Updates on breast biomarkers

Najjar, Saleh; Allison, Kimberly H.

doi:10.1007/s00428-022-03267-x

Cited by 53 publications

(36 citation statements)

References 70 publications

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“…However, more recently an association between tumor stage and ATP2B1 was identified [ 40 ]. Meanwhile, ERBB2 (erb-b2 receptor tyrosine kinase 2) is a member of the epidermal growth factor (EGF) receptor family genes encoding for well-known HER2 protein, which is known to play an essential role in breast cancer progression and treatment selection [ 41 , 42 ]. Moreover, 35 unique ERBB2 fusions are present in ChimerDB, and at least 3 were previously described in scientific papers [ 43 , 44 ].…”

Section: Discussionmentioning

confidence: 99%

Experimentally Deduced Criteria for Detection of Clinically Relevant Fusion 3′ Oncogenes from FFPE Bulk RNA Sequencing Data

Rabushko

Suntsova

Seryakov³

et al. 2022

Biomedicines

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Drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins demonstrate impressive anti-cancer activities. The fusion presence in the cancer is the respective drug prescription biomarker, but their identification is challenging as both the breakpoint and the exact fusion partners are unknown. RNAseq offers the advantage of finding both fusion parts by screening sequencing reads. Paraffin (FFPE) tissue blocks are the most common way of storing cancer biomaterials in biobanks. However, finding RTK fusions in FFPE samples is challenging as RNA fragments are short and their artifact ligation may appear in sequencing libraries. Here, we annotated RNAseq reads of 764 experimental FFPE solid cancer samples, 96 leukemia samples, and 2 cell lines, and identified 36 putative clinically relevant RTK fusions with junctions corresponding to exon borders of the fusion partners. Where possible, putative fusions were validated by RT-PCR (confirmed for 10/25 fusions tested). For the confirmed 3′RTK fusions, we observed the following distinguishing features. Both moieties were in-frame, and the tyrosine kinase domain was preserved. RTK exon coverage by RNAseq reads upstream of the junction site were lower than downstream. Finally, most of the true fusions were present by more than one RNAseq read. This provides the basis for automatic annotation of 3′RTK fusions using FFPE RNAseq profiles.

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Section: Discussionmentioning

confidence: 99%

Experimentally Deduced Criteria for Detection of Clinically Relevant Fusion 3′ Oncogenes from FFPE Bulk RNA Sequencing Data

Rabushko

Suntsova

Seryakov³

et al. 2022

Biomedicines

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“…Transcriptomic analysis has revealed high HER2 mRNA levels in HER2-enriched breast cancer subtypes using the PAM50 probe, suggesting another possible subtype signature. Dual HER2blockade led to positive results in patients with higher HER2 mRNA levels; thus, it is a newly proposed biomarker for chemotherapy de-escalation [13][14][15] . Despite evolving modalities of HER2 testing, they are currently awaiting approval and the IHC-ISH approach remains the "gold standard" [16] .…”

Section: Historical Perspectivementioning

confidence: 99%

Improving HER2 testing reproducibility in HER2-low breast cancer

Sajjadi¹,

Venetis²,

Ivanova³

et al. 2022

Cancer Drug Resist

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HER2 is a pillar biomarker in breast cancer, and it is assessed by immunohistochemistry (IHC) using a three-tier scoring system and reflex in situ hybridization (ISH) for IHC score 2+. Novel HER2-directed antibody-drug conjugates have demonstrated significant antitumor activity in breast cancers with low levels of HER2 expression, i.e. IHC score 1+ or ISH-negative IHC score 2+. Both primary and acquired resistance to anti-HER2 therapies remains a challenge in the treatment of breast cancers according to the HER2 positivity continuum. Thus, the ability to precisely discriminate among HER2-zero, HER2-low, and HER2-positive breast cancers is no longer a mere academic exercise. HER2 testing criteria, guidelines, and quality controls are re-gaining momentum for this new clinical need. Therefore, all preanalytical and analytical variables that might trouble the sensitivity and reproducibility of this test should be carefully considered to address all possible issues and open all possible therapeutic opportunities for breast cancer patients.

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“…Such methods include the use of next-generation sequencing (NGS), RT-qPCR, in situ hybridization, microRNA tracking and multigene assays [ 24 ]. The purpose is to provide the best suited personalized therapy in order to avoid of overtreatment and side effects in patients with good prognosis, yet to provide sufficient therapeutic effect to the patients with worse prognosis [ 25 ]. It is also important to consider an economic relevance of methods to be designated as standard care [ 4 , 6 , 18 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

Classic and New Markers in Diagnostics and Classification of Breast Cancer

Benacka

Szabóová

Guľašová

et al. 2022

Cancers

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Breast cancer remains the most frequently diagnosed form of female’s cancer, and in recent years it has become the most common cause of cancer death in women worldwide. Like many other tumours, breast cancer is a histologically and biologically heterogeneous disease. In recent years, considerable progress has been made in diagnosis, subtyping, and complex treatment of breast cancer with the aim of providing best suited tumour-specific personalized therapy. Traditional methods for breast cancer diagnosis include mammography, MRI, biopsy and histological analysis of tumour tissue in order to determine classical markers such as estrogen and progesterone receptors (ER, PR), cytokeratins (CK5/6, CK14, C19), proliferation index (Ki67) and human epidermal growth factor type 2 receptor (HER2). In recent years, these methods have been supplemented by modern molecular methodologies such as next-generation sequencing, microRNA, in situ hybridization, and RT-qPCR to identify novel molecular biomarkers. MicroRNAs (miR-10b, miR-125b, miR145, miR-21, miR-155, mir-30, let-7, miR-25-3p), altered DNA methylation and mutations of specific genes (p16, BRCA1, RASSF1A, APC, GSTP1), circular RNA (hsa_circ_0072309, hsa_circRNA_0001785), circulating DNA and tumour cells, altered levels of specific proteins (apolipoprotein C-I), lipids, gene polymorphisms or nanoparticle enhanced imaging, all these are promising diagnostic and prognostic tools to disclose any specific features from the multifaceted nature of breast cancer to prepare best suited individualized therapy.

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Updates on breast biomarkers

Cited by 53 publications

References 70 publications

Experimentally Deduced Criteria for Detection of Clinically Relevant Fusion 3′ Oncogenes from FFPE Bulk RNA Sequencing Data

Experimentally Deduced Criteria for Detection of Clinically Relevant Fusion 3′ Oncogenes from FFPE Bulk RNA Sequencing Data

Improving HER2 testing reproducibility in HER2-low breast cancer

Classic and New Markers in Diagnostics and Classification of Breast Cancer

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