Prognostic impact of ACTN4 gene copy number alteration in hormone receptor-positive, HER2-negative, node-negative invasive breast carcinoma

Abstract Background Hepatocellular carcinoma (HCC) is the most common type of liver cancer that occurs predominantly in patients with previous liver conditions. In the absence of an ideal screening modality, HCC is usually diagnosed at an advanced stage. Recent studies show that loss or gain of genomic materials can activate the oncogenes or inactivate the tumor suppressor genes to predispose cells toward carcinogenesis. Here, we evaluated both the copy number alteration (CNA) and RNA sequencing data of 361 HCC samples in order to locate the frequently altered chromosomal regions and identify the affected genes. Results Our data show that the chr1q and chr8p are two hotspot regions for genomic amplifications and deletions respectively. Among the amplified genes, YY1AP1 (chr1q22) possessed the largest correlation between CNA and gene expression. Moreover, it showed a positive correlation between CNA and tumor grade. Regarding deleted genes, CHMP7 (chr8p21.3) possessed the largest correlation between CNA and gene expression. Protein products of both genes interact with other cellular proteins to carry out various functional roles. These include ASH1L, ZNF496, YY1, ZMYM4, CHMP4A, CHMP5, CHMP2A and CHMP3, some of which are well-known cancer-related genes. Conclusions Our in-silico analysis demonstrates the importance of copy number alterations in the pathology of HCC. These findings open a door for future studies that evaluate our results by performing additional experiments.

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Abstract P2-05-14: Prognostic impact of genomic risk stratification with breast cancer index in patients with clinically low risk, hormone receptor-positive, node-negative, T1 breast cancer

10.1158/1538-7445.sabcs16-p2-05-14 ◽

2017 ◽

Author(s):

BE Schroeder ◽

Y Zhang ◽

O Stal ◽

T Fornander ◽

A Brufsky ◽

...

Keyword(s):

Breast Cancer ◽

Risk Stratification ◽

Hormone Receptor ◽

Low Risk ◽

Positive Node ◽

Prognostic Impact ◽

Node Negative ◽

Hormone Receptor Positive ◽

Breast Cancer Index ◽

Genomic Risk

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Prognostic impact of RUNX1 and ETV6 gene copy number on pediatric B-cell precursor acute lymphoblastic leukemia with or without hyperdiploidy

International Journal of Hematology ◽

10.1007/s12185-016-2034-y ◽

2016 ◽

Vol 104 (3) ◽

pp. 368-377 ◽

Cited By ~ 1

Author(s):

Nuket Yurur Kutlay ◽

Esra Pekpak ◽

Sule Altıner ◽

Talia Ileri ◽

Arzu Nedime Vicdan ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

B Cell ◽

Copy Number ◽

Lymphoblastic Leukemia ◽

Gene Copy Number ◽

Gene Copy ◽

Prognostic Impact ◽

Cell Precursor

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Prognostic impact of discrepant Ki67 and mitotic index on hormone receptor-positive, HER2-negative breast carcinoma

British Journal of Cancer ◽

10.1038/bjc.2015.239 ◽

2015 ◽

Vol 113 (7) ◽

pp. 996-1002 ◽

Cited By ~ 9

Author(s):

L Rossi ◽

E Laas ◽

P Mallon ◽

A Vincent-Salomon ◽

J-M Guinebretiere ◽

...

Keyword(s):

Breast Carcinoma ◽

Mitotic Index ◽

Hormone Receptor ◽

Prognostic Impact ◽

Hormone Receptor Positive

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Prognostic impact of gene copy number instability and tumor mutation burden in patients with resectable gastric cancer

Cancer Communications ◽

10.1002/cac2.12007 ◽

2020 ◽

Vol 40 (1) ◽

pp. 63-66

Author(s):

Lisheng Cai ◽

Linhai Li ◽

Dandan Ren ◽

Xue Song ◽

Beibei Mao ◽

...

Keyword(s):

Gastric Cancer ◽

Copy Number ◽

Gene Copy Number ◽

Gene Copy ◽

Prognostic Impact ◽

Tumor Mutation Burden ◽

Mutation Burden ◽

Resectable Gastric Cancer

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SOX2 and FGFR1 gene copy number in surgically resected non-small cell lung cancer (NSCLC).

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.7061 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. 7061-7061

Author(s):

Luca Toschi ◽

Giovanna Finocchiaro ◽

Teresa T. Nguyen ◽

Margaret Skokan ◽

Laura Giordano ◽

...

Keyword(s):

Lung Cancer ◽

Gene Amplification ◽

Squamous Cell ◽

Cell Lung Cancer ◽

Copy Number ◽

Gene Copy Number ◽

Gene Copy ◽

Prognostic Impact ◽

Prognostic Relevance ◽

Fgfr1 Gene

7061 Background: SOX2 is a member of the SRY-related HMG-box family of transcription factors and has been shown to be frequently amplified and overexpressed in squamous cell lung cancer, with conflicting results regarding its prognostic relevance. Similarly, FGFR1, a transmembrane tyrosine kinase receptor belonging to the fibroblast growth factor receptor family, has been recently reported to be amplified in squamous cell lung carcinomas, suggesting a potential role for FGFR1 as a therapeutic target in NSCLC. Aim of the present study is to evaluate SOX2 and FGFR1 gene copy number in surgically resected NSCLCs, to investigate their prognostic relevance and their association with clinico-pathological characteristics. Methods: SOX2 and FGFR1 gene copy number was assessed by fluorescence in situ hybridization (FISH) in tissue microarray cores from 447 surgically resected NSCLCs. Each patient was given a score ranging from 1 to 6 according to increasing mean copy number per cell of each gene, with 6 indicating true gene amplification. Results: SOX2 and FGFR1 FISH was successfully performed in 445 patients (pts), which were grouped as + (score 5-6) and - (score 1-4). Using this scoring system 105 (23.6%) pts tested SOX2+, while 74 (16.6%) pts resulted FGFR1+. True gene amplification for SOX2 and FGFR1 was observed in 19 (4.3%) and 37 (8.3%) cases, respectively. SOX2+ and FGFR1+ status was significantly associated with squamous histology (p<.001). Additionally, SOX2+ pts had a significantly higher chance of being former/current smokers, male and FGFR1+. FGFR1 gene status had no prognostic impact in the whole population and in the squamous cell carcinoma subgroup. Conversely, SOX2+ pts had significantly longer overall survival compared with SOX2- pts (HR 0.68, p=.020). When restricting survival analysis to squamous cell histology, stage I-II SOX2+ pts had a significant survival advantage compared with SOX2- group (HR 0.38, p=.006), while no difference was observed in stage III-IV pts. Conclusions: Increased SOX2 and FGFR1 gene copy number is a common event in lung cancer pts with squamous cell histology. SOX2 gene gain is a favorable prognostic factor in surgically resected pts, particularly in early stage squamous cell cancers.

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