| Literature DB >> 32322420 |
Auhood Nassar1, Mohamed Abouelhoda2, Osman Mansour3, Samah A Loutfy1, Mohamed M Hafez1, M Gomaa4, Abeer Bahnassy5, Amira Salah El-Din Youssef1, Mai M Lotfy1, Hoda Ismail5, Ola S Ahmed1, Amany Abd-Elhameed Abou-Bakr5, Abdel-Rahman N Zekri1.
Abstract
Breast cancer (BC) incidence is progressively increasing in Egypt. However, there is insufficient knowledge of the acquired somatic mutations in Egyptian BC patients which limit our understanding of its progression. To the best of our knowledge, this is the first Egyptian cohort to sequence a multiple-gene panel of cancer related genes on BC patients. Four hundred and nine cancer related genes were sequenced in 46 fresh breast tumors of Egyptian BC patients to identify somatic mutations and their frequencies. TP53 and PIK3CA were the most top two frequently mutated genes. We detected 15 different somatic mutations in TP53 and 8 different ones in PIK3CA, each in 27 samples (58.7%). According to Clinvar database; we found 19 pathogenic somatic mutations: 7 in Tp53, 5 in PIK3CA, and single variants of VHL, STK11, AKT1, KRAS, IDH2, PTEN and ERBB2. We also identified 5 variants with uncertain significance (4 in TP53 and 1 in CEBPA) and 4 variants with conflicting interpretations of pathogenicity (2 in TP53 and 1 in each of APC and JAK3). Moreover, one drug response variant (p.P72R) in TP53 was detected in 8 samples. Furthermore, four novel variants were identified in JAK2, MTOR, KIT and EPHB. Further analysis, by Ingenuity Variant Analysis software (IVA), showed that PI3K/AKT signaling is altered in greater than 50% of Egyptian BC patients which implicates PI3K/AKT signaling as a therapeutic target. In this cohort, we shed the light on the most frequently detected somatic mutations and the most altered pathway in Egyptian BC patients.Entities:
Keywords: Breast cancer; Ion torrent sequencing; Next Generation Sequencing; Somatic mutations; Target sequencing
Year: 2020 PMID: 32322420 PMCID: PMC7167517 DOI: 10.1016/j.jare.2020.04.001
Source DB: PubMed Journal: J Adv Res ISSN: 2090-1224 Impact factor: 10.479
Clinical features of the studied 46 Egyptian patients.
| Characteristics | Number | ||
|---|---|---|---|
| Age (Years) | Mean: 54.75 | <40 y | 5 |
| 40–50 y | 8 | ||
| 50–60 y | 18 | ||
| ≥60 y | 15 | ||
| HR status | ER+ | 33 | |
| ER- | 13 | ||
| PR+ | 27 | ||
| PR- | 19 | ||
| Grade | I | 3 | |
| II | 33 | ||
| III | 10 | ||
| Histological type | Invasive duct carcinoma | 41 | |
| Invasive tubular carcinoma | 1 | ||
| Invasive micropapillary carcinoma | 1 | ||
| Invasive tubulolobular carcinoma | 2 | ||
| Invasive duct & Invasive lobular carcinoma (mixed) | 1 | ||
| Molecular classification | Luminal A | 25 | |
| Luminal B | 9 | ||
| Her2- enriched | 8 | ||
| Basal like (triple negative) | 4 | ||
Fig. 1aSummary of types and numbers of the detected somatic mutations.
Fig. 1bClassification of the identified variants.
Fig. 2Oncoplot showing the distribution of somatic mutations in the studied breast cancer patients. The Oncoplot provided an overview of somatic mutations in particular genes (rows) affecting individual samples (columns). According to the logic of oncoplot, if a sample has more variants, it is counted once, and not with the total frequencies. The plot shows total positive 44 samples. The substitution mutations were shown in green, indels were shown in red.
Fig. 3a. PI3K/AKT signaling pathway identified using ingenuity variant analysis (IVA). Blue represents loss of function, orange represents gain of function, and grey inferred normal.
Fig. 3bPI3K/AKT signaling pathway identified using ingenuity variant analysis (IVA). Blue represents loss of function, orange represents gain of function, grey inferred normal, and entities outlined in red are potential drug targets.
Somatic mutations detected in 46 Egyptian BC patients:
| Gene | Function | AA mutation | CDS mutation | Mutation type | Samples with mutation | Zygosity | CADD Phred prediction | Hot spot | Clinvar |
|---|---|---|---|---|---|---|---|---|---|
| Exonic; splicing | p.L862L | c.2586G > C | Substitution – coding silent | 10 | Het. | – | – | Benign | |
| Exonic; splicing | p.M541L | c.1621A > C | Substitution – Missense | 6 | Het. | – | 4-55593464 | Benign | |
| Exonic; splicing | p.K546K | c.1638A > G | Substitution – coding silent | 5 | Het. | – | 4-55593481 | Benign | |
| Exonic | p.F608Lfs*21 | c.1824del | Frame shift deletion | 12 | Hom. | D | – | Not reported | |
| Exonic | p.L203Cfs*7 | c.608del | Frame shift deletion | 2 | Hom. | D | – | Not reported | |
| Exonic | p.F298Lfs*65 | c.894del | Frame shift deletion | 3 | Hom. | D | – | Not reported | |
| Exonic | p.A176V | c.527C > T | Substitution – Missense | 7 | Het. | D | – | Uncertain significance | |
| Splicing | – | c.575-9G > A | Substitution- Intronic | 6 | Het. | – | – | Benign | |
| Exonic | p.G12V | c.35G > T | Substitution – Missense | 1 | Het. | D | 12-25398284 | Pathogenic | |
| Exonic | – | c.2472C > T | Substitution – coding silent | 6 | Het. | – | 4-55152040 | Benign | |
| Exonic | p.E288fs | c.863delA | Frame shift deletion | 6 | Hom. | – | 10-89720712 | Not reported | |
| 1 | Het. | – | |||||||
| Exonic | p.R130X | c.388C > T | Substitution – Nonense (stopgain) | 1 | Het. | D | 10-89692904 | Pathogenic | |
| Exonic | p.F148fs | c.440delT | Frame shift deletion | 5 | Hom. | – | 3-10188297 | Pathogenic | |
| Exonic | p.K117Q | c. 349A > C | Substitution – Missense | 4 | Hom. | – | – | Not reported | |
| Exonic | p.G279fs | c.837delC | Frame shift deletion | 4 | Het. | – | 19-1221314 | Pathogenic | |