Breast Invasive Carcinoma

Citation Author(s):
Giovanni
Ciriello
Department of Medical Genetics, University of Lausanne (UNIL), 1011 Lausanne, Switzerland
Michael L
Gatza
Andrew H
Beck
Matthew D
Wilkerson
Suhn K
Rhie
Alessandro
Pastore
Hailei
Zhang
Michael
McLellan
Christina
Yau
Cyriac
Kandoth
Reanne
Bowlby
Hui
Shen
Sikander
Hayat
Robert
Fieldhouse
Susan C
Lester
Gary M K
Tse
Rachel E
Factor
Laura C
Collins
Kimberly H
Allison
Yunn-Yi
Chen
Kristin
Jensen
Nicole B
Johnson
Steffi
Oesterreich
Gordon B
Mills
Andrew D
Cherniack
Gordon
Robertson
Christopher
Benz
Chris
Sander
Peter W
Laird
Katherine A
Hoadley
Tari A
King
TCGA Research
Network
Charles M
Perou
Submitted by:
Raktim Kumar Mondol
Last updated:
Tue, 06/23/2020 - 07:54
DOI:
10.21227/2wtc-wd25
Links:
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Abstract 

Invasive lobular carcinoma (ILC) is the second most prevalent histologic subtype of invasive breast cancer. Here, we comprehensively profiled 817 breast tumors, including 127 ILC, 490 ductal (IDC), and 88 mixed IDC/ILC. Besides E-cadherin loss, the best known ILC genetic hallmark, we identified mutations targeting PTEN, TBX3 and FOXA1 as ILC enriched features. PTEN loss associated with increased AKT phosphorylation, which was highest in ILC among all breast cancer subtypes. Spatially clustered FOXA1 mutations correlated with increased FOXA1 expression and activity. Conversely, GATA3 mutations and high expression characterized Luminal A IDC, suggesting differential modulation of ER activity in ILC and IDC. Proliferation and immune-related signatures determined three ILC transcriptional subtypes associated with survival differences. Mixed IDC/ILC cases were molecularly classified as ILC-like and IDC-like revealing no true hybrid features. This multidimensional molecular atlas sheds new light on the genetic bases of ILC and provides potential clinical options.

Instructions: 

RNA Seq expression median has been used and case lists have been utilized to label the dataset.
The details of the datasets are the following:
There are 605 Number of Samples (Patients) and there are 20439 Number of Features (Genes).
Luminal A is labeled as 0 (zero), Luminal B is labeled as 1 (one), Basal & Triple Negetive are labelled as 2 (two) and Her 2 Positive is labeled as 3 (three).

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Submitted by santhosh s on Thu, 12/24/2020 - 04:22