Babak Nami, Molecular Genetics

Affiliation:
Moffat lab, Donnelly Centre and Department of Molecular Genetics, University of Toronto

Supervisor:
Jason Moffat PhD, Professor, Senior Scientist, Canada Research Chair in Functional Genomics of Cancer, Anne and Max Tanenbaum Chair in Molecular Medicine, Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto

Dr. Nami studied his PhD at Department of Medical Genetics, University of Alberta under the supervision of Dr. Zhixiang Wang. His PhD research focused on targeting therapy of HER2+ subtype of breast cancer and studying the genetic and epigenetic mechanisms of drug resistance in breast cancers. As his PhD thesis outcome, he discovered a novel mechanism of action of trastuzumab (also known as Herceptin), an FDA-approved HER2 targeting monoclonal antibody, and described the epigenetic mechanism of trastuzumab resistance in HER2+ breast cancer. During his PhD Dr. Nami published several peer-reviewed articles and book chapters and received 6 graduate awards and scholarships including Women and Children's Health Research Institute (WCHRI) Graduate Scholarship and William (Bill) Preshing Award for his research and academic achievements.

Currently, Dr. Nami is a postdoctoral fellow at Dr. Jason Moffat’s lab at Department of Molecular Genetics. He received Mitacs Internship Award (2020) and CIHR Postdoctoral Fellowship Award (2021) for studying cancer intrinsic immune evasion mechanisms.

PhD Thesis:
Anti-Cancer Mechanism of Trastuzumab via Blocking Nuclear HER2 Function and Epigenetic Mechanism of Resistance

Dr. Nami in his thesis found a novel anti-cancer mechanism of trastuzumab through blocking proteolytic cleavage and nuclear localization of HER2. Trastuzumab binding to HER2 blocks HER2 cleavage and migration of its C-terminal part to the nucleus where it can regulate RNA processing such as RNA splicing. In this thesis, Dr. Nami also demonstrated a negative feedback loop between HER2 expression and cancer stemness that leads to resistance to HER2 targeting therapies. Targeting HER2+ epithelial breast cancer cells can lead to epithelial to mesenchymal transition (EMT) that results in a global epigenetic remodeling including the silencing of the ERBB2 gene (encoding for HER2) due to chromatin remodeling. Silencing of HER2 expression can cause anti-HER2 drug resistance because of the lack of HER2 surface of the cells. Following are more details of Dr. Nami’s thesis:

1. Mechanism of action of anti-HER2 monoclonal antibodies

HER2 (in human encoded by ERBB2 gene) is an epidermal growth factor receptor tyrosine kinase that mediates cell growth and survival by inducing cell cycle progress, increasing cell motility, and suppressing apoptosis. HER2 is overexpressed more than 10 times in tumor cells than that in normal cells in 20–30% of all breast cancers, 2–66% of all ovarian cancers, and 4–35% of all lung adenocarcinoma. The cancers with HER2 overexpression are known as “HER2+ cancers”. Overexpression of HER2 mostly due to gene amplification is a common oncogenic phenomenon and is associated with poor clinical outcomes. Compared to other subtypes, HER2+ cancers grow faster due to more HER2 signaling but are vulnerable to anti-HER2 targeting therapies including kinase inhibitor lapatinib, and monoclonal antibodies trastuzumab (Herceptin) and pertuzumab (Perjeta). Trastuzumab has been shown to induce antibody-dependent cell-mediated cytotoxicity (ADCC) of the tumor cells, inhibit tumor growth, and improve the survival of HER2+ breast cancer patients. However, approximately 60-70% of HER2+ breast cancer patients develop de novo resistance to trastuzumab, partially due to the loss of HER2 expression on their tumor cells during the treatment. Dr. Nami in his thesis showed that trastuzumab binding to HER2 induces NK cell-mediated ADCC but it can inhibit cell growth even in absence of immune cells as well. However, it does not inhibit HER2 canonical function including receptor homo- and heterodimerization, phosphorylation, and PI3K/Akt and MAPK signaling pathways as HER2 canonical downstream pathways. Dr. Nami also showed that trastuzumab upregulates the apoptosis pathway and inhibits proliferation of the HER2+ cells, but not via inhibiting HER2-mediated PI3K/Akt and MAPK pathways. He also demonstrated that pertuzumab is unable to inhibit HER2 homodimerization but induces HER2 phosphorylation at some phospho-Y sites and abolishes HER2 effects on cell cycle progression. Dr. Nami’s studies showed that pertuzumab inhibits HER2 heterodimers, rather than HER2 homodimers. In addition, pertuzumab binding to HER2 may inhibit non-canonical HER2 activation and function in the non-HER-mediated and dimerization-independent pathway(s).

2. A non-canonical pathway of HER2 oncogene and trastuzumab function

Dr. Nami also showed that binding trastuzumab to the extracellular domain of HER2 blocks proteolytic cleavage of HER2 from its juxtamembrane region and inhibits HER2 nuclear localization that leading to cancer cell growth inhibition. This is a new molecular anti-cancer mechanism of trastuzumab. Immunoprecipitation of nuclear HER2 followed by mass spectrometry analysis revealed that nuclear HER2 directly interacts with transcription factors and several members of the spliceosome protein complex. Nuclear HER2 may mediate RNA processing and regulation of gene expression. In addition, most of the nuclear HER2 client proteins were found as downstream targets for oncogenic/stemness transcription factors that are master regulators of breast cancer stemness. This information demonstrates that trastuzumab blocks a non-canonical function of the C-terminal HER2 fragment. This finding hints at a new strategy to target HER2 in the treatment of HER2+ breast cancers. 

3. Stemness-mediated epigenetic regulation and drug resistance

According to clinical evidence, over 60% of all HER2+ cancers develop resistance to HER2 targeting agents lapatinib and trastuzumab. This is mainly due to the loss of expression of HER2 on the tumor cells. Dr. Nami suggested that loss of HER2 expression can be due to epigenetic remodeling during EMT of HER+ tumor cells. EMT is a biological process by which epithelial cells that are normally lied on the basement membrane lose their epithelial features such as cell-cell junctions and gain mesenchymal properties with the ability to migrate. HER2 can induce EMT of cancer cell EMT by crosstalking with the stemness pathways such as TGF-β and Wnt signaling pathways resulting in an increased subpopulation of mesenchymal-like cells, which are HER2-low or HER2-, proteinase-high and trastuzumab-resistant. EMT can result in the downregulation of membrane HER2 via proteolytic cleavage by EMT-related sheddases. This regulation has been previously shown in trastuzumab-resistant/lapatinib-sensitive cells. However, the mechanism of de novo downregulation of HER2 in trastuzumab-resistant/lapatinib-resistant HER2+ breast tumors was a question mark. Dr. Nami hypothesized that EMT not only downregulates membrane HER2 but also abrogates HER2 transcription by epigenetic inactivation of ERBB2 chromatin. Epithelial-like cells are HER2-high, while mesenchymal-like cells are HER2-low. Dr. Nami showed this correlation because of active and inactive dynamics of ERBB2 chromatin in epithelial-like and mesenchymal-like cells respectively. HER2-low mesenchymal-like breast cancer cell lines revealed less promoter-enhancer interaction and larger chromatin loops compared to the HER2-high epithelial-like breast cancer cell lines. Further, the cell line with higher expression levels of HER2 showed higher numbers of chromatin-chromatin interaction, super-enhancers, and topologically associated domains (TADs) at the chromatin of ERBB2 gene and flanking regions. Dr. Nami showed that the lower HER2 expression, the higher EMT phenotype, and inactivated chromatin all were correlated with a lower response to lapatinib. He found that induction of EMT of HER2+ cancer cells results in downregulation of HER2 expression and a lower binding rate of trastuzumab. These results demonstrate that HER2+ cancer cells can develop resistance to anti-HER2 drugs by silencing HER2 gene expression that takes place by epigenetic remodeling during EMT.

Current research
The immune system is the first line of defense charged to eliminate cancer cells. However, cancer has evolved mechanisms to evade the immune system, some of which have been exposed and leveraged with powerful immunotherapies. Despite the incredible advances made with new immunotherapies in the past two decades, the majority of cancers remain refractory to immunotherapy through intrinsic and acquired genetic and/or epigenetic mechanisms of resistance. Our understanding of the genes and pathways that program cancer cells to evade the immune system is very limited. In other words, the inventory of secret weapons that cancer cells harbour against the immune system still needs to be fully catalogued. Identifying cancer intrinsic immune invasion genes and the mechanism of action by which these genes help cancer cells evade the immune system will uncover the Achilles’ heel of cancer and find new ways to weaken cancers against the immune system and immunotherapy.

Using state-of-the-art technologies in genetics including systematic genome-wide CRISPR screening, as well as a cutting edge cost-effective single-cell sequencing approach, Moffat lab identifies key genes that help cancer cells evade tumor-infiltrating immune cells. One such gene is ADAR which encodes for a double-stranded RNA-specific adenosine deaminase enzyme. ADAR is charged to edit double-stranded RNA (dsRNA) by deamination and converting adenosine (A) to inosine (I). This edit can determine the dsRNA faith in several ways including altering the dsRNA structure, changing amino acid codons, reducing RNA stability, altering splice site recognition sequences, and guiding miRNAs to target the edited RNA that helps cancer cells resist the immune system. It is not known how ADAR contributes to resistance to immunotherapy; however, preliminary results by Dr. Nami and other groups suggest that ADAR is has a prominent role in negative regulation of innate immunity. Dr. Nami studies how ADAR regulates cancer immune evasion, and which molecular pathways synergize with ADAR activity to enhance immunotherapy. His research goals are 1) mapping the genome-scale genetic interaction network of ADAR in cancer using CRISPR/Cas9 screens, 2) mapping the protein interaction network of ADAR using BioID, 3) identifying the molecular function of ADAR in tumor immune suppression and 4) developing new techniques to identify mechanisms of cancer immune evasion. Dr. Nami is collaborating with pharmaceutical companies to translate his findings to clinical medicine by developing new anti-cancer treatments based on targeting ADAR-mediated pathways.

Scholarships/Awards
CIHR Postdoctoral Fellowship (2021)
Mitacs Postdoctoral Internship (2020)
William (Bill) Preshing Graduate Excellence Award (2019)
University of Alberta Medical Sciences Graduate Scholarship (2018)
Kevin Lewis & Catherine Field Medical Genetics Research Fund Award (2017)
Women and Children's Health Research Institute (WCHRI) Travel Award (2017)
Women and Children's Health Research Institute (WCHRI) Graduate Scholarship (2016)
University of Alberta 75th Anniversary Graduate Student Award (2015)