Biology subjects

Sarkaria, J. N.

Publications and source records attributed to Sarkaria, J. N..

30 records · Page 2Linked to original sources

bioRxiv2020

msiPL: Non-linear Manifold and Peak Learning of Mass Spectrometry Imaging Data Using Artificial Neural Networks

Mass spectrometry imaging (MSI) is an emerging technology that holds potential for improving clinical diagnosis, biomarker discovery, metabolomics research and pharmaceutical applications. The large data size and high dimensional nature of MSI pose computational and memory complexities that hinder accurate identification of biologically-relevant molecular patterns. We propose msiPL, a robust and generic probabilistic generative model based on a fully-connected variational autoencoder for unsupervised analysis and peak learning of MSI data. The method can efficiently learn and visualize the underlying non-linear spectral manifold, reveal biologically-relevant clusters of tumor heterogeneity and identify underlying informative m/z peaks. The method provides a probabilistic parametric mapping to allow a trained model to rapidly analyze a new unseen MSI dataset in a few seconds. The computational model features a memory-efficient implementation using a minibatch processing strategy to enable the analyses of big MSI data (encompassing more than 1 million high-dimensional datapoints) with significantly less memory. We demonstrate the robustness and generic applicability of the application on MSI data of large size from different biological systems and acquired using different mass spectrometers at different centers, namely: 2D Matrix-Assisted Laser Desorption Ionization (MALDI) Fourier Transform Ion Cyclotron Resonance (FT ICR) MSI data of human prostate cancer, 3D MALDI Time-of-Flight (TOF) MSI data of human oral squamous cell carcinoma, 3D Desorption Electrospray Ionization (DESI) Orbitrap MSI data of human colorectal adenocarcinoma, 3D MALDI TOF MSI data of mouse kidney, and 3D MALDI FT ICR MSI data of a patient-derived xenograft (PDX) mouse brain model of glioblastoma. SignificanceMass spectrometry imaging (MSI) provides detailed molecular characterization of a tissue specimen while preserving spatial distributions. However, the complex nature of MSI data slows down the processing time and poses computational and memory challenges that hinder the analysis of multiple specimens required to extract biologically relevant patterns. Moreover, the subjectivity in the selection of parameters for conventional pre-processing approaches can lead to bias. Here, we present a generative probabilistic deep-learning model that can analyze and non-linearly visualize MSI data independent of the nature of the specimen and of the MSI platform. We demonstrate robustness of the method with application to different tissue types, and envision it as a new generation of rapid and robust analysis for mass spectrometry data.

bioinformatics↗

bioRxiv2020

Impact of the radiated brain microenvironment on a panel of human patient-derived xenografts.

ObjectiveRadiotherapy, combined with surgical resection and chemotherapy, remains a first-line treatment for infiltrative gliomas. However, these tumor are not surgically curable, and often recur, even within the prior radiation field, and may demonstrate a more aggressive phenotype. We recently demonstrated that the radiated brain tumor microenvironment promotes tumor aggressiveness in an orthotopic patient-derived xenograft (PDX) model of glioblastoma (Mayo GBM 143). Importantly, high grade gliomas display diverse molecular phenotypes, and whether this genetic variability leads to divergent behaviour in the radiated tumor microenvironment is unknown. Herein, we characterize the effects of the irradiated brain microenvinroment on nine additional unique GBM cell lines to better understand the nuances of how tumor molecular phenotypes influence cellular dynamics. MethodsFemale athymic nude mice were randomly divided into cranial radiation (15 Gy) and non-radiated groups. Mice then underwent intracranial implantation with one of the selected PDX GBM cell lines (GBM 6, 10, 12, 39, 46, 76, 123, 164, 196; total n=8-15, per group, per line). GBM 6 cells were additionally implanted 6 months after completion of fractionated radiation (4Gy x 10 fractions or 2Gy x 30 fractions) vs sham radiation. Kaplan-Meyer (K-M) and log-rank tests were performed to compare the survival between irradiated and non-irradiated groups. ResultOf nine previously untested human GBM lines, we found that five demonstrated shorter survival in the pre-radiated brain (GBM 6, 46, 76, 164, 196); similar to previous observations with GBM 143. GBM 6 was also evaluated 6 months after fractionated radiation yielding similar results. However, two lines yielded prolonged survival in the pre-radiated brain (GBM 10, 12); GBM12 and 10 demonstrated the fastest baseline growth in the non-radiated brain; GBM 39, 123 whose rate of growth was not impacted by the radiated brain, demonstrated a an intermediate baseline growth rate between that of those positively and negatively impacted by the radiated brain microenvironment. No other clinical or molecular phenotype was found to consistently correlate with response to the radiated microenvironment. ConclusionAmong a total of 10 total human GBM lines evaluated to date, 60% induce faster mortality in a radiated microenvironment, and 20% induce slower mortality. These results highlight the likely critical impact of the irradiated microenvironment on tumor behaviour, yet illustrate that different tumors may exhibit opposing responses. Although further evaluation will be needed to understand mechanisms of divergent behavior, our data suggest the increased rate of growth in the radiated microenvironment may not apply to the fastest-growing tumor lines, which could instead demonstrate a paradoxical response.

cancer biology↗

bioRxiv2020

Selective Vulnerability of Senescent Glioblastoma Cells to Bcl-XL Inhibition

Despite decades of research and numerous basic science advances, there have only marginal gains in improving glioblastoma multiforme survival. Therefore, new ideas and approaches for treating this aggressive disease are essential to drive progress forward. Conventional therapies, such as radiation and Temozolomide (TMZ), function to cause oxidative stress and DNA damage yielding a senescent-like state of replicative arrest in susceptible cells. However, increasing evidence demonstrates malignant cells can escape senescence leading to tumor recurrence. Ablation of non-replicating senescent tumor cells after radiation and chemotherapy may be an avenue to reduce the rates of tumor recurrence. Senolytic agents have been developed that selectively target senescent cells, but it remains unknown whether senolytics might be utilized against senescent-like glioma cells. We employed radiation or TMZ to induce a functionally senescent state in human glioblastoma cells. Viable cells that survive these treatments were then utilized to screen candidate senolytic drugs, to identify those selectively effective at ablating senescent-like cells over naive non-tumor and proliferative cells. Among 10 candidate senolytic drugs evaluated, only Bcl-XL inhibitors demonstrated reproducible senolytic activity in radiated or TMZ-treated glioma across the majority of GBM cell lines evaluated. Conversely, Bcl-2 inhibitors and other established senolytic drugs failed to show any consistent senolytic activity. In agreement with these data, Bcl-XL knockdown selectively reduced the viability of senescent-like GBM cells, whereas knockdown of Bcl-2 or Bcl-W yielded no senolytic effect. These findings demonstrate the potential to harness radiation-induced biology to ablate latent surviving cells and highlight Bcl-XL dependency as a potential vulnerability of surviving GBM cells after exposure to radiation or TMZ.

cancer biology↗

bioRxiv2020

Distinct Long-term Effects of Precision X-Radiation on Reflex Saliva Flow Rate and Tissue Integrity in a Preclinical Model of Chronic Hyposalivation

Chronic salivary hypofunction and xerostomia are common side effects of radiation therapy which is an essential component in the curative management in patients with head & neck cancers. Over the years, improvements in delivery techniques such as image-guided intensity modulated radiation therapy have led to improvement in cancer management but chronic hyposalivation continues to be a challenge that causes long-term health implications resulting in compromised quality of life. Recent advances in salivary stem cell research promise new frontier in the treatment of radiation-induced hyposalivation by initiating regeneration of radiation-damaged salivary parenchymal cells. Lack of a standard preclinical immunodeficient model to assess radiation-induced changes objectively and quantitatively in salivary flow rates will impede rapid progress towards the development of cellular therapies for chronic salivary dysfunction and attendant xerostomia. Herein, we report the first fully characterized novel cone-beam computed tomography (CBCT)-guided precision ionizing radiation (IR) induced chronic hyposalivation model in radiosensitive, immunodeficient transgenic NSG-SGM3 mice expressing three human cytokines including c-KIT ligand/stem cell factor. Additionally, we also report a novel and instantaneous method to objectively assess the kinetics of pilocarpine-stimulated salivary flowrate. Comprehensive structural and functional characterization of salivary glands revealed previously unknown and highly complex gender, age, IR dose and salivary gland subtype-specific effects of salivary-ablative precision IR.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pathology↗

bioRxiv2019

Quantifying glioblastoma drug response dynamics incorporating resistance and blood brain barrier penetrance from experimental data

Many drugs investigated for the treatment of glioblastoma (GBM) have had poor clinical outcomes, as their efficacy is dependent on adequate delivery to sensitive tumor cell populations, which is limited by the blood-brain barrier (BBB). Further complicating evaluation of therapeutic efficacy, tumors can become resistant to anti-cancer drugs, and it can be difficult to gauge the extent to which BBB limitations and resistance each contribute to a drugs failure. To address this question, we developed a minimal mathematical model to characterize these elements of overall drug response, informed by time-series bioluminescence imaging data from a treated patient-derived xenograft (PDX) experimental model. By fitting this mathematical model to a preliminary dataset in a series of nonlinear regression steps, we estimated parameter values for individual PDX subjects that correspond to the dynamics seen in experimental data. Using these estimates, we performed a parameter sensitivity analysis using Latin hypercube sampling and partial rank correlation coefficients. Results from this analysis combined with simulation results suggest that BBB permeability may play a slightly larger role in therapeutic efficacy than drug resistance. Our model and fitting technique to estimate parameters from data may be a useful tool in aiding further exploration of these challenges in future studies of drug efficacy with larger datasets.

cancer biology↗

bioRxiv2019

Single-cell based elucidation of molecularly-distinct glioblastoma states and drug sensitivity

Glioblastoma heterogeneity and plasticity remain controversial, with proposed subtypes representing the average of highly heterogeneous admixtures of independent transcriptional states. Single-cell, protein-activity-based analysis allowed full quantification of >6,000 regulatory and signaling proteins, thus providing a previously unattainable single-cell characterization level. This helped identify four novel, molecularly distinct subtypes that successfully harmonize across multiple GBM datasets, including previously published bulk and single-cell profiles and single cell profiles from seven orthotopic PDX models, representative of prior subtype diversity. GBM is thus characterized by the plastic coexistence of single cells in two mutually-exclusive developmental lineages, with additional stratification provided by their proliferative potential. Consistently, all previous subtypes could be recapitulated by single-cell mixtures drawn from newly identified states. Critically, drug sensitivity was predicted and validated as highly state-dependent, both in single-cell assays from patient-derived explants and in PDX models, suggesting that successful treatment requires combinations of multiple drugs targeting these distinct tumor states.\n\nSignificanceWe propose a new, 4-subtype GBM classification, which harmonizes across bulk and single-cell datasets. Single-cell mixtures from these subtypes effectively recapitulate all prior classifications, suggesting that the latter are a byproduct of GBM heterogeneity. Finally, we predict single-cell level activity of three clinically-relevant drugs, and validate them in patient-derived explant.

systems biology↗

bioRxiv2019

Hyaluronic acid-functionalized gelatin hydrogels reveal extracellular matrix signals temper the efficacy of erlotinib against patient-derived glioblastoma specimens

Therapeutic options to treat primary glioblastoma (GBM) tumors are scarce. GBM tumors with epidermal growth factor receptor (EGFR) mutations, in particular a constitutively active EGFRvIII mutant, have extremely poor clinical outcomes. GBM tumors with concurrent EGFR amplification and active phosphatase and tensin homolog (PTEN) are sensitive to the tyrosine kinase inhibitor erlotinib, but the effect is not durable. A persistent challenge to improved treatment is the poorly understood role of cellular, metabolic, and biophysical signals from the GBM tumor microenvironment on therapeutic efficacy and acquired resistance. The intractable nature of studying GBM cell in vivo motivates tissue engineering approaches to replicate aspects of the complex GBM tumor microenvironment. Here, we profile the effect of erlotinib on two patient-derived GBM specimens: EGFR+ GBM12 and EGFRvIII GBM6. We use a three-dimensional gelatin hydrogel to present brain-mimetic hyaluronic acid (HA) and evaluate the coordinated influence of extracellular matrix signals and EGFR mutation status on GBM cell migration, survival and proliferation, as well as signaling pathway activation in response to cyclic erlotinib exposure. Comparable to results observed in vivo for xenograft tumors, erlotinib exposure is not cytotoxic for GBM6 EGFRvIII specimens. We also identify a role of extracellular HA (via CD44) in altering the effect of erlotinib in GBM EGFR+ cells by modifying STAT3 phosphorylation status. Taken together, we report an in vitro tissue engineered platform to monitor signaling associated with poor response to targeted inhibitors in GBM.

bioengineering↗

bioRxiv2019

Estrogen-related receptor beta activation and isoform shifting by cdc2-like kinase inhibition restricts migration and intracranial tumor growth in glioblastoma

Glioblastoma (GBM; grade 4 glioma) is a highly aggressive and incurable tumor. GBM has recently been characterized as highly dependent on alternative splicing, a critical driver of tumor heterogeneity and plasticity. Estrogen-related receptor beta (ERR{beta}, ESRRB, NR3B2) is an orphan nuclear receptor expressed in the brain, where alternative splicing of the 3 end of the pre-mRNA leads to the production of three validated ERR{beta} protein products - ERR{beta} short form (ERR{beta}sf), ERR{beta}2, and ERR{beta} exon 10-deleted (ERR{beta}-{Delta}10). Our prior studies have shown the ERR{beta}2 isoform to play a role in G2/M cell cycle arrest and induction of apoptosis, in contrast to the function of the shorter ERR{beta}sf isoform in senescence and G1 cell cycle arrest. In this study, we sought to better define the role of the pro-apoptotic ERR{beta}2 isoform in GBM. We show that the ERR{beta}2 isoform is located in the nucleus, but also the cytoplasm. ERR{beta}2 suppresses GBM cell migration, interacts with the actin nucleation-promoting factor cortactin, and an ERR{beta} agonist is able to remodel the actin cytoskeleton and similarly suppress GBM cell migration. We further show that inhibition of the splicing regulatory cdc2-like kinases (CLKs) in combination with an ERR{beta} agonist shifts isoform expression in favor of ERR{beta}2 and potentiates inhibition of growth and migration in GBM cells and intracranial tumors. Financial SupportThis work was supported by R21 CA191444 (RBR), a Georgetown University Medical Center (GUMC) Dean for Researchs Toulmin Pilot Project Award (RBR), and a Partners in Research Breakthrough Award (RBR), as well as F99 CA234799 (DMT) and a student research grant from the Medical Center Graduate Student Organization (MCGSO, to DMT). Additional fellowship funding for DMT and MMH was provided by the Tumor Biology Training Grant (T32 CA009686, PI: Dr. Anna T. Riegel). Technical services were provided by the GUMC Animal Models, Flow Cytometry & Cell Sorting, Histopathology & Tissue, Microscopy & Imaging, and Tissue Culture Shared Resources, which are supported in part by Cancer Center Support Grant P30 CA051008 (PI: Dr. Louis M. Weiner). The Mayo Clinic Brain Tumor Patient-Derived Xenograft National Resource is supported in part by P50 CA108961 (JNS, PI: Dr. Patrick ONeill). The content of this article is the sole responsibility of the authors and does not represent the official views of the National Institutes of Health. Conflict of Interest and Author Contribution StatementThe authors declare no potential conflict of interest. DMT contributed to study design, performed experiments, analyzed data, and wrote the paper. SAK performed experiments, analyzed data, and wrote the paper. CJT performed experiments and analyzed data. MMH performed experiments. SDD performed experiments. JNS provided patient-derived xenograft samples. EG contributed to study design, and performed experiments. RBR contributed to study design, performed experiments, analyzed data, and wrote the paper. All authors reviewed, edited, and approved the manuscript.

cancer biology↗

bioRxiv2019

Image-based metric of invasiveness predicts response to adjuvant temozolomide for primary glioblastoma

Temozolomide (TMZ) has been the standard-of-care chemotherapy for glioblastoma (GBM) patients for more than a decade. Despite this long time in use, significant questions remain regarding how best to optimize TMZ therapy for individual patients. Understanding the relationship between TMZ response and factors such as number of adjuvant TMZ cycles, patient age, patient sex, and image-based tumor features, might help predict which GBM patients would benefit most from TMZ, particularly for those whose tumors are not MGMT methylated. Using a cohort of 90 newly-diagnosed GBM patients treated according to the Stupp protocol, we examined the relationships between several patient and tumor characteristics and volumetric and survival outcomes during adjuvant chemotherapy. Volumetric changes in MR imaging abnormalities during adjuvant therapy were used to assess TMZ response. T1Gd volumetric response is associated with younger patient age, increased number of TMZ cycles, longer time to nadir volume, and decreased tumor invasiveness. Moreover, increased adjuvant TMZ cycles corresponded with improved volumetric response only among more nodular tumors, and this volumetric response was associated with improved survival outcomes. Finally, in a subcohort of patients with known MGMT methylation status, MGMT methylated tumors were more diffusely invasive than unmethylated tumors, suggesting that the improved response in nodular tumors is not driven by a preponderance of MGMT methylated tumors. Our finding that less diffusely invasive tumors are associated with greater volumetric response to TMZ suggests that patients with these tumors may benefit from additional cycles of adjuvant TMZ, even for those without MGMT methylation.

cell biology↗

bioRxiv2018

ENvironmental Dynamics Underlying Responsive Extreme Survivors (ENDURES) of Glioblastoma: a Multi-disciplinary Team-based, Multifactorial Analytical Approach

Although glioblastoma is a fatal primary brain cancer with a short median survival of 15 months, a small number of patients survive more than 5 years after diagnosis; they are known as extreme survivors (ES). Due to their rarity, very little is known about what differentiates these outliers from other glioblastoma patients. For the purpose of identifying unknown drivers of extreme survivorship in glioblastoma, we developed the ENDURES consortium (ENvironmental Dynamics Underlying Responsive Extreme Survivors of glioblastoma). This consortium is a multicenter collaborative network of investigators focused on the integration of multiple types of clinical data and the creation of patient-specific models of tumor growth informed by radiographic and histological parameters. Leveraging our combined resources, the goals of the ENDURES consortium are two-fold: (1) to build a curated, searchable, multilayered repository housing clinical and outcome data on a large cohort of ES patients with glioblastoma and (2) to leverage the ENDURES repository for new insights on tumor behavior and novel targets for prolonging survival for all glioblastoma patients. In this article, we review the available literature and discuss what is already known about ES. We then describe the creation of our consortium and some of our preliminary results.\n\nFundingThis review was financially supported by a grant from the James S. McDonnell Foundation\n\nConflicts of InterestThe authors have declared that no conflicts of interest exist.\n\nAuthorshipConceptualized consortium: LW, RG, KME, PC, and KRS. Built consortium: SKJ, PK, NR, JS, KME, PC, and KRS. Wrote the manuscript: SKJ, PW, SCM, PK, AP, and KME. Reviewed and edited the manuscript: LFGC, MMM, AHD, PRJ, and LSH. Contributed to writing, provided feedback, and approved of final manuscript: All authors.\n\nLink to website for ENDUREShttp://mathematicalneurooncology.org/?page_id=2125

cancer biology↗

bioRxiv2018

Influence of hyaluronic acid transitions in tumor microenvironment on glioblastoma malignancy and invasive behavior

The extracellular matrix (ECM) is critical in tumor growth and invasive potential of cancer cells. In glioblastoma tumors, some components of the native brain ECM such as hyaluronic acid (HA) have been suggested as key regulators of processes associated with poor patient outlook such as invasion and therapeutic resistance. Given the importance of cell-mediated remodeling during invasion, it is likely that the molecular weight of available HA polymer may strongly influence GBM progression. Biomaterial platforms therefore provide a unique opportunity to systematically examine the influence of the molecular weight distribution of HA on GBM cell activity. Here we report the relationship between the molecular weight of matrix-bound HA within a methacrylamide-functionalized gelatin (GelMA) hydrogel, the invasive phenotype of a patient-derived xenograft GBM population that exhibits significant in vivo invasivity, and the local production of soluble HA during GBM cell invasion. Hyaluronic acid of different molecular weights spanning a range associated with cell-mediated remodeling (10, 60, and 500 kDa) was photopolymerized into GelMA hydrogels, with cell activity compared to GelMA only conditions (-HA). Polymerization conditions were tuned to create a homologous series of GelMA hydrogels with conserved poroelastic properties (i.e. shear modulus, Poissons ratio, and diffusivity). GBM migration was strongly influenced by HA molecular weight. While markers associated with active remodeling of the HA content, hyaluronan synthase and hyaluronidase, were found to be insensitive to matrix immobilized HA content. These results provide new information regarding the importance of local hyaluronic acid content on the invasive phenotype of GBM.

bioengineering↗

bioRxiv2017

H3K27me3-mediated silencing of Wilms Tumor 1 supports the proliferation of brain tumor cells harboring the H3.3K27M mutation

The lysine 27 to methionine mutation of histone H3.3 (H3.3K27M) is detected in over 75% of diffuse intrinsic pontine glioma (DIPG). The H3.3K27M mutant proteins inhibit H3K27 methyltransferase complex PRC2, resulting in a global reduction of tri-methylation of H3K27 (H3K27me3). Paradoxically, high levels of H3K27me3 were also detected at hundreds of genomic loci. However, it is not known how and why H3K27me3 is redistributed in DIPG cells. Here we show that lower levels of H3.3K27M mutant proteins at some genomic loci contribute to the retention of H3K27me3 peaks. But more importantly, Jarid2, a PRC2-associated protein, strongly correlates the presence of H3K27me3 and relieves the H3.3K27M-mediated inhibition in vivo and in vitro. Furthermore, we show that H3K27me3-mediated silencing of tumor suppressor gene Wilms Tumor 1 (WT1) supports the proliferation of DIPG cells and reaction of WT1 inhibits DIPG proliferation. Together, these studies reveal mechanisms whereby H3K27me3 is retained in the environment of global loss of this mark, and how persistence of this mark contributes to DIPG tumorigenesis.

cancer biology↗