scholarly journals Survival-Critical Genes Associated with Copy Number Alterations in Lung Adenocarcinoma

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2586
Author(s):  
Chinthalapally V. Rao ◽  
Chao Xu ◽  
Mudassir Farooqui ◽  
Yuting Zhang ◽  
Adam S. Asch ◽  
...  

Chromosome Instability (CIN) in tumors affects carcinogenesis, drug resistance, and recurrence/prognosis. Thus, it has a high impact on outcomes in clinic. However, how CIN occurs in human tumors remains elusive. Although cells with CIN (i.e., pre/early cancer cells) are proposed to be removed by apoptosis and/or a surveillance mechanism, this surveillance mechanism is poorly understood. Here we employed a novel data-mining strategy (Gene Expression to Copy Number Alterations [CNA]; “GE-CNA”) to comprehensively identify 1578 genes that associate with CIN, indicated by genomic CNA as its surrogate marker, in human lung adenocarcinoma. We found that (a) amplification/insertion CNA is facilitated by over-expressions of DNA replication stressor and suppressed by a broad range of immune cells (T-, B-, NK-cells, leukocytes), and (b) deletion CNA is facilitated by over-expressions of mitotic regulator genes and suppressed predominantly by leukocytes guided by leukocyte extravasation signaling. Among the 39 CNA- and survival-associated genes, the purine metabolism (PPAT, PAICS), immune-regulating CD4-LCK-MEC2C and CCL14-CCR1 axes, and ALOX5 emerged as survival-critical pathways. These findings revealed a broad role of the immune system in suppressing CIN/CNA and cancer development in lung, and identified components representing potential targets for future chemotherapy, chemoprevention, and immunomodulation approaches for lung adenocarcinoma.

2017 ◽  
Vol 114 (40) ◽  
pp. 10743-10748 ◽  
Author(s):  
Tali Mazor ◽  
Charles Chesnelong ◽  
Aleksandr Pankov ◽  
Llewellyn E. Jalbert ◽  
Chibo Hong ◽  
...  

IDH1 mutation is the earliest genetic alteration in low-grade gliomas (LGGs), but its role in tumor recurrence is unclear. Mutant IDH1 drives overproduction of the oncometabolite d-2-hydroxyglutarate (2HG) and a CpG island (CGI) hypermethylation phenotype (G-CIMP). To investigate the role of mutant IDH1 at recurrence, we performed a longitudinal analysis of 50 IDH1 mutant LGGs. We discovered six cases with copy number alterations (CNAs) at the IDH1 locus at recurrence. Deletion or amplification of IDH1 was followed by clonal expansion and recurrence at a higher grade. Successful cultures derived from IDH1 mutant, but not IDH1 wild type, gliomas systematically deleted IDH1 in vitro and in vivo, further suggestive of selection against the heterozygous mutant state as tumors progress. Tumors and cultures with IDH1 CNA had decreased 2HG, maintenance of G-CIMP, and DNA methylation reprogramming outside CGI. Thus, while IDH1 mutation initiates gliomagenesis, in some patients mutant IDH1 and 2HG are not required for later clonal expansions.


Pathology ◽  
2014 ◽  
Vol 46 (1) ◽  
pp. 32-36
Author(s):  
Prudence A. Russell ◽  
Y.U. Yong ◽  
D.O. Hongdo ◽  
Timothy D. Clay ◽  
Melissa M. Moore ◽  
...  

2021 ◽  
Vol 23 (Supplement_1) ◽  
pp. i40-i40
Author(s):  
Sharon Freshour ◽  
Bryan Fisk ◽  
Christopher Miller ◽  
Obi Griffith ◽  
Malachi Griffith ◽  
...  

Abstract Brain and central nervous system tumors are the most common form of solid tumor cancers and the second most common cancer overall among children. While many advances have been made in understanding the genomics of childhood brain tumors in recent years, the role of copy number alterations (CNAs) has not been fully characterized. Although the genomes of childhood brain tumor patients are generally considered to be relatively stable diploid genomes, analysis of a subset of pretreatment diagnostic samples from a cohort of 84 deceased patients from Washington University revealed widespread alterations, suggesting CNAs may play a larger role in the progression and prognosis of childhood brain tumors than originally thought. Follow up analysis of the entire cohort, containing a variety of tumor types that had low-pass whole genome sequencing performed, similarly showed evidence of CNAs across samples. 75 out 84 patients showed the presence of CNAs with an average of 16% of the genome being altered per sample and a median of 7%. Preliminary results examining correlations between the percentage of the genome that was copy number altered and event free survival or overall survival indicated that CNA percentage may have some prognostic value. For example, ependymoma samples showed positive correlation between alteration percentage and overall survival, while glioblastoma samples showed negative correlation. To explore copy number alteration in a larger cohort and increase statistical power, similar analyses are being performed using an additional 950 samples from the Pediatric Brain Tumor Atlas curated by The Children’s Brain Tumor Network (CBTN) to determine if CNVs and CNV percentage or specific alterations can serve as prognostic markers and whether the biology of this genomic instability could inform therapeutic strategy.


2012 ◽  
Vol 72 (2 Supplement) ◽  
pp. A26-A26
Author(s):  
Greg L. Stewart ◽  
Katey SS Enfield ◽  
Stephen Lam ◽  
Wan Lam

2007 ◽  
Vol 25 (16) ◽  
pp. 2164-2170 ◽  
Author(s):  
Stephane Temam ◽  
Hidetoshi Kawaguchi ◽  
Adel K. El-Naggar ◽  
Jaroslav Jelinek ◽  
Hongli Tang ◽  
...  

Purpose Overexpression of epidermal growth factor receptor (EGFR) is common in head and neck squamous cell carcinoma (HNSCC). Recent studies showed that EGFR inhibitors are effective for patients with HNSCC. This study analyzed the genetic nature of EGFR gene in HNSCC and its clinical correlations. Patients and Methods The EGFR gene copy numbers in 134 HNSCC tumors were determined using quantitative real-time polymerase chain reaction. The status of EGFR gene copy numbers was analyzed with clinical parameters including clinical outcome. Mutation status of EGFR exons 18, 19, and 21 was determined in the HNSCC tumors. Results Aberrant EGFR copy numbers were found in 32 (24%) of 134 tumors, including 22 (17%) with increased copy number and 10 (7%) with decreased copy number. Patients whose tumors had EGFR copy number alterations (particularly patients with increased copy numbers) had significantly poorer overall, cancer-specific, and disease-free survivals compared with patients with normal copy numbers (P < .0001). At 5 years after initial diagnosis, 20 (91%) of the 22 patients with increased copy numbers died of disease compared with 30 (29%) of the 102 patients with normal copy number. No mutations on EGFR exons 18, 19, and 21 were detected in any of the tumors. Conclusion A subset of HNSCC manifests EGFR copy number alterations, and this is associated with a poor clinical outcome, suggesting a biologic role of the alterations. The rare mutation or small deletion at EGFR exons 18 to 21 indicates a minimal role of these events in HNSCC.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Haiquan Chen ◽  
Jian Carrot-Zhang ◽  
Yue Zhao ◽  
Haichuan Hu ◽  
Samuel S. Freeman ◽  
...  

AbstractAdenocarcinoma in situ and minimally invasive adenocarcinoma are the pre-invasive forms of lung adenocarcinoma. The genomic and immune profiles of these lesions are poorly understood. Here we report exome and transcriptome sequencing of 98 lung adenocarcinoma precursor lesions and 99 invasive adenocarcinomas. We have identified EGFR, RBM10, BRAF, ERBB2, TP53, KRAS, MAP2K1 and MET as significantly mutated genes in the pre/minimally invasive group. Classes of genome alterations that increase in frequency during the progression to malignancy are revealed. These include mutations in TP53, arm-level copy number alterations, and HLA loss of heterozygosity. Immune infiltration is correlated with copy number alterations of chromosome arm 6p, suggesting a link between arm-level events and the tumor immune environment.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 971-971
Author(s):  
Motohiro Kato ◽  
Masashi Sanada ◽  
Itaru Kato ◽  
Yasuharu Sato ◽  
Junko Takita ◽  
...  

Abstract Abstract 971 NFκB is a tightly regulated transcription factor of lymphocyte activation, proliferation and development. Controlled activity of NF κ B signaling pathway plays critical roles in coordination of immune and inflammatory response. Constitutive NFκB activation is recognized as a key pathological feature in several subsets of B-cell malignant lymphoma, and it is well known that lymphoma frequently occurred in association with chronic inflammation. Recently, our group showed frequent inactivation of A20, a negative regulator of NF κ B, in B-lineage malignant lymphomas. However, the molecular mechanism underlying the aberrant NF κ B activation in lymphomagenesis has not fully understood. In this study, to clarify the genetic basis of the aberrant NFκB activation, we performed genome-wide analysis of copy number alterations as well as allelic imbalances of primary B-lineage lymphoma specimens using Affymetrix GeneChip 250K genomic microarray with the CNAG/AsCNAR algorithm. We also searched for possible mutations in CARD11, CYLD, IKK and TRAF family genes and IκB genes, to obtain comprehensive registry of lesions in genes regulating NFκB pathway. This study included 238 primary lymphoma samples, including 64 samples of diffuse large B-cell lymphomas (DLBCL), 52 of follicular lymphomas (FL), 35 of mantle cell lymphomas (MCL), and 87 of mucosa-associated tissue (MALT) lymphomas. Five Hodgkin lymphoma-derived cell line (KM-H2, L1236, HDLM2, RPMI1666, L540) was also analyzed. Through a genome-wide analysis, we identified that each histology type had a unique genomic signature, suggesting a distinctive underlying molecular pathogenesis for different histology types. In contrast to the fact that A20 mutation was highly associated with loss of heterozygosity at 6q23.3, mutations of CARD11 (5 cases of DLBCL, 2 cases of MALT lymphoma) and IκB family genes (2 cases of DLBCL and 1 cases of MALT lymphoma) had no association with copy number abnormality at the locus of the genes. In total, mutations and copy number alterations in genes regulating NFκB pathway were found in more than 40% of B-cell lymphomas, which underpinned the importance of aberrant NFκB activation in lymphomagenesis. To also assess the role of uncontrolled signaling of NFκB pathway in lymphomagenesis, we re-expressed wild-type A20 in two lymphoma-derived cell lines without normal functional A20 alleles (KM-H2 and L1236). In both cells, re-expression of wild-type A20 resulted in suppression of cell growth and induction of apoptosis, accompanied by down-regulation of NFκB activation. The A20-deficient KM-H2 stably generated tumors in immunodeficient mice, whereas the tumorigenicity was effectively suppressed by re-expression of A20. We further investigated the role of A20 inactivation during clonal expansion of lymphoma by competitive proliferation assays using A20-deficient lymphoma-derived cell lines with or without re-expression of A20. The proportion of A20-expressing cells gradually decreased during competitive cell culture, and A20-expressing cells outgrew control cells in NOG mice, indicating the importance of A20 inactivation in clonal evolution of lymphoma. We demonstrated that uncontrolled NFκB signaling caused by alterations of multiple genes is a common feature of B-lineage lymphomas. Considering the physiological function of NFκB activation induced upon a variety of upstream stimuli, our observations provide an intriguing insight into and the pathogenesis of lymphoma. Our study also indicated that NFκB inhibition may have a role in lymphoma therapeutics. Disclosures: No relevant conflicts of interest to declare.


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