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Article: Actionability and precision oncology.

Schwaederle, Maria / Kurzrock, Razelle

Oncoscience

2015 Volume 2, Issue 10, Page(s) 779–780

Language	English
Publishing date	2015-09-12
Publishing country	United States
Document type	Journal Article
ISSN	2331-4737
ISSN	2331-4737
DOI	10.18632/oncoscience.236
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Article ; Online: TP53

Chang, Geraldine H / Kurzrock, Razelle / Tran, Lisa / Schwaederle, Maria / Hoh, Carl K

Oncotarget

2018 Volume 9, Issue 18, Page(s) 14306–14310

Abstract: Background: Our study explored the relationship between the molecular changes in cancer and the maximum standardized uptake value (SUVmax) determined by positron emission tomography/computed tomography (PET/CT) with [: Results: A higher SUVmax ... ...

Abstract	Background: Our study explored the relationship between the molecular changes in cancer and the maximum standardized uptake value (SUVmax) determined by positron emission tomography/computed tomography (PET/CT) with [ Results: A higher SUVmax correlated with Conclusions: A higher SUVmax on Methods: Overall, 176 patients with diverse cancers had a tumor biopsy within 6 months after a PET/CT image for SUVmax measurement. The biopsy was interrogated by next generation sequencing (182 to 315 genes).
Language	English
Publishing date	2018-02-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.24508
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Article ; Online: Fibroblast growth factor receptor signaling in hereditary and neoplastic disease: biologic and clinical implications.

Helsten, Teresa / Schwaederle, Maria / Kurzrock, Razelle

Cancer metastasis reviews

2015 Volume 34, Issue 3, Page(s) 479–496

Abstract: Fibroblast growth factors (FGFs) and their receptors (FGFRs) are transmembrane growth factor receptors with wide tissue distribution. FGF/FGFR signaling is involved in neoplastic behavior and also development, differentiation, growth, and survival. FGFR ... ...

Abstract	Fibroblast growth factors (FGFs) and their receptors (FGFRs) are transmembrane growth factor receptors with wide tissue distribution. FGF/FGFR signaling is involved in neoplastic behavior and also development, differentiation, growth, and survival. FGFR germline mutations (activating) can cause skeletal disorders, primarily dwarfism (generally mutations in FGFR3), and craniofacial malformation syndromes (usually mutations in FGFR1 and FGFR2); intriguingly, some of these activating FGFR mutations are also seen in human cancers. FGF/FGFR aberrations reported in cancers are mainly thought to be gain-of-function changes, and several cancers have high frequencies of FGFR alterations, including breast, bladder, or squamous cell carcinomas (lung and head and neck). FGF ligand aberrations (predominantly gene amplifications) are also frequently seen in cancers, in contrast to hereditary syndromes. There are several pharmacologic agents that have been or are being developed for inhibition of FGFR/FGF signaling. These include both highly selective inhibitors as well as multi-kinase inhibitors. Of note, only four agents (ponatinib, pazopanib, regorafenib, and recently lenvatinib) are FDA-approved for use in cancer, although the approval was not based on their activity against FGFR. Perturbations in the FGFR/FGF signaling are present in both inherited and malignant diseases. The development of potent inhibitors targeting FGF/FGFR may provide new tools against disorders caused by FGF/FGFR alterations.
MeSH term(s)	Fibroblast Growth Factors/genetics ; Fibroblast Growth Factors/metabolism ; Genetic Diseases, Inborn/genetics ; Humans ; Mutation ; Neoplasms/genetics ; Receptors, Fibroblast Growth Factor/genetics ; Receptors, Fibroblast Growth Factor/metabolism ; Signal Transduction/physiology
Chemical Substances	Receptors, Fibroblast Growth Factor ; Fibroblast Growth Factors (62031-54-3)
Language	English
Publishing date	2015-09
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	604857-2
ISSN	1573-7233 ; 0167-7659
ISSN (online)	1573-7233
ISSN	0167-7659
DOI	10.1007/s10555-015-9579-8
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Article ; Online: MET alterations detected in blood-derived circulating tumor DNA correlate with bone metastases and poor prognosis.

Ikeda, Sadakatsu / Schwaederle, Maria / Mohindra, Mandakini / Fontes Jardim, Denis L / Kurzrock, Razelle

Journal of hematology & oncology

2018 Volume 11, Issue 1, Page(s) 76

Abstract: Background: We analyzed clinical associations of MET alterations in the plasma of patients with diverse malignancies.: Methods: Digital sequencing of circulating tumor DNA (ctDNA) (54-70 genes) was performed in 438 patients; 263 patients also had ... ...

Abstract	Background: We analyzed clinical associations of MET alterations in the plasma of patients with diverse malignancies. Methods: Digital sequencing of circulating tumor DNA (ctDNA) (54-70 genes) was performed in 438 patients; 263 patients also had tissue sequencing (182-315 genes). The most represented tumor types were gastrointestinal (28.1%), brain (24.9%), and lung (23.2%). Most patients (71.2%) had recurrent/metastatic disease. Results: MET alterations were observed in 31 patients (7.1%) and correlated with bone metastasis (P = 0.007), with TP53 (P = 0.001) and PTEN (P = 0.003) abnormalities, and with an increased number of alterations (median, 4 vs 1, P = 0.001) (all multivariable analyses). Patients with MET alterations demonstrated a significantly shorter median time to metastasis/recurrence (1.0 vs 10.4 months, P = 0.044, multivariable) and a poorer survival (30.6 vs 58.4 months, P = 0.013, univariate only). Of the 31 patients with MET alterations, 18 also had tissue testing; only two also had tissue MET alterations (11.1%); MET alterations were detected at a lower frequency in tissue (1.14%) compared to ctDNA (7.1%), with P = 0.0002. Conclusions: In conclusion, the detection of MET alterations by liquid biopsy is feasible. MET ctDNA alterations were associated with a poorer prognosis, higher numbers of genomic abnormalities, and bone metastases. The correlation with bone metastases may explain the higher frequency of MET alterations in blood ctDNA than in tissue (since bones are rarely biopsied) and the previous observations of bone-predominant responses to MET inhibitors. The high number of co-altered genes suggests that MET inhibitors may need to be combined with other agents to induce/optimize responses.
MeSH term(s)	Aged ; Bone Neoplasms/secondary ; Circulating Tumor DNA/blood ; Female ; Hematologic Neoplasms/blood ; Hematologic Neoplasms/complications ; Hematologic Neoplasms/diagnosis ; Hematologic Neoplasms/pathology ; Humans ; Liquid Biopsy ; Middle Aged ; Prognosis ; Proto-Oncogene Proteins c-met/antagonists & inhibitors ; Proto-Oncogene Proteins c-met/genetics ; Proto-Oncogene Proteins c-met/metabolism ; Sequence Analysis, DNA
Chemical Substances	Circulating Tumor DNA ; MET protein, human (EC 2.7.10.1) ; Proto-Oncogene Proteins c-met (EC 2.7.10.1)
Language	English
Publishing date	2018-06-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2429631-4
ISSN	1756-8722 ; 1756-8722
ISSN (online)	1756-8722
ISSN	1756-8722
DOI	10.1186/s13045-018-0610-8
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Article: Genomic Assessment of Blood-Derived Circulating Tumor DNA in Patients With Colorectal Cancers: Correlation With Tissue Sequencing, Therapeutic Response, and Survival.

Kato, Shumei / Schwaederlé, Maria C / Fanta, Paul T / Okamura, Ryosuke / Leichman, Lawrence / Lippman, Scott M / Lanman, Richard B / Raymond, Victoria M / Talasaz, AmirAli / Kurzrock, Razelle

JCO precision oncology

2019 Volume 3

Abstract: Purpose: Genomic alterations in blood-derived circulating tumor DNA (ctDNA) from patients with colorectal cancers were correlated with clinical outcomes.: Patients and methods: Next-generation sequencing of ctDNA (54- to 73-gene panel) was performed ... ...

Abstract	Purpose: Genomic alterations in blood-derived circulating tumor DNA (ctDNA) from patients with colorectal cancers were correlated with clinical outcomes. Patients and methods: Next-generation sequencing of ctDNA (54- to 73-gene panel) was performed in 94 patients with colorectal cancer. Results: Most patients (96%) had metastatic or recurrent disease at the time of blood draw. The median number of nonsynonymous alterations per patient was three (range, zero to 30). The most frequently aberrant genes were Conclusion: Patients with colorectal cancer have heterogeneous ctDNA profiles, and most harbor potentially actionable ctDNA alterations. Matched therapy yielded higher rates of stable disease for 6 months or more, partial response, or complete response. ctDNA assessment may have clinical utility and merits further investigation.
Language	English
Publishing date	2019-01-25
Publishing country	United States
Document type	Journal Article
ISSN	2473-4284
ISSN	2473-4284
DOI	10.1200/PO.18.00158
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Article ; Online: An appraisal of drug development timelines in the Era of precision oncology.

Jardim, Denis Leonardo / Schwaederle, Maria / Hong, David S / Kurzrock, Razelle

Oncotarget

2016 Volume 7, Issue 33, Page(s) 53037–53046

Abstract: The effects of incorporating a biomarker-based (personalized or precision) selection strategy on drug development timelines for new oncology drugs merit investigation. Here we accessed documents from the Food and Drug Administration (FDA) database for ... ...

Abstract	The effects of incorporating a biomarker-based (personalized or precision) selection strategy on drug development timelines for new oncology drugs merit investigation. Here we accessed documents from the Food and Drug Administration (FDA) database for anticancer agents approved between 09/1998 and 07/2014 to compare drugs developed with and without a personalized strategy. Sixty-three drugs were included (28 [44%] personalized and 35 [56%] non-personalized). No differences in access to FDA-expedited programs were observed between personalized and non-personalized drugs. A personalized approach for drug development was associated with faster clinical development (Investigational New Drug [IND] to New Drug Application [NDA] submission; median = 58.8 months [95% CI 53.8-81.8] vs. 93.5 months [95% CI 73.9-112.9], P =.001), but a similar approval time (NDA submission to approval; median=6.0 months [95% CI 5.5-8.4] vs. 6.1 months [95% CI 5.9-8.3], P = .756) compared to a non-personalized strategy. In the multivariate model, class of drug stratified by personalized status (targeted personalized vs. targeted non-personalized vs. cytotoxic) was the only independent factor associated with faster total time of clinical drug development (clinical plus approval phase, median = 64.6 vs 87.1 vs. 112.7 months [cytotoxic], P = .038). Response rates (RR) in early trials were positively correlated with RR in registration trials (r = 0.63, P = <.001), and inversely associated with total time of drug development (r = -0.29, P = .049). In conclusion, targeted agents were developed faster than cytotoxic agents. Shorter times to approval were associated, in multivariate analysis, with a biomarker-based clinical development strategy.
Language	English
Publishing date	2016-08-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.10588
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Article ; Online: Topoisomerase expression and amplification in solid tumours: Analysis of 24,262 patients.

Heestand, Gregory M / Schwaederle, Maria / Gatalica, Zoran / Arguello, David / Kurzrock, Razelle

European journal of cancer (Oxford, England : 1990)

2017 Volume 83, Page(s) 80–87

Abstract: Background: Topoisomerase I (TOPO1) and topoisomerase IIα (TOP2A) are specific targets of multiple chemotherapy drugs. Increased expression of TOPO1 protein and amplification of the TOP2A gene have been associated with treatment response in colorectal ... ...

Abstract	Background: Topoisomerase I (TOPO1) and topoisomerase IIα (TOP2A) are specific targets of multiple chemotherapy drugs. Increased expression of TOPO1 protein and amplification of the TOP2A gene have been associated with treatment response in colorectal and breast cancers, respectively. TOPO1 and TOP2A may be potential therapeutic targets in other malignancies as well. Summary of methods: We analysed TOPO1 protein expression and TOP2A gene amplification in patients (n = 24,262 specimens) with diverse cancers. Since HER2 and TOP2A co-amplification have been investigated for predictive value regarding anthracycline benefit, we analysed specimens for HER2 amplification as well. Results: Overexpressed TOPO1 protein was present in 51% of the tumours. Four percent of the tumours had TOP2A amplification, with gallbladder tumours and gastroesophageal/oesophageal tumours having rates over 10%. Overall, 4903 specimens were assessed for both TOP2A and HER2 amplification; 129 (2.6%) had co-amplification. High rates (>40%) of HER2 amplification were seen in patients with TOP2A amplification in breast, ovarian, gastroesophageal/oesophageal and pancreatic cancer. Conclusion: Our data indicate that increased TOPO1 expression and TOP2A amplification, as well as HER2 co-alterations, are present in multiple malignancies. The implications of these observations regarding sensitivity to chemotherapy not traditionally administered to these tumour types merits investigation.
MeSH term(s)	Antigens, Neoplasm/metabolism ; Biomarkers, Tumor/metabolism ; DNA Topoisomerases, Type I/metabolism ; DNA Topoisomerases, Type II/metabolism ; DNA-Binding Proteins/metabolism ; Female ; Humans ; Immunohistochemistry ; Male ; Neoplasms/metabolism ; Poly-ADP-Ribose Binding Proteins
Chemical Substances	Antigens, Neoplasm ; Biomarkers, Tumor ; DNA-Binding Proteins ; Poly-ADP-Ribose Binding Proteins ; DNA Topoisomerases, Type I (EC 5.99.1.2) ; DNA Topoisomerases, Type II (EC 5.99.1.3) ; TOP2A protein, human (EC 5.99.1.3)
Language	English
Publishing date	2017-09
Publishing country	England
Document type	Journal Article
ZDB-ID	82061-1
ISSN	1879-0852 ; 0277-5379 ; 0959-8049 ; 0964-1947
ISSN (online)	1879-0852
ISSN	0277-5379 ; 0959-8049 ; 0964-1947
DOI	10.1016/j.ejca.2017.06.019
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Zs.A 456: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: VEGF-A Expression Correlates with TP53 Mutations in Non-Small Cell Lung Cancer: Implications for Antiangiogenesis Therapy.

Schwaederlé, Maria / Lazar, Vladimir / Validire, Pierre / Hansson, Johan / Lacroix, Ludovic / Soria, Jean-Charles / Pawitan, Yudi / Kurzrock, Razelle

Cancer research

2015 Volume 75, Issue 7, Page(s) 1187–1190

Abstract: Bevacizumab is one of the most widely used antiangiogenic drugs in oncology, but the overall beneficial effects of this VEGF-A targeting agent are relatively modest, in part due to the lack of a biomarker to select patients most likely to respond ... ...

Abstract	Bevacizumab is one of the most widely used antiangiogenic drugs in oncology, but the overall beneficial effects of this VEGF-A targeting agent are relatively modest, in part due to the lack of a biomarker to select patients most likely to respond favorably. Several molecular aberrations in cancer influence angiogenesis, including mutations in the tumor suppressor gene TP53, which occur frequently in many human malignancies. In this study, we present a multiple regression analysis of transcriptomic data in 123 patients with non-small cell lung cancer (NSCLC) showing that TP53 mutations are associated with higher VEGF-A expression (P = 0.006). This association was interesting given a recent retrospective study showing longer progression-free survival in patients with diverse tumors who receive bevacizumab, if tumors harbor mutant TP53 instead of wild-type TP53. Thus, our current findings linking TP53 mutation with VEGF-A upregulation offered a mechanistic explanation for why patients exhibit improved outcomes after bevacizumab treatment when their tumors harbor mutant TP53 versus wild-type TP53. Overall, this work warrants further evaluation of TP53 as a ready biomarker to predict bevacizumab response in NSCLC and possibly other tumor types.
MeSH term(s)	Adenocarcinoma/drug therapy ; Adenocarcinoma/metabolism ; Angiogenesis Inhibitors/pharmacology ; Angiogenesis Inhibitors/therapeutic use ; Bevacizumab/pharmacology ; Bevacizumab/therapeutic use ; Carcinoma, Squamous Cell/drug therapy ; Carcinoma, Squamous Cell/metabolism ; Humans ; Lung Neoplasms/drug therapy ; Lung Neoplasms/metabolism ; Mutation ; Transcriptome ; Tumor Suppressor Protein p53/genetics ; Vascular Endothelial Growth Factor A/genetics ; Vascular Endothelial Growth Factor A/metabolism
Chemical Substances	Angiogenesis Inhibitors ; TP53 protein, human ; Tumor Suppressor Protein p53 ; VEGFA protein, human ; Vascular Endothelial Growth Factor A ; Bevacizumab (2S9ZZM9Q9V)
Language	English
Publishing date	2015-04-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1432-1
ISSN	1538-7445 ; 0008-5472
ISSN (online)	1538-7445
ISSN	0008-5472
DOI	10.1158/0008-5472.CAN-14-2305
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Article ; Online: Breast Cancer Experience of the Molecular Tumor Board at the University of California, San Diego Moores Cancer Center.

Parker, Barbara A / Schwaederlé, Maria / Scur, Michael D / Boles, Sarah G / Helsten, Teresa / Subramanian, Rupa / Schwab, Richard B / Kurzrock, Razelle

Journal of oncology practice

2015 Volume 11, Issue 6, Page(s) 442–449

Abstract: Purpose: Multiplex genomic tests are enabling oncologists to interrogate the DNA of their patients. However, few oncologists are proficient with respect to the implications of complex molecular diagnostics. We initiated a Molecular Tumor Board that ... ...

Abstract	Purpose: Multiplex genomic tests are enabling oncologists to interrogate the DNA of their patients. However, few oncologists are proficient with respect to the implications of complex molecular diagnostics. We initiated a Molecular Tumor Board that focused on individual patients with advanced cancer whose tumors underwent genomic profiling, and here report our experience with breast cancer. Methods: A multidisciplinary team that included physicians, scientists, geneticists, and bioinformatics/pathway specialists attended. All molecular tests were performed in a Clinical Laboratory Improvement Amendments environment (next-generation sequencing, 182 or 236 genes). Results: Forty of 43 patients (93%; mean age, 59 years) had at least one theoretically actionable aberration (mean, 4.79 anomalies/patient). Median time from ordering to report was 27 days (median of approximately 11 days for specimen acquisition and approximately 14 days for diagnostic processing). Even if we considered distinct abnormalities in a gene as the same, there were only two patients with an identical molecular profile. Seventy-three genes (206 abnormalities; 119 distinct) were aberrant. Seventeen of the 43 patients (40%; median, seven previous therapies in the metastatic setting) were treated in a manner consistent with Molecular Tumor Board discussions; seven (16% of 43, or 41% of 17) achieved stable disease for 6 or more months (n = 2) or partial remission (n = 5). Lack of access to targeted medication was the most common reason that patients could not be treated. Conclusion: Multidisciplinary molecular tumor boards may help to optimize the management of patients with advanced, heavily pretreated breast cancer who have undergone genomic testing. Facilitating availability of appropriately targeted drugs and clinical trials is needed.
MeSH term(s)	Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; California ; Cancer Care Facilities ; Disease-Free Survival ; Female ; Genetic Testing ; Hospitals, University ; Humans ; Kaplan-Meier Estimate ; Middle Aged ; Specialty Boards
Language	English
Publishing date	2015-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2236338-5
ISSN	1935-469X ; 1554-7477
ISSN (online)	1935-469X
ISSN	1554-7477
DOI	10.1200/JOP.2015.004127
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Article ; Online: Cyclin alterations in diverse cancers: Outcome and co-amplification network.

Schwaederlé, Maria / Daniels, Gregory A / Piccioni, David E / Fanta, Paul T / Schwab, Richard B / Shimabukuro, Kelly A / Parker, Barbara A / Kurzrock, Razelle

Oncotarget

2015 Volume 6, Issue 5, Page(s) 3033–3042

Abstract: Cyclin genes are key regulatory components of the cell cycle. With the development of new agents, cyclin-related genes are becoming increasingly important as they can be targeted. Yet, the biological implications of these alterations have not been fully ... ...

Abstract	Cyclin genes are key regulatory components of the cell cycle. With the development of new agents, cyclin-related genes are becoming increasingly important as they can be targeted. Yet, the biological implications of these alterations have not been fully studied. Clinical characteristics and outcome parameters were compared for patients harboring cyclin alterations versus not. CCN alterations were found in 13% of our population (50/392; all amplifications) and were associated with breast cancer (P < 0.0001), a higher median number of concomitant molecular alterations (P < 0.0001), and liver metastases (P = 0.046). Harboring a cyclin amplification was not associated with overall survival, the time to metastasis/recurrence, nor with the best progression-free survival. In a Cox regression model, gastrointestinal histology (P < 0.0001), PTEN (P < 0.0001), and CDK alterations (P = 0.041) had a significant association with poorer overall survival. CCN amplifications significantly correlated with alterations in FGF/FGFR family genes as well as in MET and ARFRP1. An extended correlation study shed light on a network of co-amplifications influenced in part by genes that were localized on the same amplicons. CCN amplifications are common across cancers and had distinctive biological associations. Customized combinations targeting the cyclin pathway as well as the extended co- amplification network may be necessary in order to address resistance mechanisms.
MeSH term(s)	Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Cyclins/genetics ; Cyclins/metabolism ; Disease-Free Survival ; Female ; Gene Amplification ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Genetic Predisposition to Disease ; Humans ; Kaplan-Meier Estimate ; Logistic Models ; Male ; Middle Aged ; Multivariate Analysis ; Neoplasm Metastasis ; Neoplasm Recurrence, Local ; Neoplasms/enzymology ; Neoplasms/genetics ; Neoplasms/mortality ; Neoplasms/pathology ; Odds Ratio ; Phenotype ; Proportional Hazards Models ; Retrospective Studies ; Risk Factors ; Time Factors
Chemical Substances	Biomarkers, Tumor ; Cyclins
Language	English
Publishing date	2015-02-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.2848
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