Browsing by Author "Bahlis, Nizar"

Now showing 1 - 6 of 6
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    An Investigation of 53BP1 in Multiple Myeloma
    (2017) Simms, Justin; Bahlis, Nizar; Goodarzi, Aaron; Lees-Miller, Susan
    Currently, multiple myeloma is the second most common hematological malignancy, and as of yet it remains incurable. Although many therapeutic advances have been made in the recent past, there is still room for improvement in the treatment of myeloma. Here, using CRISPR/Cas9 genome editing, we show that a therapeutic combination of proteasome inhibition in combination with PARP inhibition that is in clinical trials depends on the DNA damage response protein 53BP1. These findings contribute to the understanding of the mechanisms behind potential resistance to the combination of proteasome inhibitors with PAPR inhibitors.
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    CNV Radar: an improved method for somatic copy number alteration characterization in oncology
    (2020-03-06) Soong, David; Stratford, Jeran; Avet-Loiseau, Herve; Bahlis, Nizar; Davies, Faith; Dispenzieri, Angela; Sasser, A. K; Schecter, Jordan M; Qi, Ming; Brown, Chad; Jones, Wendell; Keats, Jonathan J; Auclair, Daniel; Chiu, Christopher; Powers, Jason; Schaffer, Michael
    Abstract Background Cancer associated copy number variation (CNV) events provide important information for identifying patient subgroups and suggesting treatment strategies. Technical and logistical issues, however, make it challenging to accurately detect abnormal copy number events in a cost-effective manner in clinical studies. Results Here we present CNV Radar, a software tool that utilizes next-generation sequencing read depth information and variant allele frequency patterns, to infer the true copy number status of genes and genomic regions from whole exome sequencing data. Evaluation of CNV Radar in a public multiple myeloma dataset demonstrated that CNV Radar was able to detect a variety of CNVs associated with risk of progression, and we observed > 70% concordance with fluorescence in situ hybridization (FISH) results. Compared to other CNV callers, CNV Radar showed high sensitivity and specificity. Similar results were observed when comparing CNV Radar calls to single nucleotide polymorphism array results from acute myeloid leukemia and prostate cancer datasets available on TCGA. More importantly, CNV Radar demonstrated its utility in the clinical trial setting: in POLLUX and CASTOR, two phase 3 studies in patients with relapsed or refractory multiple myeloma, we observed a high concordance rate with FISH for del17p, a risk defining CNV event (88% in POLLUX and 90% in CASTOR), therefore allowing for efficacy assessments in clinically relevant disease subgroups. Our case studies also showed that CNV Radar is capable of detecting abnormalities such as copy-neutral loss of heterozygosity that elude other approaches. Conclusions We demonstrated that CNV Radar is more sensitive than other CNV detection methods, accurately detects clinically important cytogenetic events, and allows for further interrogation of novel disease biology. Overall, CNV Radar exhibited high concordance with standard methods such as FISH, and its success in the POLLUX and CASTOR clinical trials demonstrated its potential utility for informing clinical and therapeutic decisions.
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    Epigenetic Investigation of PF(A) Ependymoma
    (2024-09-13) Hasheminasabgorji, Elham; Gallo, Marco; Nikolic, Ana; Bahlis, Nizar; Chan, Jennifer
    Posterior Fossa type A (PFA) ependymoma in infants presents therapeutic challenges with a 60% survival rate and significant treatment-associated neurocognitive sequalae. Our research revealed a distinctive 3D genomic architecture — Type B Ultra-Long Interactions in PFA (TULIPs) - universally present in PFA samples and occurring at recurrent regions of the genome. Here, we investigate the molecular origins of TULIPs in PFA ependymoma. We hypothesized that EZHIP expression may underlie TULIP formation, given its widespread expression in virtually all PFAs. To test this hypothesis, EZHIP was expressed in human neural progenitor cell (hNPC) cultures, and we validated the models using immunofluorescence and western blot assays. Our results demonstrated the nuclear localization of EZHIP and its association with chromatin. Moreover, the expression of EZHIP induced profound alterations in the conformation and localization of heterochromatin in the cells, consistent with the induction of TULIPs. Additionally, functional EdU incorporation assays provided evidence that the expression of EZHIP positively influences cell proliferation. Based on our immunofluorescence results, TULIPs appear as large H3K9me3-rich foci in the nucleus of cells. In various cell types, regions of heterochromatin marked by H3K9me3 are typically associated with HP1 proteins. Considering that HP1 proteins are involved in maintaining the liquid-liquid phase separation (LLPS) state of H3K9me3, we assessed whether TULIPs were in fact condensates. hNPCs expressing EZHIP were treated with 1,6-hexanediol, a compound widely used to disrupt liquid condensates. Our results indicated that 1,6-hexanediol treatment caused disruption of the H3K9me3 configuration, suggesting that TULIPs are in fact in LLPS states. In conclusion, our study provides valuable insights into the molecular origins of TULIPs in PFA ependymoma, elucidating the role of EZHIP expression and its impact on chromatin conformation and cell proliferation. While our data suggest that TULIPs may exist in an LLPS state, further investigation is required to confirm this. These findings enrich our understanding of the molecular landscape of PFA ependymomas and offer potential therapeutic targets.
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    A General Strategy for the Preparation of Thalidomide-Conjugate Linkers
    (2017-01) Papatzimas, James; Gorobets, Evgueni; Brownsey, Duncan; Maity, Ranjan; Bahlis, Nizar; Derksen, Darren
    The synthesis of small-molecule linkers for installation of thalidomide-based conjugates is described. Linker properties have been recognized as vital to conjugate success in drug discovery and delivery systems. These small-molecule tethers act as linkages between molecules, can also aid in cell permeability, and act as solubilizing agents. This work shows our progress in synthesizing conjugates with a variety of linker characteristics. The adaptability and manipulation of these and other linkers holds potential in improving synthetic control of chemical connectivities toward therapeutic development.
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    Investigating T Cell Exhaustion in Multiple Myeloma
    (2023-04-26) Barakat, Elie; Bahlis, Nizar; Mahoney, Douglas; Yong, Wee
    Multiple Myeloma (MM) is a currently incurable malignancy of plasma cells. Immunotherapies are widely agreed upon to be the most likely avenue through which a cure could be found, however, to become longer lasting, permanent solutions, immunotherapies must overcome persistent antigenic stimulation and immune exhaustion. To this end, there is no currently agreed upon immune signature that denotes which cells are exhausted, and which are healthy. The aim of this thesis was to define this exhaustion signature, using only surface antigens and flow cytometry, in order to sort these exhausted T cells from peripheral blood mononuclear cells (PBMC). Based upon the logic that patients who respond poorly to immunotherapy will have on average more exhausted T cells than patients who respond well to immunotherapy, this project developed and optimized a flow cytometry panel designed to use 14 different T cell markers to phenotypically characterize T cells isolated from patient bone marrow aspirates (BMA). While this project did not succeed in generating a full exhaustion signature due to issues concerning censorship within the cohort which shrunk the sample size, it does show that a repetition of this experiment could elucidate the exhaustion signature with a larger sample size and slight adjustments to the antibody panel. An exhaustion signature for T cells can be generated, using surface markers that can be used for flow cytometric sorting in the future.
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    Targeting Selective Receptor Tyrosine Kinases in Refractory Embryonal Tumors of Childhood
    (2016) Singh, Anjali; Narendran, Aru; Kurz, Ebba; Krawetz, Roman; Bahlis, Nizar
    Embryonal tumors are a collection of biologically heterogeneous malignancies and the exact cellular origin of these tumors is not known. Neuroblastoma (NB) and atypical teratoid/rhabdoid tumor (AT/RT) are highly malignant tumors of embryonal origin that primarily affect infants and young children. Neuroblastoma is the most common type of extra cranial solid tumor in children. In the case of AT/RT, the survival rate of children affected by this disease is the lowest when compared to all embryonal tumors. Despite intensifying multimodal treatments, children affected with refractory AT/RT and NB have unacceptably high treatment failure and mortality rates. To improve the clinical outcome of these malignancies, it is important to identify the key molecules and cellular pathways responsible for tumor progression, survival and invasion. Many childhood cancers have high activation levels of selective receptor tyrosine kinase signaling pathways. Activation of these signaling pathways promotes cell proliferation, differentiation and cell survival. Therefore, receptor tyrosine kinases (RTKs) have become attractive therapeutic targets and the use of small molecule kinase inhibitors to block their signal transduction functions has led to the discovery of a number of novel therapeutics agents. This research presents the relevant background information on two pediatric neoplasms that we have selected to study and aims to provide the rationale for the development of useful new therapies for their treatment. Presented in details are the data with respect to the establishment of a screening approach to identify effective therapeutic agents with information on target validation and target modulation activities that can be utilized to design future clinical trials for these cancers.