Meet Batsheva Kerem, an Israeli geneticist who helped discover the gene, CFTR, which, when mutated, is responsible for causing the disease cystic fibrosis (CF). In addition to finding the globally most common CFTR mutation, she discovered many more mutations, including the most common CFTR mutation among Ashkenazi Jews. She currently studies types of mutations which affect CFTR production (namely nonsense mutations and splicing mutations – don’t worry, I’ll de-jargonize those!) and she works to develop targeted therapies to counteract the mutations so that functional CFTR is made. ⠀

CF is a terrible genetic disease that causes mucus to get thick and gunky, trapping bacteria in lungs and making it hard to breathe, blocking pancreatic ducts and making it hard to digest food, and more. This is all caused by problems with a protein called CFTR, which is an ion transporter (a protein that lets charged particles, in the case of CFTR, chloride and bicarbonate ions, into and out of cells). CF is an autosomal recessive disease meaning that, barring spontaneous mutations, patients with CF have inherited 2 “bad copies” of the CFTR gene – one from each biological parent. People like the parents, who only have a single mutated copy, don’t have the disease and are instead called carriers. ⠀

Obtaining the genetic sequence of the gene which contains instructions for making CFTR has allowed scientists to better understand the condition and develop targeted treatments. The groundbreaking discovery and characterization of the CFTR gene in 1989 was achieved through a collaborative effort between groups of researchers at the Hospital for Sick Children (aka SickKids – seriously) in Toronto, Canada led by Lap-Chee Tsui and at the University of Michigan, led by Francis Collins (that name might sound familiar because he went on to become director of the U.S. National Institutes of Health (NIH)). Collaboration for the CF win!⠀

More on that in last week’s post: http://bit.ly/cysticfibrosisscience

In researching for that post, I became intrigued about a couple of the postdoctoral researchers (scientists who had recently earned their PhDs and were looking for further training) working in Tsui’s laboratory who played key roles in the discovery – Batsheva Kerem and Johanna Rommens. When I went to learn more about them I found to my dismay that they didn’t have Wikipedia articles. So I made them. You can check them out (and improve them please) but I also want to give them a shout-out here, starting with Kerem (don’t worry, Rommens will get a post too!)⠀

Education & Career

Batsheva Kerem was born in Tel-Aviv in 1955 and raised in Israel, where she served as an an IDF officer in the military. She received a B.Sc. with distinction in biology from the Hebrew University in 1979, followed by a Ph.D. from the direct doctoral program of Hebrew University’s Department of Genetics in 1986 (supervised by Menashe Marcus and Howard Cedar in case you happen to know them or were otherwise just super curious). She did a brief post doctoral fellowship with Tamar Schaap in the Department of Genetics at Jerusalem’s Hadassah Medical School, then moved to Canada for further postdoctoral training. There, she worked in Tsui’s lab at SickKids from from 1987-1990 while juggling caring for two children. The reason Batsheva chose a postdoctoral fellowship in Tsui’s lab at SickKids was in part because she and her husband Eitan, a pediatric pulmonologist, were looking for job opportunities where they would be able to work nearby one another (they’d collaborate a lot on CF work in the future).⠀

After her work with Tsui, Kerem moved back to Israel, where she has spent her career at the Hebrew University. She was hired as a senior lecturer in 1990, at which time she established the Israel National Center for CF Genetic Research. She was promoted to associate professor in 1998 and Full Professor in 2003. So let’s talk about some of her work, starting back with that initial CFTR discovery…⠀

Research

As I mentioned, and as I go into great detail on in last week’s post, Kerem helped identify the gene behind cystic fibrosis, the CFTR gene, while a postdoc in Tsui’s lab. Like all genes, CFTR is a stretch of DNA that’s present in a really really long piece of coiled-up DNA called a chromosome. You can think of genes as recipes and chromosomes like cookbooks. You get one copy of each somatic (non-sex) chromosome from each biological parent and these chromosomes are kept locked up in a membranous compartment in the cell called the nucleus. ⠀

The CFTR gene was discovered through something called genetic linkage analysis which involved looking for genetic markers that were present in patients with cystic fibrosis but were not present in their non-affected relatives. Due to the phenomenon of recombination, whereby parts of chromosomes swap homologous (“matching”) segments during germ cell development, each chromosome a child inherits is a mix of the both of that parent’s copies of that chromosome. Markers (bits of DNA that could be detected and serve as “landmarks”) would only be consistently co-inherited with the gene behind cystic fibrosis if they were close together on the chromosome and thus stayed together during those swaps. So, Kerem and other researchers used markers to find the approximate location of the gene. They then used a combination of chromosome walking and chromosome hopping or jumping to locate the CF gene, which they named cystic fibrosis transmembrane conductance regulator (CFTR). ⠀

When comparing the sequence of the CFTR gene of a patient to that of the patient’s healthy relative, they found the patient’s CFTR gene was missing a few DNA letters (nucleotides) – that is, they’d found a deletion mutation. But would that mutation matter? ⠀

This gets us to the point where I need to step back a sec and explain different types of mutations and why some mutations matter and some don’t. Mutations are changes that occur at the DNA level (changes to the sequence of the gene gene) but proteins are actually made from RNA copies of those genes… bear with me! ⠀

Basically, the nucleus is a bit like the reference section of a library – you can make copies of the stuff in there, but you can’t take the originals outside. So, when a cell wants to make a protein, it first makes RNA copies of the genetic recipe and “edits” those copies in a process called “splicing” to remove regulatory regions called introns (which are a bit like extra pages in between the instruction pages). With a little more processing (involving the addition of a molecular “cap” and “tail”) you get mature messenger RNA (mRNA), which is shipped out of the nucleus and into the general interior of the cell (the cytoplasm) where protein-making complexes called ribosomes are standing by to read the instructions and piece together the specified amino acids (protein letters) into a long polypeptide chain that folds up (based on those amino acids’ unique properties) to form a functional protein. ⠀

Each amino acid is “spelled” by a 3-RNA-letter “word” referred to as a codon. So, for example, GCA calls for alanine (Ala, A) whereas GAA calls for lysine (Lys, K). Things get a little complicated terminology-wise because those RNA codons are themselves the complements of DNA codons, but hopefully the pictures can help you understand what I mean by that. ⠀

The key thing to remember is that mutations are changes to the DNA (that permanent copy of the recipe) and, if these mutations occur in a region of the gene that gets copied into mRNA, the mutations will also be present in the mRNA copies. There’s some degeneracy (redundancy) in the genetic code, meaning that some amino acids are spelled by multiple codons. For example, GCA and GCU both spell alanine. Therefore, some letter swaps don’t cause any difference in the recipe (we call these synonymous mutations). But, if the  mutations cause the mRNA to spell a different protein letter (a missense mutation) or specify extra letters or missing letters (insertions or deletions, respectively), you can get dysfunctional proteins. ⠀

The mutation Kerem and the team had identified *was* consequential at the protein level – it was in an exon (a protein-instruction-containing part) and it caused a deletion of the 508th amino acid in the CFTR protein, which is normally a phenylalanine (abbreviated F), thus the abbreviation F508del, or ΔF508. Scientists would later show that this change was consequential at the protein *functional* level too. Some mutations cause such minor changes to a protein that they don’t make a functional difference, but this wasn’t such a case – this mutation mattered. It mattered because, as scientists would find out it causes the protein to misfold and get removed by the cell’s quality control system. And, any protein that did make it all the way to the membrane wouldn’t work very well. ⠀

Kerem found 2 copies of the ΔF508 mutation in 68% of the Canadian CF patients whose DNA she tested and NONE of their tested healthy relatives had 2 copies of it. This turned out to be the definitive proof that they’d found the gene responsible for CF. ⠀

And, ΔF508 turns out to be the globally most common CFTR mutation. But what about the remaining 32% of the patients Kerem tested? Some of them had one copy of the ΔF508 mutation and some had no copies of that mutation – but they still had the disease. At the time, they could only test for that specific mutation, but Kerem knew that there must be additional mutations in the CFTR gene that were capable of causing CF. And she would make it part of her life goal to find (and counteract) them. ⠀

The “68%” figure was for the Canadian CF patients in that initial set of samples. But, as word spread of her work, Kerem started getting sent CF DNA samples from around the world. When looking at the CFTR gene in samples sent from Israeli patients, she found that they didn’t carry ΔF508 or any other known mutation. She became intrigued so, when she moved back to Israel in September 1990, she collected blood from most Israeli CF patients and searched their CFTR genes for mutations. She discovered that about 60% of Israel’s Ashkenazi Jewish CF patients had a mutation called W1282X (more on what this means in a second). She published this finding in 1992 and in 1997, Israel’s government introduced population carrier screening for it. ⠀

W1282X is an example of a “nonsense mutation” – in this type of mutation, an amino-acid-spelling codon (which makes “sense”) gets changed to a “stop codon” (nonsense!) which tells the ribosome that its job is done before it gets finished making the protein. This Premature Termination Codon (PTC) leads to truncated proteins being made and often the faulty mRNA being destroyed through a process called nonsense-mediated decay (NMD). More on NMD here: https://bit.ly/nmdecay  but the gist is that, when splicing occurs, it leaves marks in the form of proteins left at splicing junctions. Those proteins get removed when the ribosome plows through them in the pioneering round of translation. But, if you have a PTC, junctions after the PTC don’t have the pleasure of having a ribosome plow through them, so the proteins stay on. And this alerts the cell that all is not well! The mRNA is recognized as defective and destroyed. So you can’t make protein from it. ⠀

The abbreviation “W1282X” signifies that the genetic instructions for 1282rd amino acid in the protein, which is normally a tryptophan (W), has been mutated to a stop signal (X)). Since her discovery of W1282X, additional nonsense mutations have been discovered. Kerem is now investigating how pharmaceutical compounds that promote read-through of PTCs (i.e. tell the ribosome to keep going) might be able to counteract problems caused by such mutations. Since nonsense mutations in other proteins can cause other diseases, this strategy can have wider use. (You might be wondering why this doesn’t mess up all the normal stop signals, but the read-through compounds aren’t fully efficient and it turns out that most genes have multiple stop codons at their end so if the first one gets read-through there’s still back-up!)⠀

Kerem also identified and classified a wide spectrum of CFTR mutations. The search wasn’t easy, in part because some mutations occur in “regulatory” regions of DNA that don’t even make it into mRNA but rather affect the processing of mRNA-to-be. These include mutations that can interfere with proper splicing. refresher: RNA splicing is where regulatory regions called introns are removed from the protein-instruction-containing exons in order to make mature mRNAs that ribosomes can use as instructions for making proteins. Mutations at or around splice sites (intron:exon junctions) can alter the splicing pattern, messing up protein production. Kerem invented a discovery platform which serves as the basis of the biotechnology company SpliSense, which is working to develop antisense oligonucleotides (ASOs) to counteract mRNA splicing mutations by using small segments of DNA complementary to specific regions of the RNA in order to hide improper splice sites and promote proper splicing. (this is a similar strategy to that of nusinersen (Spinraza), a groundbreaking treatment for Spinal Muscular Atrophy (SMA) https://bit.ly/spinrazasma )⠀

Kerem’s work broadened beyond CF – in the late 1990s, she began studying chromosome structure and function. She has investigated genome instability and made significant contributions to knowledge of the involvement of frequent fragile sites in cancer – such “fragile sites” are regions of chromosomes that are prone to breaking and recombining, etc., potentially causing cellular mayhem if they separate genes from their regulatory elements, splice together parts of different genes, etc.⠀

Honors and positions

Since I had all this info from making the Wikipedia article, I thought I might as well share it here too:⠀

Kerem has received numerous awards and, when, in 2008, she was one of the few women to receive an EMET Prize (a prestigious Israeli prize), she used the opportunity to advocate for better representation of women among prize recipients. Other awards include the Julodan Prize for Contribution to Medicine (1993); the Teva Prize for Excellence in Human Genome Research (1993); the Joels Senior Lectureship for Excellence in Science (1996); and the Abisch-Frenkel Prize for Excellence in Life Sciences (2004).⠀

In addition to establishing the Israel National Center for CF Genetic Research, she established the National Genomic Knowledge Center at Hebrew University’s Institute of Life Sciences and served as its chair from 2000-2014. She also served as the Head of Authority for research students from 2007-2011. She was appointed President Advisor for Promotion of Women in Science in 2013. She is a member of the European Research Council (ERC) for advanced scientists and has served on the editorial board of the European Journal of Human Genetics and EMBO Reports. She was appointed President of the Genetic Society of Israel in 2007.⠀

You can find sources for all those goodies in her new Wikipedia article: https://en.wikipedia.org/wiki/Batsheva_Kerem

here’s one of them: https://www.isracast.com/prof-batsheva-kerem/

there’s a lot of great info on Kerem’s involvement in the CFTR discovery in the book “Breath from Salt” by Trijal Trivedi⠀

here’s a link to her lab’s website: https://scholars.huji.ac.il/kerem

and a couple of her key papers:⠀

more on Wikipedia editing: http://bit.ly/wikieditingintro ⠀

more on topics mentioned (& others) #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0

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