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Article ; Online: Real-world insights on preferred treatments for steroid-refractory immune checkpoint inhibitor-induced pneumonitis.

Gatti-Mays, Margaret / Gulley, James L

2021 Volume 9, Issue 2

MeSH term(s)	Carcinoma, Non-Small-Cell Lung/drug therapy ; Humans ; Immune Checkpoint Inhibitors ; Lung Neoplasms/drug therapy ; Pneumonia/drug therapy ; Steroids/therapeutic use
Chemical Substances	Immune Checkpoint Inhibitors ; Steroids
Language	English
Publishing date	2021-02-18
Publishing country	England
Document type	Editorial ; Comment
ZDB-ID	2719863-7
ISSN	2051-1426 ; 2051-1426
ISSN (online)	2051-1426
ISSN	2051-1426
DOI	10.1136/jitc-2020-002252
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Article ; Online: Genomic assays for Epstein-Barr virus-positive gastric adenocarcinoma.

Gulley, Margaret L

Experimental & molecular medicine

2015 Volume 47, Page(s) e134

Abstract: A small set of gastric adenocarcinomas (9%) harbor Epstein-Barr virus (EBV) DNA within malignant cells, and the virus is not an innocent bystander but rather is intimately linked to pathogenesis and tumor maintenance. Evidence comes from unique genomic ... ...

Abstract	A small set of gastric adenocarcinomas (9%) harbor Epstein-Barr virus (EBV) DNA within malignant cells, and the virus is not an innocent bystander but rather is intimately linked to pathogenesis and tumor maintenance. Evidence comes from unique genomic features of host DNA, mRNA, microRNA and CpG methylation profiles as revealed by recent comprehensive genomic analysis by The Cancer Genome Atlas Network. Their data show that gastric cancer is not one disease but rather comprises four major classes: EBV-positive, microsatellite instability (MSI), genomically stable and chromosome instability. The EBV-positive class has even more marked CpG methylation than does the MSI class, and viral cancers have a unique pattern of methylation linked to the downregulation of CDKN2A (p16) but not MLH1. EBV-positive cancers often have mutated PIK3CA and ARID1A and an amplified 9p24.1 locus linked to overexpression of JAK2, CD274 (PD-L1) and PDCD1LG2 (PD-L2). Multiple noncoding viral RNAs are highly expressed. Patients who fail standard therapy may qualify for enrollment in clinical trials targeting cancer-related human gene pathways or promoting destruction of infected cells through lytic induction of EBV genes. Genomic tests such as the GastroGenus Gastric Cancer Classifier are available to identify actionable variants in formalin-fixed cancer tissue of affected patients.
MeSH term(s)	Adenocarcinoma/diagnosis ; Adenocarcinoma/etiology ; Adenocarcinoma/therapy ; DNA Methylation ; Epstein-Barr Virus Infections/complications ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Expression Regulation, Viral ; Genomics/methods ; Herpesvirus 4, Human/physiology ; Host-Pathogen Interactions/genetics ; Humans ; MicroRNAs/genetics ; Mutation ; RNA, Messenger/genetics ; Signal Transduction ; Stomach Neoplasms/diagnosis ; Stomach Neoplasms/etiology ; Stomach Neoplasms/therapy ; Virus Integration
Chemical Substances	MicroRNAs ; RNA, Messenger
Language	English
Publishing date	2015-01-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1328915-9
ISSN	2092-6413 ; 1226-3613 ; 0378-8512
ISSN (online)	2092-6413
ISSN	1226-3613 ; 0378-8512
DOI	10.1038/emm.2014.93
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Article ; Online: Immune correlates with response in patients with metastatic solid tumors treated with a tumor targeting immunocytokine NHS-IL12.

Toney, Nicole J / Gatti-Mays, Margaret E / Tschernia, Nicholas P / Strauss, Julius / Gulley, James L / Schlom, Jeffrey / Donahue, Renee N

International immunopharmacology

2023 Volume 116

Abstract: The immunocytokine NHS-IL12 delivers IL-12 to the tumor microenvironment by targeting DNA/histones in necrotic areas. The first-in-human clinical trial administered NHS-IL12 subcutaneously in 59 patients treated every four weeks (Q4W), with a maximum ... ...

Abstract	The immunocytokine NHS-IL12 delivers IL-12 to the tumor microenvironment by targeting DNA/histones in necrotic areas. The first-in-human clinical trial administered NHS-IL12 subcutaneously in 59 patients treated every four weeks (Q4W), with a maximum tolerated dose of 16.8 mcg/kg. The phase I study was expanded to include a high-exposure cohort that received bi-weekly treatment (Q2W) with two dose levels of NHS-IL12: 12.0 mcg/kg and 16.8 mcg/kg. Here, patients given NHS-IL12 were analyzed both prior to and early after treatment for effects on 10 serum soluble analytes, complete blood counts, and 158 peripheral immune subsets. Higher levels of immune activation were seen with a dose of 16.8 mcg/kg versus 12.0 mcg/kg in patients in the high-exposure cohort, as evidenced by greater increases in serum IFNγ, TNFα, and soluble PD-1, and greater increases in frequencies of peripheral ki67
MeSH term(s)	Humans ; Ki-67 Antigen ; State Medicine ; Interleukin-12 ; Neoplasms/drug therapy ; Killer Cells, Natural ; Tumor Microenvironment
Chemical Substances	Ki-67 Antigen ; Interleukin-12 (187348-17-0)
Language	English
Publishing date	2023-02-16
Publishing country	Netherlands
Document type	Clinical Trial, Phase I ; Journal Article
ZDB-ID	2043785-7
ISSN	1878-1705 ; 1567-5769
ISSN (online)	1878-1705
ISSN	1567-5769
DOI	10.1016/j.intimp.2023.109736
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Article ; Online: Calibration of cell-free DNA measurements by next-generation sequencing.

Hoerres, Derek / Dai, Qunsheng / Elmore, Sandra / Sheth, Siddharth / Gupta, Gaorav P / Kumar, Sunil / Gulley, Margaret L

American journal of clinical pathology

2023 Volume 160, Issue 3, Page(s) 314–321

Abstract: Objectives: Accurate monitoring of disease burden depends on accurate disease marker quantification. Although next-generation sequencing (NGS) is a promising technology for noninvasive monitoring, plasma cell-free DNA levels are often reported in ... ...

Abstract	Objectives: Accurate monitoring of disease burden depends on accurate disease marker quantification. Although next-generation sequencing (NGS) is a promising technology for noninvasive monitoring, plasma cell-free DNA levels are often reported in misleading units that are confounded by non-disease-related factors. We proposed a novel strategy for calibrating NGS assays using spiked normalizers to improve precision and to promote standardization and harmonization of analyte concentrations. Methods: In this study, we refined our NGS protocol to calculate absolute analyte concentrations to (1) adjust for assay efficiency, as judged by recovery of spiked synthetic normalizer DNAs, and (2) calibrate NGS values against droplet digital polymerase chain reaction (ddPCR). As a model target, we chose the Epstein-Barr virus (EBV) genome. In patient (n = 12) and mock (n = 12) plasmas, NGS and 2 EBV ddPCR assays were used to report EBV load in copies per mL of plasma. Results: Next-generation sequencing was equally sensitive to ddPCR, with improved linearity when NGS values were normalized for spiked DNA read counts (R2 = 0.95 for normalized vs 0.91 for raw read concentrations). Linearity permitted NGS calibration to each ddPCR assay, achieving equivalent concentrations (copies/mL). Conclusions: Our novel strategy for calibrating NGS assays suggests potential for a universal reference material to overcome biological and preanalytical variables hindering traditional NGS strategies for quantifying disease burden.
MeSH term(s)	Humans ; Epstein-Barr Virus Infections ; Cell-Free Nucleic Acids ; Herpesvirus 4, Human/genetics ; Calibration ; High-Throughput Nucleotide Sequencing/methods
Chemical Substances	Cell-Free Nucleic Acids
Language	English
Publishing date	2023-05-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2944-0
ISSN	1943-7722 ; 0002-9173
ISSN (online)	1943-7722
ISSN	0002-9173
DOI	10.1093/ajcp/aqad055
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Article ; Online: Evaluating Elevated Hemoglobin.

Reeves, Brandi N / Gulley, Margaret L

JAMA

2016 Volume 316, Issue 10, Page(s) 1114–1115

MeSH term(s)	Fetal Hemoglobin ; Glycated Hemoglobin A ; Hematologic Diseases ; Hemoglobins ; Humans
Chemical Substances	Glycated Hemoglobin A ; Hemoglobins ; Fetal Hemoglobin (9034-63-3)
Language	English
Publishing date	2016-09-13
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	2958-0
ISSN	1538-3598 ; 0254-9077 ; 0002-9955 ; 0098-7484
ISSN (online)	1538-3598
ISSN	0254-9077 ; 0002-9955 ; 0098-7484
DOI	10.1001/jama.2016.11326
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Article: M7824: A promising new strategy to combat cancer immune evasion.

Gatti-Mays, Margaret E / Gulley, James L

Oncoscience

2018 Volume 5, Issue 11-12, Page(s) 269–270

Language	English
Publishing date	2018-08-22
Publishing country	United States
Document type	Journal Article
ISSN	2331-4737
ISSN	2331-4737
DOI	10.18632/oncoscience.451
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Article ; Online: Current and Emerging Molecular Tests for Human Papillomavirus-Related Neoplasia in the Genomic Era.

Leal, Sixto M / Gulley, Margaret L

The Journal of molecular diagnostics : JMD

2017 Volume 19, Issue 3, Page(s) 366–377

Abstract: Laboratory tests have a key role in preventing human papillomavirus (HPV)-driven carcinomas and in guiding therapeutic interventions. An understanding of the virology, immunology, and carcinogenesis of HPV is essential for choosing appropriate diagnostic ...

Abstract	Laboratory tests have a key role in preventing human papillomavirus (HPV)-driven carcinomas and in guiding therapeutic interventions. An understanding of the virology, immunology, and carcinogenesis of HPV is essential for choosing appropriate diagnostic test modalities and developing new and even more effective cancer prevention strategies. HPV infects basal epithelial cells on multiple surfaces and induces carcinoma primarily in the cervix and the oropharynx. HPV types are stratified as high risk or low risk based on their carcinogenic potential. During oncogenesis, HPV interferes with cell cycle regulation and incites DNA damage responses that thwart apoptosis and enable mutations to accumulate. Such mutations are an adverse effect of innate and adaptive antiviral immune responses that up-regulate DNA-editing enzymes, with natural selection of cells having a chromosomally integrated viral genome lacking expression of viral proteins targeted by the immune system. Infected cancers share a similar mutation signature, reflecting the effect of apolipoprotein B mRNA-editing catalytic polypeptide enzyme DNA-editing enzymes. It is feasible that genomic tests for characteristic mutations or methylation signatures, along with tests for dysregulated HPV gene expression, add value in predicting behavior of premalignant lesions. Furthermore, these tumor markers in cell-free DNA of plasma or body fluids may one day assist in early detection or monitoring cancer burden during treatment.
MeSH term(s)	DNA Damage/genetics ; DNA Methylation/genetics ; DNA, Viral/genetics ; Humans ; Papillomaviridae/genetics ; Papillomaviridae/pathogenicity ; Papillomavirus Infections/complications ; Papillomavirus Infections/genetics ; Uterine Cervical Dysplasia/genetics ; Uterine Cervical Dysplasia/virology
Chemical Substances	DNA, Viral
Language	English
Publishing date	2017-03-18
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2017.01.006
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Article ; Online: Molecular oncology testing in resource-limited settings.

Gulley, Margaret L / Morgan, Douglas R

The Journal of molecular diagnostics : JMD

2014 Volume 16, Issue 6, Page(s) 601–611

Abstract: Cancer prevalence and mortality are high in developing nations, where resources for cancer control are inadequate. Nearly one-quarter of cancers in resource-limited nations are infection related, and molecular assays can capitalize on this relationship ... ...

Abstract	Cancer prevalence and mortality are high in developing nations, where resources for cancer control are inadequate. Nearly one-quarter of cancers in resource-limited nations are infection related, and molecular assays can capitalize on this relationship by detecting pertinent pathogen genomes and human gene variants to identify those at highest risk for progression to cancer, to classify lesions, to predict effective therapy, and to monitor tumor burden over time. Prime examples are human papillomavirus in cervical neoplasia, Helicobacter pylori and Epstein-Barr virus in gastric adenocarcinoma and lymphoma, and hepatitis B or C virus in hepatocellular cancer. Research is underway to engineer devices that overcome social, economic, and technical barriers limiting effective laboratory support. Additional challenges include an educated workforce, infrastructure for quality metrics and record keeping, and funds to sustain molecular test services. The combination of well-designed interfaces, novel and robust electrochemical technology, and telemedicine tools will promote adoption by frontline providers. Fast turnaround is crucial for surmounting loss to follow-up, although increased use of cell phones, even in rural areas, enhances options for patient education and engagement. Links to a broadband network facilitate consultation and centralized storage of medical data. Molecular technology shows promise to address gaps in health care through rapid, user-friendly, and cost-effective devices reflecting clinical priorities in resource-poor areas.
MeSH term(s)	Communicable Diseases/complications ; Developing Countries ; Health Care Rationing ; Humans ; Neoplasms/complications ; Neoplasms/diagnosis ; Neoplasms/genetics
Language	English
Publishing date	2014-09-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2014.07.002
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Zs.A 5146: Show issues

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Article: Public policy recommendations for oversight of molecular laboratory tests.

Gulley, Margaret L

North Carolina medical journal

2007 Volume 68, Issue 2, Page(s) 109–111

MeSH term(s)	Clinical Laboratory Techniques/standards ; Guidelines as Topic ; Health Policy ; Hospitals ; Humans ; Molecular Diagnostic Techniques/standards ; North Carolina ; Pathology, Clinical/legislation & jurisprudence ; Pharmacogenetics
Language	English
Publishing date	2007-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	422795-5
ISSN	0029-2559
ISSN	0029-2559
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Article ; Online: Use of Spiked Normalizers to More Precisely Quantify Tumor Markers and Viral Genomes by Massive Parallel Sequencing of Plasma DNA.

Gulley, Margaret L / Elmore, Sandra / Gupta, Gaorav P / Kumar, Sunil / Egleston, Matthew / Hoskins, Ian J / Garnett, Aaron

The Journal of molecular diagnostics : JMD

2020 Volume 22, Issue 4, Page(s) 437–446

Abstract: A problematic aspect of massive parallel sequencing is that somatic mutations and viral loads are typically quantified as a fraction relative to wild-type human DNA, yet wild-type levels vary with diverse biologic and preanalytic interferences. A novel ... ...

Abstract	A problematic aspect of massive parallel sequencing is that somatic mutations and viral loads are typically quantified as a fraction relative to wild-type human DNA, yet wild-type levels vary with diverse biologic and preanalytic interferences. A novel strategy was devised to quantify target analytes in copies per mL of plasma after normalizing for read counts of spiked DNAs. Five synthetic DNAs (called EndoGenus spikes) were added to plasma before library preparation (modified ArcherDX LiquidPlex 28). By normalizing to the fractional recovery of EndoGenus spike reads, numerical values for each disease marker were reportable in units of copies per mL. To show how well this system operates, replicate assays were performed on 40 mock plasmas having 23 engineered mutations and on 21 natural plasmas. Reads for all five EndoGenus spikes were recovered (means, 313 and 376 copies/mL in mock and natural plasmas, respectively). Normalizing read counts for the proportional recovery of spikes helped control for variables in the multistep protocol, reducing the CV in replicate tests from 34% to 22% for mutations and from 25% to 7% for viral loads. In conclusion, the EndoGenus system is useful for evaluating efficiency of the total test system and for precisely quantifying target molecules. This system may benefit patients being monitored for disease burden while also tracking emerging subclones.
MeSH term(s)	Alleles ; Biomarkers, Tumor ; Cell-Free Nucleic Acids ; Circulating Tumor DNA ; DNA, Neoplasm ; DNA, Viral ; Genetic Variation ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mutation ; Neoplasms/diagnosis ; Neoplasms/genetics ; Real-Time Polymerase Chain Reaction
Chemical Substances	Biomarkers, Tumor ; Cell-Free Nucleic Acids ; Circulating Tumor DNA ; DNA, Neoplasm ; DNA, Viral
Language	English
Publishing date	2020-02-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2020.01.012
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