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Article: Quantitative proteomic analysis of HER2 protein expression in PDAC tumors.

Randall, Jamie / Hunt, Allison L / Nutcharoen, Aratara / Johnston, Laura / Chouraichi, Safae / Wang, Hongkun / Winer, Arthur / Wadlow, Raymond / Huynh, Jasmine / Davis, Justin / Corgiat, Brian / Bateman, Nicholas W / Deeken, John F / Petricoin, Emanuel F / Conrads, Thomas P / Cannon, Timothy L

Clinical proteomics

2024 Volume 21, Issue 1, Page(s) 24

Abstract: Metastatic pancreatic adenocarcinoma (PDAC) is the third leading cause of cancer-related death in the United States, with a 5-year survival rate of only 11%, necessitating identification of novel treatment paradigms. Tumor tissue specimens from patients ... ...

Abstract	Metastatic pancreatic adenocarcinoma (PDAC) is the third leading cause of cancer-related death in the United States, with a 5-year survival rate of only 11%, necessitating identification of novel treatment paradigms. Tumor tissue specimens from patients with PDAC, breast cancer, and other solid tumor malignancies were collected and tumor cells were enriched using laser microdissection (LMD). Reverse phase protein array (RPPA) analysis was performed on enriched tumor cell lysates to quantify a 32-protein/phosphoprotein biomarker panel comprising known anticancer drug targets and/or cancer-related total and phosphorylated proteins, including HER2
Language	English
Publishing date	2024-03-20
Publishing country	England
Document type	Letter
ZDB-ID	2205154-5
ISSN	1542-6416
ISSN	1542-6416
DOI	10.1186/s12014-024-09476-7
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Zs.A 6222: Show issues

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Article ; Online: Effectiveness of an Electronic Medical Record-Based Recognition Tool for the Identification of Incidental Pulmonary Nodules.

Mahajan, Amit K / Collar, Nancy / Bari, Mahwish / Nader, Abe / Muldowney, Frances / Patel, Priya P / Weyant, Michael J / Druckenbrod, Glenn G / Oliverio, Patrick / Moynihan, John / Deeken, John F

Journal of bronchology & interventional pulmonology

2023 Volume 30, Issue 4, Page(s) 373–378

Abstract: Background: Incidental pulmonary nodules (IPNs) are lung nodules detected on imaging studies performed for an unrelated reason. Approximately 1.6 million IPNs are detected in the United States every year. Unfortunately, close to 1.1 million (69%) of ... ...

Abstract	Background: Incidental pulmonary nodules (IPNs) are lung nodules detected on imaging studies performed for an unrelated reason. Approximately 1.6 million IPNs are detected in the United States every year. Unfortunately, close to 1.1 million (69%) of these IPNs are not managed with appropriate follow-up care. The goal of this study was to assess the utility of a noncommercial electronic medical record (EMR)-based IPN keyword recognition program in identifying IPNs and the ability of lung navigators to communicate these findings to patients. Methods: This is a observational, implementation study aimed identify IPNs using an EMR-based protocol and to relay results of findings to patients. The patient population included patients 16 and older undergoing computed tomography (CT) chest, CT chest/abdomen, CT angiogram chest, CT chest/abdomen/pelvis, and chest radiography through the radiology department within a large community tertiary medical campus between June 2019 and August 2020. EPIC EMR were queried using criteria designed to find IPNs. A lung navigator reviewed these cases and sorted them into categories based on their size and risk status. After identification of risk factors, actions were taken to directly communicate results to patients. Results: Seven hundred and fifty-three patients were found to have true IPNs without a history of active malignancy involving the lung. On the basis of radiographic measurements, 60% of the nodules identified were <6 mm, 17% were between 6 and 8 mm, 22% were >8 mm, and 12% were deemed nodular opacities. Lung navigators were able to contact a total of 637 (87%) individuals with IPNs and results were directly communicated. Of the 637 patients identified to have an IPN, a total of 12 (2%) cancers were diagnosed. Conclusion: We have here demonstrated that the development of an EMR-based keyword recognition platform for the identification of IPNs is a useful and successful tool for communication of IPN findings to patients using lung navigators.
MeSH term(s)	Humans ; Lung Neoplasms/diagnostic imaging ; Electronic Health Records ; Multiple Pulmonary Nodules/diagnostic imaging ; Lung ; Tomography, X-Ray Computed/methods ; Incidental Findings
Language	English
Publishing date	2023-10-01
Publishing country	United States
Document type	Observational Study ; Journal Article
ZDB-ID	2478320-1
ISSN	1948-8270 ; 1944-6586
ISSN (online)	1948-8270
ISSN	1944-6586
DOI	10.1097/LBR.0000000000000905
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Zs.A 4027: Show issues

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Article ; Online: Endosomal trafficking defects in patient cells with

Kane, Megan S / Diamonstein, Callie J / Hauser, Natalie / Deeken, John F / Niederhuber, John E / Vilboux, Thierry

Genes & diseases

2019 Volume 6, Issue 1, Page(s) 56–67

Abstract: The uncharacterized ... ...

Abstract	The uncharacterized gene
Language	English
Publishing date	2019-01-07
Publishing country	China
Document type	Journal Article
ZDB-ID	2821806-1
ISSN	2352-3042 ; 2352-3042
ISSN (online)	2352-3042
ISSN	2352-3042
DOI	10.1016/j.gendis.2018.12.004
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Article ; Online: Integration of Multi-omic Data in a Molecular Tumor Board Reveals EGFR-Associated ALK-Inhibitor Resistance in a Patient With Inflammatory Myofibroblastic Cancer.

Hunt, Allison L / Nutcharoen, Aratara / Randall, Jamie / Papazian, Alyssa / Deeken, John / Maxwell, G Larry / Bateman, Nicholas W / Petricoin, Emanuel F / Benyounes, Amin / Conrads, Thomas P / Cannon, Timothy L

The oncologist

2023 Volume 28, Issue 8, Page(s) 730–736

Abstract: Inflammatory myofibroblastic tumors (IMTs) are intermediate-grade mesenchymal neoplasms commonly characterized by chromosomal rearrangements causing constitutive activation of anaplastic lymphoma kinase (ALK) and/or ALK mutations causing reduced ... ...

Abstract	Inflammatory myofibroblastic tumors (IMTs) are intermediate-grade mesenchymal neoplasms commonly characterized by chromosomal rearrangements causing constitutive activation of anaplastic lymphoma kinase (ALK) and/or ALK mutations causing reduced sensitivity to ALK tyrosine kinase inhibitors (TKI). We present a patient with an IMT who initially responded to first-line alectinib, but who later suffered disease relapse and presently survives with moderate residual disease after receiving second-line lorlatinib. Biopsy specimens were analyzed using next generation sequencing (DNA-seq and RNA-seq) and reverse phase protein microarray (RPPA) as part of an institutional Molecular Tumor Board (MTB) study. An EML4-ALK rearrangement and EGFR activation (pEGFRY1068) were present in both the primary and recurrent tumors, while a secondary ALK I1171N mutation was exclusive to the latter. EGFR signaling in the background of a secondary ALK mutation is correlated with reduced ALK TKI sensitivity in vitro, implicating an important mechanism of drug resistance development in this patient. The RPPA results also critically demonstrate that ALK signaling (ALKY1604) was not activated in the recurrent tumor, thereby indicating that standard-of-care use of third- or fourth-line ALK TKI would not likely be efficacious or durable. These results underscore the importance of real-time clinical integration of functional protein drug target activation data with NGS in the MTB setting for improving selection of patient-tailored therapy.
MeSH term(s)	Humans ; Lung Neoplasms/drug therapy ; Multiomics ; Drug Resistance, Neoplasm/genetics ; Neoplasm Recurrence, Local/drug therapy ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/therapeutic use ; Protein-Tyrosine Kinases/therapeutic use ; ErbB Receptors/metabolism
Chemical Substances	Protein Kinase Inhibitors ; Protein-Tyrosine Kinases (EC 2.7.10.1) ; ErbB Receptors (EC 2.7.10.1) ; EGFR protein, human (EC 2.7.10.1)
Language	English
Publishing date	2023-05-31
Publishing country	England
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1409038-7
ISSN	1549-490X ; 1083-7159
ISSN (online)	1549-490X
ISSN	1083-7159
DOI	10.1093/oncolo/oyad129
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Zs.A 4845: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 494: Show issues

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Article ; Online: Publisher Correction: Germline de novo mutation clusters arise during oocyte aging in genomic regions with high double-strand-break incidence.

Goldmann, Jakob M / Seplyarskiy, Vladimir B / Wong, Wendy S W / Vilboux, Thierry / Neerincx, Pieter B / Bodian, Dale L / Solomon, Benjamin D / Veltman, Joris A / Deeken, John F / Gilissen, Christian / Niederhuber, John E

Nature genetics

2021 Volume 53, Issue 8, Page(s) 1270

Language	English
Publishing date	2021-07-23
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-021-00905-z
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Zs.A 3613: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 46: Show issues

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Article ; Online: Supportive treatments for oncology patients: not just icing on the cake.

Deeken, John F / Weiner, Louis M

Annals of internal medicine

2010 Volume 153, Issue 6, Page(s) 411–412

MeSH term(s)	Adolescent ; Adult ; Aged ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Female ; Fibroblast Growth Factor 7/administration & dosage ; Fibroblast Growth Factor 7/adverse effects ; Humans ; Male ; Middle Aged ; Neoplasms/drug therapy ; Sarcoma/drug therapy ; Stomatitis/drug therapy ; Stomatitis/prevention & control ; Young Adult
Chemical Substances	Fibroblast Growth Factor 7 (126469-10-1)
Language	English
Publishing date	2010-09-20
Publishing country	United States
Document type	Comment ; Editorial
ZDB-ID	336-0
ISSN	1539-3704 ; 0003-4819
ISSN (online)	1539-3704
ISSN	0003-4819
DOI	10.7326/0003-4819-153-6-201009210-00010
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Ua VI Zs.178/2: Show issues

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Article ; Online: RAS Mutations Beyond KRAS Exon 2: A Review and Discussion of Clinical Trial Data.

Cannon, Timothy L / Kokon, Megan A / Shafqat, Sara / Deeken, John F

Current treatment options in oncology

2015 Volume 16, Issue 7, Page(s) 33

Abstract: Opinion statement: The addition of targeted therapy to a 5-FU chemotherapy backbone is now a standard of care in metastatic colorectal cancer. Epidermal growth factor receptor (EGFR) inhibitors have been demonstrated to improve progression-free survival ( ...

Abstract	Opinion statement: The addition of targeted therapy to a 5-FU chemotherapy backbone is now a standard of care in metastatic colorectal cancer. Epidermal growth factor receptor (EGFR) inhibitors have been demonstrated to improve progression-free survival (PFS) and overall survival (OS) in the first line for patients with tumors that do not harbor KRAS exon 2 mutations. Eligibility criteria for most clinical trials involving EGFR inhibitors in recent years have used the absence of KRAS exon 2 mutation as the sole criteria for entry, as this specific mutation has been consistently shown to be predictive of a poor response to EGFR inhibitors. However, expanded analyses of first-line metastatic trials reveal that other RAS mutations, such as other KRAS mutations in exons 3 and 4, along with NRAS mutations, are predictive of poor responses to EGFR inhibitors as well. Testing for a full panel of these RAS mutations should be done prior to initiating treatment with an EGFR inhibitor. Further clinical trials are required to determine the predictive impact of each of these individual mutations. To date, they have been analyzed in the aggregate. The addition of targeted therapy, bevacizumab or an EGFR inhibitor, to a chemotherapy backbone should be considered for all appropriate patients. The relevant clinical trials that evaluated patients without any RAS mutation and compared an EGFR inhibitor to chemotherapy alone show a distinct advantage in overall survival and progression-free survival to the groups that received EGFR inhibition. The largest trial that compared bevacizumab with an EGFR inhibitor in the first line, CALGB/SWOG 80405, did not show a statistically significant difference between the two groups, making the use of bevacizumab, cetuximab, or panitumumab reasonable in the first line.
MeSH term(s)	Antibodies, Monoclonal/administration & dosage ; Antineoplastic Agents/administration & dosage ; Antineoplastic Combined Chemotherapy Protocols ; Bevacizumab/administration & dosage ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/mortality ; Colorectal Neoplasms/pathology ; Disease-Free Survival ; Exons ; Humans ; Molecular Targeted Therapy/methods ; Mutation/drug effects ; Proto-Oncogene Proteins p21(ras)/drug effects ; Randomized Controlled Trials as Topic ; Receptor, Epidermal Growth Factor/antagonists & inhibitors ; Treatment Outcome
Chemical Substances	Antibodies, Monoclonal ; Antineoplastic Agents ; KRAS protein, human ; Bevacizumab (2S9ZZM9Q9V) ; Receptor, Epidermal Growth Factor (EC 2.7.10.1) ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
Language	English
Publishing date	2015-07
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2057351-0
ISSN	1534-6277 ; 1527-2729
ISSN (online)	1534-6277
ISSN	1527-2729
DOI	10.1007/s11864-015-0350-8
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Zs.A 5523: Show issues

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Article ; Online: Association of Ancestral Genetic Admixture and Excess Weight at Twelve Months of Age.

Hazrati, Sahel / Huddleston, Kathi / Sadat-Hossieny, Sara / Tilman, Laura W / Fuller, Alma / Deeken, John F / Wong, Wendy S W / Niederhuber, John E / Hourigan, Suchitra K

Childhood obesity (Print)

2019 Volume 16, Issue 1, Page(s) 59–64

Abstract: Background/Objective: ...

Abstract	Background/Objective:
Language	English
Publishing date	2019-10-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2639910-6
ISSN	2153-2176 ; 2153-2168
ISSN (online)	2153-2176
ISSN	2153-2168
DOI	10.1089/chi.2019.0055
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Article ; Online: Endosomal trafficking defects in patient cells with KIAA1109 biallelic variants

Megan S. Kane / Callie J. Diamonstein / Natalie Hauser / John F. Deeken / John E. Niederhuber / Thierry Vilboux

Genes and Diseases, Vol 6, Iss 1, Pp 56-

2019 Volume 67

Abstract: The uncharacterized gene KIAA1109 has recently been associated with a congenital neurological malformation disorder that variably presents with arthrogryposis, craniofacial and/or cardiac abnormalities. We have identified two additional patients with ... ...

Abstract	The uncharacterized gene KIAA1109 has recently been associated with a congenital neurological malformation disorder that variably presents with arthrogryposis, craniofacial and/or cardiac abnormalities. We have identified two additional patients with compound heterozygous KIAA1109 variants presenting with the same neurological malformations. The mechanism whereby KIAA1109 loss of function causes this spectrum of disorders was the primary focus of our studies. We hypothesized that KIAA1109 function could be conserved relative to the fly gene tweek and examined endocytosis and endosome recycling in patient fibroblasts. Furthermore, we examined the structure of the cytoskeleton and cilia based on functional overlap with endocytosis and several known etiologies for neuronal migration disorders. Utilizing primary dermal fibroblasts from one patient and a healthy donor, we performed immunofluorescence and endocytosis assays to examine the endosomal, cytoskeletal, and ciliary cellular phenotypes. We found notable abnormalities in endosomal trafficking and endosome recycling pathways. We also observed changes in the actin cytoskeleton and cilia structural dynamics. We conclude that the function of KIAA1109 in humans may indeed overlap with the function of the Drosophila ortholog, resulting in perturbations to endosomal trafficking and the actin cytoskeleton. These alterations have ripple effects, altering many pathways that are critical for proper neuronal migration and embryonic development. Keywords: Cilia, Endocytosis, KIAA1109, Neurological malformation, Vesicular trafficking
Keywords	Medicine (General) ; R5-920 ; Genetics ; QH426-470
Subject code	612
Language	English
Publishing date	2019-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: EPG5 Variants with Modest Functional Impact Result in an Ameliorated and Primarily Neurological Phenotype in a 3.5-Year-Old Patient with Vici Syndrome.

Kane, Megan S / Zhao, Jia / Muskett, Julie / Diplock, Amelia / Srivastava, Siddharth / Hauser, Natalie / Deeken, John F / Niederhuber, John E / Smith, Wendy E / Vilboux, Thierry / Ebrahimi-Fakhari, Darius

Neuropediatrics

2019 Volume 50, Issue 4, Page(s) 257–261

Abstract: Congenital disorders of autophagy are multisystem disorders with significant neurological involvement. Ectopic p-granules protein 5 ( ...

Abstract	Congenital disorders of autophagy are multisystem disorders with significant neurological involvement. Ectopic p-granules protein 5 (
MeSH term(s)	Agenesis of Corpus Callosum/diagnostic imaging ; Agenesis of Corpus Callosum/genetics ; Autophagy-Related Proteins/genetics ; Cataract/diagnostic imaging ; Cataract/genetics ; Child, Preschool ; Corpus Callosum/diagnostic imaging ; Humans ; Magnetic Resonance Imaging ; Male ; Mutation ; Phenotype ; Severity of Illness Index ; Vesicular Transport Proteins/genetics
Chemical Substances	Autophagy-Related Proteins ; EPG5 protein, human ; Vesicular Transport Proteins
Language	English
Publishing date	2019-06-21
Publishing country	Germany
Document type	Case Reports ; Journal Article
ZDB-ID	573291-8
ISSN	1439-1899 ; 0174-304X
ISSN (online)	1439-1899
ISSN	0174-304X
DOI	10.1055/s-0039-1692129
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