Genome-Wide DNA Methylation Profiling as Frontline Diagnostics for Central Nervous System Embryonal Tumors in Hong Kong

This paper examines the link between CNS tumor biology and heterogeneity and the use of genome-wide DNA methylation profiling as a clinical diagnostic platform. CNS tumors are the most common solid tumors in children, and their prognosis remains poor. This study retrospectively analyzed pediatric patients with CNS embryonal tumors in Hong Kong between 1999 and 2017, using data from the territory-wide registry and available formalin-fixed paraffin-embedded tumor tissue. After processing archival tumor tissue via DNA extraction, quantification, and methylation profiling, the data were analyzed by using the web-based DKFZ classifier (Molecular Neuropathology (MNP) 2.0 v11b4) and t-SNE analysis. Methylation profiles were deemed informative in 85 samples. Epigenetic data allowed molecular subgrouping and confirmed diagnosis in 65 samples, verified histologic diagnosis in 8, and suggested an alternative diagnosis in 12. This study demonstrates the potential of DNA methylation profiling in characterizing pediatric CNS embryonal tumors in a large cohort from Hong Kong, which should enable regional and international collaboration in future pediatric neuro-oncology research.

Failure of human rhombic lip differentiation underlies medulloblastoma formation

Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal neoplasms of the hindbrain with strong links to early development of the hindbrain^1-4. Mutations that activate Sonic hedgehog signalling lead to Sonic hedgehog MB in the upper rhombic lip (RL) granule cell lineage^5-8. By contrast, mutations that activate WNT signalling lead to WNT MB in the lower RL^9,10. However, little is known about the more commonly occurring group 4 (G4) MB, which is thought to arise in the unipolar brush cell lineage^3,4. Here we demonstrate that somatic mutations that cause G4 MB converge on the core binding factor alpha (CBFA) complex and mutually exclusive alterations that affect CBFA2T2, CBFA2T3, PRDM6, UTX and OTX2. CBFA2T2 is expressed early in the progenitor cells of the cerebellar RL subventricular zone in Homo sapiens, and G4 MB transcriptionally resembles these progenitors but are stalled in developmental time. Knockdown of OTX2 in model systems relieves this differentiation blockade, which allows MB cells to spontaneously proceed along normal developmental differentiation trajectories. The specific nature of the split human RL, which is destined to generate most of the neurons in the human brain, and its high level of susceptible EOMES⁺KI67⁺ unipolar brush cell progenitor cells probably predisposes our species to the development of G4 MB.

Subgroup and subtype-specific outcomes in adult medulloblastoma

Medulloblastoma, a common pediatric malignant central nervous system tumour, represent a small proportion of brain tumours in adults. Previously it has been shown that in adults, Sonic Hedgehog (SHH)-activated tumours predominate, with Wingless-type (WNT) and Group 4 being less common, but molecular risk stratification remains a challenge. We performed an integrated analysis consisting of genome-wide methylation profiling, copy number profiling, somatic nucleotide variants and correlation of clinical variables across a cohort of 191 adult medulloblastoma cases identified through the Medulloblastoma Advanced Genomics International Consortium. We identified 30 WNT, 112 SHH, 6 Group 3, and 41 Group 4 tumours. Patients with SHH tumours were significantly older at diagnosis compared to other subgroups (p < 0.0001). Five-year progression-free survival (PFS) for WNT, SHH, Group 3, and Group 4 tumours was 64.4 (48.0-86.5), 61.9% (51.6-74.2), 80.0% (95% CI 51.6-100.0), and 44.9% (95% CI 28.6-70.7), respectively (p = 0.06). None of the clinical variables (age, sex, metastatic status, extent of resection, chemotherapy, radiotherapy) were associated with subgroup-specific PFS. Survival among patients with SHH tumours was significantly worse for cases with chromosome 3p loss (HR 2.9, 95% CI 1.1-7.6; p = 0.02), chromosome 10q loss (HR 4.6, 95% CI 2.3-9.4; p < 0.0001), chromosome 17p loss (HR 2.3, 95% CI 1.1-4.8; p = 0.02), and PTCH1 mutations (HR 2.6, 95% CI 1.1-6.2; p = 0.04). The prognostic significance of 3p loss and 10q loss persisted in multivariable regression models. For Group 4 tumours, chromosome 8 loss was strongly associated with improved survival, which was validated in a non-overlapping cohort (combined cohort HR 0.2, 95% CI 0.1-0.7; p = 0.007). Unlike in pediatric medulloblastoma, whole chromosome 11 loss in Group 4 and chromosome 14q loss in SHH was not associated with improved survival, where MYCN, GLI2 and MYC amplification were rare. In sum, we report unique subgroup-specific cytogenetic features of adult medulloblastoma, which are distinct from those in younger patients, and correlate with survival disparities. Our findings suggest that clinical trials that incorporate new strategies tailored to high-risk adult medulloblastoma patients are urgently needed.

OMIC-07. FEASIBILITY AND UTILITY OF EPIGENOMIC PROFILING FOR CHILDHOOD CNS TUMORS IN HONG KONG

Genome-wide DNA methylation profiling has emerged as an important diagnostic tool that complements histopathology for CNS tumors in children and adults. Literature describing its application in Asian countries is nonetheless limited. Herein, we report the feasibility and utility of adopting such platform for children diagnosed with CNS tumors in Hong Kong. A multi-institutional cohort (n=94, 97% of Chinese ethnicity) with CNS embryonal or high grade neuroepithelial tumors (HGNET) diagnosed in Hong Kong from 1996–2020 was assembled based on tissue availability. DNA was extracted from FFPE tumor material (median 301ng, range 13-1000ng), bisulfite converted and profiled with the Infinium Methylation EPIC BeadChip kit. Raw data were analyzed on the German Cancer Research Center MNP 2.0 classifier and through unsupervised dimensionality-reduction analysis (t-SNE) referencing a published CNS tumor reference dataset (GSE90496). The radio-histologic diagnosis included medulloblastoma (n=65), ATRT (n=9), pineal parenchymal tumors (n=7), ETMR (n=5), CNS-PNET (n=4) and other embryonal tumors/HGNETs (n=4). Methylation class could be assigned based on results from MNP 2.0 (calibrated score ≥ 0.9) in 62 patients (66%, including 2 clustering with control) and t-SNE in 22 (23%), while no-match was encountered in 10 (11%). Methylation-based analysis allowed confirmation of diagnosis and assignment of molecular subgroup in 64 patients (68%), confirmation of histologic diagnosis alone in 5 (5%) and resulted in revision/reassignment of diagnosis in 13 (14%). Among medulloblastoma samples that were assigned molecular tumor classes (n=57), 8 clustered with WNT-activated medulloblastoma, 13 with SHH-activated medulloblastoma, 10 with Group 3 medulloblastoma, 21 with Group 4 medulloblastoma, and 5 with non-medulloblastoma entities (high-grade gliomas=3, ETMR=1, ATRT=1). In conclusion, epigenomic profiling allowed refinement of disease classification for pediatric CNS tumors. Availability of such methodology in Asia sets the stage for international collaborations in molecularly-driven trials.

Clinical features and prognostic factors of Klebsiella endophthalmitis-10-year experience in an endemic region

AimsTo identify the clinical features and prognostic factors of endogenous endophthalmitis caused by Klebsiella pneumoniae.MethodsThis is a retrospective case series of all patients with Klebsiella endophthalmitis managed from January 2006 to December 2015 by Kowloon East Ophthalmic Service. Statistical analysis involved hypothesis testing on the SPSS 18.0 software (SPSS). A significance level of P<0.05 was taken.ResultsIn the 10-year period, K. pneumoniae accounted for 19 out of 39 cases of endogenous endophthalmitis (48.7%). The mean age of patients was 67.9 years. Bilateral involvement occurred in five patients (26.3%). More than half of the patients (10/19, 52.6%) had underlying diabetes mellitus. Most patients had concurrent liver abscess (18/19, 94.74%). Ten patients (52.6%) had disseminated intravascular coagulopathy. Eight patients (42.1%) were in shock. The overall mortality was 21.1% (4/19). Septic shock was associated with a significantly higher mortality (50.0 vs 0%, P=0.018). Among the 15 survivors, nine patients (60.0%) required evisceration and three patients (20.0%) had no light perception in an involved eye. Eyes with diffuse posterior involvement were less likely to have a final visual acuity of logMAR 0.30 or better than those with focal posterior involvement (4.76 vs 100% 4.76%, P=0.002). Patients with hypopyon were more likely to require evisceration (85.71 vs 25.00%, P=0.02).ConclusionsKlebsiella endophthalmitis is associated with a high incidence of diabetes mellitus and liver abscess. Prognosis remains poor. Universal ocular screening and systemic control in patients with Klebsiella sepsis are recommended.

Focal choroidal excavation-morphological features and clinical correlation

PurposeTo describe and correlate the morphological and clinical features of focal choroidal excavation (FCE).MethodsThis is a consecutive case series from the review of the 4436 optical coherence tomography scans performed by Kowloon East Cluster Ophthalmic Service from 1 August 2014-31 January 2016. Statistical analysis was performed on SPSS 18.0 (SPSS, Chicago, IL, USA). A significance level of P<0.05 was taken.ResultsAll 16 patients with FCE had unilateral involvement. The mean age of diagnosis was 52.56±14.00. The mean greatest linear dimension (GLD) of FCE was 636.25±265.11 μm. The mean choroidal thickness was 183.63±52.39 μm. Fourteen FCEs (87.5%) were conforming and two were non-conforming (12.5%). In the eyes with FCE, concurrent macular pathology was present in four cases (25.0%). Tractional pathologies of macular pucker and macular scar corresponded to the two non-conforming FCEs in the series. Polypoidal choroidal vasculopathy (PCV) and lacquer crack had a close topographic relationship with the FCE. The mean GLD was significantly larger in eyes with concurrent macular pathology than those without (878.00 vs 555.67 μm, P=0.029). In the fellow eyes, concurrent macular pathology was present in 5 cases (31.3%): PCV in 3 cases and chronic central serous chorioretinopathy in 2 cases.ConclusionAs a significant proportion of FCE is associated with concurrent macular pathology in the involved or fellow eye, angiography for both eyes is recommended even for asymptomatic cases. The GLD of FCE may have clinical value in risk stratification.

Overexpression of HMGA1 deregulates tumor growth via cdc25A and alters migration/invasion through a cdc25A-independent pathway in medulloblastoma

Overexpression of high mobility group AT-hook 1 (HMGA1) is common in human cancers. Little is known about the mechanisms underlying its deregulation and downstream targets, and information about its clinical and biological significance in medulloblastoma (MB) is lacking. Here, we demonstrated frequent genomic gain at 6p21.33-6p21.31 with copy number increase leading to overexpression of HMGA1 in MB. The overexpression correlated with a high proliferation index and poor prognosis. Moreover, we found that hsa-miR-124a targeted 3'UTR of HMGA1 and negatively modulated the expression in MB cells, indicating that loss/downregulation of hsa-miR-124a reported in our previous study could contribute to the overexpression. Regarding the biological significance of HMGA1, siRNA knockdown and ectopic expression studies revealed the crucial roles of HMGA1 in controlling MB cell growth and migration/invasion through modulation of apoptosis and formation of filopodia and stress fibers, respectively. Furthermore, we identified cdc25A as a target of HMGA1 and showed that physical interaction between HMGA1 and the cdc25A promoter is required for transcriptional upregulation. In clinical samples, HMGA1 and cdc25A were concordantly overexpressed. Functionally, cdc25A is involved in the HMGA1-mediated control of MB cell growth. Finally, netropsin, which competes with HMGA1 in DNA binding, reduced the expression of cdc25A by suppression of its promoter activity and inhibited in vitro and in vivo intracranial MB cell growth. In conclusion, our results delineate the mechanisms underlying the deregulation and reveal the functional significance of HMGA1 in controlling MB cell growth and migration/invasion. Importantly, the results highlight the therapeutic potential of targeting HMGA1 in MB patients.

Anticancer activity of a series of platinum complexes integrating demethylcantharidin with isomers of 1,2-diaminocyclohexane

A series of platinum complexes derived from integrating demethylcantharidin (DMC) with different isomers of 1,2-diaminocyclohexane (DACH) has been synthesized and found to exhibit superior in vitro anticancer activity against colorectal and human hepatocellular cancer cell lines when compared with oxaliplatin, cisplatin, and carboplatin. Flow cytometric analysis revealed that the trans-DACH-Pt-DMC analogues showed similar behavior to oxaliplatin on affecting the cell cycle of the HCT116 colorectal cancer cell line, but distinct from that of cisplatin or carboplatin. The DACH component apparently dictates the trans-DACH-Pt-DMC complexes to behave mechanistically similar to oxaliplatin, whereas the DMC ligand appears to enhance the compounds' overall anticancer activity, probably by accelerating the cell cycle from G1 to S-phase with subsequent onset of G2/M arrest and accompanying apoptosis.

Recurrent genomic aberrations in gastric carcinomas associated with Helicobacter pylori and Epstein-Barr virus

Helicobacter pylori and Epstein-Barr virus (EBV) both have been associated with gastric carcinoma. No specific genomic aberrations have been reported in association with these agents. We studied 20 cases of primary gastric carcinoma (including 11 positive for and 6 for EBV) by comparative genomic hybridization with validation of results by fluorescence in situ hybridization, loss of heterozygosity analysis, and immunohistochemistry. The results were analyzed in respect to presence or absence of and EBV. The tumors were also compared in terms of histologic type, tumor location, and lymph node metastases. The most frequently observed aberrations in the gastric carcinomas were gains of chromosome 19, 17, 1p, 11, 20q, and 22. The more common losses were found in 4q, 6q, 13q, and 15q. Gains in chromosome 19 and losses in 9p23-pter were found more commonly in cases with (P < 0.05). Gains in centromeric region of chromosome 19 were more common in the EBV-negative cases (P < 0.05). Immunohistochemical expression of and correlated with gains in the regions containing these genes. Gains in chromosome 11 and losses in 15q15 were more common in cases with EBV (P < 0.01 and P < 0.001, respectively). There was no significant association between any genomic aberration and histologic type, tumor location, or nodal metastases. and EBV are associated with different genomic imbalances, suggesting that these infectious agents exert different influences in the development of gastric carcinoma.

Activation of cyclin-dependent kinases CDC2 and CDK2 in hepatocellular carcinoma

BACKGROUND

The cyclin-dependent kinases (CDKs) CDC2 and CDK2 are key regulators of the cell cycle. The expression of the CDK alone does not necessary reflect their true activities because they are highly regulated by post-translational mechanisms. Human hepatocellular carcinoma (HCC) is one of the most common cancers in the world, but the kinase activities of CDKs in HCC have not been examined.

METHODS

Here we examined the protein expression and kinase activities associated with CDC2 and CDK2 in HCC and the corresponding non-tumorous liver tissues.

RESULTS

CDC2 and CDK2 are activated in HCC in over 70% and 80% of the cases, respectively, but have little correlation with clinical parameters and PCNA expression. Interestingly, PCNA was readily detectable in extracts from non-tumorous liver, but more than 60% of samples contain higher concentration of PCNA in HCC than the corresponding non-tumorous tissues. CDC2 and CDK2 are generally activated in the same HCC samples, but the extent of their activation varied significantly, suggesting that the pathways leading to the activation of CDC2 and CDK2 can be regulated independently. Both positive regulators of CDK activity like cyclins and CDKs, and negative regulators of CDK activity like p21(CIP1/WAF1) and Thr14/Tyr15 phosphorylation were up-regulated in HCC.

CONCLUSION

CDC2 and CDK2 are activated in HCC, and this may be due to a complex interplay between the level of the cyclin, CDK, CDK inhibitors, and inhibitory phosphorylation.