Construction of multi-gene classifier for prediction of response to and prognosis after neoadjuvant chemotherapy for estrogen receptor positive breast cancers

Tsunashima, Ryo; Naoi, Yasuto; Kagara, Naofumi; Shimoda, Masashi; Shimomura, Atsushi; Maruyama, Naomi; Shimazu, Kenzo; Kim, Seung Jin; Noguchi, Shinzaburo

doi:10.1016/j.canlet.2015.05.030

Cited by 11 publications

(13 citation statements)

References 39 publications

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“…A complete absence of invasive tumor cells in the breast and lymph nodes was defined as pathological complete response (pCR), irrespective of the presence or absence of non-invasive breast cancer cells. ER, PR, and Ki67 levels in the tumor biopsy samples were immunohistochemically determined as previously described (10)(11)(12). The cut-off values were 10% for ER, 10% for PR and 20% for Ki67.…”

Section: Gc -----------------------------------------------------mentioning

confidence: 99%

Development of recurrence risk score using 95‑gene classifier and its application to formalin‑fixed paraffin‑embedded tissues in ER‑positive, HER2‑negative and node‑negative breast cancer

et al. 2019

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We previously developed a 95-gene classifier (95GC) to classify ER-positive/HER2-negative/node-negative (ER + /HER2-/N0) breast cancer as high-and low-risk. The present study aimed to devise a 95GC recurrence score (95GC RS) to estimate recurrence risk more precisely and, although the 95GC was originally developed using fresh-frozen (FF) tissues, this was applied to formalin-fixed paraffin-embedded (FFPE) tissues. 95GC RS was calculated using between-group analysis and denominated as a value from 0 to 100. Correlation of 95GC RS with distant recurrence rate and response to neoadjuvant chemotherapy (NAC) was evaluated in 257 patients with ER + /HER2 − /N0 breast cancer treated with adjuvant hormonal therapy at Osaka University Hospital and in 425 patients with ER + breast cancer treated with NAC at Osaka University Hospital and the University of Texas MD Anderson Cancer Center (GSE25066 dataset). Correlation of 95GC RS between FF and FFPE tissues was evaluated in paired tissues from 56 ER + /HER2-/N0 breast cancer types obtained from patients without NAC treatment. Distant recurrence rates were remarkably low in patients with 95GC RS ≤50 and increased proportionally in patients with 95GC RS >50. Pathological complete response (pCR) rates to NAC were increased in proportion to 95GC RS, indicating a greater sensitivity of breast cancers with high 95GC RS to chemotherapy. 95GC RS was highly correlated (R=0.92) between FF and FFPE tissues, and the concordance rate (94.6%) of high-and low-risk groups was also considerably high. Overall, the present study developed a 95GC RS that correlated with distant recurrence rate and pCR rate to NAC. The 95GC was applicable to FFPE tissues with a high concordance rate in FF tissues.

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Section: Gc -----------------------------------------------------mentioning

confidence: 99%

Development of recurrence risk score using 95‑gene classifier and its application to formalin‑fixed paraffin‑embedded tissues in ER‑positive, HER2‑negative and node‑negative breast cancer

et al. 2019

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“…Multigene approaches perform single-gene prognosis and diagnosis methods [ 29 , 30 ]. The data obtained in our laboratory [ 31 – 33 ] and other groups [ 34 ] suggest that aberrations in the human chromosome 3 frequently accompany the formation of tumors of the epithelial origin.…”

Section: Introductionmentioning

confidence: 99%

Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis

et al. 2015

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A significant need for reliable and accurate cancer diagnostics and prognosis compels the search for novel biomarkers that would be able to discriminate between indolent and aggressive tumors at the early stages of disease. The aim of this work was identification of potential diagnostic biomarkers for characterization of different types of prostate tumors. NotI-microarrays with 180 clones associated with chromosome 3 genes/loci were applied to determine genetic and epigenetic alterations in 33 prostate tumors. For 88 clones, aberrations were detected in more than 10% of tumors. The major types of alterations were DNA methylation and/or deletions. Frequent methylation of the discovered loci was confirmed by bisulfite sequencing on selective sampling of genes: FGF12, GATA2, and LMCD1. Three genes (BHLHE40, BCL6, and ITGA9) were tested for expression level alterations using qPCR, and downregulation associated with hypermethylation was shown in the majority of tumors. Based on these data, we proposed the set of potential biomarkers for detection of prostate cancer and discrimination between prostate tumors with different malignancy and aggressiveness: BHLHE40, FOXP1, LOC285205, ITGA9, CTDSPL, FGF12, LOC440944/SETD5, VHL, CLCN2, OSBPL10/ZNF860, LMCD1, FAM19A4, CAND2, MAP4, KY, and LRRC58. Moreover, we probabilistically estimated putative functional relations between the genes within each set using the network enrichment analysis.

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“…Therefore,weattemptedtodevelopanMGAthatcanclassify ER+/HER2− breast cancer patients treated with NAC into lowrisk and high-risk groups. 19 RNAs extracted from vacuum-assisted biopsy specimens obtained before NAC were subjected to the Affymetrix microarray assay, and the differentially expressed genes between poor responders (grade 1 by histological assessment) 20 and good responders (grades 2 and 3) were determined in the training set. Optimization of the MGA using these genes by the leave-one-out cross-validation method resulted in the con- High-CS; this was the case as well as in patients with residual cancerburden(RCBIIorRCBIII)inthevalidationcohort(Figure6).…”

Section: The 155g C For the Pred I C Ti On Of Recurren Ce Of Er+/hementioning

confidence: 99%

The multigene classifiers 95GC/42GC/155GC for precision medicine in ER‐positive HER2‐negative early breast cancer

et al. 2021

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Construction of multi-gene classifier for prediction of response to and prognosis after neoadjuvant chemotherapy for estrogen receptor positive breast cancers

Cited by 11 publications

References 39 publications

Development of recurrence risk score using 95‑gene classifier and its application to formalin‑fixed paraffin‑embedded tissues in ER‑positive, HER2‑negative and node‑negative breast cancer

Development of recurrence risk score using 95‑gene classifier and its application to formalin‑fixed paraffin‑embedded tissues in ER‑positive, HER2‑negative and node‑negative breast cancer

Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis

The multigene classifiers 95GC/42GC/155GC for precision medicine in ER‐positive HER2‐negative early breast cancer

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