong collaboration emerged when Linc married another member of our class, Gail Entner, who worked with Ned Holt and went on to become a professor at Boston University Medical School and Tufts Medical School. Mike Newlon also married a classmate, Carol Shaw, who was also in the Holt lab and has been a professor at the University of Iowa and Rutgers Medical School.
Linc and Rich are proud to have trained many students (six of whom went on to be postdocs at MIT) and multiple postdocs who have continued productive careers in their own labs based on our beloved B. subtilis bacterium. Indeed one such individual went on to become the chairman of the very department for which we have written these recollections.
Memories fade with time, but we have recreated at least a partial list of the entering class of 1965 and their mentors.
Entering Class of 1965: Name (Lab) Academic/Industry Employment
Roberta Berrien (B. Magasanik) MD, VA Health Center
Lynne Brown (V. Ingram) Penn State University
Gail Bruns (V. Ingram) Children’s Hospital, Harvard Medical School
Judith Ebel Tsipis (M. Fox) Brandeis University
Charles Emerson (moved to UCSD) UMass Medical School
Gail Entner Sonenshein (C. Holt) Boston University Medical School, Tufts Medical School
Stephen Fahnestock (A. Rich) Penn State University, DuPont
Costa Georgopoulos (S. Luria) University of Utah, University of Geneva
John Lisman (J. Brown) Brandeis University
Richard Losick (P. Robbins) Harvard University
Susan Neiman Offner (B. Magasanik) Plymouth, Milton, and Lexington High Schools
Michael Newlon (S. Luria) University of Iowa, Rutgers
Steven Raymond (J. Lettvin) MIT, Harvard Medical School, Personal Health Technologies, Inc.
Carol Shaw Newlon (C. Holt) University of Iowa, Rutgers Med School
Abraham L. Sonenshein (S. Luria) Tufts Medical School
Joel Sussman (A. Rich) Weizmann Institute
Walter Vinson (E. Bell)
Raymond White (M. Fox) UMass Med School, University of Utah, UC San Francisco
Faculty director discusses the future of the initiative and Africa’s position as a global priority for the Institute.
Sarah McDonnell | MIT News Office
May 8, 2018
In 2017, MIT released a report entitled “A Global Strategy for MIT,” which offered a framework for the Institute’s ever-growing international activities in education, research, and innovation. The report, written by Richard Lester, associate provost for MIT overseeing international activities, offered recommendations organized around three broad themes: bringing MIT to the world, bringing the world to MIT, and strengthening governance and operations.
Specifically, Lester identified China, Latin America, and Africa as global priorities and regions where the Institute should expand engagement.
Reflecting that increased focus, the MIT-Africa initiative, led by Faculty Director Hazel Sive, a professor in the Department of Biology and member of the Whitehead Institute for Biomedical Research, has launched a new website, africa.mit.edu, to further formalize MIT’s commitment to expanding its already robust presence in Africa. Sive spoke with MIT News about the initiative’s future and Africa’s position as a global priority for MIT.
Q: Can you start by explaining what the MIT-Africa initiative is?
A: MIT-Africa began in 2014 as a mechanism to promote and communicate connections between MIT students, faculty, and staff, and African counterparts in the spheres of research, education, and innovation.
Together with the enthusiastic participation of many faculty, senior staff, and students, I originated the MIT-Africa initiative because a number of us who are either from Africa (I am from South Africa) or interested in the continent were doing important work together with African colleagues. We thought that the strong connections MIT was making in Africa should be understood more broadly, and that tremendous synergies would develop from sharing our work and promoting joint projects.
The initiative provided the first public face of MIT engagement with Africa, comprising a portal to disseminate information, and a means to invite potential collaborators to connect with MIT. We developed community through the MIT-Africa Interest Group; through supporting student groups such as the African Students Association and through a growing network of MIT students who have interned or worked in Africa.
MIT-Africa both consolidates Africa-relevant opportunities and directly promotes new programs. Multiple MIT initiatives and units include an Africa focus: the MIT International Science and Technology Initiatives (MISTI), D-Lab, the Abdul Latif Jameel Poverty Action Lab (J-PAL), the Abdul Latif Jameel World Water and Food Security Lab (J-WAFS), the Abdul Latif Jameel World Education Lab (J-WEL), the Environmental Solutions Initiative (ESI), MITx, the Legatum Center, and others.
The tagline for MIT-Africa is “Collaborating for impact,” and through the pillars of research, education, and innovation, our goal is to develop even more substantial collaborations between the MIT community and in Africa.
Q: What are your thoughts on Africa’s inclusion as a priority in MIT’s recent global strategy report?
A: We are very pleased that MIT has recognized the importance of Africa in the world and as a focus for the Institute.
At the outset of the MIT-Africa initiative, we brought together an Africa Advisory Committee for strategic discussions. Last year, at the request of Richard Lester, we put together a strategic plan for MIT engagement in Africa, and the findings in this document interfaced with his decision to define Africa as a global priority for MIT.
In our plan, we made it clear that MIT priorities overlap with issues of vital importance to Africa — in tackling critical challenges relating to the environment, climate change, energy, population growth, food, health, education, industry, and urbanization. We are confident that this emphasis will facilitate expanded connections between MIT and our African collaborators and supporters.
A useful outcome of formalizing MIT’s priority of Africa engagement is recognition of our already extensive engagement with Africa. MIT has projects in half the countries of Africa! There are hundreds of examples in progress, from water utilization in Mozambique to entrepreneurship in South Africa and education in Nigeria. We are well-represented, and this engagement is growing rapidly.
The new website is both a way to acknowledge the outstanding scholarship and work already progressing on the continent, as well as a call to expand collaborations in a high impact way.
Q: What’s next for MIT-Africa?
A: Our strategic discussions identified key priorities over the next five years. These include: higher visibility of MIT in Africa through “MIT-Africa” branding, coordination in purpose and scope of MIT engagement in Africa, increased student internship and travel opportunities, increased research funding, new collaborations in education, expanded innovation presence, revised Africa-relevant education at MIT, and increased numbers of African trainees at MIT.
We are well on our way to meeting these goals, aided by a team with broad experience. For example, in 2014, we sent two students to Africa through MISTI, and last year we sent 92, so this has been a hugely fast-growing program. The MISTI Global Seed Fund Program newly includes Africa, and units such as J-WAFS, J-WEL, and ESI offer research funding that can be focused on Africa. A key aspect encompasses our alumni who envision a significant and influential African and African diaspora alumni group.
The distinguished MIT-Africa Working Group advises on policy, strategy, and implementation. Many members are leaders of other MIT initiatives, facilitating development of intersecting and productive joint programs with MIT-Africa.
All of this takes effort and collaborators, and we look forward to an expanded set of connections. We extend an invitation to potential collaborators: Come and speak with us. The expertise at MIT is enormous, and our focus on Africa-relevant engagement will have outcomes that advance intellectual, societal, and economic trajectories.
Study in worms reveals gene loss can lead to accumulation of waste products in cells.
Anne Trafton | MIT News Office
May 4, 2018
MIT biologists have discovered a function of a gene that is believed to account for up to 40 percent of all familial cases of amyotrophic lateral sclerosis (ALS). Studies of ALS patients have shown that an abnormally expanded region of DNA in a specific region of this gene can cause the disease.
In a study of the microscopic worm Caenorhabditis elegans, the researchers found that the gene has a key role in helping cells to remove waste products via structures known as lysosomes. When the gene is mutated, these unwanted substances build up inside cells. The researchers believe that if this also happens in neurons of human ALS patients, it could account for some of those patients’ symptoms.
“Our studies indicate what happens when the activities of such a gene are inhibited — defects in lysosomal function. Certain features of ALS are consistent with their being caused by defects in lysosomal function, such as inflammation,” says H. Robert Horvitz, the David H. Koch Professor of Biology at MIT, a member of the McGovern Institute for Brain Research and the Koch Institute for Integrative Cancer Research, and the senior author of the study.
Mutations in this gene, known as C9orf72, have also been linked to another neurodegenerative brain disorder known as frontotemporal dementia (FTD), which is estimated to affect about 60,000 people in the United States.
“ALS and FTD are now thought to be aspects of the same disease, with different presentations. There are genes that when mutated cause only ALS, and others that cause only FTD, but there are a number of other genes in which mutations can cause either ALS or FTD or a mixture of the two,” says Anna Corrionero, an MIT postdoc and the lead author of the paper, which appears in the May 3 issue of the journal Current Biology.
Genetic link
Scientists have identified dozens of genes linked to familial ALS, which occurs when two or more family members suffer from the disease. Doctors believe that genetics may also be a factor in nonfamilial cases of the disease, which are much more common, accounting for 90 percent of cases.
Of all ALS-linked mutations identified so far, the C9orf72 mutation is the most prevalent, and it is also found in about 25 percent of frontotemporal dementia patients. The MIT team set out to study the gene’s function in C. elegans, which has an equivalent gene known as alfa-1.
In studies of worms that lack alfa-1, the researchers discovered that defects became apparent early in embryonic development. C. elegans embryos have a yolk that helps to sustain them before they hatch, and in embryos missing alfa-1, the researchers found “blobs” of yolk floating in the fluid surrounding the embryos.
This led the researchers to discover that the gene mutation was affecting the lysosomal degradation of yolk once it is absorbed into the cells. Lysosomes, which also remove cellular waste products, are cell structures which carry enzymes that can break down many kinds of molecules.
When lysosomes degrade their contents — such as yolk — they are reformed into tubular structures that split, after which they are able to degrade other materials. The MIT team found that in cells with the alfa-1 mutation and impaired lysosomal degradation, lysosomes were unable to reform and could not be used again, disrupting the cell’s waste removal process.
“It seems that lysosomes do not reform as they should, and material accumulates in the cells,” Corrionero says.
For C. elegans embryos, that meant that they could not properly absorb the nutrients found in yolk, which made it harder for them to survive under starvation conditions. The embryos that did survive appeared to be normal, the researchers say.
Neuronal effects
The researchers were able to partially reverse the effects of alfa-1 loss in the C. elegans embryos by expressing the human protein encoded by the c9orf72 gene. “This suggests that the worm and human proteins are performing the same molecular function,” Corrionero says.
If loss of C9orf72 affects lysosome function in human neurons, it could lead to a slow, gradual buildup of waste products in those cells. ALS usually affects cells of the motor cortex, which controls movement, and motor neurons in the spinal cord, while frontotemporal dementia affects the frontal areas of the brain’s cortex.
“If you cannot degrade things properly in cells that live for very long periods of time, like neurons, that might well affect the survival of the cells and lead to disease,” Corrionero says.
Many pharmaceutical companies are now researching drugs that would block the expression of the mutant C9orf72. The new study suggests certain possible side effects to watch for in studies of such drugs.
“If you generate drugs that decrease c9orf72 expression, you might cause problems in lysosomal homeostasis,” Corrionero says. “In developing any drug, you have to be careful to watch for possible side effects. Our observations suggest some things to look for in studying drugs that inhibit C9orf72 in ALS/FTD patients.”
The research was funded by an EMBO postdoctoral fellowship, an ALS Therapy Alliance grant, a gift from Rose and Douglas Barnard ’79 to the McGovern Institute, and a gift from the Halis Family Foundation to the MIT Aging Brain Initiative.
A drug treatment that mimics fasting can also provide the same benefit, study finds.
Anne Trafton | MIT News Office
May 1, 2018
As people age, their intestinal stem cells begin to lose their ability to regenerate. These stem cells are the source for all new intestinal cells, so this decline can make it more difficult to recover from gastrointestinal infections or other conditions that affect the intestine.
This age-related loss of stem cell function can be reversed by a 24-hour fast, according to a new study from MIT biologists. The researchers found that fasting dramatically improves stem cells’ ability to regenerate, in both aged and young mice.
In fasting mice, cells begin breaking down fatty acids instead of glucose, a change that stimulates the stem cells to become more regenerative. The researchers found that they could also boost regeneration with a molecule that activates the same metabolic switch. Such an intervention could potentially help older people recovering from GI infections or cancer patients undergoing chemotherapy, the researchers say.
“Fasting has many effects in the intestine, which include boosting regeneration as well as potential uses in any type of ailment that impinges on the intestine, such as infections or cancers,” says Omer Yilmaz, an MIT assistant professor of biology, a member of the Koch Institute for Integrative Cancer Research, and one of the senior authors of the study. “Understanding how fasting improves overall health, including the role of adult stem cells in intestinal regeneration, in repair, and in aging, is a fundamental interest of my laboratory.”
David Sabatini, an MIT professor of biology and member of the Whitehead Institute for Biomedical Research and the Koch Institute, is also a senior author of the paper, which appears in the May 3 issue of Cell Stem Cell.
“This study provided evidence that fasting induces a metabolic switch in the intestinal stem cells, from utilizing carbohydrates to burning fat,” Sabatini says. “Interestingly, switching these cells to fatty acid oxidation enhanced their function significantly. Pharmacological targeting of this pathway may provide a therapeutic opportunity to improve tissue homeostasis in age-associated pathologies.”
The paper’s lead authors are Whitehead Institute postdoc Maria Mihaylova and Koch Institute postdoc Chia-Wei Cheng.
Boosting regeneration
For many decades, scientists have known that low caloric intake is linked with enhanced longevity in humans and other organisms. Yilmaz and his colleagues were interested in exploring how fasting exerts its effects at the molecular level, specifically in the intestine.
Intestinal stem cells are responsible for maintaining the lining of the intestine, which typically renews itself every five days. When an injury or infection occurs, stem cells are key to repairing any damage. As people age, the regenerative abilities of these intestinal stem cells decline, so it takes longer for the intestine to recover.
“Intestinal stem cells are the workhorses of the intestine that give rise to more stem cells and to all of the various differentiated cell types of the intestine. Notably, during aging, intestinal stem function declines, which impairs the ability of the intestine to repair itself after damage,” Yilmaz says. “In this line of investigation, we focused on understanding how a 24-hour fast enhances the function of young and old intestinal stem cells.”
After mice fasted for 24 hours, the researchers removed intestinal stem cells and grew them in a culture dish, allowing them to determine whether the cells can give rise to “mini-intestines” known as organoids.
The researchers found that stem cells from the fasting mice doubled their regenerative capacity.
“It was very obvious that fasting had this really immense effect on the ability of intestinal crypts to form more organoids, which is stem-cell-driven,” Mihaylova says. “This was something that we saw in both the young mice and the aged mice, and we really wanted to understand the molecular mechanisms driving this.”
Metabolic switch
Further studies, including sequencing the messenger RNA of stem cells from the mice that fasted, revealed that fasting induces cells to switch from their usual metabolism, which burns carbohydrates such as sugars, to metabolizing fatty acids. This switch occurs through the activation of transcription factors called PPARs, which turn on many genes that are involved in metabolizing fatty acids.
The researchers found that if they turned off this pathway, fasting could no longer boost regeneration. They now plan to study how this metabolic switch provokes stem cells to enhance their regenerative abilities.
They also found that they could reproduce the beneficial effects of fasting by treating mice with a molecule that mimics the effects of PPARs. “That was also very surprising,” Cheng says. “Just activating one metabolic pathway is sufficient to reverse certain age phenotypes.”
Jared Rutter, a professor of biochemistry at the University of Utah School of Medicine, described the findings as “interesting and important.”
“This paper shows that fasting causes a metabolic change in the stem cells that reside in this organ and thereby changes their behavior to promote more cell division. In a beautiful set of experiments, the authors subvert the system by causing those metabolic changes without fasting and see similar effects,” says Rutter, who was not involved in the research. “This work fits into a rapidly growing field that is demonstrating that nutrition and metabolism has profound effects on the behavior of cells and this can predispose for human disease.”
The findings suggest that drug treatment could stimulate regeneration without requiring patients to fast, which is difficult for most people. One group that could benefit from such treatment is cancer patients who are receiving chemotherapy, which often harms intestinal cells. It could also benefit older people who experience intestinal infections or other gastrointestinal disorders that can damage the lining of the intestine.
The researchers plan to explore the potential effectiveness of such treatments, and they also hope to study whether fasting affects regenerative abilities in stem cells in other types of tissue.
The research was funded by the National Institutes of Health, the V Foundation, a Sidney Kimmel Scholar Award, a Pew-Stewart Trust Scholar Award, the Kathy and Curt Marble Cancer Research Fund, the MIT Stem Cell Initiative through Fondation MIT, the Koch Institute Frontier Research Program through the Kathy and Curt Marble Cancer Research Fund, the American Federation of Aging Research, the Damon Runyon Cancer Research Foundation, the Robert Black Charitable Foundation, a Koch Institute Ludwig Postdoctoral Fellowship, a Glenn/AFAR Breakthroughs in Gerontology Award, and the Howard Hughes Medical Institute.
Meena Chakraborty ’19 has spent two years in the lab of Nobel Prize winner Philip Sharp, combining computer science and wet lab techniques to study the impact of microRNAs on gene expression.
Raleigh McElvery
May 2, 2018
When Meena Chakraborty was eleven years old, her parents took her to South Africa to show her what life was like outside her hometown of Lexington, Massachusetts. The trip was first and foremost a family vacation, but what struck Chakraborty, now a junior at MIT, was neither the sights nor safaris, but their visit to a children’s hospital. Looking back, she identifies that experience as the catalyst that spurred her current career path, centered on three years of biology research with implications for human health.
“I remember being astounded that the patients there were my age,” she says. “I had all these things in my life to look forward to, while they were fighting HIV and might not survive. That’s when I started thinking that I could do something to counter disease, and studying biology seemed like the best way to do that.”
Up until that point, she’d intended to be a writer. So when it came time to choose a college, she initially shied away from MIT, fearing it would be too “tech-focused.”
“Even though I was primarily interested in biology, I still wanted diversity in terms of the academic subjects and the people around me,” she says. “But it became clear that MIT really encourages you to step outside your major. Every undergrad has to complete a Humanities, Arts, or Social Sciences concentration, and I chose philosophy. Those classes have become a staple of my undergrad experience, and allowed me to keep in touch with my love for writing while still focusing on my science.”
Given her propensity for math, she declared Course 6-7 (Computer Science and Molecular Biology), as a means to develop analytical tools to decipher large data sets and better understand biological systems. The summer after her freshman year, she had her first chance to marry these two skills in a real-world setting: she began working in the lab of Nobel Prize winner Philip Sharp, located in the Koch Institute for Integrative Cancer Research.
This was her first foray into computational biology, but it wasn’t her first time at the Koch — she’d shadowed two graduates students in the Irvine lab for a summer as a junior in high school. This time, though, as an undergraduate, she was assigned her own project, under the guidance of postdoctoral fellow Salil Garg. Together, they’ve studied a type of RNA known as microRNA (miRNA) for the past two years.
Messenger RNA (mRNA) — perhaps the most well-known of the RNAs — constitutes the intermediate step between DNA and the final product of gene expression: the protein. In contrast, miRNAs are never translated into proteins. Instead, they bind to complementary sequences in target mRNAs, preventing those mRNAs from being turned into proteins, and blocking gene expression.
This miRNA-directed silencing is widespread and complex. In some cases, miRNAs silence single genes. In others, multiple miRNAs coordinate to turn groups of genes on and off in concert, thereby controlling entire sets of genes that interact with one another. For example, two years ago, Chakraborty’s mentor used computational methods to pinpoint a group of poorly expressed, understudied “nonclassical” miRNAs that appear to coordinate the expression of pluripotency genes. Pluripotency gene levels dictate the behavior and fate of embryonic stem cells — non-specialized cells awaiting instructions to “differentiate” and assume a particular cell type (skin cell, blood cell, neuron, and so on).
Chakraborty then used a technique known as fluorescence-activated cell sorting (FACS) to determine how nonclassical miRNAs affect gene expression in embryonic stem cells. She used a FACS assay to detect miRNA activity, engineering special DNA and inserting it into mouse embryonic stem cells. The DNA contained two genes: one encoding a red fluorescent protein with a place for miRNAs to bind, and another that makes a blue fluorescent protein and lacks this miRNA attachment site. When the miRNA binds to the gene expressing the red fluorescing protein, it is silenced, and the cell makes fewer red proteins compared to blue ones, whose production remains unhindered.
“We know when miRNAs are active, they will reduce the expression of the red florescent protein, but not the blue one,” she says. “And that’s precisely what we’ve seen with these nonclassical miRNAs, suggesting that they are active in the cell.”
Chakraborty is excited about what this finding could mean for cancer research. A growing number of studies have shown that some cancers arise when miRNAs fail to help embryonic stem cells interconvert between cell states.
Although she spends anywhere from four to 20 hours a week in lab, Chakraborty hasn’t lost sight of her extracurriculars. As co-president of the Biology Undergraduate Student Association, she serves as a liaison between biology students and faculty, coordinating events to connect the two. As the discussion chair for the Effective Altruism Club, she promotes dialogue between student club members regarding charities — how these organizations can maximize their donations, and how the public should decide which ones to support. As a volunteer for the non-profit Help at Your Door, she inputs grocery lists from senior citizens and disabled individuals into a computer program, and then coordinates with community members to deliver the specified order.
Last summer, she was accepted into the Johnson & Johnson UROP Scholars Program, joining approximately 20 fellow undergraduate women in STEM research at MIT during the summer term. Her cohort attended faculty presentations, workshops, and networking events geared towards post-graduate careers in the sciences.
“I really appreciated that program, because I think a lot of women are afraid of science due to societal norms,” she says. “I remember originally thinking I wouldn’t be good at computer science or math, and now here I am combining both skills with wet lab techniques in my research.”
Most recently, Chakraborty was a recipient of the 2017-2018 Barry Goldwater Scholarship Award, selected from a nationwide field of candidates nominated by university faculty. She will also remain on campus this coming summer to conduct faculty-mentored research as part of the MIT Amgen Scholars Program.
After she graduates in 2019, Chakraborty intends to pursue a PhD in a biology-related discipline, perhaps computational biology. After that, the options are endless — professor, consultant, research scientist. She’s still weighing the possibilities, and doesn’t seem too concerned about selecting one just yet.
“I know I’m going in the right direction, because it hits me every time I finish a challenging assignment or whenever I figure out a new approach in the lab,” she says. “When I complete a task like that with the help of friends and mentors, there’s this sense of pride and a feeling that I can’t believe how much I’ve learned in just once semester. The way my brain considers problems and finds solutions is just so different from the way it was three years ago when I first started out as a freshman.”
Photo credit: Raleigh McElvery
Whitehead team analyzes transcriptomes for roughly 70,000 cells in planarians, creates publicly available database to drive further research.
Nicole Davis | Whitehead Institute
April 20, 2018
A team at Whitehead Institute and MIT has harnessed single-cell technologies to analyze over 65,000 cells from the regenerative planarian flatworm, Schmidtea mediterranea, revealing the complete suite of actives genes (or “transcriptome”) for practically every type of cell in a complete organism. This transcriptome atlas represents a treasure trove of biological information on planarians, which is the subject of intense study in part because of its unique ability to regrow lost or damaged body parts. As described in the April 19 advance online issue of the journal Science, this new, publicly available resource has already fueled important discoveries, including the identification of novel planarian cell types, the characterization of key transition states as cells mature from one type to another, and the identity of new genes that could impart positional cues from muscles cells — a critical component of tissue regeneration.
“We’re really at the beginning of an amazing era,” says senior author Peter Reddien, a member of Whitehead Institute, professor of biology at MIT, and investigator with the Howard Hughes Medical Institute. “Just as genome sequences became indispensable resources for studying the biology of countless organisms, analyzing the transcriptomes of every cell type will become another fundamental tool — not just for planarians, but for many different organisms.”
The ability to systematically reveal which genes in the genome are active within an individual cell flows from a critical technology known as single-cell RNA sequencing. Recent advances in the technique have dramatically reduced the per-cell cost, making it feasible for a single laboratory to analyze a suitably large number of cells to capture the cell type diversity present in complex, multi-cellular organisms.
Reddien has maintained a careful eye on the technology from its earliest days because he believed it offered an ideal way to unravel planarian biology. “Planarians are relatively simple, so it would be theoretically possible for us to capture every cell type. Yet they still have a sufficiently large number of cells — including types we know little or even nothing about,” he explains. “And because of the unusual aspects of planarian biology — essentially, adults maintain developmental information and progenitor cells that in other organisms might be present transiently only in embryos — we could capture information about mature cells, progenitor cells, and information guiding cell decisions by sampling just one stage, the adult.”
Two and a half years ago, Reddien and his colleagues — led by first author Christopher Fincher, a graduate student in Reddien’s laboratory — set out to apply single-cell RNA sequencing systematically to planarians. The group isolated individual cells from five regions of the animal and gathered data from a total of 66,783 cells. The results include transcriptomes for rare cell types, such as those that comprise on the order of 10 cells out of an adult animal that consists of roughly 500,000 to 1 million cells.
In addition, the researchers uncovered some cell types that have yet to be described in planarians, as well cell types common to many organisms, making the atlas a valuable tool across the scientific community. “We identified many cells that were present widely throughout the animal, but had not been previously identified. This surprising finding highlights the great value of this approach in identifying new cells, a method that could be applied widely to many understudied organisms,” Fincher says.
“One main important aspect of our transcriptome atlas is its utility for the scientific community,” Reddien says. “Because many of the cell types present in planarians emerged long ago in evolution, similar cells still exist today in various organisms across the planet. That means these cell types and the genes active within them can be studied using this resource.”
The Whitehead team also conducted some preliminary analyses of their atlas, which they’ve dubbed “Planarian Digiworm.” For example, they were able to discern in the transcriptome data a variety of transition states that reflect the progression of stem cells into more specialized, differentiated cell types. Some of these cellular transition states have been previously analyzed in painstaking detail, thereby providing an important validation of the team’s approach.
In addition, Reddien and his colleagues knew from their own prior, extensive research that there is positional information encoded in adult planarian muscle — information that is required not only for the general maintenance of adult tissues but also for the regeneration of lost or damaged tissue. Based on the activity pattern of known genes, they could determine roughly which positions the cells had occupied in the intact animal, and then sort through those cells’ transcriptomes to identify new genes that are candidates for transmitting positional information.
“There are an unlimited number of directions that can now be taken with these data,” Reddien says. “We plan to extend our initial work, using further single-cell analyses, and also to mine the transcriptome atlas for addressing important questions in regenerative biology. We hope many other investigators find this to be a very valuable resource, too.”
This work was supported by the National Institutes of Health, the Howard Hughes Medical Institute, and the Eleanor Schwartz Charitable Foundation.
Nicole Giese Rura | Whitehead Institute
April 11, 2018
Cambridge, MA – According to research conducted in mice by Whitehead Institute scientists, surgery in breast cancer patients, which while often curative, may trigger a systemic immunosuppressive response, allowing the outgrowth of dormant cancer cells at distant sites whose ability to generate tumors had previously been kept in check by the immune system. Taking a non-steroidal anti-inflammatory drug (NSAID) around the time of surgery may thwart such early metastatic relapse without impeding post-surgical wound healing.
The team’s work was published in the April 11 issue of the journal Science Translational Medicine.
“This represents the first causative evidence of surgery having this kind of systemic response,” says Jordan Krall, the first author of the paper and a former postdoctoral researcher in the lab of Whitehead Founding Member Robert Weinberg. “Surgery is essential for treating a lot of tumors, especially breast cancer. But there are some side effects of surgery, just as there are side effects to any treatment. We’re starting to understand what appears to be one of those potential side effects, and this could lead to supportive treatment alongside of surgery that could mitigate some of those effects.”
Although the association between surgery and metastatic relapse has been documented, a causal line between the two has never been established, leading many to consider early metastatic relapse to be the natural disease progression in some patients. Previous studies of breast cancer patients have shown a marked peak in metastatic relapse 12-18 months following surgery. Although the underlying mechanism for such a spike has not been understood, a 2010 retrospective clinical trial conducted in Belgium provides a clue: Breast cancer patients taking a non-steroidal anti-inflammatory (NSAID) for pain following tumor resection had lower rates of this early type of metastatic relapse than patients taking opioids for post-surgical pain. Anti-inflammatory drugs also have previously been shown to directly inhibit tumor growth, but Krall and Weinberg thought that the NSAIDs’ effects in these studies may be independent of the mechanism responsible for the effects noted in the retrospective clinical trial.
To investigate the causes of early metastatic relapse after surgery, the team created a mouse model that seems to mirror the immunological detente keeping in check dormant, disseminated tumor cells in breast cancer patients. In this experimental model, the mice’s T cells stall the growth of tumors that are seeded by injected cancer cells. When mice harboring dormant cancer cells underwent simulated surgeries at sites distant from the tumor cells, tumor incidence and size dramatically increased. Analysis of the blood and tumors from wounded mice showed that wound healing increases levels of cells called inflammatory monocytes, which differentiate into tumor-associated macrophages. Such macrophages, in turn, can act at distant sites to suppress the actions of T lymphocytes that previously succeeded in keeping the implanted tumors under control. Krall and Weinberg then tested the effects of the NSAID meloxicam (Mobic®), thinking that this anti-inflammatory drug might block the effects of immuno-suppressive effects of wound healing. In fact, when mice received the NSAID after or at the time of surgery, the drug prevented a systemic inflammatory response created by the wound healing and the meloxicam-treated mice developed significantly smaller tumors than wounded, untreated mice; often these tumors completely disappeared. Notably, meloxicam did not impede the mice’s wound healing
Still, Weinberg cautions that scientists are just beginning to understand the connections between post-surgical wound healing, inflammation, and metastasis.
“This is an important first step in exploring the potential importance of this mechanism in oncology,” says Weinberg, who is also a professor of biology at Massachusetts Institute of Technology (MIT) and director of the MIT/Ludwig Center for Molecular Oncology.
This work was supported by the Advanced Medical Research Foundation, the Transcend Program (a partnership between the Koch Institute and Janssen Pharmaceuticals Inc.), the Breast Cancer Research Foundation, the Ludwig Center for Molecular Oncology at MIT, and the Samuel Waxman Cancer Research Foundation, the American Cancer Society, Hope Funds for Cancer Research, the Charles A. King Trust, the National Health and Medical Research Council of Australia (NHMRC APP1071853), the National Institutes of Health (NIH/NCI 1K99CA201574-01A1), the American Cancer Society Ellison Foundation (PF-15-131-01-CSM), and the U.S. Department of Defense (W81XWH-10-1-0647).