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  • 1
    In: Blood Cancer Journal, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2020-01-27)
    Type of Medium: Online Resource
    ISSN: 2044-5385
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2600560-8
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  • 2
    In: Leukemia, Springer Science and Business Media LLC, Vol. 35, No. 4 ( 2021-04), p. 1225-1225
    Type of Medium: Online Resource
    ISSN: 0887-6924 , 1476-5551
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2008023-2
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  • 3
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 4111-4111
    Abstract: Background Hodgkin lymphoma (HL) accounts for 15% of all cancer diagnosis in young adults. Standard of care is ABVD (Adriamycin, Bleomycin, Vinblastine, Dacarbazine), which has resulted in overall cures of 70-90%. In the setting of HL, bleomycin is still one of the cornerstones in its treatment with the omission of bleomycin in the randomized trial of GHSG HD13 showing poorer outcomes. A major complication of HL treatment is Bleomycin induced pneumonitis (BIP) occurring in 0.4-28% of patients, with up to 10% mortality. Currently, we are unable to predict which patients are more prone. Given that human genomic variations underlie both disease susceptibility and drug response, uncovering genetic biomarkers predisposing to BIP is imperative to predicting and preventing BIP. Methods In this first pharmacogenomics study of BIP in South-East Asian patients, we perform both candidate gene and GWAS analyses. 96 HL patients were recruited from the National University Cancer Institute, Singapore (NCIS). BIP was clinically characterized and graded by CTCAEv4. Genetic association analysis was performed by regression (additive model) accounting for non-genetic predictor variables. Results Age at the start of bleomycin treatment, sex, genetic ancestry, concomitant chemotherapy treatment, treatment with G-CSF, stage of HL disease, pretreatment creatinine clearance, weight, chest irradiation and smoking history did not differ significantly between patients with and without BIP. The total number of treatment cycles (P=0.006) , cumulative exposure (P=0.01) and total exposure (P=0.028) were significantly lower in the BIP group as Bleomycin was omitted from further chemotherapy regimens once BIP was diagnosed. We independently replicated the association of HFE rs1799945 (H63D) with BIP (Cases: 15.38% vs Controls: 1.72%, P=0.0069, OR(95%CI)=2.89 (1.88-88.59)), while BLMH rs1050565 was not associated with BIP (P=0.92, OR(95%CI)=1.07 (0.29-3.93)). H63D carriers have 12.44 (1.98-78.17) times the odds of developing BIP compared to non-carriers (P=0.0088). We uncover a significant association of H63D with the severity of BIP (P=0.00087). HIST1H1T rs198846, a downstream variant in LD with H63D was also associated with BIP and its severity. H63D was predicted to be highly pathogenic (CADD Score=24.40) and at the top 1% of the most deleterious mutations in the human genome. The GWAS uncovered 4 novel genetic biomarkers with suggestive evidence of association with BIP (Unknown locus on Chr 17, MRC2 rs8072984, TMEM260 rs1124062 and KIF26B rs12747330). MRC2 rs8072984 is involved with remodeling of extracellular matrix, and defects in this could cause poor lung remodeling after bleomycin insult. TMEM260 rs1124062 and KIF26B rs12747330 are both involved with renal anomalies and development suggesting that defects in these could affect bleomycin clearance. Conclusion This is the first pharmacogenomics study of BIP in South East Asian patients, looking at both candidate gene and GWAS analyses. Our results suggest that iron regulation could be the driver in the etiopathogenesis of BIP, supporting the utility of H63D testing in the risk stratification of patients receiving Bleomycin. Moreover, GWAS analyses have discovered 4 novel markers that suggest an association with BIP, which will be further evaluated and should be independently replicated in a larger cohort. Disclosures Chng: Celgene: Consultancy, Honoraria, Other: Travel, accommodation, expenses, Research Funding; Takeda: Consultancy, Honoraria, Other: Travel, accommodation, expenses; Janssen: Consultancy, Honoraria, Other: Travel, accommodation, expenses, Research Funding; Merck: Research Funding; Amgen: Consultancy, Honoraria, Other: Travel, accommodation, expenses; Aslan: Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 4
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 2915-2915
    Abstract: The genetic landscape of Natural killer/T-cell nasal-type lymphoma (NKTL) has been recently unraveled by discoveries describing recurring mutations altering the JAK-STAT pathway, epigenetic modifiers, the DDX3X gene and genetic predisposition in the HLA-DPB1 gene but none has employed whole-genome sequencing (WGS). Whole-genome sequencing was performed for 11 pairs of tumor-blood samples to study the association between somatic mutations and response to pembrolizumab. Interestingly, recurrent PD-L1 SRs were validated in four of the seven complete responders (CR) cases. JAK3-activating (p.A573V) mutations were also validated in another two pembrolizumab-treated patients who have achieved CR. Lastly, we also found a homozygous 3 bp insertion (p.Q131_H132insQ) in the ARID1B gene, a chromatin remodeler gene and a subunit in the SWI/SNF complex in the last remaining CR case. A recent study has also reported PBRM1-deficient and ARID2-deficient tumors correlated with better response to anti-PD1/PD-L1 therapy renal cell carcinoma. There seems to be a relationship between truncating alterations in the subunits of the SWI/SNF complex and response to PD1/PD-L1 therapy. However, the exact mechanisms behind these associations remain to be elucidated for NKTL. Analysis of the WGS data from the four remaining progressive disease (PD) patients' tumors did not reveal similar alterations in the PD-L1 and JAK3 genes. A careful inspection was also carried out on the genes associated with major histocompatibility complex and interferon gamma pathways, which are known to associate with resistance to immune checkpoint blockade in melanoma, but no further mutation in these groups of genes was found in our cohort. Furthermore, a TP53 (p.W14X) stop-gain mutation, a hallmark tumor suppressor gene, was detected in a patient who had progressive disease after given pembrolizumab. We went on to check if PD-L1 IHC staining could explain the response of these NKTL patients to pembrolizumab. In this study, tumors were stained and assessed for PD-L1 positivity by the same pathologist. All cases, except two cases, have greater than 20% of tumor cells stained positive for PD-L1. Interesting, both cases are CR. In addition, all four PD cases were strongly stained for PD-L1 with an average of 69% PD-L1 positive cells (range, 50% - 90%) but their outcomes were dismal. This suggests that there could be a companion biomarker that could be added to PD-L1 IHC positivity for better predictive power of response to PD1 blockade therapy. Here we report retrospectively, for the first time, the genomic mutational profiles of anti-PD1 blockade in 11 relapsed/refractory NKTL patients using WGS data, which provide proof-of-concept data that the response to anti-PD1 is relevant and correlates with recurrent PD-L1 and JAK3 genomic alterations in this malignancy. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 5
    In: Cancer Discovery, American Association for Cancer Research (AACR), Vol. 13, No. 5 ( 2023-05-04), p. 1144-1163
    Abstract: Cancers often overexpress multiple clinically relevant oncogenes, but it is not known if combinations of oncogenes in cellular subpopulations within a cancer influence clinical outcomes. Using quantitative multispectral imaging of the prognostically relevant oncogenes MYC, BCL2, and BCL6 in diffuse large B-cell lymphoma (DLBCL), we show that the percentage of cells with a unique combination MYC+BCL2+BCL6− (M+2+6−) consistently predicts survival across four independent cohorts (n = 449), an effect not observed with other combinations including M+2+6+. We show that the M+2+6− percentage can be mathematically derived from quantitative measurements of the individual oncogenes and correlates with survival in IHC (n = 316) and gene expression (n = 2,521) datasets. Comparative bulk/single-cell transcriptomic analyses of DLBCL samples and MYC/BCL2/BCL6-transformed primary B cells identify molecular features, including cyclin D2 and PI3K/AKT as candidate regulators of M+2+6− unfavorable biology. Similar analyses evaluating oncogenic combinations at single-cell resolution in other cancers may facilitate an understanding of cancer evolution and therapy resistance. Significance: Using single-cell–resolved multiplexed imaging, we show that selected subpopulations of cells expressing specific combinations of oncogenes influence clinical outcomes in lymphoma. We describe a probabilistic metric for the estimation of cellular oncogenic coexpression from IHC or bulk transcriptomes, with possible implications for prognostication and therapeutic target discovery in cancer. This article is highlighted in the In This Issue feature, p. 1027
    Type of Medium: Online Resource
    ISSN: 2159-8274 , 2159-8290
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
    detail.hit.zdb_id: 2607892-2
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 5557-5557
    Abstract: Background: Cancers often overexpress multiple clinically relevant oncogenes. However, it is not known if multiple oncogenes within a cancer combineuniquely in specific cellular sub-populations to influence clinical outcome.We studied this phenomenon using the prognostically relevantoncogenes MYC, BCL2 and BCL6 in Diffuse Large B-Cell Lymphoma(DLBCL). Methods: Quantitative multispectral imaging simultaneously measured oncogene co-expression at single-cell resolution in reactive lymphoid tissue (n=12)and four independent cohorts (n=409) of DLBCL. Mathematically derived co-expression phenotypes were evaluated in DLBCLs with immunohistochemistry (n=316) and nine DLBCL cohorts with gene expression data (n=3974). Bulk and single-cell RNA sequencing was performed on patient-derived B-cells with induced co-expression of MYC,BCL2 and BCL6. Results: Unlike in non-malignant lymphoid tissue where the co-expression of MYC, BCL2 and BCL6 in a B-cell is limited, DLBCLs show multiple permutations of oncogenic co-expression in malignant B-cells. The percentage of cells with a unique combination MYC+BCL2+BCL6-(M+2+6-) consistently predicts survival in contrast to that of other combinations (including M+2+6+). An estimated percentage of M+2+6-cells can be derived from any quantitative measurement of the component individual oncogenes, and correlates with survival in immunohistochemistry and gene expression datasets. Comparative transcriptomic analysis of DLBCLs and transformed patient-derived B-cells identifies cyclin D2 (CCND2) as a potential BCL6-repressedregulator of proliferation in the M+2+6- population. Conclusions: Unique patterns of oncogene co-expression at single-cell resolution affect clinical outcomes in DLBCL. Similar analyses evaluating oncogenic combinations at the cellular level may impact diagnostics and target discovery in other cancers. Citation Format: Michal M. Hoppe, Patrick Jaynes, Shuangyi Fan, Yanfen Peng, Shruti Sridhar, Phuong Mai Hoang, Xin Liu, Sanjay de Mel, Limei Poon, Esther Chan, Joanne Lee, Choon Kiat Ong, Tiffany Tang, Soon Thye Lim, Chandramouli Nagarajan, Nicholas F. Grigoropoulos, Soo-Yong Tan, Susan Swee-Shan Hue, Sheng-Tsung Chang, Shih-Sung Chuang, Shaoying Li, Joseph D. Khoury, Hyungwon Choi, Pedro Farinha, Anja Mottok, David W. Scott, Carl Harris, Alessia Bottos, Gayatri Kumar, Kasthuri Kannan, Laura J. Gay, Hendrik F. Runge, Ilias Moutsopoulos, Irina Mohorianu, Daniel J. Hodson, Yen-Chee Lin, Wee-Joo Chng, Siok-Bian Ng, Claudio Tripodo, Anand D. Jeyasekharan. Patterns of oncogene co-expression at single cell resolution influence survival in diffuse large B-cell lymphoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5557.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 7
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 2949-2949
    Abstract: Monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL) is a type of rare aggressive lymphoma accounting for 5.4% of primary intestinal peripheral T-cell lymphoma and 10-25% of all primary intestinal lymphoma. MEITL also has an extremely poor prognosis with the median overall survival of only seven months. No effective treatment or targeted therapies are currently available to manage this disease. Therefore, there is an urgent need to devise and establish an appropriate preclinical model for a better understanding of this disease and for new therapeutic strategies to be developed on it. Here, we present the first MEITL patient derived xenograft (PDX) as both orthotropic intestinal and as a subcutaneous model. The histological analysis demonstrated high similarity in the overall immunomorphologic features between the primary tumour and PDX tumours. Importantly, all the PDX tumors carried the distinctive MEITL immunophenotype; CD3+CD4-CD8+CD56+ and extensive nuclear expression of MATK. We also had Sanger sequenced 83 somatic mutations in the original tumour and rediscovered them in the 6th passage of our xenografts, which suggest that the generated MEITL PDX tumours were genetically stable. Moreover, whole exome sequencing results showed that the clonal architecture in the primary tumour was well preserved in the PDX tumours. The clonal architecture was further analysed with single cell whole genome amplification following by Sanger sequencing. We found that the most of heterozygous mutations in the primary tumour were a mixture of wild type alleles and heterozygous/homozygous mutations from separated clones, including DUPS14 heterozygous mutation (p.R300W) which was known to activate MEK pathway, and SETD2 mutations, (g.chr3:47061285_ 47061286insA and g.chr3:47127805C & gt;A) which were the synthetic lethal partner of Wee1. Interestingly, we found that the two SETD2 mutations alone were able to differentiate three subclones. This result indicates that the tumour was highly subclonal, which could have a strong impact on the selection of drug resistant clones in the drug treatment. In order to verify this hypothesis, we proceeded to test the efficacy of MEK inhibitor, Trametinib and Wee1 inhibitor, AZD1775 both separately and combined treatment, in our PDX subcutaneous model. The results showed that both 1mg/kg/day of Trametinib and 60mg/kg/day of AZD1775 treatments significantly delayed 60-70% of tumour growth as compared with the vehicle group. The tumour growth was completely arrested in the combined treatment group. In addition, 20% and 40% of the mice exhibited Trametinib and AZD1775 resistance, respectively. From our genomic analysis, all DUPS14 and SETD2 mutations from the pretreated tumours were preserved in the treatment-resistant tumours but absent in the sensitive post-treated residual tumours. The clonality analysis from the sequencing data of the pretreated tumour supports and suggests that single-agent regimes will often not be able to induce a complete response in MEITL patients. Altogether, the current results demonstrated that our MEITL PDX model preserved the principal histological and genetic characteristics of its original tumour and is genomic stable across passages. The model also showed that MEITL could be highly subclonal and combined targeted therapy might achieve a higher efficacy for MEITL treatment. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 8
    In: American Journal of Hematology, Wiley, Vol. 97, No. 9 ( 2022-09), p. 1159-1169
    Abstract: With lowering costs of sequencing and genetic profiling techniques, genetic drivers can now be detected readily in tumors but current prognostic models for Natural‐killer/T cell lymphoma (NKTCL) have yet to fully leverage on them for prognosticating patients. Here, we used next‐generation sequencing to sequence 260 NKTCL tumors, and trained a genomic prognostic model (GPM) with the genomic mutations and survival data from this retrospective cohort of patients using LASSO Cox regression. The GPM is defined by the mutational status of 13 prognostic genes and is weakly correlated with the risk‐features in International Prognostic Index (IPI), Prognostic Index for Natural‐Killer cell lymphoma (PINK), and PINK‐Epstein–Barr virus (PINK‐E). Cox‐proportional hazard multivariate regression also showed that the new GPM is independent and significant for both progression‐free survival (PFS, HR: 3.73, 95% CI 2.07–6.73; p   〈  .001) and overall survival (OS, HR: 5.23, 95% CI 2.57–10.65; p  = .001) with known risk‐features of these indices. When we assign an additional risk‐score to samples, which are mutant for the GPM, the Harrell's C‐indices of GPM‐augmented IPI, PINK, and PINK‐E improved significantly ( p   〈  .001, χ 2 test) for both PFS and OS. Thus, we report on how genomic mutational information could steer toward better prognostication of NKTCL patients.
    Type of Medium: Online Resource
    ISSN: 0361-8609 , 1096-8652
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 1492749-4
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  • 9
    In: Blood Cancer Discovery, American Association for Cancer Research (AACR), Vol. 1, No. 3_Supplement ( 2020-11-01), p. PO-35-PO-35
    Abstract: MYC, BCL2, and BCL6 are commonly used markers for immunohistochemistry of Diffuse large B-cell lymphomas (DLBCL). Coexpression of MYC and BCL2 in particular constitutes a subgroup of “double expressor lymphomas” (DEL) with a distinct poor clinical outcome. However, it is not known if MYC and BCL2/BCL6 coexpression occurs in the same cell or in different cells within the tumor, as traditional immunohistochemistry (IHC) is limited by the number of markers that can be simultaneously assessed within formalin-fixed, paraffin-embedded (FFPE) samples. We set out to discover the clinical significance of MYC, BCL2, and BCL6 colocalization at single-cell resolution using multiplexed quantitative immunofluorescence (qIF) based on sequential OPAL-TSA staining and spectral microscopy on the Vectra platform. The initial discovery cohort comprised 90 cases of DLBCL from NUH Singapore with adequate clinical follow-up after R-CHOP therapy. We stratified each DLBCL tumor into 8 “clonal fractions” based on the possible permutations of MYC (M), BCL2 (2), and BCL6 (6) colocalization: M+2+6+, M+2+6-, M+2-6+, M+2-6-, M-2+6+, M-2-6+, M-2+6-, and M-2-6-. Interestingly, even within cases that fit traditional IHC criteria for “positivity” of MYC, BCL2, and BCL6, only a subset of cells within each case expressed multiple markers concurrently. Using the fraction of each of these clones as a continuous variable, Cox regression analysis revealed that the percentage of M+2+6- cells in a case was most predictive of poor survival. Importantly, the same clonal fraction (M+2+6-) was a significant poor prognostic feature in 2 smaller validation cohorts from SGH Singapore (n=41) and MD Anderson Cancer Centre USA (n=36). The single-cell staining pattern of these markers revealed a stark contrast between healthy tonsil tissue and DLBCL tissue. In the tonsil, colocalization of each marker was nonrandom (mutually exclusive BCL2 positivity in B cells outside the germinal center and BCL6 positivity inside the germinal center), whereas in DLBCL samples the mutual exclusivity pattern noted in the tonsil was lost, leading to a random distribution of colocalization of MYC, BCL2, and BCL6. The random nature of this colocalization allowed us to mathematically predict the “extent” of these 8 subclones from any data set with quantitative data of each single marker (MYC, BCL2, and BCL6). We therefore attempted to evaluate this model in RNA expression datasets of DLBCL cases with clinically annotated data. Remarkably, in concordance with our IF data, the “predicted” M+2+ 6- subgroup consistently was associated with an unfavorable prognosis in 3 independent mRNA datasets (GSE10846 n=233, GSE117556 n=469, GSE32918 n=140). In summary, we have for the first time assessed the expression of MYC, BCL2, and BCL6 at the single-cell level in DLBCL. These results may explain the apparent protective function of BCL6 expression in prior cohort studies of DEL, and provide a quantitative tool for the identification of DLBCL cases with poor survival on R-CHOP. Citation Format: Michal Hoppe, Shuangyi Fan, Patrick Jaynes, Phuong Mai Hoang, Liu Xin, Sanjay De Mel, Li Mei Poon, Esther Chan, Joanne Lee, Yen Lin Chee, Choon Kiat Ong, Tiffany Tang, Soon Thye Lim, Nicholas Francis Grigoropoulos, Sheng-Tsung Chang, Shih-Sung Chuang, Joseph Khoury, Hyungwon Choi, Wee Joo Chng, Siok-Bian Ng, Claudio Tripodo, Anand D. Jeyasekharan. Prognostic significance of MYC, BCL2, and BCL6 colocalization at single-cell resolution in DLBCL [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-35.
    Type of Medium: Online Resource
    ISSN: 2643-3230 , 2643-3249
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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  • 10
    In: The Lancet Oncology, Elsevier BV, Vol. 21, No. 2 ( 2020-02), p. 306-316
    Type of Medium: Online Resource
    ISSN: 1470-2045
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2020
    detail.hit.zdb_id: 2049730-1
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