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Article ; Online: Overview of Research on Germline Genetic Variation in Immune Genes and Cancer Outcomes.

Chao, Brittany N / Carrick, Danielle M / Filipski, Kelly K / Nelson, Stefanie A

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

2022 Volume 31, Issue 3, Page(s) 495–506

Abstract: Since the late 19th century, the immune system has been known to play a role in cancer risk, initiation, and progression. Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for autoimmune and inflammatory diseases, yet ... ...

Abstract	Since the late 19th century, the immune system has been known to play a role in cancer risk, initiation, and progression. Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for autoimmune and inflammatory diseases, yet the connection between human genetic variation and immune-mediated response to cancer treatments remains less well-explored. Understanding inherited genetic variation, with respect to germline genetic polymorphisms that affect immune system pathways, could lead to greater insights about how these processes may best be harnessed to successfully treat cancer. Our goal in this manuscript was to understand progress and challenges in assessing the role of inherited genetic variation in response to cancer treatments. Overall, the 39 studies reviewed here suggest that germline genetic variation in immune system-related genes may potentially affect responses to cancer treatments. Although further research is needed, considering information on germline immune genetic variation may help, in some cases, to optimize cancer treatment.
MeSH term(s)	Genetic Predisposition to Disease ; Genetic Variation/genetics ; Genome-Wide Association Study/methods ; Germ Cells ; Humans ; Neoplasms/genetics ; Neoplasms/therapy ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2022-01-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	1153420-5
ISSN	1538-7755 ; 1055-9965
ISSN (online)	1538-7755
ISSN	1055-9965
DOI	10.1158/1055-9965.EPI-21-0583
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Article ; Online: Unraveling Links between Chronic Inflammation and Long COVID: Workshop Report.

Tandon, Pushpa / Abrams, Natalie D / Avula, Leela Rani / Carrick, Danielle M / Chander, Preethi / Divi, Rao L / Dwyer, Johanna T / Gannot, Gallya / Gordiyenko, Nataliya / Liu, Qian / Moon, Kyung / PrabhuDas, Mercy / Singh, Anju / Tilahun, Mulualem E / Satyamitra, Merriline M / Wang, Chiayeng / Warren, Ronald / Liu, Christina H

Journal of immunology (Baltimore, Md. : 1950)

2024 Volume 212, Issue 4, Page(s) 505–512

Abstract: As COVID-19 continues, an increasing number of patients develop long COVID symptoms varying in severity that last for weeks, months, or longer. Symptoms commonly include lingering loss of smell and taste, hearing loss, extreme fatigue, and "brain fog." ... ...

Abstract	As COVID-19 continues, an increasing number of patients develop long COVID symptoms varying in severity that last for weeks, months, or longer. Symptoms commonly include lingering loss of smell and taste, hearing loss, extreme fatigue, and "brain fog." Still, persistent cardiovascular and respiratory problems, muscle weakness, and neurologic issues have also been documented. A major problem is the lack of clear guidelines for diagnosing long COVID. Although some studies suggest that long COVID is due to prolonged inflammation after SARS-CoV-2 infection, the underlying mechanisms remain unclear. The broad range of COVID-19's bodily effects and responses after initial viral infection are also poorly understood. This workshop brought together multidisciplinary experts to showcase and discuss the latest research on long COVID and chronic inflammation that might be associated with the persistent sequelae following COVID-19 infection.
MeSH term(s)	Humans ; Post-Acute COVID-19 Syndrome ; COVID-19 ; SARS-CoV-2 ; Inflammation ; Disease Progression
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
DOI	10.4049/jimmunol.2300804
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Article ; Online: Epidemiologic Research of Rare Cancers: Trends, Resources, and Challenges.

Gallicchio, Lisa / Daee, Danielle L / Rotunno, Melissa / Barajas, Rolando / Fagan, Sarah / Carrick, Danielle M / Divi, Rao L / Filipski, Kelly K / Freedman, Andrew N / Gillanders, Elizabeth M / Lam, Tram K / Martin, Damali N / Rogers, Scott / Verma, Mukesh / Nelson, Stefanie A

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

2021 Volume 30, Issue 7, Page(s) 1305–1311

Abstract: Background: The goals of this project were to assess the status of NCI's rare cancer-focused population science research managed by the Division of Cancer Control and Population Sciences (DCCPS), to develop a framework for evaluation of rare cancer ... ...

Abstract	Background: The goals of this project were to assess the status of NCI's rare cancer-focused population science research managed by the Division of Cancer Control and Population Sciences (DCCPS), to develop a framework for evaluation of rare cancer research activities, and to review available resources to study rare cancers. Methods: Cancer types with an overall age-adjusted incidence rate of less than 20 cases per 100,000 individuals were identified using NCI Surveillance, Epidemiology and End Results (SEER) Program data. SEER data were utilized to develop a framework based on statistical commonalities. A portfolio analysis of DCCPS-supported active grants and a review of three genomic databases were conducted. Results: For the 45 rare cancer types included in the analysis, 123 active DCCPS-supported rare cancer-focused grants were identified, of which the highest percentage (18.7%) focused on ovarian cancer. The developed framework revealed five clusters of rare cancer types. The cluster with the highest number of grants ( Conclusions: This article provides an overview of the rare cancer-focused population sciences research landscape as well as information on gaps and opportunities. Impact: The findings of this article can be used to develop efficient and comprehensive strategies to accelerate rare cancer research.
MeSH term(s)	Biomedical Research/statistics & numerical data ; Biomedical Research/trends ; Epidemiologic Studies ; Humans ; Incidence ; National Cancer Institute (U.S.)/statistics & numerical data ; Neoplasms/epidemiology ; Neoplasms/prevention & control ; Prevalence ; Professional Practice Gaps/statistics & numerical data ; Professional Practice Gaps/trends ; Rare Diseases/epidemiology ; Rare Diseases/prevention & control ; SEER Program/statistics & numerical data ; Survival Rate ; United States/epidemiology
Language	English
Publishing date	2021-04-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1153420-5
ISSN	1538-7755 ; 1055-9965
ISSN (online)	1538-7755
ISSN	1055-9965
DOI	10.1158/1055-9965.EPI-20-1796
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Article ; Online: Robustness of RNA sequencing on older formalin-fixed paraffin-embedded tissue from high-grade ovarian serous adenocarcinomas.

Zhao, Yongmei / Mehta, Monika / Walton, Ashley / Talsania, Keyur / Levin, Yelena / Shetty, Jyoti / Gillanders, Elizabeth M / Tran, Bao / Carrick, Danielle Mercatante

PloS one

2019 Volume 14, Issue 5, Page(s) e0216050

Abstract: Formalin-fixed paraffin-embedded (FFPE) tissues are among the most widely available clinical specimens. Their potential utility as a source of RNA for transcriptome studies would greatly enhance population-based cancer studies. Although preliminary ... ...

Abstract	Formalin-fixed paraffin-embedded (FFPE) tissues are among the most widely available clinical specimens. Their potential utility as a source of RNA for transcriptome studies would greatly enhance population-based cancer studies. Although preliminary studies suggest FFPE tissue may be used for RNA sequencing, the effect of storage time on these specimens needs to be determined. We conducted this study to determine whether RNA in archived FFPE high-grade ovarian serous adenocarcinomas from Surveillance, Epidemiology and End Results (SEER) registries was present in sufficient quantity and quality for RNA-Seq analysis. FFPE tissues, stored from 7 to 32 years, were obtained from three SEER sites. RNA was extracted, quantified, quality assessed, and subjected to RNA-Seq (a whole transcriptome sequencing technology). FFPE specimens stored for longer periods of time had poorer RNA sample quality as indicated by negative correlations between specimen storage time and fragment distribution values (DV). In addition, sample contamination was a common issue among the RNA, with 41 of 67 samples having 5% to 48% bacterial contamination. However, regardless of specimen storage time and bacterial contamination, 60% of the samples yielded data that enabled gene expression quantification, identifying more than 10,000 genes, with the correlations among most biological replicates above 0.7. This study demonstrates that FFPE high-grade ovarian serous adenocarcinomas specimens stored in repositories for up to 32 years and under varying storage conditions are a promising source of RNA for RNA-Seq. We also describe certain caveats to be considered when designing RNA-Seq studies using archived FFPE tissues.
MeSH term(s)	Cystadenocarcinoma, Serous/genetics ; Female ; Formaldehyde ; Gene Expression Profiling/methods ; Gene Library ; Humans ; Ovarian Neoplasms/genetics ; Paraffin Embedding/methods ; RNA, Neoplasm/genetics ; RNA-Seq/methods ; SEER Program ; Time Factors ; Tissue Fixation/methods
Chemical Substances	RNA, Neoplasm ; Formaldehyde (1HG84L3525)
Language	English
Publishing date	2019-05-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0216050
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Article ; Online: Metabolic Regulation of Inflammation and Its Resolution: Current Status, Clinical Needs, Challenges, and Opportunities.

Tandon, Pushpa / Abrams, Natalie D / Carrick, Danielle M / Chander, Preethi / Dwyer, Johanna / Fuldner, Rebecca / Gannot, Gallya / Laughlin, Maren / McKie, George / PrabhuDas, Mercy / Singh, Anju / Tsai, Shang-Yi Anne / Vedamony, Merriline M / Wang, Chiayeng / Liu, Christina H

Journal of immunology (Baltimore, Md. : 1950)

2021 Volume 207, Issue 11, Page(s) 2625–2630

Abstract: Metabolism and inflammation have been viewed as two separate processes with distinct but critical functions for our survival: metabolism regulates the utilization of nutrients, and inflammation is responsible for defense and repair. Both respond to an ... ...

Abstract	Metabolism and inflammation have been viewed as two separate processes with distinct but critical functions for our survival: metabolism regulates the utilization of nutrients, and inflammation is responsible for defense and repair. Both respond to an organism's stressors to restore homeostasis. The interplay between metabolic status and immune response (immunometabolism) plays an important role in maintaining health or promoting disease development. Understanding these interactions is critical in developing tools for facilitating novel preventative and therapeutic approaches for diseases, including cancer. This trans-National Institutes of Health workshop brought together basic scientists, technology developers, and clinicians to discuss state-of-the-art, innovative approaches, challenges, and opportunities to understand and harness immunometabolism in modulating inflammation and its resolution.
MeSH term(s)	Humans ; Inflammation/immunology ; Inflammation/metabolism ; Neoplasms/immunology ; Neoplasms/metabolism
Language	English
Publishing date	2021-11-23
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
DOI	10.4049/jimmunol.2100829
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Article ; Online: Robustness of RNA sequencing on older formalin-fixed paraffin-embedded tissue from high-grade ovarian serous adenocarcinomas.

Yongmei Zhao / Monika Mehta / Ashley Walton / Keyur Talsania / Yelena Levin / Jyoti Shetty / Elizabeth M Gillanders / Bao Tran / Danielle Mercatante Carrick

PLoS ONE, Vol 14, Iss 5, p e

2019 Volume 0216050

Abstract	Formalin-fixed paraffin-embedded (FFPE) tissues are among the most widely available clinical specimens. Their potential utility as a source of RNA for transcriptome studies would greatly enhance population-based cancer studies. Although preliminary studies suggest FFPE tissue may be used for RNA sequencing, the effect of storage time on these specimens needs to be determined. We conducted this study to determine whether RNA in archived FFPE high-grade ovarian serous adenocarcinomas from Surveillance, Epidemiology and End Results (SEER) registries was present in sufficient quantity and quality for RNA-Seq analysis. FFPE tissues, stored from 7 to 32 years, were obtained from three SEER sites. RNA was extracted, quantified, quality assessed, and subjected to RNA-Seq (a whole transcriptome sequencing technology). FFPE specimens stored for longer periods of time had poorer RNA sample quality as indicated by negative correlations between specimen storage time and fragment distribution values (DV). In addition, sample contamination was a common issue among the RNA, with 41 of 67 samples having 5% to 48% bacterial contamination. However, regardless of specimen storage time and bacterial contamination, 60% of the samples yielded data that enabled gene expression quantification, identifying more than 10,000 genes, with the correlations among most biological replicates above 0.7. This study demonstrates that FFPE high-grade ovarian serous adenocarcinomas specimens stored in repositories for up to 32 years and under varying storage conditions are a promising source of RNA for RNA-Seq. We also describe certain caveats to be considered when designing RNA-Seq studies using archived FFPE tissues.
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Comparative expression of tristetraprolin (TTP) family member transcripts in normal human tissues and cancer cell lines.

Carrick, Danielle M / Blackshear, Perry J

Archives of biochemistry and biophysics

2007 Volume 462, Issue 2, Page(s) 278–285

Abstract: The tristetraprolin (TTP) family of tandem zinc finger proteins comprises three members in man and most other mammals, with a fourth expressed in rodents. In mice, gene disruption of TTP itself leads to a systemic inflammatory syndrome that is mediated ... ...

Abstract	The tristetraprolin (TTP) family of tandem zinc finger proteins comprises three members in man and most other mammals, with a fourth expressed in rodents. In mice, gene disruption of TTP itself leads to a systemic inflammatory syndrome that is mediated in large part by over-expression of tumor necrosis factor alpha (TNF). This increased expression is secondary to stabilization of the TNF mRNA in the TTP KO mice, a finding that led to the characterization of TTP as an mRNA binding protein that can promote the removal of the poly(A) tail from selected mRNAs and facilitate their nucleolytic destruction. The other human family members behave similarly to TTP in over-expression studies of transfected cells, but gene disruption experiments have implicated them in different physiological processes. In the present study, we developed a real-time PCR assay for all three human family members that allowed for comparative measurements of all three family members in the same tissues and cells. We used this assay to quantitate expression levels of all three transcripts in a variety of normal human tissues, as well as in the ;;NCI 60", a well characterized panel of human tumor cell lines. Although studies in fibroblasts and macrophages derived from knockout mice have failed to demonstrate compensatory expression of the family members in terms of transcript levels, it remains possible that the different family members can function as ;;TTP equivalents" in certain physiological or pathological circumstances.
MeSH term(s)	Cell Line, Tumor ; Cells, Cultured ; Gene Expression Regulation, Neoplastic ; Humans ; Multigene Family ; Neoplasms/metabolism ; Organ Specificity ; Transcription Factors/metabolism ; Tristetraprolin/metabolism
Chemical Substances	Transcription Factors ; Tristetraprolin ; ZFP36 protein, human
Language	English
Publishing date	2007-06-15
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2007.04.011
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Article ; Online: Imaging inflammation and its resolution in health and disease: current status, clinical needs, challenges, and opportunities.

Liu, Christina H / Abrams, Natalie D / Carrick, Danielle M / Chander, Preethi / Dwyer, Johanna / Hamlet, Michelle R J / Kindzelski, Andrei L / PrabhuDas, Mercy / Tsai, Shang-Yi Anne / Vedamony, Merriline M / Wang, Chiayeng / Tandon, Pushpa

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

2019 Volume 33, Issue 12, Page(s) 13085–13097

Abstract: Inflammation is a normal process in our body; acute inflammation acts to suppress infections and support wound healing. Chronic inflammation likely leads to a wide range of diseases, including cancer. Tools to locate and monitor inflammation are critical ...

Abstract	Inflammation is a normal process in our body; acute inflammation acts to suppress infections and support wound healing. Chronic inflammation likely leads to a wide range of diseases, including cancer. Tools to locate and monitor inflammation are critical for developing effective interventions to arrest inflammation and promote its resolution. To identify current clinical needs, challenges, and opportunities in advancing imaging-based evaluations of inflammatory status in patients, the U.S. National Institutes of Health convened a workshop on imaging inflammation and its resolution in health and disease. Clinical speakers described their needs for image-based capabilities that could help determine the extent of inflammatory conditions in patients to guide treatment planning and undertake necessary interventions. The imaging speakers showcased the state-of-the-art
MeSH term(s)	Atherosclerosis/diagnostic imaging ; Atherosclerosis/immunology ; Atherosclerosis/metabolism ; Biomarkers/metabolism ; Humans ; Immunotherapy ; Inflammation/diagnostic imaging ; Inflammation/immunology ; Inflammation/metabolism ; Magnetic Resonance Imaging ; Non-alcoholic Fatty Liver Disease/diagnostic imaging ; Non-alcoholic Fatty Liver Disease/immunology ; Non-alcoholic Fatty Liver Disease/metabolism ; Positron-Emission Tomography
Chemical Substances	Biomarkers
Language	English
Publishing date	2019-10-09
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	639186-2
ISSN	1530-6860 ; 0892-6638
ISSN (online)	1530-6860
ISSN	0892-6638
DOI	10.1096/fj.201902024
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Article ; Online: Biomarkers of chronic inflammation in disease development and prevention: challenges and opportunities.

Liu, Christina H / Abrams, Natalie D / Carrick, Danielle M / Chander, Preethi / Dwyer, Johanna / Hamlet, Michelle R J / Macchiarini, Francesca / PrabhuDas, Mercy / Shen, Grace L / Tandon, Pushpa / Vedamony, Merriline M

Nature immunology

2017 Volume 18, Issue 11, Page(s) 1175–1180

MeSH term(s)	Biomarkers/analysis ; Chronic Disease ; Humans ; Inflammation/complications ; Inflammation/diagnosis
Chemical Substances	Biomarkers
Language	English
Publishing date	2017-10-13
Publishing country	United States
Document type	Congress
ZDB-ID	2016987-5
ISSN	1529-2916 ; 1529-2908
ISSN (online)	1529-2916
ISSN	1529-2908
DOI	10.1038/ni.3828
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Article ; Online: Eastern Association for the Surgery of Trauma Multicenter Trial: Comparison of pre-injury antithrombotic use and reversal strategies among severe traumatic brain injury patients.

Yorkgitis, Brian K / Tatum, Danielle M / Taghavi, Sharven / Schroeppel, Thomas J / Noorbakhsh, Matthew R / Philps, Frances Hite / Bugaev, Nikolay / Mukherjee, Kaushik / Bellora, Mellody / Ong, Adrian W / Ratnasekera, Asanthi / Nordham, Kristen D / Carrick, Matthew M / Haan, James M / Lightwine, Kelly L / Lottenberg, Lawrence / Borrego, Robert / Cullinane, Daniel C / Berne, John D /

Rodriguez Mederos, Dalier / Hayward, Thomas Z / Kerwin, Andy J / Crandall, Marie

The journal of trauma and acute care surgery

2021 Volume 92, Issue 1, Page(s) 88–92

Abstract: Background: Trauma teams are often faced with patients on antithrombotic (AT) drugs, which is challenging when bleeding occurs. We sought to compare the effects of different AT medications on head injury severity and hypothesized that AT reversal would ... ...

Abstract	Background: Trauma teams are often faced with patients on antithrombotic (AT) drugs, which is challenging when bleeding occurs. We sought to compare the effects of different AT medications on head injury severity and hypothesized that AT reversal would not improve mortality in severe traumatic brain injury (TBI) patients. Methods: An Eastern Association for the Surgery of Trauma-sponsored prospective, multicentered, observational study of 15 trauma centers was performed. Patient demographics, injury burden, comorbidities, AT agents, and reversal attempts were collected. Outcomes of interest were head injury severity and in-hospital mortality. Results: Analysis was performed on 2,793 patients. The majority of patients were on aspirin (acetylsalicylic acid [ASA], 46.1%). Patients on a platelet chemoreceptor blocker (P2Y12) had the highest mean Injury Severity Score (9.1 ± 8.1). Patients taking P2Y12 inhibitors ± ASA, and ASA-warfarin had the highest head Abbreviated Injury Scale (AIS) mean (1.2 ± 1.6). On risk-adjusted analysis, warfarin-ASA was associated with a higher head AIS (odds ratio [OR], 2.43; 95% confidence interval [CI], 1.34-4.42) after controlling for Injury Severity Score, Charlson Comorbidity Index, initial Glasgow Coma Scale score, and initial systolic blood pressure. Among patients with severe TBI (head AIS score, ≥3) on antiplatelet therapy, reversal with desmopressin (DDAVP) and/or platelet transfusion did not improve survival (82.9% reversal vs. 90.4% none, p = 0.30). In severe TBI patients taking Xa inhibitors who received prothrombin complex concentrate, survival was not improved (84.6% reversal vs. 84.6% none, p = 0.68). With risk adjustment as described previously, mortality was not improved with reversal attempts (antiplatelet agents: OR 0.83; 85% CI, 0.12-5.9 [p = 0.85]; Xa inhibitors: OR, 0.76; 95% CI, 0.12-4.64; p = 0.77). Conclusion: Reversal attempts appear to confer no mortality benefit in severe TBI patients on antiplatelet agents or Xa inhibitors. Combination therapy was associated with severity of head injury among patients taking preinjury AT therapy, with ASA-warfarin possessing the greatest risk. Level of evidence: Prognostic, level II.
MeSH term(s)	Aged ; Anticoagulant Reversal Agents/administration & dosage ; Aspirin/adverse effects ; Aspirin/therapeutic use ; Brain Injuries, Traumatic/complications ; Brain Injuries, Traumatic/diagnosis ; Brain Injuries, Traumatic/mortality ; Brain Injuries, Traumatic/therapy ; Cardiovascular Diseases/drug therapy ; Cardiovascular Diseases/epidemiology ; Comorbidity ; Deamino Arginine Vasopressin/administration & dosage ; Factor Xa Inhibitors/adverse effects ; Factor Xa Inhibitors/therapeutic use ; Female ; Fibrinolytic Agents/adverse effects ; Fibrinolytic Agents/classification ; Fibrinolytic Agents/therapeutic use ; Hemorrhage/etiology ; Hemorrhage/mortality ; Hemorrhage/therapy ; Hospital Mortality ; Humans ; Male ; Platelet Transfusion/statistics & numerical data ; Risk Assessment/methods ; Risk Assessment/statistics & numerical data ; Trauma Severity Indices ; Treatment Outcome ; United States/epidemiology ; Warfarin/adverse effects ; Warfarin/therapeutic use
Chemical Substances	Anticoagulant Reversal Agents ; Factor Xa Inhibitors ; Fibrinolytic Agents ; Warfarin (5Q7ZVV76EI) ; Deamino Arginine Vasopressin (ENR1LLB0FP) ; Aspirin (R16CO5Y76E)
Language	English
Publishing date	2021-09-23
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2651070-4
ISSN	2163-0763 ; 2163-0755
ISSN (online)	2163-0763
ISSN	2163-0755
DOI	10.1097/TA.0000000000003421
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