Jelle Wesseling - Academia.edu (original) (raw)
Papers by Jelle Wesseling
Breast Cancer Research, Jun 19, 2023
Background The introduction of pertuzumab has greatly improved pathological complete response (pC... more Background The introduction of pertuzumab has greatly improved pathological complete response (pCR) rates in HER2-positive breast cancer, yet effects on long-term survival have been limited and it is uncertain which patients derive most benefit. In this study, we determine the prognostic value of BluePrint subtyping in HER2-positive breast cancer. Additionally, we evaluate its use as a biomarker for predicting response to trastuzumab-containing neoadjuvant chemotherapy with or without pertuzumab. Methods From a cohort of patients with stage II-III HER2-positive breast cancer who were treated with neoadjuvant chemotherapy and trastuzumab with or without pertuzumab, 836 patients were selected for microarray gene expression analysis, followed by readout of BluePrint standard (HER2, Basal and Luminal) and dual subtypes (HER2-single, Basal-single, Luminal-single, HER2-Basal, Luminal-HER2, Luminal-HER2-Basal). The associations between subtypes and pathological complete response (pCR), overall survival (OS) and breast cancer-specific survival (BCSS) were assessed, and pertuzumab benefit was evaluated within the BluePrint subgroups. Results BluePrint results were available for 719 patients. In patients with HER2-type tumors, the pCR rate was 71.9% in patients who received pertuzumab versus 43.5% in patients who did not (adjusted Odds Ratio 3.43, 95% CI 2.36-4.96). Additionally, a significantly decreased hazard was observed for both OS (adjusted hazard ratio [aHR] 0.45, 95% CI 0.25-0.80) and BCSS (aHR 0.46, 95% CI 0.24-0.86) with pertuzumab treatment. Findings were similar in the HER2-single subgroup. No significant benefit of pertuzumab was seen in other subtypes. Conclusions In patients with HER2-type or HER2-single-type tumors, pertuzumab significantly improved the pCR rate and decreased the risk of breast cancer mortality, which was not observed in other subtypes. BluePrint subtyping may be valuable in future studies to identify patients that are likely to be highly sensitive to HER2-targeting agents.
British Journal of Cancer, Feb 10, 2023
BACKGROUND: Studies have shown that blood platelets contain tumour-specific mRNA profiles tumour-... more BACKGROUND: Studies have shown that blood platelets contain tumour-specific mRNA profiles tumour-educated platelets (TEPs). Here, we aim to train a TEP-based breast cancer detection classifier. METHODS: Platelet mRNA was sequenced from 266 women with stage I-IV breast cancer and 212 female controls from 6 hospitals. A particle swarm optimised support vector machine (PSO-SVM) and an elastic net-based classifier (EN) were trained on 71% of the study population. Classifier performance was evaluated in the remainder (29%) of the population, followed by validation in an independent set (37 cases and 36 controls). Potential confounding was assessed in post hoc analyses. RESULTS: Both classifiers reached an area under the curve (AUC) of 0.85 upon internal validation. Reproducibility in the independent validation set was poor with an AUC of 0.55 and 0.54 for the PSO-SVM and EN classifier, respectively. Post hoc analyses indicated that 19% of the variance in gene expression was associated with hospital. Genes related to platelet activity were differentially expressed between hospitals. CONCLUSIONS: We could not validate two TEP-based breast cancer classifiers in an independent validation cohort. The TEP protocol is sensitive to within-protocol variation and revision might be necessary before TEPs can be reconsidered for breast cancer detection.
Breast Cancer Research, May 15, 2014
Introduction: BRCA-mutated breast cancer cells lack the DNA-repair mechanism homologous recombina... more Introduction: BRCA-mutated breast cancer cells lack the DNA-repair mechanism homologous recombination that is required for error-free DNA double-strand break (DSB) repair. Homologous recombination deficiency (HRD) may cause hypersensitivity to DNA DSB-inducing agents, such as bifunctional alkylating agents and platinum salts. HRD can be caused by BRCA mutations, and by other mechanisms. To identify HRD, studies have focused on triple-negative (TN) breast cancers as these resemble BRCA1-mutated breast cancer closely and might also share this hypersensitivity. However, ways to identify HRD in non-BRCA-mutated, estrogen receptor (ER)-positive breast cancers have remained elusive. The current study provides evidence that genomic patterns resembling BRCA1-or BRCA2-mutated breast cancers can identify breast cancer patients with TN as well as ER-positive, HER2-negative tumors that are sensitive to intensified, DSB-inducing chemotherapy. Methods: Array comparative genomic hybridization (aCGH) was used to classify breast cancers. Patients with tumors with similar aCGH patterns as BRCA1-and/or BRCA2-mutated breast cancers were defined as having a BRCA-like CGH status, others as non-BCRA-like CGH. Stage-III patients (n = 249) had participated in a randomized controlled trial of adjuvant high-dose (HD) cyclophosphamide-thiotepa-carboplatin (CTC) versus 5-fluorouracil-epirubicin-cyclophosphamide (FE 90 C) chemotherapy. Results: Among patients with BRCA-like CGH tumors (81/249, 32%), a significant benefit of HD-CTC compared to FE 90 C was observed regarding overall survival (adjusted hazard ratio 0.19, 95% CI: 0.08 to 0.48) that was not seen for patients with non-BRCA-like CGH tumors (adjusted hazard ratio 0.90, 95% CI: 0.53 to 1.54) (P = 0.004). Half of all BRCA-like CGH tumors were ER-positive. Conclusions: Distinct aCGH patterns differentiated between HER2-negative patients with a markedly improved outcome after adjuvant treatment with an intensified DNA-DSB-inducing regimen (BRCA-like CGH patients) and those without benefit (non-BRCA-like CGH patients).
Cancer Research
Introduction: Ductal Carcinoma In Situ (DCIS) is a proliferation of neoplastic cells confined to ... more Introduction: Ductal Carcinoma In Situ (DCIS) is a proliferation of neoplastic cells confined to the ducto-lobular system. Due to uncertainty which DCIS lesions progress to invasive breast cancer women with DCIS receive surgery and radiotherapy. The PRECISION (PREvent ductal carcinoma In Situ Invasive Overtreatment Now) initiative intends to improve the management of DCIS including reduction of unnecessary treatment. Histological high grade is an unfavorable prognostic indicator used to guide treatment decisions, and used as an exclusion criterion for DCIS trials that randomize between active surveillance and standard treatment. Hence, accurate assessment of grade is important in current clinical practice. Pathologists within PRECISION setup this study to compare histological parameters of four retrospective DCIS cohorts from three different countries to investigate interobserver variability particularly in grading of DCIS. Method: Tissue slides from two population-based cohorts (UK...
PLOS ONE, 2017
Pathological response of breast cancer to neoadjuvant chemotherapy (NAC) presents great variabili... more Pathological response of breast cancer to neoadjuvant chemotherapy (NAC) presents great variability, and new prognostic biomarkers are needed. Our aim was to evaluate the association of the epidermal growth factor receptor gene (EGFR) polymorphism R497K (rs2227983) with prognostic features and clinical outcomes of breast cancer, including the pathological response to NAC and the recurrence-free survival (RFS). Tumoral complete response (tCR) was defined by no remaining invasive cancer in the excised breast, whereas pathological complete response (pCR) was defined by no remaining invasive cancer both in the excised breast and lymph nodes. Two independent cohorts were analyzed: one from Brazil (INCA, n = 288) and one from The Netherlands (NKI-AVL, n = 255). In the INCA cohort, the variant (Lys-containing) genotypes were significantly associated with lower proportion of tCR (OR adj = 0.92; 95%CI = 0.85-0.99), whereas in the NKI-AVL cohort they were associated with tumor grade 3 (p = 0.035) and with triple-negative subtype (p = 0.032), but not with clinical outcomes. Such distinct prognostic associations may have arisen due to different neoadjuvant protocols (p < 0.001), or to lower age at diagnosis (p < 0.001) and higher proportion of tumor grade 3 (p = 0.018) at the NKI-AVL cohort. Moreover, NKI-AVL patients achieved better proportion of pCR (21.2% vs 8.3%, p < 0.001) and better RFS (HR adj = 0.48; 95% adj CI = 0.26-0.86) than patients from INCA. In conclusion, large scale studies comprehending different populations are needed to evaluate the impact of genome variants on breast cancer outcomes.
Nederlands Tijdschrift voor Geneeskunde, 2016
Since population-based breast cancer screening was implemented in the Netherlands, the incidence ... more Since population-based breast cancer screening was implemented in the Netherlands, the incidence of Ductal Carcinoma In Situ of the breast, regarded as a non-obligate precursor lesion of breast cancer, has strongly increased. However, the incidence of invasive breast cancer has not decreased. This suggests that a percentage of all the DCIS lesions would never have become symptomatic if no screening was performed. This phenomenon is known as 'overdiagnosis'. Nonetheless, almost all DCIS lesions are managed surgically, often followed by radiotherapy in those having breast-conserving treatment, to avoid potential progression to breast cancer. To prevent potential over- or undertreatment, further studies are required to distinguish low from high risk DCIS. Ultimately this could help avoid non-beneficial intensive treatment for women with low risk DCI
The Breast, 2020
Objective: The majority of 'low-risk' (grade I/II) Ductal Carcinoma In Situ (DCIS) may not progre... more Objective: The majority of 'low-risk' (grade I/II) Ductal Carcinoma In Situ (DCIS) may not progress to invasive breast cancer during a women's lifetime. Therefore, the safety of active surveillance versus standard surgical treatment for DCIS is prospectively being evaluated in clinical trials. If proven safe and selectively implemented in clinical practice, a significant group of women with low-risk DCIS may forego surgery and radiotherapy in the future. Identification of modifiable and non-modifiable risk factors associated with prognosis after a primary DCIS would also enhance our care of women with low-risk DCIS. Methods: To identify modifiable and non-modifiable risk factors for subsequent breast events after DCIS, we performed a systematic literature search in PUBMED, EMBASE and Scopus. Results: Six out of the 3870 articles retrieved were included for final data extraction. These six studies included a total of 4950 patients with primary DCIS and 640 recorded subsequent breast events. There was moderate evidence for an association of a family history of breast cancer, premenopausal status, high BMI, and high breast density with a subsequent breast cancer or further DCIS. Conclusion: There is a limited number of recent studies published on the impact of modifiable and nonmodifiable risk factors on subsequent events after DCIS. The available evidence is insufficient to identify potential targets for risk reduction strategies, reflecting the relatively small numbers and the lack of longterm follow-up in DCIS, a low-event condition.
American Journal of Surgical Pathology, 2019
Ductal carcinoma in situ (DCIS) is considered a potential precursor of invasive breast carcinoma ... more Ductal carcinoma in situ (DCIS) is considered a potential precursor of invasive breast carcinoma (IBC). Studies aiming to find markers involved in DCIS progression generally have compared characteristics of IBC lesions with those of adjacent synchronous DCIS lesions. The question remains whether synchronous DCIS and IBC comparisons are a good surrogate for primary DCIS and subsequent IBC. In this study, we compared both primary DCIS and synchronous DCIS with the associated IBC lesion, on the basis of immunohistochemical marker expression. Immunohistochemical analysis of ER, PR, HER2, p53, and cyclo-oxygenase 2 (COX-2) was performed for 143 primary DCIS and subsequent IBC lesions, including 81 IBC lesions with synchronous DCIS. Agreement between DCIS and IBC was assessed using kappa, and symmetry tests were performed to assess the pattern in marker conversion. The primary DCIS and subsequent IBC more often showed discordant marker expression than synchronous DCIS and IBC. Strikingly, 18 of 49 (36%) women with HER2-positive primary DCIS developed an HER2-negative IBC. Such a difference in HER2 expression was not observed when comparing synchronous DCIS and IBC. The frequency of discordant marker expression did not increase with longer time between primary DCIS and IBC. In conclusion, comparison of primary DCIS and subsequent IBC yields different results than a comparison of synchronous DCIS and IBC, in particular with regard to HER2 status. To gain more insight into the progression of DCIS to IBC, it is essential to focus on the relationship between primary DCIS and subsequent IBC, rather than comparing IBC with synchronous DCIS.
Cancer Research, 2017
Background Cancer classification, prognostication, and prediction of treatment sensitivity increa... more Background Cancer classification, prognostication, and prediction of treatment sensitivity increasingly rely on DNA and RNA-based tests. This approach requires sufficiently high tumor cell percentages to yield enough DNA or RNA for reliable test results. As a consequence, samples of insufficient quality may drop out, e.g. due to poor cellularity or high numbers of tumor infiltrating lymphocytes. We hypothesized that requiring a high tumor cell percentage and high quality RNA causes systemic bias when interpreting genomic test results in breast cancer, as specific breast cancer subgroups may be over- or underrepresented. Patients and methods For this analysis, we used pre-treatment frozen samples from patients included in neoadjuvant chemotherapy trials at the Netherlands Cancer Institute between 2004 and 2012. Histological features and tumor cell percentage were reviewed and assessed by a consultant breast pathologist. Gene expression profiling was done if the tumor cell percentage ...
Cancer Research, 2017
Background Neoadjuvant chemotherapy is standard of care for locally advanced breast cancer. Unfor... more Background Neoadjuvant chemotherapy is standard of care for locally advanced breast cancer. Unfortunately not all patients benefit from this treatment. Even after decades of research, we still cannot predict which tumor will or will not respond. This may in part be due to tumor heterogeneity, as the sample taken before treatment not necessarily represents the tumor cell population that causes therapy resistance. Methods To test this hypothesis, we collected pre-treatment biopsies, resection specimens, and matched blood from 21 breast cancer patients treated with doxorubicin and cyclophosphamide in a neoadjuvant setting. Specifically, tumors were selected with a tumor percentage >50% after chemotherapy to enrich for resistant samples and ensure high quality data. RNA and whole exome sequencing were performed to characterize somatic mutations, copy number alterations and gene expression profiles. Histopathological characteristics were determined to obtain a comprehensive profile of...
International Journal of Radiation Oncology*Biology*Physics, 2017
moiety on AuNPs from an agonist of FRa, to anti-FRa Ig, an antibody (Ab) that binds to FRa withou... more moiety on AuNPs from an agonist of FRa, to anti-FRa Ig, an antibody (Ab) that binds to FRa without inducing proliferative or mitogenic effects. Materials/Methods: Pegylated 20 nm AuNPs (pAuNPs) were synthesized and conjugated to nonspecific rabbit IgG Ab (rAuNPs) or targeted anti-FRa Ab (aAuNPs). AuNPs were characterized by zeta potential, hydrodynamic diameters and absorption spectra. Uptake by MDA-MB-231 cells was analyzed qualitatively using dark field microscopy. In-vitro radiosensitization potential by aAuNPs was assessed via clonogenic assay using clinically relevant, 6MV RT. Results: Surface plasmon resonance peaks of pAuNPs, rAuNPs, and aAuNPs were observed at 521AE2 nm. AuNP zeta potentials were:-34AE6 mV (bare AuNPs),-8AE4 mV (pAuNPs),-1AE6 mV (rAuNPs), and-5AE5 mV (aAuNPs). Hydrodynamic diameters determined by dynamic light scattering were: 33AE12 nm (bare AuNPs), 56AE18 nm (pAuNPs), 64AE22 nm (rAuNPs), and 62AE17 nm (aAuNPs). aAuNPs demonstrated significant radiosensitization with a dose enhancement factor of 1.15 calculated at 10% cell survival relative to RT alone. Conclusion: AuNPs conjugated to anti-FRa Ab sensitize triple negative breast cancer cells to radiation and present a viable strategy to target cancer cells at the molecular level.
Molecular Cancer Research, 2013
Background: BRCA1 mutated breast tumor cells are defective in DNA repair by homologous recombinat... more Background: BRCA1 mutated breast tumor cells are defective in DNA repair by homologous recombination and therefore especially sensitive to treatment with DNA double-strand break (DSB) inducing agents, such as alkylators and PARP inhibitors. However, such tumors can eventually develop therapy resistance. Understanding the underlying mechanisms may help in designing strategies to avoid or overcome acquired therapy resistance. Methods: We have developed patient derived xenograft (PDX) models of BRCA1-deficient triple-negative breast cancer (TNBC) by implantating fresh human breast tumor pieces and subsequent serial passaging. These models show epigenetic loss of BRCA1 due to promoter hypermethylation or genetic inactivation of BRCA1 due to a frameshift mutation (c.2210delC) resulting in a premature stop codon (p.Thr737LeufsX15). We have used these 3 BRCA1-deficient TNBC models to study response and acquisition of resistance to alkylating therapy (cisplatin, melphalan, nimustine) and th...
Purpose: Extensive work in preclinical models has shown that microenvironmental cells influence m... more Purpose: Extensive work in preclinical models has shown that microenvironmental cells influence many aspects of cancer cell behavior, including metastatic potential and their sensitivity to therapeutics. In the human setting, this behavior is mainly correlated with the presence of immune cells. Here, in addition to T cells, B cells, macrophages, and mast cells, we identified the relevance of nonimmune cell types for breast cancer survival and therapy benefit, including fibroblasts, myoepithelial cells, muscle cells, endothelial cells, and seven distinct epithelial cell types. Experimental Design: Using single-cell sequencing data, we generated reference profiles for all these cell types. We used these reference profiles in deconvolution algorithms to optimally detangle the cellular composition of more than 3,500 primary breast tumors of patients that were enrolled in the SCAN-B and MATADOR clinical trials, and for which bulk mRNA sequencing data were available. Results: This large data set enables us to identify and subsequently validate the cellular composition of microenvironments that distinguish differential survival and treatment benefit for different treatment regimens in patients with primary breast cancer. In addition to immune cells, we have identified that survival and therapy benefit are characterized by various contributions of distinct epithelial cell types. Conclusions: From our study, we conclude that differential survival and therapy benefit of patients with breast cancer are characterized by distinct microenvironments that include specific populations of immune and epithelial cells.
medRxiv (Cold Spring Harbor Laboratory), Nov 11, 2022
Invasive breast cancer patients are increasingly being treated with neoadjuvant chemotherapy, how... more Invasive breast cancer patients are increasingly being treated with neoadjuvant chemotherapy, however, only a fraction of the patients respond to it completely. To prevent over-treating patients with a toxic drug, there is an urgent need for biomarkers capable of predicting treatment response before administering the therapy. In this retrospective study, we developed interpretable, deep-learning based biomarkers to predict the pathological complete response (pCR, i.e. the absence of tumor cells in the surgical resection specimens) to neoadjuvant chemotherapy from digital pathology H&E images of pre-treatment breast biopsies. Experimental Design: Our approach consists of two steps: In the first step, using deep learning, mitoses are detected and the tissue segmented into several morphology compartments including tumor, lymphocytes and stroma. In the second step, computational biomarkers are derived from the segmentation and detection output to encode slide-level relationships between the morphological structures with focus on tumor infiltrating lymphocytes (TILs). We developed and evaluated our method on slides from N=721 patients from three European medical centers with triple-negative and Luminal B breast cancers. Results: The investigated biomarkers yield statistically significant prediction performance for pCR with areas under the receiver operating characteristic curve between 0.66 and 0.88 depending on the cancer subtype and center. Conclusion: The proposed computational biomarkers predict pathological complete response, but will require more evaluation and finetuning for clinical
British Journal of Cancer, Apr 4, 2013
Background: BRCAness is defined as shared tumour characteristics between sporadic and BRCA-mutate... more Background: BRCAness is defined as shared tumour characteristics between sporadic and BRCA-mutated cancers. However, how to exactly measure BRCAness and its frequency in breast cancer is not known. Assays to establish BRCAness would be extremely valuable for the clinical management of these tumours. We assessed BRCAness characteristics frequencies in a large cohort of triple-negative breast cancers (TNBCs). Methods: As a measure of BRCAness, we determined a specific BRCA1-like pattern by array Comparative Genomic Hybridisation (aCGH), and BRCA1 promoter methylation in 377 TNBCs, obtained from 3 different patient cohorts. Clinicopathological data were available for all tumours, BRCA1-germline mutation status and chemotherapy response data were available for a subset. Results: Of the tumours, 66-69% had a BRCA1-like aCGH profile and 27-37% showed BRCA1 promoter methylation. BRCA1germline mutations and BRCA1 promoter methylation were mutually exclusive events (P ¼ 1 Â 10 À 5). BRCAness was associated with younger age and grade 3 tumours. Chemotherapy response was significantly higher in BRCA1-mutated tumours, but not in tumours with BRCAness (63% (12 out of 19) vs 35% (18 out of 52) pathological complete remission rate, respectively). Conclusion: The majority of the TNBCs show BRCAness, and those tumours share clinicopathological characteristics with BRCA1-mutated tumours. A better characterisation of TNBC and the presence of BRCAness could have consequences for both hereditary breast cancer screening and the treatment of these tumours.
Purpose: Ductal carcinoma in situ (DCIS) is treated to prevent progression to invasive breast can... more Purpose: Ductal carcinoma in situ (DCIS) is treated to prevent progression to invasive breast cancer. Yet, most lesions will never progress, implying that overtreatment exists. Therefore, we aimed to identify factors distinguishing harmless from potentially hazardous DCIS using a nested case–control study.Experimental Design: We conducted a case–control study nested in a population-based cohort of patients with DCIS treated with breast-conserving surgery (BCS) alone (N = 2,658) between 1989 and 2005. We compared clinical, pathologic, and IHC DCIS characteristics of 200 women who subsequently developed ipsilateral invasive breast cancer (iIBC; cases) and 474 women who did not (controls), in a matched setting. Median follow-up time was 12.0 years (interquartile range, 9.0–15.3). Conditional logistic regression models were used to assess associations of various factors with subsequent iIBC risk after primary DCIS.Results: High COX-2 protein expression showed the strongest association w...
Nature Reviews Cancer, Dec 15, 2022
npj Breast Cancer
When locally advanced breast cancer is treated with neoadjuvant chemotherapy, the recurrence risk... more When locally advanced breast cancer is treated with neoadjuvant chemotherapy, the recurrence risk is significantly higher if no complete pathologic response is achieved. Identification of the underlying resistance mechanisms is essential to select treatments with maximal efficacy and minimal toxicity. Here we employed gene expression profiles derived from 317 HER2-negative treatment-naïve breast cancer biopsies of patients who underwent neoadjuvant chemotherapy, deep whole exome, and RNA-sequencing profiles of 22 matched pre- and post-treatment tumors, and treatment outcome data to identify biomarkers of response and resistance mechanisms. Molecular profiling of treatment-naïve breast cancer samples revealed that expression levels of proliferation, immune response, and extracellular matrix (ECM) organization combined predict response to chemotherapy. Triple negative patients with high proliferation, high immune response and low ECM expression had a significantly better treatment res...
Breast Cancer Research, Jun 19, 2023
Background The introduction of pertuzumab has greatly improved pathological complete response (pC... more Background The introduction of pertuzumab has greatly improved pathological complete response (pCR) rates in HER2-positive breast cancer, yet effects on long-term survival have been limited and it is uncertain which patients derive most benefit. In this study, we determine the prognostic value of BluePrint subtyping in HER2-positive breast cancer. Additionally, we evaluate its use as a biomarker for predicting response to trastuzumab-containing neoadjuvant chemotherapy with or without pertuzumab. Methods From a cohort of patients with stage II-III HER2-positive breast cancer who were treated with neoadjuvant chemotherapy and trastuzumab with or without pertuzumab, 836 patients were selected for microarray gene expression analysis, followed by readout of BluePrint standard (HER2, Basal and Luminal) and dual subtypes (HER2-single, Basal-single, Luminal-single, HER2-Basal, Luminal-HER2, Luminal-HER2-Basal). The associations between subtypes and pathological complete response (pCR), overall survival (OS) and breast cancer-specific survival (BCSS) were assessed, and pertuzumab benefit was evaluated within the BluePrint subgroups. Results BluePrint results were available for 719 patients. In patients with HER2-type tumors, the pCR rate was 71.9% in patients who received pertuzumab versus 43.5% in patients who did not (adjusted Odds Ratio 3.43, 95% CI 2.36-4.96). Additionally, a significantly decreased hazard was observed for both OS (adjusted hazard ratio [aHR] 0.45, 95% CI 0.25-0.80) and BCSS (aHR 0.46, 95% CI 0.24-0.86) with pertuzumab treatment. Findings were similar in the HER2-single subgroup. No significant benefit of pertuzumab was seen in other subtypes. Conclusions In patients with HER2-type or HER2-single-type tumors, pertuzumab significantly improved the pCR rate and decreased the risk of breast cancer mortality, which was not observed in other subtypes. BluePrint subtyping may be valuable in future studies to identify patients that are likely to be highly sensitive to HER2-targeting agents.
British Journal of Cancer, Feb 10, 2023
BACKGROUND: Studies have shown that blood platelets contain tumour-specific mRNA profiles tumour-... more BACKGROUND: Studies have shown that blood platelets contain tumour-specific mRNA profiles tumour-educated platelets (TEPs). Here, we aim to train a TEP-based breast cancer detection classifier. METHODS: Platelet mRNA was sequenced from 266 women with stage I-IV breast cancer and 212 female controls from 6 hospitals. A particle swarm optimised support vector machine (PSO-SVM) and an elastic net-based classifier (EN) were trained on 71% of the study population. Classifier performance was evaluated in the remainder (29%) of the population, followed by validation in an independent set (37 cases and 36 controls). Potential confounding was assessed in post hoc analyses. RESULTS: Both classifiers reached an area under the curve (AUC) of 0.85 upon internal validation. Reproducibility in the independent validation set was poor with an AUC of 0.55 and 0.54 for the PSO-SVM and EN classifier, respectively. Post hoc analyses indicated that 19% of the variance in gene expression was associated with hospital. Genes related to platelet activity were differentially expressed between hospitals. CONCLUSIONS: We could not validate two TEP-based breast cancer classifiers in an independent validation cohort. The TEP protocol is sensitive to within-protocol variation and revision might be necessary before TEPs can be reconsidered for breast cancer detection.
Breast Cancer Research, May 15, 2014
Introduction: BRCA-mutated breast cancer cells lack the DNA-repair mechanism homologous recombina... more Introduction: BRCA-mutated breast cancer cells lack the DNA-repair mechanism homologous recombination that is required for error-free DNA double-strand break (DSB) repair. Homologous recombination deficiency (HRD) may cause hypersensitivity to DNA DSB-inducing agents, such as bifunctional alkylating agents and platinum salts. HRD can be caused by BRCA mutations, and by other mechanisms. To identify HRD, studies have focused on triple-negative (TN) breast cancers as these resemble BRCA1-mutated breast cancer closely and might also share this hypersensitivity. However, ways to identify HRD in non-BRCA-mutated, estrogen receptor (ER)-positive breast cancers have remained elusive. The current study provides evidence that genomic patterns resembling BRCA1-or BRCA2-mutated breast cancers can identify breast cancer patients with TN as well as ER-positive, HER2-negative tumors that are sensitive to intensified, DSB-inducing chemotherapy. Methods: Array comparative genomic hybridization (aCGH) was used to classify breast cancers. Patients with tumors with similar aCGH patterns as BRCA1-and/or BRCA2-mutated breast cancers were defined as having a BRCA-like CGH status, others as non-BCRA-like CGH. Stage-III patients (n = 249) had participated in a randomized controlled trial of adjuvant high-dose (HD) cyclophosphamide-thiotepa-carboplatin (CTC) versus 5-fluorouracil-epirubicin-cyclophosphamide (FE 90 C) chemotherapy. Results: Among patients with BRCA-like CGH tumors (81/249, 32%), a significant benefit of HD-CTC compared to FE 90 C was observed regarding overall survival (adjusted hazard ratio 0.19, 95% CI: 0.08 to 0.48) that was not seen for patients with non-BRCA-like CGH tumors (adjusted hazard ratio 0.90, 95% CI: 0.53 to 1.54) (P = 0.004). Half of all BRCA-like CGH tumors were ER-positive. Conclusions: Distinct aCGH patterns differentiated between HER2-negative patients with a markedly improved outcome after adjuvant treatment with an intensified DNA-DSB-inducing regimen (BRCA-like CGH patients) and those without benefit (non-BRCA-like CGH patients).
Cancer Research
Introduction: Ductal Carcinoma In Situ (DCIS) is a proliferation of neoplastic cells confined to ... more Introduction: Ductal Carcinoma In Situ (DCIS) is a proliferation of neoplastic cells confined to the ducto-lobular system. Due to uncertainty which DCIS lesions progress to invasive breast cancer women with DCIS receive surgery and radiotherapy. The PRECISION (PREvent ductal carcinoma In Situ Invasive Overtreatment Now) initiative intends to improve the management of DCIS including reduction of unnecessary treatment. Histological high grade is an unfavorable prognostic indicator used to guide treatment decisions, and used as an exclusion criterion for DCIS trials that randomize between active surveillance and standard treatment. Hence, accurate assessment of grade is important in current clinical practice. Pathologists within PRECISION setup this study to compare histological parameters of four retrospective DCIS cohorts from three different countries to investigate interobserver variability particularly in grading of DCIS. Method: Tissue slides from two population-based cohorts (UK...
PLOS ONE, 2017
Pathological response of breast cancer to neoadjuvant chemotherapy (NAC) presents great variabili... more Pathological response of breast cancer to neoadjuvant chemotherapy (NAC) presents great variability, and new prognostic biomarkers are needed. Our aim was to evaluate the association of the epidermal growth factor receptor gene (EGFR) polymorphism R497K (rs2227983) with prognostic features and clinical outcomes of breast cancer, including the pathological response to NAC and the recurrence-free survival (RFS). Tumoral complete response (tCR) was defined by no remaining invasive cancer in the excised breast, whereas pathological complete response (pCR) was defined by no remaining invasive cancer both in the excised breast and lymph nodes. Two independent cohorts were analyzed: one from Brazil (INCA, n = 288) and one from The Netherlands (NKI-AVL, n = 255). In the INCA cohort, the variant (Lys-containing) genotypes were significantly associated with lower proportion of tCR (OR adj = 0.92; 95%CI = 0.85-0.99), whereas in the NKI-AVL cohort they were associated with tumor grade 3 (p = 0.035) and with triple-negative subtype (p = 0.032), but not with clinical outcomes. Such distinct prognostic associations may have arisen due to different neoadjuvant protocols (p < 0.001), or to lower age at diagnosis (p < 0.001) and higher proportion of tumor grade 3 (p = 0.018) at the NKI-AVL cohort. Moreover, NKI-AVL patients achieved better proportion of pCR (21.2% vs 8.3%, p < 0.001) and better RFS (HR adj = 0.48; 95% adj CI = 0.26-0.86) than patients from INCA. In conclusion, large scale studies comprehending different populations are needed to evaluate the impact of genome variants on breast cancer outcomes.
Nederlands Tijdschrift voor Geneeskunde, 2016
Since population-based breast cancer screening was implemented in the Netherlands, the incidence ... more Since population-based breast cancer screening was implemented in the Netherlands, the incidence of Ductal Carcinoma In Situ of the breast, regarded as a non-obligate precursor lesion of breast cancer, has strongly increased. However, the incidence of invasive breast cancer has not decreased. This suggests that a percentage of all the DCIS lesions would never have become symptomatic if no screening was performed. This phenomenon is known as 'overdiagnosis'. Nonetheless, almost all DCIS lesions are managed surgically, often followed by radiotherapy in those having breast-conserving treatment, to avoid potential progression to breast cancer. To prevent potential over- or undertreatment, further studies are required to distinguish low from high risk DCIS. Ultimately this could help avoid non-beneficial intensive treatment for women with low risk DCI
The Breast, 2020
Objective: The majority of 'low-risk' (grade I/II) Ductal Carcinoma In Situ (DCIS) may not progre... more Objective: The majority of 'low-risk' (grade I/II) Ductal Carcinoma In Situ (DCIS) may not progress to invasive breast cancer during a women's lifetime. Therefore, the safety of active surveillance versus standard surgical treatment for DCIS is prospectively being evaluated in clinical trials. If proven safe and selectively implemented in clinical practice, a significant group of women with low-risk DCIS may forego surgery and radiotherapy in the future. Identification of modifiable and non-modifiable risk factors associated with prognosis after a primary DCIS would also enhance our care of women with low-risk DCIS. Methods: To identify modifiable and non-modifiable risk factors for subsequent breast events after DCIS, we performed a systematic literature search in PUBMED, EMBASE and Scopus. Results: Six out of the 3870 articles retrieved were included for final data extraction. These six studies included a total of 4950 patients with primary DCIS and 640 recorded subsequent breast events. There was moderate evidence for an association of a family history of breast cancer, premenopausal status, high BMI, and high breast density with a subsequent breast cancer or further DCIS. Conclusion: There is a limited number of recent studies published on the impact of modifiable and nonmodifiable risk factors on subsequent events after DCIS. The available evidence is insufficient to identify potential targets for risk reduction strategies, reflecting the relatively small numbers and the lack of longterm follow-up in DCIS, a low-event condition.
American Journal of Surgical Pathology, 2019
Ductal carcinoma in situ (DCIS) is considered a potential precursor of invasive breast carcinoma ... more Ductal carcinoma in situ (DCIS) is considered a potential precursor of invasive breast carcinoma (IBC). Studies aiming to find markers involved in DCIS progression generally have compared characteristics of IBC lesions with those of adjacent synchronous DCIS lesions. The question remains whether synchronous DCIS and IBC comparisons are a good surrogate for primary DCIS and subsequent IBC. In this study, we compared both primary DCIS and synchronous DCIS with the associated IBC lesion, on the basis of immunohistochemical marker expression. Immunohistochemical analysis of ER, PR, HER2, p53, and cyclo-oxygenase 2 (COX-2) was performed for 143 primary DCIS and subsequent IBC lesions, including 81 IBC lesions with synchronous DCIS. Agreement between DCIS and IBC was assessed using kappa, and symmetry tests were performed to assess the pattern in marker conversion. The primary DCIS and subsequent IBC more often showed discordant marker expression than synchronous DCIS and IBC. Strikingly, 18 of 49 (36%) women with HER2-positive primary DCIS developed an HER2-negative IBC. Such a difference in HER2 expression was not observed when comparing synchronous DCIS and IBC. The frequency of discordant marker expression did not increase with longer time between primary DCIS and IBC. In conclusion, comparison of primary DCIS and subsequent IBC yields different results than a comparison of synchronous DCIS and IBC, in particular with regard to HER2 status. To gain more insight into the progression of DCIS to IBC, it is essential to focus on the relationship between primary DCIS and subsequent IBC, rather than comparing IBC with synchronous DCIS.
Cancer Research, 2017
Background Cancer classification, prognostication, and prediction of treatment sensitivity increa... more Background Cancer classification, prognostication, and prediction of treatment sensitivity increasingly rely on DNA and RNA-based tests. This approach requires sufficiently high tumor cell percentages to yield enough DNA or RNA for reliable test results. As a consequence, samples of insufficient quality may drop out, e.g. due to poor cellularity or high numbers of tumor infiltrating lymphocytes. We hypothesized that requiring a high tumor cell percentage and high quality RNA causes systemic bias when interpreting genomic test results in breast cancer, as specific breast cancer subgroups may be over- or underrepresented. Patients and methods For this analysis, we used pre-treatment frozen samples from patients included in neoadjuvant chemotherapy trials at the Netherlands Cancer Institute between 2004 and 2012. Histological features and tumor cell percentage were reviewed and assessed by a consultant breast pathologist. Gene expression profiling was done if the tumor cell percentage ...
Cancer Research, 2017
Background Neoadjuvant chemotherapy is standard of care for locally advanced breast cancer. Unfor... more Background Neoadjuvant chemotherapy is standard of care for locally advanced breast cancer. Unfortunately not all patients benefit from this treatment. Even after decades of research, we still cannot predict which tumor will or will not respond. This may in part be due to tumor heterogeneity, as the sample taken before treatment not necessarily represents the tumor cell population that causes therapy resistance. Methods To test this hypothesis, we collected pre-treatment biopsies, resection specimens, and matched blood from 21 breast cancer patients treated with doxorubicin and cyclophosphamide in a neoadjuvant setting. Specifically, tumors were selected with a tumor percentage >50% after chemotherapy to enrich for resistant samples and ensure high quality data. RNA and whole exome sequencing were performed to characterize somatic mutations, copy number alterations and gene expression profiles. Histopathological characteristics were determined to obtain a comprehensive profile of...
International Journal of Radiation Oncology*Biology*Physics, 2017
moiety on AuNPs from an agonist of FRa, to anti-FRa Ig, an antibody (Ab) that binds to FRa withou... more moiety on AuNPs from an agonist of FRa, to anti-FRa Ig, an antibody (Ab) that binds to FRa without inducing proliferative or mitogenic effects. Materials/Methods: Pegylated 20 nm AuNPs (pAuNPs) were synthesized and conjugated to nonspecific rabbit IgG Ab (rAuNPs) or targeted anti-FRa Ab (aAuNPs). AuNPs were characterized by zeta potential, hydrodynamic diameters and absorption spectra. Uptake by MDA-MB-231 cells was analyzed qualitatively using dark field microscopy. In-vitro radiosensitization potential by aAuNPs was assessed via clonogenic assay using clinically relevant, 6MV RT. Results: Surface plasmon resonance peaks of pAuNPs, rAuNPs, and aAuNPs were observed at 521AE2 nm. AuNP zeta potentials were:-34AE6 mV (bare AuNPs),-8AE4 mV (pAuNPs),-1AE6 mV (rAuNPs), and-5AE5 mV (aAuNPs). Hydrodynamic diameters determined by dynamic light scattering were: 33AE12 nm (bare AuNPs), 56AE18 nm (pAuNPs), 64AE22 nm (rAuNPs), and 62AE17 nm (aAuNPs). aAuNPs demonstrated significant radiosensitization with a dose enhancement factor of 1.15 calculated at 10% cell survival relative to RT alone. Conclusion: AuNPs conjugated to anti-FRa Ab sensitize triple negative breast cancer cells to radiation and present a viable strategy to target cancer cells at the molecular level.
Molecular Cancer Research, 2013
Background: BRCA1 mutated breast tumor cells are defective in DNA repair by homologous recombinat... more Background: BRCA1 mutated breast tumor cells are defective in DNA repair by homologous recombination and therefore especially sensitive to treatment with DNA double-strand break (DSB) inducing agents, such as alkylators and PARP inhibitors. However, such tumors can eventually develop therapy resistance. Understanding the underlying mechanisms may help in designing strategies to avoid or overcome acquired therapy resistance. Methods: We have developed patient derived xenograft (PDX) models of BRCA1-deficient triple-negative breast cancer (TNBC) by implantating fresh human breast tumor pieces and subsequent serial passaging. These models show epigenetic loss of BRCA1 due to promoter hypermethylation or genetic inactivation of BRCA1 due to a frameshift mutation (c.2210delC) resulting in a premature stop codon (p.Thr737LeufsX15). We have used these 3 BRCA1-deficient TNBC models to study response and acquisition of resistance to alkylating therapy (cisplatin, melphalan, nimustine) and th...
Purpose: Extensive work in preclinical models has shown that microenvironmental cells influence m... more Purpose: Extensive work in preclinical models has shown that microenvironmental cells influence many aspects of cancer cell behavior, including metastatic potential and their sensitivity to therapeutics. In the human setting, this behavior is mainly correlated with the presence of immune cells. Here, in addition to T cells, B cells, macrophages, and mast cells, we identified the relevance of nonimmune cell types for breast cancer survival and therapy benefit, including fibroblasts, myoepithelial cells, muscle cells, endothelial cells, and seven distinct epithelial cell types. Experimental Design: Using single-cell sequencing data, we generated reference profiles for all these cell types. We used these reference profiles in deconvolution algorithms to optimally detangle the cellular composition of more than 3,500 primary breast tumors of patients that were enrolled in the SCAN-B and MATADOR clinical trials, and for which bulk mRNA sequencing data were available. Results: This large data set enables us to identify and subsequently validate the cellular composition of microenvironments that distinguish differential survival and treatment benefit for different treatment regimens in patients with primary breast cancer. In addition to immune cells, we have identified that survival and therapy benefit are characterized by various contributions of distinct epithelial cell types. Conclusions: From our study, we conclude that differential survival and therapy benefit of patients with breast cancer are characterized by distinct microenvironments that include specific populations of immune and epithelial cells.
medRxiv (Cold Spring Harbor Laboratory), Nov 11, 2022
Invasive breast cancer patients are increasingly being treated with neoadjuvant chemotherapy, how... more Invasive breast cancer patients are increasingly being treated with neoadjuvant chemotherapy, however, only a fraction of the patients respond to it completely. To prevent over-treating patients with a toxic drug, there is an urgent need for biomarkers capable of predicting treatment response before administering the therapy. In this retrospective study, we developed interpretable, deep-learning based biomarkers to predict the pathological complete response (pCR, i.e. the absence of tumor cells in the surgical resection specimens) to neoadjuvant chemotherapy from digital pathology H&E images of pre-treatment breast biopsies. Experimental Design: Our approach consists of two steps: In the first step, using deep learning, mitoses are detected and the tissue segmented into several morphology compartments including tumor, lymphocytes and stroma. In the second step, computational biomarkers are derived from the segmentation and detection output to encode slide-level relationships between the morphological structures with focus on tumor infiltrating lymphocytes (TILs). We developed and evaluated our method on slides from N=721 patients from three European medical centers with triple-negative and Luminal B breast cancers. Results: The investigated biomarkers yield statistically significant prediction performance for pCR with areas under the receiver operating characteristic curve between 0.66 and 0.88 depending on the cancer subtype and center. Conclusion: The proposed computational biomarkers predict pathological complete response, but will require more evaluation and finetuning for clinical
British Journal of Cancer, Apr 4, 2013
Background: BRCAness is defined as shared tumour characteristics between sporadic and BRCA-mutate... more Background: BRCAness is defined as shared tumour characteristics between sporadic and BRCA-mutated cancers. However, how to exactly measure BRCAness and its frequency in breast cancer is not known. Assays to establish BRCAness would be extremely valuable for the clinical management of these tumours. We assessed BRCAness characteristics frequencies in a large cohort of triple-negative breast cancers (TNBCs). Methods: As a measure of BRCAness, we determined a specific BRCA1-like pattern by array Comparative Genomic Hybridisation (aCGH), and BRCA1 promoter methylation in 377 TNBCs, obtained from 3 different patient cohorts. Clinicopathological data were available for all tumours, BRCA1-germline mutation status and chemotherapy response data were available for a subset. Results: Of the tumours, 66-69% had a BRCA1-like aCGH profile and 27-37% showed BRCA1 promoter methylation. BRCA1germline mutations and BRCA1 promoter methylation were mutually exclusive events (P ¼ 1 Â 10 À 5). BRCAness was associated with younger age and grade 3 tumours. Chemotherapy response was significantly higher in BRCA1-mutated tumours, but not in tumours with BRCAness (63% (12 out of 19) vs 35% (18 out of 52) pathological complete remission rate, respectively). Conclusion: The majority of the TNBCs show BRCAness, and those tumours share clinicopathological characteristics with BRCA1-mutated tumours. A better characterisation of TNBC and the presence of BRCAness could have consequences for both hereditary breast cancer screening and the treatment of these tumours.
Purpose: Ductal carcinoma in situ (DCIS) is treated to prevent progression to invasive breast can... more Purpose: Ductal carcinoma in situ (DCIS) is treated to prevent progression to invasive breast cancer. Yet, most lesions will never progress, implying that overtreatment exists. Therefore, we aimed to identify factors distinguishing harmless from potentially hazardous DCIS using a nested case–control study.Experimental Design: We conducted a case–control study nested in a population-based cohort of patients with DCIS treated with breast-conserving surgery (BCS) alone (N = 2,658) between 1989 and 2005. We compared clinical, pathologic, and IHC DCIS characteristics of 200 women who subsequently developed ipsilateral invasive breast cancer (iIBC; cases) and 474 women who did not (controls), in a matched setting. Median follow-up time was 12.0 years (interquartile range, 9.0–15.3). Conditional logistic regression models were used to assess associations of various factors with subsequent iIBC risk after primary DCIS.Results: High COX-2 protein expression showed the strongest association w...
Nature Reviews Cancer, Dec 15, 2022
npj Breast Cancer
When locally advanced breast cancer is treated with neoadjuvant chemotherapy, the recurrence risk... more When locally advanced breast cancer is treated with neoadjuvant chemotherapy, the recurrence risk is significantly higher if no complete pathologic response is achieved. Identification of the underlying resistance mechanisms is essential to select treatments with maximal efficacy and minimal toxicity. Here we employed gene expression profiles derived from 317 HER2-negative treatment-naïve breast cancer biopsies of patients who underwent neoadjuvant chemotherapy, deep whole exome, and RNA-sequencing profiles of 22 matched pre- and post-treatment tumors, and treatment outcome data to identify biomarkers of response and resistance mechanisms. Molecular profiling of treatment-naïve breast cancer samples revealed that expression levels of proliferation, immune response, and extracellular matrix (ECM) organization combined predict response to chemotherapy. Triple negative patients with high proliferation, high immune response and low ECM expression had a significantly better treatment res...