Integrative multi-omics approach to targeted therapy for glioblastoma

This review describes recent technological advances applied to glioblastoma (GBM), a brain tumor with dismal prognosis. International consortial efforts suggest the presence of molecular subtypes within histologically identical GBM tumors. This emphasizes that future treatment decisions should no longer be made based solely on morphological analyses, but must now take into consideration such molecular and cellular heterogeneity. The use of single-cell technologies has advanced our understanding and assignation of functional subtypes revealing therapeutic vulnerabilities. Our team has developed stratification approaches in the past few years, and we have been able to identify patient cohorts enriched for various signaling pathways. Importantly, our Glioportal brain tumor resource has been established under the National Neuroscience Institute Tissue Bank in 2021. This resource offers preclinical capability to validate working hypotheses established from patient clinical datasets. This review highlights recent developments with the ultimate goal of assigning functional meaning to molecular subtypes, revealing therapeutic vulnerabilities.

Abstract 2123: Chromatin profiling of glioblastoma tissues identifies core oncogenic dependency and therapeutic opportunities

Background: Glioblastoma (GBM) is the most aggressive and therapy-refractory brain tumor in adults. Molecular profiling of GBM on the basis of gene expression, DNA methylation and genomic variations has advanced both cancer research and clinical diagnosis. However, the enhancer architectures and regulatory circuitries governing tumor-intrinsic transcriptional diversity and subtype identity are still elusive.

Methods: Chromatin immunoprecipitation followed by sequencing analysis was applied to examine H3K27ac deposition and to map the active regulatory landscapes across 95 GBM biopsies and 12 normal brain tissues. RNA-sequencing analysis was performed to measure transcriptome and to classify transcriptional subtypes. Super-enhancer associated genes and master transcriptional factors were identified. Function of novel cancer associated genes was explored using both patient-derived GBM propagating cells and orthotopic xenograft models.

Results: Analyses of differentially regulated enhancers and super-enhancers uncovered previously unrecognized layers of inter-tumor heterogeneity. Integrative analysis of variant enhancer loci and transcriptome identified topographies of transcriptional enhancers and core regulatory circuitries in four molecular subtypes of primary tumors: AC1-mesenchymal, AC1-classical, AC2-proneural and AC3-proneural. Subtype-specific enhancer domains contributed to transcriptional diversity and shaped subtype identity. Moreover, this study reveals novel oncogenic dependency of GBM on various super-enhancer-driven transcriptional factors and druggable targets (e.g., BRD4).

Conclusion: Through profiling of transcriptional enhancers, we provide clinically relevant insights into the molecular classification, pathogenesis and therapeutic intervention of GBM.

Citation Format: Liang Xu, Ye Chen, Yulun Huang, Edwin Sandanaraj, John S. Yu, Ruby Yu-Tong Lin, Pushkar Dakle, Xin-Yu Ke, Yuk Kien Chong, Lynnette Koh, Anand Mayakonda, Kassoum Nacro, Jeffrey Hill, Mo-Li Huang, Sigal Gery, See Wee Lim, Zhengyun Huang, Ying Xu, Jianxiang Chen, Longchuan Bai, Shaomeng Wang, Hiroaki Wakimoto, Tseng Tsai Yeo, Beng Ti Ang, Markus Müschen, Carol Tang, Tuan Zea Tan, Phillip H. Koeffler. Chromatin profiling of glioblastoma tissues identifies core oncogenic dependency and therapeutic opportunities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2123.

Topography of transcriptionally active chromatin in glioblastoma

Molecular profiling of the most aggressive brain tumor glioblastoma (GBM) on the basis of gene expression, DNA methylation, and genomic variations advances both cancer research and clinical diagnosis. The enhancer architectures and regulatory circuitries governing tumor-intrinsic transcriptional diversity and subtype identity are still elusive. Here, by mapping H3K27ac deposition, we analyze the active regulatory landscapes across 95 GBM biopsies, 12 normal brain tissues, and 38 cell line counterparts. Analyses of differentially regulated enhancers and super-enhancers uncovered previously unrecognized layers of intertumor heterogeneity. Integrative analysis of variant enhancer loci and transcriptome identified topographies of transcriptional enhancers and core regulatory circuitries in four molecular subtypes of primary tumors: AC1-mesenchymal, AC1-classical, AC2-proneural, and AC3-proneural. Moreover, this study reveals core oncogenic dependency on super-enhancer-driven transcriptional factors, long noncoding RNAs, and druggable targets in GBM. Through profiling of transcriptional enhancers, we provide clinically relevant insights into molecular classification, pathogenesis, and therapeutic intervention of GBM.

CSIG-03. STAT3-BASED PATIENT STRATIFICATION IN PRECISION NEURO-ONCOLOGY

Glioblastoma (GBM) displays both spatial and temporal heterogeneity, whereupon mesenchymal tumors fare more poorly than the proneural molecular subtype. STAT3 was selected because its activation preceeds the proneural-mesenchymal transition. We first defined a STAT3 gene signature that stratified GBM patients into STAT3-high and -low cohorts. STAT3 inhibitor treatment selectively mitigated STAT3-high cell viability and tumorigenicity in orthotopic mouse xenograft models. In addition, we elucidated the mechanism underlying resistance in STAT3-low cells by combining STAT3 signature analysis with kinome screen data on STAT3 inhibitor-treated cells, allowing us to draw connections between kinases affected by STAT3 inhibitors, their associated transcription factors and target genes. As such, we show that dual inhibition of IGF-1R and STAT3 sensitized STAT3-low cells and improved survival in mice. Our study emphasizes the clinical implications of molecular subtype switching and demonstrates the importance of serially profiling GBM tumors upon recurrence so as to facilitate effective therapy.

Abstract 1524: BCL6 modulates the TP53 and STAT pathways in glioma

Glioblastoma multiforme (GBM) remains the most aggressive brain malignancy with little improvement in prognosis or therapy for decades. Recently, we identified BCL6, also known as ZBTB27, to be a novel oncogene in GBM. In this study, we performed IHC analysis of 153 primary human glioma specimens and 8 normal brain samples. BCL6 expression is robustly elevated in tumor samples and positively correlated with glioma pathological grade. High BCL6 expression strongly predicts a worse prognosis of GBM patients. Depletion of BCL6 in human GBM cells reduced the incorporation of BrdU, promoted the cellular senescence and inhibited the growth of human GBM cells in vivo. Next, genome-wide occupancy of BCL6 in GBM cells was characterized by ChIP-seq assay. Genomic regions centered on BCL6 peaks are co-enriched with RNA-Pol II and flanked with strong H3K27ac and H3K4me3 modifications. MYC and two long non-coding RNAs MALAT1 and NEAT1 were identified as novel BCL6 targets in GBM. Moreover, pathway enrichment analysis of BCL6 peak-associated genes reveals a significant enrichment of JAK-STAT, TP53, ERBB and MAPK pathways. We demostrated further that BCL6 represses the TP53 pathway and promotes the JAK-STAT pathway activation in GBM cells. Together, our findings uncover potential downstream targets and provide a better understanding of BCL6 function in GBM.

Citation Format: Ye Chen, Liang Xu, Marina Dutra-Clarke, Anand Mayakonda, De-Chen Lin, Lynnette Koh, Yuk Kien Chong, Edwin Sandanaraj, Vikas Madan, Henry Yang, Ngan Doan, Jonathan W. Said, William H. Yong, Markus Müschen, Beng Ti Ang, Carol Tang, Joshua J. Breunig, Phillip Koeffler. BCL6 modulates the TP53 and STAT pathways in glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1524. doi:10.1158/1538-7445.AM2017-1524

Abstract 4470: ST3GAL1-associated transcriptomic program portends poor prognosis in glioblastoma

Cell surface sialylation has been associated with tumor cell invasiveness in several cancers. Patients with grade IV glioblastoma multiforme (GBM) often show a median survival period of fifteen months, even with the current standard-of-care treatment. Among the reasons for this poor prognosis lies in the cellular and molecular heterogeneity of tumor cells. The Cancer Genome Atlas efforts have shown that histologically identical GBM tumors can be divided into four molecular subtypes based on gene expression, with each subtype corresponding to unique genomic aberrations and clinical outcome. These findings highlight the limitation of relying solely on morphological approaches to diagnose and subsequently treat patients. We conducted a lectin screen with the goal of identifying candidates that stained normal and tumor cells differentially. We identified a sialyltransferase, ST3Gal1 as a mediator of the binding pattern of one such lectin, Peanut Agglutinin. We demonstrate that ST3Gal1 promotes tumor cell invasiveness and enriches for self-renewal potential in the mesenchymal tumor subclass of patients, typified by highly aggressive and recurrent profiles. Depletion of ST3Gal1 extends tumor latency and prolongs survival in mice. Importantly, an enrichment of the ST3GAL1 transcriptomic program portends poor prognosis in glioma patients. Moving forward, since there are no mutations or changes in copy number of ST3GAL1, we explored epigenetic regulation as a possible mechanism. By tapping into data from the NIH Roadmap Epigenome, and transcriptomic analysis of our patient tumor-derived cells, we identified a histone clustering signature that correlates with survival outcome and disease progression. We are currently investigating one such histone modifier, lysine (K)-specific demethylase 1A (LSD1) and its role at modifying ST3GAL1 transcription and activity.

Citation Format: Yuk Kien Chong, Edwin Sandanaraj, Lynnette Koh, Moogaambikai Thangaveloo, Melanie SY Tan, Geraldene Koh, Tan Boon Toh, Grace GY Lim, Joanna Holbrook, Oi Lian Kon, Mahendran Nadarajah, Ivan Ng, Wai Hoe Ng, Nguan Soon Tan, Kah Leong Lim, Carol S. Tang, Beng Ti Ang. ST3GAL1-associated transcriptomic program portends poor prognosis in glioblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4470.

Regional survey of tuberculosis risk assessment in rheumatology outpatients commencing anti-TNF-alpha treatment in relation to British Thoracic Society guidelines

The aim of this study was to analyse tuberculosis (TB) risk assessment for rheumatology patients commencing anti-tumour necrosis factor-alpha (anti-TNF-alpha) therapy using the British Thoracic Society (BTS) guidelines. Data were obtained retrospectively on 856 outpatients regionally receiving anti-TNF-alpha. Prior to commencing treatment, patients had the following assessments documented: respiratory examination, 47.4%; chest X-ray, 84.5%; TB history, 92.9%; and advice about TB risk, 45.8%. Of the 856 patients, 94.3% were on immunosuppressives but 27% had a tuberculin test; 12.6% had > or =1 high-risk factors for TB. In total, 3.4% were referred to a TB specialist and of these, 24.1% had no risk factors for TB. Of patients with > or =1 risk factor, 76.9% were not referred. Only 4/28 patients at high risk for TB due to ethnicity or birthplace received chemoprophylaxis. Marked inter-unit variation was demonstrated and it was evident that patients require improved screening for TB. Greater awareness is necessary of patients with risk factors, particularly ethnicity, to facilitate more appropriate targeting of chemoprophylaxis. Multi-centre audit is a valuable clinical governance tool.

Subarachnoid injection of Microfil reveals connections between cerebrospinal fluid and nasal lymphatics in the non-human primate

Based on quantitative and qualitative studies in a variety of mammalian species, it would appear that a significant portion of cerebrospinal fluid (CSF) drainage is associated with transport along cranial and spinal nerves with absorption taking place into lymphatic vessels external to the central nervous system. CSF appears to convect primarily through the cribriform plate into lymphatics associated with the submucosa of the olfactory and respiratory epithelium. However, the significance of this pathway for CSF absorption in primates has never been established unequivocally. In past studies, we infused Microfil into the subarachnoid compartment of numerous species to visualize CSF transport pathways. The success of this method encouraged us to use a similar approach in the non-human primate. Yellow Microfil was injected post mortem into the cisterna magna of 6 years old Barbados green monkeys (Cercopithecus aethiops sabeus, n = 6). Macroscopic and microscopic examination revealed that Microfil was (1) distributed throughout the subarachnoid compartment, (2) located in the perineurial spaces associated with the fila olfactoria, (3) present within the olfactory submucosa, and (4) situated within an extensive network of lymphatic vessels in the nasal submucosa, nasal septum and turbinate tissues. We conclude that the Microfil distribution patterns in the monkey were very similar to those observed in many other species suggesting that significant nasal lymphatic uptake of CSF occurs in the non-human primate.

Integrating the roles of extracranial lymphatics and intracranial veins in cerebrospinal fluid absorption in sheep

At relatively low cerebrospinal fluid (CSF) pressures, the majority of CSF drainage in 6- to 8-month-old sheep occurs through the cribriform plate into lymphatic vessels in the nasal submucosa. As CSF pressures are elevated, other absorption sites are recruited and these may include transport through arachnoid projections. To test for the transport of CSF directly into the venous sinus, the concentration of a tracer (131I-human serum albumin [HSA]) administered into the CSF compartment was measured in the confluence of the intracranial venous sinuses (torcular) and in the peripheral blood (inferior vena cava). CSF pressures were adjusted to favor absorption. Enrichment of the CSF tracer in the cranial venous system was most evident when the CSF-venous sinus pressure gradients were high. Peak concentration differences occurred 90 s after the CSF pressures were elevated. When pressure gradients approached 30 cm H(2)O, tracer concentrations in the torcular were approximately twofold higher than those observed in peripheral blood. The greatest concentration differences favoring the torcular were obtained when the CSF-venous sinus pressure gradients were elevated to high levels (20- to 40 cm H(2)O) and when CSF access to the paranasal lymphatics and CSF transport into the spinal subarachnoid compartment were prevented. In conjunction with previous studies, these results are compatible with the view that CSF absorption in the adult animal can occur directly into the cranial venous system. However, contrary to the established view, this pathway may represent a secondary system that is recruited to compliment lymphatic transport when global absorption capacity is stressed or compromised.

Restless legs symptoms in thyroid disorders

Dopaminergic dysfunction is associated with thyroid disorders and restless legs syndrome (RLS). In a 'face-to-face' interview, we evaluated for RLS using the diagnostic criteria of the International Restless Legs Syndrome Study Group (IRLSSG) in patients diagnosed biochemically with either hyper- or hypothyroidism, and in controls without thyroid disorders. Amongst 146 consecutive patients with biochemically confirmed thyroid disorders, none satisfied all the IRLSSG criteria of RLS, similar to the control population (0.2%, 1/434). However, we found 8.2% (12/146) with RLS-like symptoms (satisfied the first 3 IRLSSG criteria) compared to 0.9% (4/434) in the controls (p < 0.0001). Four (33.3%) of these patients reported complete resolution of these symptoms after treatment for their thyroid condition. In conclusion, while RLS-like symptoms were observed in some patients with thyroid disorders, our study demonstrates no significant difference of RLS prevalence between patients with thyroid disorders and euthyroid controls.

Gemcitabine in metastatic nasopharyngeal carcinoma of the undifferentiated type

BACKGROUND

We conducted two parallel phase II trials in chemonaïve and previously treated patients with metastatic nasopharyngeal carcinoma (NPC) to evaluate the tumour response, progression-free and overall survival, and toxicity of gemcitabine.

PATIENTS AND METHODS

Gemcitabine 1250 mg/m2 was given on days 1 and 8 of a 21-day cycle. Patients with an Eastern Cooperative Oncology Group performance status <2, adequate renal, hepatic and bone marrow function, and radiologically measurable NPC were eligible.

RESULTS

Twenty-five chemonaïve and 27 previously treated patients were enrolled. The overall response rate was 28% [95% confidence interval (CI) 14% to 48%] for the chemonaïve and 48% (95% CI 31% to 66%) for previously treated patients. Toxicities greater than or equal to grade 3 occurred in 15 (60%) chemonaïve and 13 (48%) previously treated patients. Neutropenia was uncommon in chemonaïve patients, but occurred in 37% of previously treated patients. The median time to progression was 3.6 months (range 0.9-7.9) for chemonaïve and 5.1 months (0.9-13.1) for previously treated patients. Median overall survival time was 7.2 months (1.4-15.6) and 10.5 months (2.4-15.0) for chemonaïve and previously treated patients, respectively.

CONCLUSIONS

Gemcitabine has moderate activity in NPC with minimal toxicity, and is also an effective salvage agent for patients who have failed or progressed after treatment with other agents.

Primary intrathoracic malignant effusion: a descriptive study

BACKGROUND

Patients who present with malignant pleural/malignant effusion without a definite primary site are not well described in the medical literature. In the course of our clinical practice, we have observed certain traits that are peculiar to patients with such a presentation. We have applied the term primary intrathoracic malignant effusion (PIME) to describe this condition.

STUDY OBJECTIVES

Patients must fulfill the following criteria before a diagnosis of PIME can be made: clinical presentation dominated by pleural/pericardial effusion; histologic proof of malignancy obtained from the pleura and/or pericardium; no definite primary site in the lungs or elsewhere from CT scan of the chest, chest radiograph, or physical and endoscopic examination; no history of malignancy; and no history of asbestos exposure. Exposure to environmental tobacco smoke (ETS) among the nonsmokers was examined in a case-control setting.

METHODS

We conducted a retrospective search of our database of patients who were referred to the Department of Medical Oncology with a diagnosis of pleural/pericardial effusion from January 1993 to January 2000.

RESULTS

Seventy-one of 200 patients from our database met the criteria. A significant majority of the patients were women (65%) and nonsmokers (72%). All patients had adenocarcinoma shown on biopsy. The majority of patients (63%) had disease localized to the intrathoracic serosal surfaces; the rest had distant metastases involving the lung (50%), bone (27%), liver (19%), brain (8%), and skin (4%). Six patients had two or more sites of distant metastases. There was a significant association with ETS exposure when compared to a control group comprised of patients with colonic cancer, matched for sex and age. The median survival was 10 months for patients with disease localized to the pleura/pericardium and 7 months for those with distant metastases. Thirty-eight patients (54%) received chemotherapy. All had platinum-based chemotherapy, except for three patients. The median survival for patients treated or not treated with chemotherapy was 12 months and 5 months, respectively. This difference in survival was statistically significant (p = 0.003).

CONCLUSIONS

PIME should be viewed as a distinct entity. Its etiology remains largely unknown, although exposure to environmental tobacco smoke may play a part. Platinum-based chemotherapy may have a positive biological effect on this disease. More studies are required to elucidate the epidemiology, possible etiologic factors, and treatment options for this group of patients.

Project 2000--initial experiences

The need for adequate preparation in colleges of nursing for the introduction of Project 2000 courses, and the necessity for comprehensive and detailed forward planning, are emphasised in this article. The staff of St Mary's School of Nursing accept that some mistakes were made in their implementation arrangements, but the process was ultimately an extremely beneficial and rewarding one.

Lung immunoglobulins in the sudden infant death syndrome

The incidence of the sudden infant death syndrome parallels that of respiratory tract infections in the paediatric community. On the basis that the aetiology of the sudden infant death syndrome may lie in an unusual response to a trivial intercurrent respiratory infection a necropsy study was carried out investigating pulmonary immunoglobulins in 16 victims of the syndrome and a series of infants (controls) who had died of non-pulmonary causes. Compared with the controls victims of the sudden infant death syndrome had grossly raised concentrations of IgG, IgM, and to a less extent IgA in lung lavage samples. In addition, pulmonary interstitial and terminal airway cells expressing these immunoglobulins were identified far more often in victims than controls. The study failed to determine whether the increased immunoglobulin concentrations were a consequence of an unusual response to a trivial infection or an expression of otherwise altered immunological control in the respiratory tract. Epidemiological evidence and the findings of this study suggest that the respiratory tract is the prime target organ in the sudden infant death syndrome.

Immunoglobulin profile of tracheal aspirate fluid in intubated children

Pulmonary lavage immunoglobulins IgG, IgA and IgM were measured in intubated ventilated neonates during their period of intubation (range 1-64 days, mean 12). The neonates were divided into two groups based on gestational age (group 1 26-32 weeks, group 2 33-40 weeks). IgG levels were high at birth, and decreased exponentially throughout the period of intubation. There was no statistical difference in IgG levels between the two groups. IgA and IgM levels were low at birth, and increased linearly, there being a significantly greater increase with age in Group 2 (the more mature gestationally) for both immunoglobulins. Two groups of older children were also studied (2-4 year olds, and 8-10 year olds). In the 2-4 year age group, IgG levels were similar to those seen in the immediate newborn period, were quantitatively greater than IgA and IgM, and were not significantly different from levels in the 8-10 year olds. IgA and IgM levels were also not significantly different between the two groups.

Responses of 'mature' human B lymphocyte lines to inducers of maturation and activation

Four human B cell lines with a mature phenotype (immunoglobulin secretion and expression of membrane markers associated with maturation) were cultured in the presence of phorbol ester (PMA), dimethyl sulphoxide (DMSO) and two conditioned media. PMA and DMSO led to changes in phenotype which suggested the cells were being activated, whilst the conditioned media resulted in increased immunoglobulin secretion, accompanied by phenotypic changes more consistent with maturation towards the plasma cell stage. The four cell lines, which had different origins (EBV-transformed normal B cell, Burkitt's lymphoma, prolymphocytic leukaemia and multiple myeloma) responded differently to the culture stimuli. These differences suggest that the changes associated with transformation affect the way in which these cells respond to agents which stimulate activation and maturation.

Plasma prostaglandin F levels and malignant tumours of the female genital tract

Plasma prostaglandin F (PGF) was measured by a radioimmunoassay method in 24 subjects with tumours of the female genital tract. Levels in the tumour group ranged from 25 pg/ml to 134 pg/ml and were almost all greater than the values observed in a control group of 41 healthy women who had a mean (+/-SD) level of 21 (+/-3.4)pg/ml. There was a relationship between plasma PGF levels and the stage of the disease. Patients with resectable tumours showed a fall in PGF levels postoperatively and those with disseminated malignancy demonstrated increasing levels as the disease progressed. Plasma PGF may provide a clinical prognostic marker in the management of patients with malignant tumours.