There are multiple applications of molecular tests in clinical oncology. Mutation analysis is now routinely utilized for the diagnosis of hereditary cancer syndromes. Healthy carriers of ...cancer-predisposing mutations benefit from tight medical surveillance and various preventive interventions. Cancers caused by germ-line mutations often require significant modification of the treatment strategy. Personalized selection of cancer drugs based on the presence of actionable mutations has become an integral part of cancer therapy. Molecular tests underlie the administration of EGFR, BRAF, ALK, ROS1, PARP inhibitors as well as the use of some other cytotoxic and targeted drugs. Tumors almost always shed their fragments (single cells or their clusters, DNA, RNA, proteins) into various body fluids. So-called liquid biopsy, i.e., the analysis of circulating DNA or some other tumor-derived molecules, holds a great promise for non-invasive monitoring of cancer disease, analysis of drug-sensitizing mutations and early cancer detection. Some tumor- or tissue-specific mutations and expression markers can be efficiently utilized for the diagnosis of cancers of unknown primary origin (CUPs). Systematic cataloging of tumor molecular portraits is likely to uncover a multitude of novel medically relevant DNA- and RNA-based markers.
Highlights • Ovarian carcinomas arising in BRCA1/2 germ-line mutation carriers show high sensitivity to platinum-based neoadjuvant therapy. • Chemonaive hereditary ovarian cancers frequently ...demonstrate somatic loss of the wild-type BRCA1 allele. • Platinum therapy results in a rapid selection of tumor cell clones with restored heterozygous BRCA1 status.
There are over a dozen of approved cancer drugs, whose administration is tailored to predictive laboratory tests. The examples include estrogen and progesterone receptor status determination for the ...use of endocrine therapy, HER2 assessment for the administration of HER2-targeting agents, EGFR and ALK gene testing for lung cancer treatment, BRAF analysis in melanoma, etc. While first predictive tests relied on relatively easy laboratory procedures, more recent developments require rather sophisticated assays. For example, administration of PARP inhibitors is tailored to a comprehensive testing of BRCA1 and BRCA2 genes, and is likely to be supplemented in the future by even more systematic assessment of DNA repair pathways. The detection of an androgenindependent splice-variant of androgen-receptor (AR-V7) in castration-resistant prostate cancer is achieved through the isolation of circulating tumor cells (CTCs). The efficacy of immune check-point inhibitors correlates with the overall mutational tumor load, therefore the companion diagnostic assays may involve genome-wide scanning. Integration of next-generation sequencing (NGS) into clinical oncology is expected to boost the use of predictive tests in the forthcoming years.
Our study aimed to analyze the evolution of molecular portraits of BRCA1‐driven ovarian cancer (OC) during treatment. BRCA1 loss‐of‐heterozygosity status (LOH) and exome profiles were investigated in ...serial OC samples from 13 patients, which included primary tumors (n = 11) obtained before neoadjuvant therapy (NACT) or at primary debulking surgery, residual post‐NACT cancer tissues (n = 13) and tumor relapses (16 samples from 13 patients). Loss of the wild‐type BRCA1 allele was detected in 11/11 (100%) primary tumors, 6/13 (46%) residual post‐NACT OC samples and 15/16 (94%) OC relapses. Full tumor triplets were available for four patients undergoing NACT; whereas primary carcinomas from these patients demonstrated BRCA1 LOH, the retention of the wild‐type allele was detected in all four post‐NACT residual tumors. These four women provided to the study 5 recurrent OC samples; 4 out of 5 tumor relapses had BRCA1 LOH thus resembling BRCA1 status observed in primary but not residual OC tissues. TP53 mutation was detected in 12 out of 13 patients and was retained across all serial samples. OC relapses tended to acquire additional intragenic mutations in genes involved in cell migration, adhesion and cell junction assembly. BRCA1‐driven OCs demonstrate the plasticity of BRCA1 status during the treatment course. NACT results in rapid selection of pre‐existing BRCA1‐proficient cells. However, BRCA1 proficiency appears to be disadvantageous in the absence of platinum exposure, as tumor relapses usually re‐acquire BRCA1 LOH during therapy holidays.
What's new?
Ovarian cancers carrying BRCA1 mutations are characterized by intratumoural heterogeneity, in which most malignant cells show a loss of the remaining BRCA1 allele, while some cells retain BRCA1 function. Here, investigation of BRCA1 mutation among ovarian cancer patients over the course of treatment reveals plasticity in somatic BRCA1 status, with impacts on primary cancer development, therapeutic response, and disease relapse. In particular, relapses following treatment holidays were characterized by the re‐appearance of somatic BRCA1 inactivation. Plasticity in BRCA1 status likely explains the failure of systemic therapy to eradicate tumor clones and accounts for platinum sensitivity in recurrent BRCA1‐driven ovarian cancers.
Neoadjuvant chemotherapy (NACT) for breast cancer (BC) often results in pathologic complete response (pCR), i.e., the complete elimination of visible cancer cells. It is unclear whether the use of ...ultrasensitive genetic methods may still detect residual BC cells in complete responders. Breast carcinomas arising in
mutation carriers almost always carry alterations of the
gene thus providing an opportunity to address this question. The analysis of consecutive BC patients treated by NACT revealed a higher pCR rate in
-driven vs.
-wildtype BCs (13/24 (54%) vs. 29/192 (15%),
< 0.0001). Twelve pre-/post-NACT tissue pairs obtained from
mutation carriers were available for the study. While
mutation was identified in all chemonaive tumors, droplet digital PCR (ddPCR) analysis of the post-NACT tumor bed revealed the persistence of this alteration in all seven pCR-non-responders but in none of five pCR responders. Eleven patients provided to the study post-NACT tissue samples only; next-generation sequencing (NGS) analysis revealed mutated
copies in all six cases without pCR but in none of five instances of pCR. In total,
mutation was present in post-NACT tissues in all 13 cases without pCR, but in none of 10 patients with pCR (
< 0.000001). Therefore, the lack of visible tumor cells in the post-NACT tumor bed is indeed a reliable indicator of the complete elimination of transformed clones. Failure of ultrasensitive methods to identify patients with minimal residual disease among pCR responders suggests that the result of NACT is a categorical rather than continuous variable, where some patients are destined to be cured while others ultimately fail to experience tumor eradication.
Novel ALK fusion partners in lung cancer Iyevleva, Aglaya G; Raskin, Grigory A; Tiurin, Vladislav I ...
Cancer letters,
06/2015, Letnik:
362, Številka:
1
Journal Article
Recenzirano
Highlights • Combination of two distinct PCR assays is a highly reliable approach for detection of both known and new ALK translocations. • Two novel ALK fusion partners, DCTN1 and SQSTM1, have been ...identified. • Increased frequency of ALK rearrangements among female patients is attributed to the low prevalence of smoking, not to the gender per se.
Purpose
Germline mutations in CHEK2 gene represent the second most frequent cause of hereditary breast cancer (BC) after BRCA1/2 lesions. This study aimed to identify the molecular characteristics of ...CHEK2-driven BCs.
Methods
Loss of heterozygosity (LOH) for the remaining CHEK2 allele was examined in 50 CHEK2-driven BCs using allele-specific PCR assays for the germline mutations and analysis of surrounding single-nucleotide polymorphisms (SNPs). Paired tumor and normal DNA samples from 25 cases were subjected to next-generation sequencing analysis.
Results
CHEK2 LOH was detected in 28/50 (56%) BCs. LOH involved the wild-type allele in 24 BCs, mutant CHEK2 copy was deleted in 3 carcinomas, while in one case the origin of the deleted allele could not be identified. Somatic PIK3CA and TP53 mutations were present in 13/25 (52%) and 4/25 (16%) tumors, respectively. Genomic features of homologous recombination deficiency (HRD), including the HRD score ≥ 42, the predominance of BRCA-related mutational signature 3, and the high proportion of long (≥ 5 bp) indels, were observed only in 1/20 (5%) BC analyzed for chromosomal instability. Tumors with the deleted wild-type CHEK2 allele differed from LOH-negative cases by elevated HRD scores (median 23 vs. 7,
p
= 0.010) and higher numbers of chromosomal segments affected by copy number aberrations (
p
= 0.008).
Conclusion
Somatic loss of the wild-type CHEK2 allele is observed in approximately half of CHEK2-driven BCs. Tumors without CHEK2 LOH are chromosomally stable. BCs with LOH demonstrate some signs of chromosomal instability; however, its degree is significantly lower as compared to BRCA1/2-associated cancers.
Purpose
Large genomic rearrangements (LGRs) constitute a significant share of pathogenic
BRCA1
mutations. Multiplex ligation-dependent probe amplification (MLPA) is a leading method for LGR ...detection; however, it is entirely based on the use of commercial kits, includes relatively time-consuming hybridization step, and is not convenient for large-scale screening of recurrent LGRs.
Materials and methods
We developed and validated the droplet digital PCR (ddPCR) assay, which covers the entire coding region of
BRCA1
gene and is capable to precisely quantitate the copy number for each exon.
Results
141 breast cancer (BC) patients, who demonstrated evident clinical features of hereditary BC but turned out to be negative for founder
BRCA1/2
mutations, were subjected to the LGR analysis. Four patients with LGR were identified, with three cases of exon 8 deletion and one women carrying the deletion of exons 5–7. Excellent concordance with MLPA test was observed. Exon 8 copy number was tested in additional 720 BC and 184 ovarian cancer (OC) high-risk patients, and another four cases with the deletion were revealed; MLPA re-analysis demonstrated that exon 8 loss was a part of a larger genetic alteration in two cases, while the remaining two patients had isolated defect of exon 8. Long-range PCR and next generation sequencing of DNA samples carrying exon 8 deletion revealed two types of recurrent LGRs.
Conclusion
Droplet digital PCR is a reliable tool for the detection of large genomic rearrangements.
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