scholarly journals Genetic mutation and biological pathway prediction based on whole slide images in breast carcinoma using deep learning

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Hui Qu ◽  
Mu Zhou ◽  
Zhennan Yan ◽  
He Wang ◽  
Vinod K. Rustgi ◽  
...  

AbstractBreast carcinoma is the most common cancer among women worldwide that consists of a heterogeneous group of subtype diseases. The whole-slide images (WSIs) can capture the cell-level heterogeneity, and are routinely used for cancer diagnosis by pathologists. However, key driver genetic mutations related to targeted therapies are identified by genomic analysis like high-throughput molecular profiling. In this study, we develop a deep-learning model to predict the genetic mutations and biological pathway activities directly from WSIs. Our study offers unique insights into WSI visual interactions between mutation and its related pathway, enabling a head-to-head comparison to reinforce our major findings. Using the histopathology images from the Genomic Data Commons Database, our model can predict the point mutations of six important genes (AUC 0.68–0.85) and copy number alteration of another six genes (AUC 0.69–0.79). Additionally, the trained models can predict the activities of three out of ten canonical pathways (AUC 0.65–0.79). Next, we visualized the weight maps of tumor tiles in WSI to understand the decision-making process of deep-learning models via a self-attention mechanism. We further validated our models on liver and lung cancers that are related to metastatic breast cancer. Our results provide insights into the association between pathological image features, molecular outcomes, and targeted therapies for breast cancer patients.

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A993-A994
Author(s):  
Caddie Dy Laberiano ◽  
Edwin Parra ◽  
Qiong Gan ◽  
Heladio Ibarguen ◽  
Shanyu Zang ◽  
...  

BackgroundBreast cancer(BC) is the second most common cause after lung cancer of malignant pleural effusions(MPEs),in approximately one third of all MPEs.Although,MPEs are relativity easy to be collated are still not well characterized in their cellular compositions. This opens new avenues to characterize the cellular milieu comprising the MPE, as it has the potential to be highly informative about mutational markers and immune response –ultimately guiding targeted therapy and predicting therapeutic outcomes with their study. The proposed study will characterize immune landscape of the cellular composition of MPE from patients with metastatic breast carcinoma and characterize their relationship with clinicopathologic features in these patients.Abstract 945 Figure 1Comparison between the cell block in H-E and mIF expression CK, CD68 and CD3Abstract 945 Figure 2Composite image in mIF expressing 8 markers. In higher magnification is possible to observe the co expression of CK+Ki67+, CK PDL1, CD3+Foxp3+ and CD3+CD8+Abstract 945 Table 1Results: cell phenotypes in percentage in the six cases analyzedAbstract 945 Table 2Clinical data of the six patients. L: left . R: right , BR : Breast cáncer, CRC: Colorrectal cáncer, NE: No evaluable , IDC : Invasive ductal carcinoma , CT: chemotherapy and BT : biotherapy* Last appointment of the patient.MethodsFive microns thickness paraffin cell pellet blocks from six cases randomly selected of breast carcinoma MPE were stained using a quantitative multiplex immunofluorescence(mIF) panel containing 8 markers against pancytokeratin(CK), PD-L1, PD-1, CD3, CD8, Foxp3, CD68, Ki67, and DAPI (figure 1). Representative regions of interest were scanned using a multispectral scanner (Vectra Polaris) in high magnification (20x) to capture different cell populations. Markers co-expression were processed and analyzed using a quantitative image analysis software (InForm). The final results were obtained as absolute number of cells from each phenotype and were characterized with clinicopathologic features.ResultsWe analyzed and stained six breast cancer MPE cases with previously optimized and validated mIF panel for formalin fixed and paraffin embedded (FFPE) tumor tissues against CK, CD3, CD68, CD8, Foxp3, Ki67, PD1 and PD-L1 (figure 2). The median cellular density was 5870.53 cells. Median for each marker: CK+ was presented in 75.9% (between malignant cells and reactive mesothelial cells) in these cells the expression of Ki67 was 8% and PD-L1+ was present in 0.2%.CD3+ was 0.72% and being the cytotoxic T-cells CD3+CD8+ was 12.13% of these cells and it expression for CD3+PD1+ was in 1.14% without concomitant expression for PD-L1. The median of the macrophages CD68+ was 8.1% of the total cells (table 2).ConclusionsmIF is a promising tool to study diverse corporal effusion from different origin. Although more studies are needed, this new perspective can help us to resolve some clues and possible prognosis in advanced stages of BC.ReferenceNicholas D T, Matthew A. S. Diagnosis and Management of Pleural Metastases and Malignant Effusion in Breast Cancer.En: Kirby I B, Edward M C, V. Suzanne K, William J. G. The Breast (Fifth Edition): Elsevier; 2018. P 934.


2019 ◽  
Vol 5 (1) ◽  
Author(s):  
David B. Page ◽  
Harry Bear ◽  
Sangeetha Prabhakaran ◽  
Margaret E. Gatti-Mays ◽  
Alexandra Thomas ◽  
...  

Abstract Antibodies blocking programmed death 1 (anti-PD-1) or its ligand (anti-PD-L1) are associated with modest response rates as monotherapy in metastatic breast cancer, but are generally well tolerated and capable of generating dramatic and durable benefit in a minority of patients. Anti-PD-1/L1 antibodies are also safe when administered in combination with a variety of systemic therapies (chemotherapy, targeted therapies), as well as with radiotherapy. We summarize preclinical, translational, and preliminary clinical data in support of combination approaches with anti-PD-1/L1 in metastatic breast cancer, focusing on potential mechanisms of synergy, and considerations for clinical practice and future investigation.


2009 ◽  
Vol 16 (4) ◽  
Author(s):  
Susan Faye Dent ◽  
Shailendra Verma ◽  
Kathleen I Pritchard ◽  
Jean Latreille ◽  
Daniel Rayson ◽  
...  

2020 ◽  
Vol 2020 (8) ◽  
Author(s):  
Saifullah Mohamed ◽  
Khurum Mazhar ◽  
Ahmed Osman ◽  
Akshay Patel ◽  
Lakshmi Srinivasan ◽  
...  

Abstract Metastatic breast carcinoma is a relatively common clinical entity. However, the prognosis of oligometastatic and polygometastatic disease differs considerably pertaining to five-year survival. Metastatic breast carcinoma to the sternum has been described as early as 1988. We describe two cases in our institution who presented with solitary sternal metastases with a previous history of treated breast cancer. In both cases, there had been a history of previous left breast cancer treated aggressively with surgical resection and adjuvant oncological therapy and maintenance hormonal therapy. Partial sternectomy or total sternectomy for solitary metastatic sternal deposits is well established with relatively low morbidity and mortality and improvement in quality of life and possible improvement in long-term survival. Furthermore, reconstructive options are inherently dependent on extent of resection performed. These techniques can incorporate the use of sternal plates in order to approximate defects and reinforce the sternum in the setting of partial sternectomy.


1994 ◽  
Vol 12 (2) ◽  
pp. 336-341 ◽  
Author(s):  
A Romero ◽  
M G Rabinovich ◽  
C T Vallejo ◽  
J E Perez ◽  
R Rodriguez ◽  
...  

PURPOSE A phase II trial was performed to evaluate the efficacy and toxicity of vinorelbine (VNB) as first-line chemotherapy for metastatic breast carcinoma. PATIENTS AND METHODS Between August 1991 and February 1993, 45 patients with metastatic breast cancer were entered onto the study. Therapy consisted of VNB 30 mg/m2 diluted in 500 mL of normal saline administered as a 1-hour intravenous infusion. Injections were repeated weekly until evidence of progressive disease (PD) or severe toxicity developed. RESULTS One patient was considered not assessable for response. An objective response (OR) was observed in 18 of 44 patients (41%; 95% confidence interval, 26% to 56%). Three patients (7%) had a complete response (CR) and 15 (34%) had a partial response (PR). The median time to treatment failure for the entire group was 6 months (range, 1 to 15), and the median duration of response was 9 months (range, 1 to 15). The median survival duration has not been reached yet. There were no treatment-related deaths. The dose-limiting toxicity was myelosuppression. Leukopenia occurred in 35 patients (78%) and was grade 3 or 4 in 16 (36%). Phlebitis was observed in 19 of 29 patients (66%) who did not have central implantable venous systems. Fifteen patients (33%) developed peripheral neurotoxicity. Myalgia occurred in 20 patients (44%). CONCLUSION VNB is an active drug against metastatic breast cancer with moderate toxicity, which justifies further evaluation in association with other agents.


2020 ◽  
Vol 38 (29_suppl) ◽  
pp. 282-282
Author(s):  
Sandhya Mehta ◽  
Jinlin Song ◽  
Melissa Pavilack ◽  
Jipan Xie ◽  
Xiaoyu Nie ◽  
...  

282 Background: HER2-positive (+) metastatic breast cancer (mBC) has a poor prognosis and many patients require multiple lines of HER2 targeted regimens. This study aims to examine the treatment sequencing of anti-HER2 regimens for HER2+ mBC among Medicare beneficiaries. Methods: A retrospective study was conducted using linked 1999-2016 Surveillance, Epidemiology, and End Results (SEER) cancer registries and Medicare claims. Adults patients who had mBC diagnosis, HER2+ status documented in SEER or claims of ≥1 anti-HER2 drug, continuous enrollment in Medicare from the date of mBC diagnosis until end of study period/death, and 2 anti-HER2 regimens with or without chemotherapy (Ch) or hormonal therapy (HT) were included. Discontinuation of anti-HER2 regimen was defined as the absence of claims for all anti-HER2 drugs for >60 days, or initiation of a different anti-HER2 drug. Re-initiation of the same regimen after >60 days was considered as a new regimen. The first two anti-HER2 regimens and subsequent therapies were summarized. Results: 804 patients with 2 anti-HER2 regimens were included. Trastuzumab (T) based regimen (defined as: T±Ch/HT; without other anti-HER2 drugs) was the most common 1st regimen (82%), followed by T+ pertuzumab (P) (14%) and lapatinib (L) (3%). For the 2nd regimen, T (52%) was most common, followed by T+P (18%), L (11%), trastuzumab emtansine (T-DM1) (11%) and T+L (7%). After a 2nd regimen, 578 (72%) initiated a subsequent therapy, with over half switching to non-targeted therapies [52%; HT alone (35%), Ch±HT (17%)] followed by T (17%), T-DM1 (12%) and T+P (7%). Among those with subsequent therapy, 2 T-based regimens followed by HT alone (21%) was the most common sequence. After the 1st regimen, 52% patients reused the same anti-HER2 drugs in the 2nd regimen, 21% added another anti-HER2 drug and 27% switched to a different anti-HER2 regimen. After the 2nd regimen, 14% reused anti-HER2 drugs and 6% added another anti-HER2 drug, 25% switched to a different anti-HER2 regimen; 15% reused anti-HER2 drugs from the 1st regimen. Conclusions: Trastuzumab based regimen was the mainstay of anti-HER2 drug regimens during the study timeframe. Despite availability of multiple anti-HER2 drugs, reuse of prior anti-HER2 drugs and switching to non-targeted therapies alone were common after using 2 anti-HER2 regimens. These findings underscore the unmet needs in later lines of therapy. Recently approved anti-HER2 agents may provide additional treatment options for pre-treated HER2+ metastatic breast cancer patients.


2020 ◽  
Vol 38 (15_suppl) ◽  
pp. TPS1115-TPS1115
Author(s):  
Shruti Trehan ◽  
Suzan S. Cheng ◽  
Aleck Hercbergs

TPS1115 Background: It is estimated that there are approximately 155,000 people living with metastatic breast cancer in the US. Studies exploring the connection between hypothyroidism or hyperthyroidism and breast cancer have yielded varying results with up to 33% prevalence of thyroid disease in these patients. L-thyroxine (T4) is the most commonly prescribed agent in the US to manage hypothyroidism. However, there are data suggesting that T4 is a pro-oncogenic agent with proposed mechanisms such as stimulation of mitogenesis, angiogenesis, resistance to apoptosis. In addition, T4 May counter anti-PDL-1 and radiation effects. Triiodothyronine (T3), which is deiodinated form of T4 and also commercially available, is felt to be less oncogenic and less mitogenic. Therefore, exogenous supplementation of T3 would decrease the T4 levels creating the desired state of EUTHYROID HYPOTHYROXINEMIA. The study hypothesizes that replacing L-thyroxine (T4) with Triiodothyronine (T3) in hypothyroid patients with metastatic breast carcinoma, while they simultaneously continue to receive standard systemic therapy, with titrating T3 dose to achieve a state of Euthyroid Hypothyroxinemia would result in improved disease outcomes. Methods: Eligible participants are adults with metastatic breast carcinoma with estimated life expectancy of > 3months, hypothyroidism, and with normal TSH on L-thyroxine (T4). Following consent, participants will discontinue L-thyroixne (T4) and initiate Triiodothyronine (T3) dose based on current T4 dose after an appropriate washout period. Drug titration will be in accordance with thyroid function testing to maintain levels of free T4 at < 50% normal range. The treatment period will continue for 9 months with periodic assessment of disease status, quality of life (FACT-B) and laboratory measures. The primary endpoint is the progression free survival at 12 months while the secondary endpoints are prevalence of hypothyroidism in the cohort, overall survival, quality of life, and duration of time to achieve the Euthyroid Hypothyroxinemia state. Given many uncertainties to calculate power precisely, the sample size is estimated to be approximately 30 patients. Clinical trial information: NCT03787303 .


Cancer ◽  
2016 ◽  
Vol 122 (17) ◽  
pp. 2654-2662 ◽  
Author(s):  
Jeffrey S. Ross ◽  
Laurie M. Gay ◽  
Kai Wang ◽  
Siraj M. Ali ◽  
Saranya Chumsri ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document