GRC NPC – Lo, KW

Leave a Comment / By /


2018 GRC NPC

  • [NPC tumorigenesis model]
  • WES-seq of 111 NPC patient Nat Commun 18: 14121, 2017
  • LCM enrichment of tumor cells. -> higher somatic mutation than the Singapore study (because of LCM?)
  • LMP1 activates both canonical and non-canonical NFKB pathways
  • Homozygous deletion f BIRC2(cIAP) and BIRC3(cIAP2) in primary NPC
  • Identification of a novel 12p13.3 amplicon in NPC
  • Cancer 2017 -May Hayek M, Issaeva N et al
  • TRAF3/CYLD mutations identify a distinct subset of HPVC associated HNSCC
  • TRAF3/CYLD/TRAF3
  • Development of sub lines with logistics of MHC Class I expression
  • Resistant to immunmotherapy?
  • Somatic genetic changes in a paired primary and recurrent NPC tumors
  • TLR3/IRF3/IRF7 —> NFKB
  • Catalogue of genetic alterations in NPC cell lines and PDXs
  • C15 LMP1 overexpression —> coupled wiht no NFKB mutation
  • NFKB addiction f EBV-positive NPC
  • KO of BCL3, p50 and
    • BCL-3
    • PI3K/MAPK activator mutations associated with poor outcome in patients with recurrent or metastatic tumors
    • ARID1A mutation is rare in this cohort



2016 GRC NPC

Kwok-Wai Lo (The Chinese University of Hong Kong, Hong Kong SAR China) “NPC Genetics: Progressive Genomic Changes” 羅國煒 (https://goo.gl/gdha6A)

  1. Undifferentiated NP cells abundantly infiltrated with immune cells
  2. Loss of chromosome 3p is a common event in NPC
  3. Ch 9p21 (p16/CDKN2A) deletion is an early event in NPC development in > 95% of EBV +ve NPC
  4. All EBV +ve gastric cancers are with p16 hypermethylation
  5. Singapore Nat Gene paper: WES 56 NPC normal/tumor pairs + capture-seq of 66 NPC samples. Results: low mutation rate and wide mutational diversity
  6. Lo’s group: WES (111/111) and WGS (15/111) of micro-dissected EBV +ve NPC tissues (> 95% non-keratinizing cells; 78 primary, 11 local, 22 distant meta mostly from lung and liver; mean age 45-yr old)
  7. By using NMF algorithm, identifying: (1) deamination of 5-methylcytosine process (2) defective DNA mismatch repair (3) high mutation load is associated with poor outcome
  8. Loss of 3p, 14q, gain of 12p, 16q
  9. High LMP1 vs low LMP1 (CYLD matters, somatic alterations of CYLD and TRAF3)
  10. Somatic gene alterations in NF-KB pathways in NPC cell lines/PDXs
  11. Xeno-2117 BCL3, p50 & RelB by siRNAs inhibit in vitro growth of EBV+ve NPC cells (local inflammatory, NF-KB involved pathway in NPC tissues was referred in their previous paper: Cheng et al., J Pathol (Chung et al., J Pathol, 2013)
  12. EBV oncoprotein LMP1 → activates NF-KB signaling pathway; nonetheless, only 30-40% primary NPC express LMP1 and even fewer NPC cell lines express LMP1 (eg C15)
  13. Mutually exclusivity between LMP1 (~30%) and NF-KB (~30%), the remaining are still mysterious
  14. NPC 後期, mutation load 多時 (may due to mutation of downstream genes CYLD, TRAF), LMP1表現量降低
  15. He cited a review paper at the end, talking about heterogeneity (Alizadeh et al., Nat Med, 2015)
From Ming-Han


NPC overall:
  • 100% EBV+
  • HEAVILY INFILTRATED with lymphocytes
  • Loss of Chr3p is a common event of NPC (nearly 100% cases): LOH in 40% and highly methylated in 40%
  • Loss of 9p21 (P16 and P14) is an early event in NPC development (Chan et al, 2002; Lun et al, 2012)
  • p16 inactivation and cyclin D1 oeverexpression in > 95% NPC cases.
  • ALL EBVaGC are p16 hypermethylation.
  • @@@@@EBV can only exist in hTERT+ cell line with KO p16 or over expression of cyclin D1; or the cell will not grow or loss EBV.
  • NPC associated pathways? (1) ERBB-PI3K pathway (if activated; survival less than 40; if at low level; survival > 80%)
  • Chromatin modification pathways.
Experiment:
Whole genome exome sequencing of 105 EBV+ NPC
Method: 
use micro dissection specifically cut off tumor regions from paraffins and send for sequencing
Samples: 
78 original tumor; 11 recurrent tumours at the same site; 28 metastasis tumours -> further separated into high survival or low survival.
Results:
  1. Microssection gets overall much higher mutation rates than the previous study (by whole tumor mass)
  2. Deamination of 5-methyl-cytosine process, by error mismatch DNA repair.  (SF: 這不是和Kenney 新PNAS 相呼應? pdf 4557)
  3. TP53 mutation ONLY in 9.5 cases (15% in recurrent and 6.4% in original tumor) overall is low.
  4. PI3K/MAPK pathway: higher mutated in recurrent tumours but low in original tumor. If have PI3K/MAPK mutations then survival is less than 5%. If without mutation survival rate is > 80%.
  5. Chromatin remodeling genes (found in 38/105 cases): ARID1A, ARID2, KMT2D, KMT2C, EP300.
  6. Comparing ORIGINAL TUMOR AND RECURRENT TUMORS:
  7. Primary tumor: LMP1 hi, SKY mut (?), loss chr 3p, 14q, 16q.
  8. Recurrent tumor: LMP1 low, SYKmut(?), further lost 12p.
  9. CYLD: (LOH) in NPC 18.6%
  10. 1TRAF3 (LOH) in NPC around 10% (Note: most of LMP1low cases need to have either CYLD or TRAF3 mutant)
  11. NFKB1A: in come cases.
  12. NFkB constitutive activation seems required for NPC (note: TRAF3 and CYLD and LMP1 all involved in NFKB) (Chung et at. J: pathol 2013) If KD NFKB pathway can reduce C666 xenograft in mice. (only p65/RelA kd is not enough; BCL3, p105/p50, RelB also)?
  13. G6 dendrimer + Bcl3 siRNA: cause C666 no tumor or extremely small in xenograft. (G6 dendrimer is a way to elevate siRNA effect?)
  14. Downstream of NFkB involved in many pathways (cytokines, chemokinesm TF factors, antiapoptosis, signal pathways)
  15. BamHIA transcript is very high in NPC cell lines; LMP1 is actually not very high; only cell line C15 is high.
  16. LMP1 is important but only 30% cases of NPC have high level of LMP1. Importantly the in vitro NPC culture cell line only C15 have LMP1 detecting level. Perhaps the downstream already mutated (i.e.; CYLD, TRAF3..)
  17. High level of LMP1 with lower survival rate. But in the cases of LMP1 low tumor; they ALWAYS HAVE EITHER CYLD or TRAF3 mutation!!
  18. J Pathol. 2013 Nov;231(3):311-22.  http://www.ncbi.nlm.nih.gov/pubmed/23868181#
Summary of NPC and GC
EBV+ NPC EBV+ GC
Histology Squamous carcinoma, LELC Adenocarcinoma
Lymphoid infiltration Highly infiltration Moderate
P53 mut 9% rare
LMP1 expression 30-80% rare
Alter NFKB >40% rare
PI3K/PTEN mutation 4-5% >70%
ARID1A inactivating mutation rare 55%
CDKN2A inactivation (p16) 90% 100%
Epigenome global hypermethylation global hypermethylation

EBV Meeting Session 10:
Whole exome and genome sequencing identifies frequent NF-kappaB pathway activating mutations in EBV-associated nasopharyngeal carcinoma.
Kwok-Wai Lo, The Chinese University of Hong Kong, China


    Leave a Comment

    Scroll to Top