Clinicopathologic Features And Whole Exome Sequencing Of Very Young Breast Cancer

Objective: The incidence and mortality of breast cancer are extremely high,ranking first and fifth among female malignancies,respectively.According to statistics,the incidence of young breast cancer under 35 years of old is significantly higher in China than the west.The pathological,clinical and prognostic of very young breast cancer(VYBC,age?25)have not been determined.Some driver genes affecting breast cancer have been found by some researches,but it still cannot fully explain the risk of breast cancer in young women.And there is no genomics research on VYBC up to now.Based on the above issues,the research focus of this paper is to explore the pathological and clinical prognostic characteristics of VYBC;explore the driving genes that cause VYBC to prematurely;explore the correlation between VYBC genomics and molecular characteristics by combining clinical,pathological and genomics studies;Construction of VYBC single nucleotide variation(SNV),germline mutation,copy number variation(CNV)and other genomics maps.Methods: Clinico-pathologic data of 215 VYBC patients were retrospectively collected.The clinicopathological characteristics of young breast cancer(YBC,age?40)were compared.Formalin-fixed paraffin-embedded(FFPE)glands and matched tumor tissue from VYBC patients without preoperative chemotherapy were collected,and the pathologists confirmed that there were no tumor cells in the glandular tissue.The proportion of tumor cells in the matched tumor tissue reached 80% or more.A total of 64 patients met the enrollment requirements.TIANamp FFPE DNA Kit(Tiangen Biotech)was used for the enrolled specimens genomic DNA extraction.Qubit? 3.0 Fluorometer(Life technologies)and gel electrophoresis were used to detect the amount and integrity of DNA,fragmentation to 250 bps with Covaris E220(Covaris),library construction,Sure Select Human All Exon V5(Agilent)perform exome capture and enrichment,and perform whole exom sequencing(WES)on DNA samples using the illumina Hiseq-Xten platform.The reads obtained by sequencing were compared with the human reference genome(hg19)using BWA(v0.7.7-r441),and the base quality recalibration was performed by a genomic analysis tool(GATK,v3.7).Mu Tect detects single nucleotide variants(SNVs).Var Scan detects small cell insertions or deletions(Indel).The identified mutations were annotated with Oncotator-1.5.1.0.BIC-seq2 was used to detect copy number variation(CNV).Results: The clinical and molecular characteristics of 215 VYBC patients were retrospectively analyzed and compared with YBC-TJ(n = 965)patients in Tianjin Medical University Cancer Institute and Hospital.Compared with YBC-TJ,VYBC patients had a lower number of lymph node dissections(p = 6.70e-13)and a higher positive lymph node detection rate(p = 0.048).VYBC had more patients with clinical stage I(p = 5.20e-6)and significantly more histological grade III(p = 1.58e-13).In terms of molecular typing,VYBC has more ER+/HER2+ subtype,and the proportion of HER2 overexpression is significantly higher than that of YBC-TJ(p = 0.001).VYBC's three-and five-year survival rates are 94.9% and 89.9%,respectively.VYBC has unique genomics characteristics.We found a total of 2139 non-synonymous mutations,with an average of 21 mutations per Mb base.In combination with TCGA database analysis,we found that the number of mutations increased with age.The signatures of the mutations are mainly Signature A and Signature B.The mutations are mainly C> G(19%)and C> T(45%)mutations,which are attributed to DNA mismatch repair defects or ERCC2/Smoking and Cytidine Deaminase.The five most significant mutant genes(SMGs)with the highest mutation frequency were PIK3CA(35.9%),TP53(34.4%),ARID1A(9.4%),GATA3(7.8%),and MAP3K1(6.3%).CNV analysis revealed that the corresponding MYC and ERBB2 amplification frequencies of chromosome 8(chr8q)and chromosome 17(chr17q)in the two genomic regions were significantly higher than those in the TCGA database over 40 years of age(p = 0.013;p = 0.006).The enrichment analysis found that about 6.8% of the mutant genes were enriched in the morphogenesis-related pathways of differentiation-related cells.Germline mutation analysis showed that 14.1% of patients had pathogenic mutations,germline mutation frequency of TP53 was 4.68%,and germline mutation frequency of BRCA2 was 7.81%.Further analysis found that 70.4% of VYBC's PIK3 CA gene mutations occurred in the kinase region,and the proportion of mutations in the helical region was significantly less than in samples older than 40 years(p = 0.008)Conclusion: VYBC patients have unique clinicopathological and genomic characteristics.Signature A indicating the mutation process occurs in the early stage of malignant transformation;the amplification frequencies of 8q and 17 q of VYBC are higher;BRCA2 germline mutation frequency is higher at 12.5%;PIK3CA mutations occur more in the kinase domain may related to the onset of tumor.In summary,our research shows that the mutation signatures,SMGs,CNV,germline mutation,and PIK3 CA point mutation domain have been shown to be associated with early onset of breast cancer.