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Johansen AM, Forsythe SD, McGrath CT, Barker G, Jimenez H, Paluri RK, Pasche BC. TGFβ in Pancreas and Colorectal Cancer: Opportunities to Overcome Therapeutic Resistance. Clin Cancer Res 2024; 30:3676-3687. [PMID: 38916900 PMCID: PMC11371528 DOI: 10.1158/1078-0432.ccr-24-0468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/16/2024] [Accepted: 05/30/2024] [Indexed: 06/26/2024]
Abstract
TGFβ is a pleiotropic signaling pathway that plays a pivotal role in regulating a multitude of cellular functions. TGFβ has a dual role in cell regulation where it induces growth inhibition and cell death; however, it can switch to a growth-promoting state under cancerous conditions. TGFβ is upregulated in colorectal cancer and pancreatic cancer, altering the tumor microenvironment and immune system and promoting a mesenchymal state. The upregulation of TGFβ in certain cancers leads to resistance to immunotherapy, and attempts to inhibit TGFβ expression have led to reduced therapeutic resistance when combined with chemotherapy and immunotherapy. Here, we review the current TGFβ inhibitor drugs in clinical trials for pancreatic and colorectal cancer, with the goal of uncovering advances in improving clinical efficacy for TGFβ combinational treatments in patients. Furthermore, we discuss the relevance of alterations in TGFβ signaling and germline variants in the context of personalizing treatment for patients who show lack of response to current therapeutics.
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Affiliation(s)
- Allan M Johansen
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Steven D Forsythe
- Neuroendocrine Therapy Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Callum T McGrath
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Grayson Barker
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Hugo Jimenez
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Ravi K Paluri
- Section of Hematology/Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Boris C Pasche
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
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2
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Scatolini M, Grisanti S, Tomaiuolo P, Grosso E, Basile V, Cosentini D, Puglisi S, Laganà M, Perotti P, Saba L, Rossini E, Palermo F, Sigala S, Volante M, Berruti A, Terzolo M. Germline NGS targeted analysis in adult patients with sporadic adrenocortical carcinoma. Eur J Cancer 2024; 205:114088. [PMID: 38714106 DOI: 10.1016/j.ejca.2024.114088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/11/2024] [Accepted: 04/21/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND Adrenocortical carcinoma (ACC) is a rare cancer that arises sporadically or due to hereditary syndromes. Data on germline variants (GVs) in sporadic ACC are limited. Our aim was to characterize GVs of genes potentially related to adrenal diseases in 150 adult patients with sporadic ACC. METHODS This was a retrospective analysis of stage I-IV ACC patients with sporadic ACC from two reference centers for ACC in Italy. Patients were included in the analysis if they had confirmed diagnosis of ACC, a frozen peripheral blood sample and complete clinical and follow-up data. Next generation sequencing technology was used to analyze the prevalence of GVs in a custom panel of 17 genes belonging to either cancer-predisposition genes or adrenocortical-differentiation genes categories. RESULTS We identified 18 GVs based on their frequency, enrichment and predicted functional characteristics. We found six pathogenic (P) or likely pathogenic (LP) variants in ARMC5, CTNNB1, MSH2, PDE11A and TP53 genes; and twelve variants lacking evidence of pathogenicity. New unique P/LP variants were identified in TP53 (p.G105D) and, for the first time, in ARMC5 (p.P731R). The presence of P/LP GVs was associated with reduced survival outcomes and had a significant and independent impact on both progression-free survival and overall survival. CONCLUSIONS GVs were present in 6.7 % of patients with sporadic ACC, and we identified novel variants of ARMC5 and TP53. These findings may improve understanding of ACC pathogenesis and enable genetic counseling of patients and their families.
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Affiliation(s)
- Maria Scatolini
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy
| | - Salvatore Grisanti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Pasquale Tomaiuolo
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy; Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Enrico Grosso
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy
| | - Vittoria Basile
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Deborah Cosentini
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Soraya Puglisi
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy.
| | - Marta Laganà
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Paola Perotti
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Laura Saba
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Elisa Rossini
- Department of Molecular & Translational Medicine, Section of Pharmacology, University of Brescia, 25123 Brescia, Italy
| | - Flavia Palermo
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy
| | - Sandra Sigala
- Department of Molecular & Translational Medicine, Section of Pharmacology, University of Brescia, 25123 Brescia, Italy
| | - Marco Volante
- Pathology Unit, Oncology department, University of Turin, San Luigi Gonzaga University Hospital, Regione Gonzole 10, 10043 Orbassano, Turin, Italy
| | - Alfredo Berruti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Massimo Terzolo
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
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Iacobas DA. Advanced Molecular Solutions for Cancer Therapy-The Good, the Bad, and the Ugly of the Biomarker Paradigm. Curr Issues Mol Biol 2024; 46:1694-1699. [PMID: 38534725 DOI: 10.3390/cimb46030109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024] Open
Abstract
Identifying the most effective actionable molecules whose "smart" manipulation might selectively kill/slow down/stop the proliferation of cancer cells, with few side effects on the normal cells of the tissue, was for decades the single major objective of countless investigators [...].
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Affiliation(s)
- Dumitru Andrei Iacobas
- Laboratory of Personalized Genomics, Undergraduate Medical Academy, Prairie View A&M University, Prairie View, TX 77446, USA
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4
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Ibrahim M, Illa-Bochaca I, Fa’ak F, Monson KR, Ferguson R, Lyu C, Vega-Saenz de Miera E, Johannet P, Chou M, Mastroianni J, Darvishian F, Kirchhoff T, Zhong J, Krogsgaard M, Osman I. Kinase Insert Domain Receptor Q472H Pathogenic Germline Variant Impacts Melanoma Tumor Growth and Patient Treatment Outcomes. Cancers (Basel) 2023; 16:18. [PMID: 38201446 PMCID: PMC10778134 DOI: 10.3390/cancers16010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND We previously reported a higher incidence of a pathogenic germline variant in the kinase insert domain receptor (KDR) in melanoma patients compared to the general population. Here, we dissect the impact of this genotype on melanoma tumor growth kinetics, tumor phenotype, and response to treatment with immune checkpoint inhibitors (ICIs) or targeted therapy. METHODS The KDR genotype was determined and the associations between the KDR Q472H variant (KDR-Var), angiogenesis, tumor immunophenotype, and response to MAPK inhibition or ICI treatment were examined. Melanoma B16 cell lines were transfected with KDR-Var or KDR wild type (KDR-WT), and the differences in tumor kinetics were evaluated. We also examined the impact of KDR-Var on the response of melanoma cells to a combination of VEGFR inhibition with MAPKi. RESULTS We identified the KDR-Var genotype in 81/489 (37%) patients, and it was associated with a more angiogenic (p = 0.003) and immune-suppressive tumor phenotype. KDR-Var was also associated with decreased PFS to MAPKi (p = 0.022) and a trend with worse PFS to anti-PD1 therapy (p = 0.06). KDR-Var B16 murine models had increased average tumor volume (p = 0.0027) and decreased CD45 tumor-infiltrating lymphocytes (p = 0.0282). The anti-VEGFR treatment Lenvatinib reduced the tumor size of KDR-Var murine tumors (p = 0.0159), and KDR-Var cells showed synergistic cytotoxicity to the combination of dabrafenib and lenvatinib. CONCLUSIONS Our data demonstrate a role of germline KDR-Var in modulating melanoma behavior, including response to treatment. Our data also suggest that anti-angiogenic therapy might be beneficial in patients harboring this genotype, which needs to be tested in clinical trials.
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Affiliation(s)
- Milad Ibrahim
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY 10016, USA; (M.I.); (I.I.-B.); (E.V.-S.d.M.)
| | - Irineu Illa-Bochaca
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY 10016, USA; (M.I.); (I.I.-B.); (E.V.-S.d.M.)
| | - Faisal Fa’ak
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY 10016, USA; (M.I.); (I.I.-B.); (E.V.-S.d.M.)
| | - Kelsey R. Monson
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (K.R.M.); (R.F.); (C.L.); (T.K.); (J.Z.)
| | - Robert Ferguson
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (K.R.M.); (R.F.); (C.L.); (T.K.); (J.Z.)
| | - Chen Lyu
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (K.R.M.); (R.F.); (C.L.); (T.K.); (J.Z.)
| | - Eleazar Vega-Saenz de Miera
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY 10016, USA; (M.I.); (I.I.-B.); (E.V.-S.d.M.)
| | - Paul Johannet
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY 10016, USA; (M.I.); (I.I.-B.); (E.V.-S.d.M.)
| | - Margaret Chou
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY 10016, USA; (M.I.); (I.I.-B.); (E.V.-S.d.M.)
| | - Justin Mastroianni
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA (M.K.)
| | - Farbod Darvishian
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA (M.K.)
| | - Tomas Kirchhoff
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (K.R.M.); (R.F.); (C.L.); (T.K.); (J.Z.)
- Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, 522 First Ave, New York, NY 10016, USA
| | - Judy Zhong
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (K.R.M.); (R.F.); (C.L.); (T.K.); (J.Z.)
- Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, 522 First Ave, New York, NY 10016, USA
| | - Michelle Krogsgaard
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA (M.K.)
- Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, 522 First Ave, New York, NY 10016, USA
| | - Iman Osman
- Ronald O Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY 10016, USA; (M.I.); (I.I.-B.); (E.V.-S.d.M.)
- Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, 522 First Ave, New York, NY 10016, USA
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Teague AG, Quintero M, Karimi Dermani F, Cagan RL, Bangi E. A polycistronic transgene design for combinatorial genetic perturbations from a single transcript in Drosophila. PLoS Genet 2023; 19:e1010792. [PMID: 37267433 PMCID: PMC10266610 DOI: 10.1371/journal.pgen.1010792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/14/2023] [Accepted: 05/18/2023] [Indexed: 06/04/2023] Open
Abstract
Experimental models that capture the genetic complexity of human disease and allow mechanistic explorations of the underlying cell, tissue, and organ interactions are crucial to furthering our understanding of disease biology. Such models require combinatorial manipulations of multiple genes, often in more than one tissue at once. The ability to perform complex genetic manipulations in vivo is a key strength of Drosophila, where many tools for sophisticated and orthogonal genetic perturbations exist. However, combining the large number of transgenes required to establish more representative disease models and conducting mechanistic studies in these already complex genetic backgrounds is challenging. Here we present a design that pushes the limits of Drosophila genetics by allowing targeted combinatorial ectopic expression and knockdown of multiple genes from a single inducible transgene. The polycistronic transcript encoded by this transgene includes a synthetic short hairpin cluster cloned within an intron placed at the 5' end of the transcript, followed by two protein-coding sequences separated by the T2A sequence that mediates ribosome skipping. This technology is particularly useful for modeling genetically complex diseases like cancer, which typically involve concurrent activation of multiple oncogenes and loss of multiple tumor suppressors. Furthermore, consolidating multiple genetic perturbations into a single transgene further streamlines the ability to perform combinatorial genetic manipulations and makes it readily adaptable to a broad palette of transgenic systems. This flexible design for combinatorial genetic perturbations will also be a valuable tool for functionally exploring multigenic gene signatures identified from omics studies of human disease and creating humanized Drosophila models to characterize disease-associated variants in human genes. It can also be adapted for studying biological processes underlying normal tissue homeostasis and development that require simultaneous manipulation of many genes.
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Affiliation(s)
- Alexander G. Teague
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Maria Quintero
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Fateme Karimi Dermani
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Ross L. Cagan
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Erdem Bangi
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
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6
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Richardson A, Darst B, Wojcik G, Wagle N, Haricharan S. Research Silos in Cancer Disparities: Obstacles to Improving Clinical Outcomes for Underserved Patient Populations. Clin Cancer Res 2023; 29:1194-1199. [PMID: 36638200 PMCID: PMC10073283 DOI: 10.1158/1078-0432.ccr-22-3182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/08/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Despite much vaunted progress in cancer therapeutics and diagnostics, outcomes for many groups of non-White patients with cancer remain worse than those for their White compatriots. One reason for this is the lack of inclusion and representation of non-White patients in clinical trials, preclinical datasets, and among researchers, a shortfall that is gaining wide recognition within the cancer research community and the lay public. Several reviews and editorials have commented on the negative impacts of the status quo on progress in cancer research toward medical breakthroughs that help all communities and not just White patients with cancer. In this perspective, we describe the existence of research silos focused either on the impact of socioeconomic factors proceeding from systemic racism on cancer outcomes, or on genetic ancestry as it affects the molecular biology of cancer developing in specific patient populations. While both these research areas are critical for progress toward precision medicine equity, breaking down these silos will help us gain an integrated understanding of how race and racism impact cancer development, progression, and patient outcomes. Bringing this comprehensive approach to cancer disparities research will undoubtedly improve our overall understanding of how stress and environmental factors affect the molecular biology of cancer, which will lead to the development of new diagnostics and therapeutics that are applicable across cancer patient demographics.
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Affiliation(s)
| | - Burcu Darst
- Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Genevieve Wojcik
- Dept of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Nikhil Wagle
- Dept of Medicine, Harvard Medical School, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
| | - Svasti Haricharan
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
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7
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Chat V, Dagayev S, Moran U, Snuderl M, Weber J, Ferguson R, Osman I, Kirchhoff T. A genome-wide association study of germline variation and melanoma prognosis. Front Oncol 2023; 12:1050741. [PMID: 36741706 PMCID: PMC9894711 DOI: 10.3389/fonc.2022.1050741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/23/2022] [Indexed: 01/20/2023] Open
Abstract
Background The high mortality of cutaneous melanoma (CM) is partly due to unpredictable patterns of disease progression in patients with early-stage lesions. The reliable prediction of advanced disease risk from early-stage CM, is an urgent clinical need, especially given the recent expansion of immune checkpoint inhibitor therapy to the adjuvant setting. In our study, we comprehensively investigated the role of germline variants as CM prognostic markers. Methods We performed a genome-wide association analysis in two independent cohorts of N=551 (discovery), and N=550 (validation) early-stage immunotherapy-naïve melanoma patients. A multivariable Cox proportional hazard regression model was used to identify associations with overall survival in the discovery group, followed by a validation analysis. Transcriptomic profiling and survival analysis were used to elucidate the biological relevance of candidate genes associated with CM progression. Results We found two independent associations of germline variants with melanoma prognosis. The alternate alleles of these two SNPs were both associated with an increased risk of death [rs60970102 in MELK: HR=3.14 (2.05-4.81), p=1.48×10-7; and rs77480547 in SH3BP4: HR=3.02 (2.02-4.52), p=7.58×10-8, both in the pooled cohort]. The addition of the combined risk alleles (CRA) of the identified variants into the prognostic model improved the predictive power, as opposed to a model of clinical covariates alone. Conclusions Our study provides suggestive evidence of novel melanoma germline prognostic markers, implicating two candidate genes: an oncogene MELK and a tumor suppressor SH3BP4, both previously suggested to affect CM progression. Pending further validation, these findings suggest that the genetic factors may improve the prognostic stratification of high-risk early-stage CM patients, and propose putative biological insights for potential therapeutic investigation of these targets to prevent aggressive outcome from early-stage melanoma.
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Affiliation(s)
- Vylyny Chat
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Sasha Dagayev
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Una Moran
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Matija Snuderl
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Jeffrey Weber
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Robert Ferguson
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States,*Correspondence: Tomas Kirchhoff, ; Robert Ferguson,
| | - Iman Osman
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States,Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, United States
| | - Tomas Kirchhoff
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States,*Correspondence: Tomas Kirchhoff, ; Robert Ferguson,
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Epidemiological, Clinical, and Genomic Profile in Head and Neck Cancer Patients and Their Families. Biomedicines 2022; 10:biomedicines10123278. [PMID: 36552033 PMCID: PMC9775590 DOI: 10.3390/biomedicines10123278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Inherited cancer predisposition genes are described as risk factors in head and neck cancer (HNC) families. To explore the clinical and epidemiological data and their association with a family history of cancer, we recruited 74 patients and 164 relatives affected by cancer. The germline copy number alterations were evaluated in 18 patients using array comparative genomic hybridization. Two or more first-degree relatives with HNC, tobacco-associated tumor sites (lung, esophagus, and pancreas), or other related tumors (breast, colon, kidney, bladder, cervix, stomach carcinomas, and melanoma) were reported in 74 families. Ten index patients had no exposure to any known risk factors. Family members presented tumors of 19 topographies (30 head and neck, 26 breast, 21 colon). In first-degree relatives, siblings were frequently affected by cancer (n = 58, 13 had HNC). Breast cancer (n = 21), HNC (n = 19), and uterine carcinoma (n = 15) were commonly found in first-degree relatives and HNC in second-degree relatives (n = 11). Nineteen germline genomic imbalances were detected in 13 patients; three presented gains of WRD genes. The number of HNC patients, the degree of kinship, and the tumor types detected in each relative support the role of heredity in these families. Germline alterations may potentially contribute to cancer development.
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DeLouize AM, Eick G, Karam SD, Snodgrass JJ. Current and future applications of biomarkers in samples collected through minimally invasive methods for cancer medicine and population-based research. Am J Hum Biol 2022; 34:e23665. [PMID: 34374148 PMCID: PMC9894104 DOI: 10.1002/ajhb.23665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/04/2023] Open
Abstract
Despite advances in cancer medicine and research, invasive and potentially risky procedures such as biopsies, venous blood tests, imaging, colonoscopy, and pap smear tests are still primarily used for screening, staging, and assessing response to therapy. The development and interdisciplinary use of biomarkers from urine, feces, saliva, scent, and capillary blood collected with minimally invasive methods represents a potential opportunity for integration with biomarker analysis for cancers, both in clinical practice (e.g., in screening, treatment, and disease monitoring, and improved quality of life for patients) and population-based research (e.g., in epidemiology/public health, studies of social and environmental determinants, and evolutionary medicine). In this article, we review the scientific rationale, benefits, challenges, and potential opportunities for measuring cancer-related biomarkers in samples collected through minimally invasive methods.
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Affiliation(s)
| | - Geeta Eick
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Sana D. Karam
- Department of Radiation Oncology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - J. Josh Snodgrass
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
- Center for Global Health, University of Oregon, Eugene, Oregon, USA
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Sahu D, Chatrath A, Ratan A, Dutta A. Integrated bioinformatic pipeline using whole-exome and RNAseq data to identify germline variants correlated with cancer. STAR Protoc 2022; 3:101273. [PMID: 35403010 PMCID: PMC8987392 DOI: 10.1016/j.xpro.2022.101273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Germline Variants (GVs) are effective in predicting cancer risk and may be relevant in predicting patient outcomes. Here we provide a bioinformatic pipeline to identify GVs from the TCGA lower grade glioma cohort in Genomics Data Commons. We integrate paired whole exome sequences from normal and tumor samples and RNA sequences from tumor samples to determine a patient’s GV status. We then identify the subset of GVs that are predictive of patient outcomes by Cox regression. For complete details on the use and execution of this protocol, please refer to Chatrath et al. (2019) and Chatrath et al. (2020). Integration of whole-exome and RNA sequences to determine Germline Variants (GVs) Whole-exome and RNA sequences from tumors resolve low coverage issue in normal samples High correlation of GV allele frequencies between patient data and the GnomAD database GVs predict patient cancer outcome
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Gao B, Li X, Li S, Wang S, Wu J, Li J. Pan-cancer analysis identifies RNA helicase DDX1 as a prognostic marker. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:33-49. [PMID: 36939765 PMCID: PMC9590584 DOI: 10.1007/s43657-021-00034-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
The DEAD-box RNA helicase (DDX) family plays a critical role in the growth and development of multiple organisms. DDX1 is involved in mRNA/rRNA processing and mature, virus replication and transcription, hormone metabolism, tumorigenesis, and tumor development. However, how DDX1 functions in various cancers remains unclear. Here, we explored the potential oncogenic roles of DDX1 across 33 tumors with The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. DDX1 is highly expressed in breast cancer (BRCA), cholangiocarcinoma (CHOL), and colon adenocarcinoma (COAD), but it is lowly expressed in renal cancers, including kidney renal clear cell carcinoma (KIRC), kidney chromophobe (KICH), and kidney renal papillary cell carcinoma (KIRP). Low expression of DDX1 in KIRC is correlated with a good prognosis of overall survival (OS) and disease-free survival (DFS). Highly expressed DDX1 is linked to a poor prognosis of OS for adrenocortical carcinoma (ACC), bladder urothelial carcinoma (BLCA), KICH, and liver hepatocellular carcinoma (LIHC). Also, the residue Ser481 of DDX1 had an enhanced phosphorylation level in BRCA and ovarian cancer (OV) but decreased in KIRC. Immune infiltration analysis exhibited that DDX1 expression affected CD8+ T cells, and it was significantly associated with MSI (microsatellite instability), TMB (tumor mutational burden), and ICT (immune checkpoint blockade therapy) in tumors. In addition, the depletion of DDX1 dramatically affected the cell viability of human tumor-derived cell lines. DDX1 could affect the DNA repair pathway and the RNA transport/DNA replication processes during tumorigenesis by analyzing the CancerSEA database. Thus, our pan-cancer analysis revealed that DDX1 had complicated impacts on different cancers and might act as a prognostic marker for cancers such as renal cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-021-00034-x.
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Affiliation(s)
- Baocai Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Xiangnan Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Shujie Li
- Kunming Institute of Physics, Kunming, 650223 China
| | - Sen Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
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12
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Quintanilha JC, Wang J, Sibley AB, Xu W, Espin-Garcia O, Jiang C, Etheridge AS, Ratain MJ, Lenz HJ, Bertagnolli M, Kindler HL, Dickler MN, Venook A, Liu G, Owzar K, Lin D, Innocenti F. Genome-wide association studies of survival in 1520 cancer patients treated with bevacizumab-containing regimens. Int J Cancer 2022; 150:279-289. [PMID: 34528705 PMCID: PMC8627468 DOI: 10.1002/ijc.33810] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/13/2021] [Accepted: 08/23/2021] [Indexed: 01/17/2023]
Abstract
Germline variants might predict cancer progression. Bevacizumab improves overall survival (OS) in patients with advanced cancers. No biomarkers are available to identify patients that benefit from bevacizumab. A meta-analysis of genome-wide association studies (GWAS) was conducted in 1,520 patients from Phase III trials (CALGB 80303, 40503, 80405 and ICON7), where bevacizumab was randomized to treatment without bevacizumab. We aimed to identify genes and single nucleotide polymorphisms (SNPs) associated with survival independently of bevacizumab treatment or through interaction with bevacizumab. A cause-specific Cox model was used to test the SNP-OS association in both arms combined (prognostic), and the effect of SNPs-bevacizumab interaction on OS (predictive) in each study. The SNP effects across studies were combined using inverse variance. Findings were tested for replication in advanced colorectal and ovarian cancer patients from The Cancer Genome Atlas (TGCA). In the GWAS meta-analysis, patients with rs680949 in PRUNE2 experienced shorter OS compared to patients without it (P = 1.02 × 10-7 , hazard ratio [HR] = 1.57, 95% confidence interval [CI] 1.33-1.86), as well as in TCGA (P = .0219, HR = 1.58, 95% CI 1.07-2.35). In the GWAS meta-analysis, patients with rs16852804 in BARD1 experienced shorter OS compared to patients without it (P = 1.40 × 10-5 , HR = 1.51, 95% CI 1.25-1.82) as well as in TCGA (P = 1.39 × 10-4 , HR = 3.09, 95% CI 1.73-5.51). Patients with rs3795897 in AGAP1 experienced shorter OS in the bevacizumab arm compared to the nonbevacizumab arm (P = 1.43 × 10-5 ). The largest GWAS meta-analysis of bevacizumab treated patients identified PRUNE2 and BARD1 (tumor suppressor genes) as prognostic genes of colorectal and ovarian cancer, respectively, and AGAP1 as a potentially predictive gene that interacts with bevacizumab with respect to patient survival.
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Affiliation(s)
- Julia C.F. Quintanilha
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jin Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alexander B. Sibley
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network and Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Osvaldo Espin-Garcia
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network and Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Chen Jiang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Amy S. Etheridge
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark J. Ratain
- University of Chicago Comprehensive Cancer Center, Chicago, Illinois, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Hedy L. Kindler
- University of Chicago Comprehensive Cancer Center, Chicago, Illinois, USA
| | | | - Alan Venook
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, USA
| | - Geoffrey Liu
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Danyu Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Federico Innocenti
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Correspondence: Federico Innocenti, MD, PhD. University of North Carolina at Chapel Hill, UNC Eshelman School of Pharmacy, Genetic Medicine Bldg. 120 Mason Farm Rd, Campus Box 7361, Chapel Hill, NC 27599-7361, Tel 919-966-9422 Fax 919-966-5863,
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13
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Chao BN, Carrick DM, Filipski KK, Nelson SA. Overview of Research on Germline Genetic Variation in Immune Genes and Cancer Outcomes. Cancer Epidemiol Biomarkers Prev 2022; 31:495-506. [PMID: 35027433 DOI: 10.1158/1055-9965.epi-21-0583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 10/13/2021] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
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.
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Affiliation(s)
- Brittany N Chao
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
| | - Danielle M Carrick
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
| | - Kelly K Filipski
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
| | - Stefanie A Nelson
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
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14
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Genetic and epigenetic processes linked to cancer. Cancer 2022. [DOI: 10.1016/b978-0-323-91904-3.00013-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Alhebshi H, Tian K, Patnaik L, Taylor R, Bezecny P, Hall C, Muller PAJ, Safari N, Creamer DPM, Demonacos C, Mutti L, Bittar MN, Krstic-Demonacos M. Evaluation of the Role of p53 Tumour Suppressor Posttranslational Modifications and TTC5 Cofactor in Lung Cancer. Int J Mol Sci 2021; 22:ijms222413198. [PMID: 34947995 PMCID: PMC8707832 DOI: 10.3390/ijms222413198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 01/09/2023] Open
Abstract
Mutations in the p53 tumor suppressor are found in over 50% of cancers. p53 function is controlled through posttranslational modifications and cofactor interactions. In this study, we investigated the posttranslationally modified p53, including p53 acetylated at lysine 382 (K382), p53 phosphorylated at serine 46 (S46), and the p53 cofactor TTC5/STRAP (Tetratricopeptide repeat domain 5/ Stress-responsive activator of p300-TTC5) proteins in lung cancer. Immunohistochemical (IHC) analysis of lung cancer tissues from 250 patients was carried out and the results were correlated with clinicopathological features. Significant associations between total or modified p53 with a higher grade of the tumour and shorter overall survival (OS) probability were detected, suggesting that mutant and/or modified p53 acts as an oncoprotein in these patients. Acetylated at K382 p53 was predominantly nuclear in some samples and cytoplasmic in others. The localization of the K382 acetylated p53 was significantly associated with the gender and grade of the disease. The TTC5 protein levels were significantly associated with the grade, tumor size, and node involvement in a complex manner. SIRT1 expression was evaluated in 50 lung cancer patients and significant positive correlation was found with p53 S46 intensity, whereas negative TTC5 staining was associated with SIRT1 expression. Furthermore, p53 protein levels showed positive association with poor OS, whereas TTC5 protein levels showed positive association with better OS outcome. Overall, our results indicate that an analysis of p53 modified versions together with TTC5 expression, upon testing on a larger sample size of patients, could serve as useful prognostic factors or drug targets for lung cancer treatment.
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Affiliation(s)
- Hasen Alhebshi
- School of Science, Engineering and Environment, University of Salford, Cockcroft Building 305, Manchester M5 4WT, UK; (H.A.); (N.S.); (D.P.M.C.)
| | - Kun Tian
- Institute of Biological Anthropology, School of Basical Medical Science, Jinzhou Medical University, Jinzhou 121001, China;
| | - Lipsita Patnaik
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool FY3 8NR, UK; (L.P.); (R.T.); (P.B.); (M.N.B.)
| | - Rebecca Taylor
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool FY3 8NR, UK; (L.P.); (R.T.); (P.B.); (M.N.B.)
| | - Pavel Bezecny
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool FY3 8NR, UK; (L.P.); (R.T.); (P.B.); (M.N.B.)
| | - Callum Hall
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Manchester SK10 4TG, UK; (C.H.); (P.A.J.M.)
| | - Patricia Anthonia Johanna Muller
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Manchester SK10 4TG, UK; (C.H.); (P.A.J.M.)
| | - Nazila Safari
- School of Science, Engineering and Environment, University of Salford, Cockcroft Building 305, Manchester M5 4WT, UK; (H.A.); (N.S.); (D.P.M.C.)
| | - Delta Patricia Menendez Creamer
- School of Science, Engineering and Environment, University of Salford, Cockcroft Building 305, Manchester M5 4WT, UK; (H.A.); (N.S.); (D.P.M.C.)
| | - Constantinos Demonacos
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, School of Health Sciences, The University of Manchester, Stopford Building, 3.124 Oxford Road, Manchester M13 9PT, UK;
| | - Luciano Mutti
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
| | - Mohamad Nidal Bittar
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool FY3 8NR, UK; (L.P.); (R.T.); (P.B.); (M.N.B.)
| | - Marija Krstic-Demonacos
- School of Science, Engineering and Environment, University of Salford, Cockcroft Building 305, Manchester M5 4WT, UK; (H.A.); (N.S.); (D.P.M.C.)
- Correspondence:
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16
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Prognostic Gene Signature for Squamous Cell Carcinoma with a Higher Risk for Treatment Failure and Accelerated MEK-ERK Pathway Activity. Cancers (Basel) 2021; 13:cancers13205182. [PMID: 34680330 PMCID: PMC8534038 DOI: 10.3390/cancers13205182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Squamous cell carcinoma (SCC) is the most prevalent type of human cancer worldwide and represents the majority of head and neck tumors. As SCC from aerodigestive or genitourinary tracts share not only common etiology and histological features but also molecular patterns, the major objectives of this study were the establishment of a pan-SCC-related prognostic gene signature by an integrative analysis of multi-omics data and the elucidation of underlying oncogenic pathway activities as potential vulnerabilities for a more efficient and less toxic therapy. Our approach delivers a reliable molecular classifier to identify HNSCC and other SCC patients at higher risk for treatment failure with tumors characterized by a more prominent MAPK activity, who might benefit from a targeted treatment with MEK inhibitors. Abstract Squamous cell carcinoma (SCC) is the most prevalent histological type of human cancer, including head and neck squamous cell carcinoma (HNSCC). However, reliable prognostic gene signatures for SCC and underlying genetic and/or epigenetic principles are still unclear. We identified 37 prognostic candidate genes by best cutoff computation based on survival in a pan-SCC cohort (n = 1334) of The Cancer Genome Atlas (TCGA), whose expression stratified not only the pan-SCC cohort but also independent HNSCC validation cohorts into three distinct prognostic subgroups. The most relevant prognostic genes were prioritized by a Least Absolute Shrinkage and Selection Operator Cox regression model and were used to identify subgroups with high or low risks for unfavorable survival. An integrative analysis of multi-omics data identified FN1, SEMA3A, CDH2, FBN1, COL5A1, and ADAM12 as key nodes in a regulatory network related to the prognostic phenotype. An in-silico drug screen predicted two MEK inhibitors (Trametinib and Selumetinib) as effective compounds for high-risk SCC based on the Cancer Cell Line Encyclopedia, which is supported by a higher p-MEK1/2 immunohistochemical staining of high-risk HNSCC. In conclusion, our data identified a molecular classifier for high-risk HNSCC as well as other SCC patients, who might benefit from treatment with MEK inhibitors.
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17
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Nguyen PBH, Ohnmacht AJ, Sharifli S, Garnett MJ, Menden MP. Inferred Ancestral Origin of Cancer Cell Lines Associates with Differential Drug Response. Int J Mol Sci 2021; 22:ijms221810135. [PMID: 34576298 PMCID: PMC8467551 DOI: 10.3390/ijms221810135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
Disparities between risk, treatment outcomes and survival rates in cancer patients across the world may be attributed to socioeconomic factors. In addition, the role of ancestry is frequently discussed. In preclinical studies, high-throughput drug screens in cancer cell lines have empowered the identification of clinically relevant molecular biomarkers of drug sensitivity; however, the genetic ancestry from tissue donors has been largely neglected in this setting. In order to address this, here, we show that the inferred ancestry of cancer cell lines is conserved and may impact drug response in patients as a predictive covariate in high-throughput drug screens. We found that there are differential drug responses between European and East Asian ancestries, especially when treated with PI3K/mTOR inhibitors. Our finding emphasizes a new angle in precision medicine, as cancer intervention strategies should consider the germline landscape, thereby reducing the failure rate of clinical trials.
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Affiliation(s)
- Phong B. H. Nguyen
- Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany; (P.B.H.N.); (A.J.O.); (S.S.)
- Department of Biology, Ludwig-Maximilians University Munich, 82152 Martinsried, Germany
| | - Alexander J. Ohnmacht
- Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany; (P.B.H.N.); (A.J.O.); (S.S.)
- Department of Biology, Ludwig-Maximilians University Munich, 82152 Martinsried, Germany
| | - Samir Sharifli
- Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany; (P.B.H.N.); (A.J.O.); (S.S.)
- Department of Mathematics, Technical University Munich, 85748 Garching, Germany
| | - Mathew J. Garnett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK;
| | - Michael P. Menden
- Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany; (P.B.H.N.); (A.J.O.); (S.S.)
- Department of Biology, Ludwig-Maximilians University Munich, 82152 Martinsried, Germany
- German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
- Correspondence:
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18
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Ma C, Storer CE, Chandran U, LaFramboise WA, Petrosko P, Frank M, Hartman DJ, Pantanowitz L, Haritunians T, Head RD, Liu TC. Crohn's disease-associated ATG16L1 T300A genotype is associated with improved survival in gastric cancer. EBioMedicine 2021; 67:103347. [PMID: 33906066 PMCID: PMC8099593 DOI: 10.1016/j.ebiom.2021.103347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND A non-synonymous single nucleotide polymorphism of the ATG16L1 gene, T300A, is a major Crohn's disease (CD) susceptibility allele, and is known to be associated with increased apoptosis induction in the small intestinal crypt base in CD subjects and mouse models. We hypothesized that ATG16L1 T300A genotype also correlates with increased tumor apoptosis and therefore could lead to superior clinical outcome in cancer subjects. METHODS T300A genotyping by Taqman assay was performed for gastric carcinoma subjects who underwent resection from two academic medical centers. Transcriptomic analysis was performed by RNA-seq on formalin-fixed paraffin-embedded cancerous tissue. Tumor apoptosis and autophagy were determined by cleaved caspase-3 and p62 immunohistochemistry, respectively. The subjects' genotypes were correlated with demographics, various histopathologic features, transcriptome, and clinical outcome. FINDINGS Of the 220 genotyped subjects, 163 (74%) subjects carried the T300A allele(s), including 55 (25%) homozygous and 108 (49%) heterozygous subjects. The T300A/T300A subjects had superior overall survival than the other groups. Their tumors were associated with increased CD-like lymphoid aggregates and increased tumor apoptosis without concurrent increase in tumor mitosis or defective autophagy. Transcriptomic analysis showed upregulation of WNT/β-catenin signaling and downregulation of PPAR, EGFR, and inflammatory chemokine pathways in tumors of T300A/T300A subjects. INTERPRETATION Gastric carcinoma of subjects with the T300A/T300A genotype is associated with repressed EGFR and PPAR pathways, increased tumor apoptosis, and improved overall survival. Genotyping gastric cancer subjects may provide additional insight for clinical stratification.
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Affiliation(s)
- Changqing Ma
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States.
| | - Chad E Storer
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Uma Chandran
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States
| | - William A LaFramboise
- UPMC Hillman Cancer Center, Cancer Genomics Facility, Pittsburgh, PA 15232, United States
| | - Patricia Petrosko
- UPMC Hillman Cancer Center, Cancer Genomics Facility, Pittsburgh, PA 15232, United States
| | - Madison Frank
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States
| | - Douglas J Hartman
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States
| | - Talin Haritunians
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Ta-Chiang Liu
- Departments of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8118, Saint Louis, MO 63110, United States.
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19
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Chatrath A, Ratan A, Dutta A. Germline variants predictive of tumor mutational burden and immune checkpoint inhibitor efficacy. iScience 2021; 24:102248. [PMID: 33786423 PMCID: PMC7988326 DOI: 10.1016/j.isci.2021.102248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 01/25/2021] [Accepted: 02/25/2021] [Indexed: 12/26/2022] Open
Abstract
High tumor mutational burden (TMB) is associated with response to checkpoint blockade in several cancers. We identify pathogenic germline variants associated with increased TMB (GVITMB). GVITMB were found in 7 genes using a pan-cancer approach (APC, FANCL, SLC25A13, ERCC3, MSH6, PMS2, and TP53) and 38 gene sets (e.g., those involved in DNA repair and programmed cell death). GVITMB were also associated with mutational signatures related to the dysfunction of the gene carrying the variant, somatic mutations that further affect the gene or pathway with the variant, or transcriptomic changes concordant with the expected effect of the variant. In a validation cohort of 140 patients with cutaneous melanoma, we found that patients with GVITMB had prolonged progression-free survival (p = 0.0349, hazard ratio = 0.688) and responded favorably (p = 0.0341, odds = 1.842) when treated with immune checkpoint inhibitors. Our results suggest that germline variants can influence the molecular phenotypes of tumors and predict the response to immune checkpoint inhibitors. GVITMB were found in 7 genes and 38 gene sets GVITMB influence the somatic mutation and gene expression profiles of tumors GVITMB predict immune checkpoint inhibitory efficacy in SKCM
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Affiliation(s)
- Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1240 Pinn Hall, Charlottesville, VA 22908, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1240 Pinn Hall, Charlottesville, VA 22908, USA
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20
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Slaught C, Berry EG, Bacik L, Skalet AH, Anadiotis G, Tuohy T, Leachman SA. Clinical challenges in interpreting multiple pathogenic mutations in single patients. Hered Cancer Clin Pract 2021; 19:15. [PMID: 33541411 PMCID: PMC7863461 DOI: 10.1186/s13053-021-00172-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 01/25/2021] [Indexed: 01/13/2023] Open
Abstract
Background In the past two decades, genetic testing for cancer risk assessment has entered mainstream clinical practice due to the availability of low-cost panels of multiple cancer-associated genes. However, the clinical value of multiple-gene panels for cancer susceptibility is not well established, especially in cases where panel testing identifies more than one pathogenic variant. The risk for specific malignancies as a result of a mutated gene is complex and likely influenced by superimposed modifier variants and/or environmental effects. Recent data suggests that the combination of multiple pathogenic variants may be fewer than reported by chance, suggesting that some mutation combinations may be detrimental. Management of patients with “incidentally” discovered mutations can be particularly challenging, especially when established guidelines call for radical procedures (e.g. total gastrectomy in CDH1) in patients and families without a classic clinical history concerning for that cancer predisposition syndrome. Case presentation We present two cases, one of an individual and one of a family, with multiple pathogenic mutations detected by multi-gene panel testing to highlight challenges practitioners face in counseling patients about pathogenic variants and determining preventive and therapeutic interventions. Conclusions Ongoing investigation is needed to improve our understanding of inherited susceptibility to disease in general and cancer predisposition syndromes, as this information has the potential to lead to the development of more precise and patient-specific counseling and surveillance strategies. The real-world adoption of new or improved technologies into clinical practice frequently requires medical decision-making in the absence of established understanding of gene-gene interactions. In the meantime, practitioners must be prepared to apply a rationale based on currently available knowledge to clinical decision-making. Current practice is evolving to rely heavily on clinical concordance with personal and family history in making specific therapeutic decisions. Supplementary Information The online version contains supplementary material available at 10.1186/s13053-021-00172-3.
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Affiliation(s)
- Christa Slaught
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Ave, Suite 16D, Portland, OR, 97239, USA
| | - Elizabeth G Berry
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Ave, Suite 16D, Portland, OR, 97239, USA.
| | - Lindsay Bacik
- Department of Dermatology, Penn State Health, Hershey, USA
| | - Alison H Skalet
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Ave, Suite 16D, Portland, OR, 97239, USA.,Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, USA.,Department of Radiation Medicine, Oregon Health & Science University, Portland, USA
| | - George Anadiotis
- Legacy Cancer Institute, Cancer Genetics Services, Legacy Health Systems, Portland, USA
| | - Therese Tuohy
- Legacy Cancer Institute, Cancer Genetics Services, Legacy Health Systems, Portland, USA
| | - Sancy A Leachman
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Ave, Suite 16D, Portland, OR, 97239, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, USA
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Chatrath A, Ratan A, Dutta A. Germline Variants That Affect Tumor Progression. Trends Genet 2020; 37:433-443. [PMID: 33203571 DOI: 10.1016/j.tig.2020.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 01/31/2023]
Abstract
Germline variants have a rich history of being studied in the context of cancer risk. Emerging studies now suggest that germline variants contribute not only to cancer risk but to tumor progression as well. In this opinion article, we discuss the initial discoveries associating germline variants with patient outcome and the mechanisms by which germline variants affect molecular pathways. Germline variants affect molecular pathways through amino acid changes, alteration of splicing patterns or expression of genes, influencing the selection for somatic mutations, and causing genome-wide mutational enrichment. These molecular alterations can lead to tumor phenotypes that become clinically apparent such as metastasis, alterations to the immune microenvironment, and modulation of therapeutic response. Overall, the growing body of evidence suggests that germline variants play a larger role in tumor progression than has been previously appreciated and that germline variation holds substantial potential for improving personalized medicine and patient outcomes.
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Affiliation(s)
- Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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