Cytogenetic polyclonality of breast carcinomas: association with clinico-pathological characteristics and outcome

Isogenic Cell Lines Derived from Specific Organ Metastases Exhibit Divergent Cytogenomic Aberrations

Aneuploidy, a deviation in chromosome numbers from the normal diploid set, is now recognized as a fundamental characteristic of all cancer types and is found in 70-90% of all solid tumors. The majority of aneuploidies are generated by chromosomal instability (CIN). CIN/aneuploidy is an independent prognostic marker of cancer survival and is a cause of drug resistance. Hence, ongoing research has been directed towards the development of therapeutics aimed at targeting CIN/aneuploidy. However, there are relatively limited reports on the evolution of CIN/aneuploidies within or across metastatic lesions. In this work, we built on our previous studies using a human xenograft model system of metastatic disease in mice that is based on isogenic cell lines derived from the primary tumor and specific metastatic organs (brain, liver, lung, and spine). As such, these studies were aimed at exploring distinctions and commonalities between the karyotypes; biological processes that have been implicated in CIN; single-nucleotide polymorphisms (SNPs); losses, gains, and amplifications of chromosomal regions; and gene mutation variants across these cell lines. Substantial amounts of inter- and intra-heterogeneity were found across karyotypes, along with distinctions between SNP frequencies across each chromosome of each metastatic cell line relative the primary tumor cell line. There were disconnects between chromosomal gains or amplifications and protein levels of the genes in those regions. However, commonalities across all cell lines provide opportunities to select biological processes as druggable targets that could have efficacy against the primary tumor, as well as metastases.

Molecular karyotyping and gene expression analysis in childhood cancer patients

Abstract

The genetic etiology of sporadic childhood cancer cases remains unclear. We recruited a cohort of 20 patients who survived a childhood malignancy and then developed a second primary cancer (2N), and 20 carefully matched patients who survived a childhood cancer without developing a second malignancy (1N). Twenty matched cancer-free (0N) and additional 1000 (0N) GHS participants served as controls. Aiming to identify new candidate loci for cancer predisposition, we compared the genome-wide DNA copy number variations (CNV) with the RNA-expression data obtained after in vitro irradiation of primary fibroblasts. In 2N patients, we detected a total of 142 genes affected by CNV. A total of 53 genes of these were not altered in controls. Six genes (POLR3F, SEC23B, ZNF133, C16orf45, RRN3, and NTAN1) that we found to be overexpressed after irradiation were also duplicated in the genome of the 2N patients. For the 1N collective, 185 genes were affected by CNV and 38 of these genes were not altered in controls. Five genes (ZCWPW2, SYNCRIP, DHX30, DHRS4L2, and THSD1) were located in duplicated genomic regions and exhibited altered RNA expression after irradiation. One gene (ABCC6) was partially duplicated in one 1N and one 2N patient. Analysis of methylation levels of THSD1 and GSTT2 genes which were detected in duplicated regions and are frequently aberrantly methylated in cancer showed no changes in patient’s fibroblasts. In summary, we describe rare and radiation-sensitive genes affected by CNV in childhood sporadic cancer cases, which may have an impact on cancer development.

Key messages

• Rare CNV’s may have an impact on cancer development in sporadic, non-familial, non-syndromic childhood cancer cases.

• In our cohort, each patient displayed a unique pattern of cancer-related gene CNVs, and only few cases shared similar CNV.

• Genes that are transcriptionally regulated after radiation can be located in CNVs in cancer patients and controls.

• THSD1 and GSTT2 methylation is not altered by CNV.

Electronic supplementary material

The online version of this article (10.1007/s00109-020-01937-4) contains supplementary material, which is available to authorized users.

Correlation of morphological markers of chromosomal instability in fine needle aspiration cytology with grade of breast cancer

OBJECTIVE

The aim of the present study was to investigate morphological markers of chromosomal instability (CI) in relation to cytological grade of breast cancer in fine needle aspiration cytology (FNAC) specimens.

METHODS

Herein we selected 55 cases of invasive ductal carcinoma diagnosed on FNAC. Representative haematoxylin and eosin (H&E)-stained smears were chosen to count chromatin bridges, multipolar mitoses per smear, and micronuclei and nuclear budding per 1000 carcinoma cells. The cases were also graded by two independent observers as grade I, II and III. The CI markers were correlated with the grade of breast carcinomas.

RESULTS

Out of 55 carcinomas, nine were grade I, nine grade II and 37 grade III. While none of the grade I carcinomas showed chromosomal bridges, the number per smear was 0.4 (± 0.7) and 3.1 (± 2.5) for grade II and III carcinomas, respectively. No multipolar mitoses were observed in grade I or II carcinomas; the number per smear was 3.7 (±3.0) in grade III carcinomas. The mean number per 1000 malignant cells of micronuclei was 1.2 (±1.7), 3.7 (±2.1) and 12.2 (±5.1) and of nuclear buds was 2.3 (±3.2), 4.7 (±2.1) and 12.4 (±4.7) in grade I, II and III carcinomas, respectively. There was a significant increase in the mean numbers of chromatin bridges, micronuclei and nuclear buds in grade I, II and III carcinomas (anova test; P < 0.001).

CONCLUSION

This is the first study of four morphological markers of CI in FNAC smears of breast cancer. This study establishes strong correlation of these markers with other criteria for cytological grading.