Team effort reveals cells reshape their nucleus to repair DNA, impacting cancer and aging

“We implemented challenging techniques and developed many approaches ourselves, but what was great was how we all worked together,” noted a recent study’s co-first authors Mitra Shokrollahi, Dr. Mia Stanic, and Anisha Hundal, who are all from the Department of Laboratory Medicine and Pathobiology at the University of Toronto. The new study, entitled “DNA double-strand break-capturing nuclear envelope tubules drive DNA repair” and published in Nature Structural & Molecular Biology, will fundamentally change how we look at DNA repair.

The study was led by Dr. Karim Mekhail from the Department of Laboratory Medicine and Pathobiology at the University of Toronto. The Mekhail lab worked closely with Dr. Razqallah Hakem (Department of Medical Biophysics and LMP faculty at the Princess Margaret Cancer Research Centre) and many other experts, including collaborators across Toronto, Spain, and Singapore.

The nucleus of our cells contains most of our DNA and is contained within a typically round ball-like structure called the nuclear envelope. Nuclear DNA is commonly broken under various conditions, especially in cancer and aging cells. This can lead to genome instability, uncontrolled cell growth, or even cell death. Particularly toxic breaks are known as DNA double-strand breaks (DSBs), where both DNA strands break, completely severing a DNA molecule in two. 

This new study reveals an intricate mechanism that human cells utilize to repair these highly toxic DNA lesions. The research uncovers that, following DNA damage, the nuclear envelope projects long tubules that infiltrate the nucleus, capturing and repairing damaged DNA. “Think of it as the nuclear envelope growing long finger-like structures that help ‘tie’ pieces of broken DNA together, akin to tying our shoelaces,” explained Mekhail. Unusually high levels of DNA damage characterize cancer cells, so they are highly dependent on these tubules – they constantly need to be repaired to stay alive and grow.

Mitra Shokrollahi is a PhD candidate focused on super-resolution microscopy and first studied the tubules by painstakingly imaging nuclei to build 3D models of the tubular network over two years. “After treating cells with chemotherapeutic drugs to trigger DSBs, I observed that microtubules, which are major components of the cytoskeleton, poke the nucleus from the cytoplasm, triggering the formation of nuclear envelope tubules inside the cell nucleus. Through elaborate 3D modeling of single nuclei using advanced microscopy software, it became apparent that not only these nuclear envelope tubules form an extended network throughout the nucleus, but they were also reaching non-peripheral DSBs.” explained Shokrollahi.

Dr. Mia Stanic joined the Mekhail Lab in early 2020 as a postdoctoral researcher and microscopy expert – a vital team member who brought everyone together. “One of the key areas I focused on was to compare how the network of nuclear envelope tubules functions when cells are experiencing a high or low number of DSBs, covering a broad range relevant to many health and disease situations,” explained Stanic. 

Only a short time after Stanic joined the Mekhail Lab, and Shokrollahi had started her studies, the labs shut down due to the COVID-19 pandemic. “It was catastrophic, but that situation brought us all together,” Stanic commented. Faced with extraordinarily restricted and challenging research conditions, the team members pulled together. “Even though we were working on different angles of the process, many parts were interconnected. As we streamlined our joint efforts, it helped speed up the whole process. The communication was excellent, the division of tasks was efficient, and it helped us have an unbiased approach to the analysis. Our joint efforts gave us confidence that we were really onto something, which was a huge boost for us all during a challenging time,” Stanic continued.

Anisha Hundal focused on expanding the translational portion of the research. Joining in 2021 as an MSc student co-supervised by Drs. Mekhail and Hakem, she worked on deciphering cytoplasmic signaling cues of the DNA repair mechanism and on breast cancer animal models. “It was so exciting to find how cells can modify the cytoplasmic filamentous proteins to drive tubule formation while also demonstrating the critical impact of the tubular nuclear envelope networks on breast cancer in vivo,” she said. 
“I got to interact with our international collaborators working within areas like bioinformatics and cytogenetics, which was great to be part of. Being involved in both labs and with our other collaborators provided me with multiple perspectives and access to a lot of resources, help, and advice”, continued Hundal, who has now converted to a PhD to continue working on the project.

“We have an amazing network connecting the Mekhail lab with key experts across Canada and internationally. I thought it was beautiful how all these perspectives could come together – this is how modern science works best”, added Shokrollahi. 

The team has also studied diseases such as BRCA1-linked breast cancer focusing on how the tubules influence cancer cell growth and existing treatments such as PARP inhibitors (a type of precision anti-cancer drug that targets the protein poly-ADP ribose polymerase). Working with Defne Urman, another graduate student in the Mekhail lab, Hundal used AI tools and algorithms in combination with advanced microscopy software to automate the detection and quantification of the nuclear envelope tubules, speeding up the study of the tubules. Hundal’s ability to see the big picture while focusing on specific mechanistic details made her a real asset to the team.

The combining of discovery science and clinical application from the beginning means this research has powerful implications for patients in many areas of aging and related diseases, particularly in cancer, which the team has initially focused on. “This is a remarkable scientific discovery by a multidisciplinary team of experts. Patients with cancers that are difficult to cure need novel therapeutic options. This is the case of women with aggressive types of breast cancer. Our study demonstrates that targeting double-strand break-capturing nuclear envelope tubules, represents a great therapeutic opportunity to kill these aggressive cancers,” commented Hakem.

“This team, particularly the co-first authors, has truly been an inspiration to me personally. They have put the team and science ahead of anything else, even though they have amazing individual talents and skills and could have prioritized differently. I am truly honored to work with them,” noted Mekhail.

More on this topic

• Dr. Karim Mekhail faculty profile
• Dr. Razqallah Hakem faculty profile
• See the announcement on Temerty Medicine News
• Q&A with Mitra Shokrollahi: how diversity in research areas fuels her PhD
• U of T Researchers Discover Intricate Process of DNA Repair in Genome Stability

The collaborators

This research was primarily supported by the Canadian Institutes of Health Research (CIHR). The authors also acknowledge additional support by the Ontario Graduate Scholarships, Ontario Women’s Health Scholars Award, Princess Margaret Cancer Foundation, Instituto Salud Carlos III, Generalitat de Catalunya, CERCA Program to IDIBELL, Lau Chair in Breast Cancer Research, and the Royal Society of Canada.

This story showcases the following pillars of the LMP strategic plan: Dynamic Collaboration (pillar 2), Impactful Research (pillar 3), Disruptive Innovation (pillar 4) and Agile Education (pillar 5)