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Nguyen LT, Pollock CA, Saad S. Extraction of high quality and high yield RNA from frozen EDTA blood. Sci Rep 2024; 14:8628. [PMID: 38622175 PMCID: PMC11018810 DOI: 10.1038/s41598-024-58576-9] [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: 01/02/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Peripheral blood RNA profiling, which can reveal systemic changes in gene expression and immune responses to disease onset and progression, is a powerful tool for diagnosis and biomarker discovery. This technique usually requires high quality RNA, which is only obtainable from fresh blood, or frozen blood that has been collected in special RNA-stabilisation systems. The current study aimed to develop a novel protocol to extract high quality RNA from frozen blood that had been collected in the conventional EDTA tubes. We determined that thawing EDTA blood in the presence of cell lysis/RNA stabilisation buffers (Paxgene or Nucleospin) significantly improved RNA quality (RIN) from below 5 to above 7, which to date has not been shown possible. The EDTA-Nucleospin protocol resulted in 5 times higher yield than the EDTA-Paxgene-PreAnalytix method. The average RIN and mRNA expression levels of five different genes including 18 s, ACTB, MCP1, TNFa and TXNIP using this protocol were also indifferent to those from Paxgene blood, suggesting similar RNA quality and blood transcriptome. Moreover, the protocol allows DNA to be extracted simultaneously. In conclusion, we have developed a practical and efficient protocol to extract high quality, high yield RNA from frozen EDTA blood.
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Affiliation(s)
- Long T Nguyen
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia.
| | - Carol A Pollock
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia
| | - Sonia Saad
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia
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2
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Touyz SJ, Ghazawi FM, Netchiporouk E, Popradi G, Michel RP, Skamene S, Lambert C, Hijal T, Litvinov IV. Cutaneous T-cell lymphoma developing in surgical scars post cardiac
surgery: A case study. SAGE Open Med Case Rep 2023; 11:2050313X231161444. [PMID: 36968985 PMCID: PMC10034272 DOI: 10.1177/2050313x231161444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Cutaneous T-cell lymphomas are a class of non-Hodgkin lymphomas characterized by
the infiltration of malignant T cells into the skin. Their precise pathogenesis
remains incompletely understood, but persistent and specific antigen stimulation
of skin-homing CD4+ memory T cells by external or internal factors, combined
with an inflammatory cytokine-rich tissue microenvironment, may be critical in
the development of cutaneous T-cell lymphomas. We present herein a case of
primary cutaneous T-cell lymphoma arising in two surgical scars that developed
6 months post-operatively and were successfully treated with external beam
radiotherapy. This case highlights the notion that primary cutaneous T-cell
lymphoma can develop locally at the site of injury/foreign body within a
relatively short time post trauma/surgery. This work contributes to the
literature of cutaneous T-cell lymphomas arising after a trauma, surgery, or a
foreign body.
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Affiliation(s)
- Sarah J Touyz
- Department of Acute Internal Medicine,
Salford Royal NHS Foundation Trust, Salford, UK
| | - Feras M Ghazawi
- Division of Dermatology, University of
Ottawa, Ottawa, ON, Canada
| | - Elena Netchiporouk
- Division of Dermatology, McGill
University Health Centre, Montreal, QC, Canada
| | - Gizelle Popradi
- Division of Hematology, McGill
University Health Centre, Montreal, QC, Canada
| | - René P Michel
- Department of Pathology, McGill
University, Montreal, QC, Canada
| | - Sonia Skamene
- Department of Radiation Oncology,
McGill University Health Centre, Montreal, QC, Canada
| | - Christine Lambert
- Department of Radiation Oncology,
McGill University Health Centre, Montreal, QC, Canada
| | - Tarek Hijal
- Department of Radiation Oncology,
McGill University Health Centre, Montreal, QC, Canada
| | - Ivan V Litvinov
- Division of Dermatology, McGill
University Health Centre, Montreal, QC, Canada
- Ivan V Litvinov, Division of Dermatology,
McGill University Health Centre, 1001 Boul Decarie, Rm. E02.0236, Montreal, QC
H4A3J1, Canada.
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3
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Borcherding N, Severson KJ, Henderson N, Ortolan LS, Rosenthal AC, Bellizzi AM, Liu V, Link BK, Mangold AR, Jabbari A. Single-cell analysis of Sézary syndrome reveals novel markers and shifting gene profiles associated with treatment. Blood Adv 2023; 7:321-335. [PMID: 35390145 PMCID: PMC9881051 DOI: 10.1182/bloodadvances.2021005991] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/08/2022] [Accepted: 03/10/2022] [Indexed: 02/02/2023] Open
Abstract
Cutaneous T-cell lymphomas (CTCLs) are a spectrum of diseases with varied clinical courses caused by malignant clonal proliferation of skin-tropic T cells. Most patients have an indolent disease course managed with skin-directed therapies. In contrast, others, especially in advanced stages of disease or with specific forms, have aggressive progression and poor median survival. Sézary syndrome (SS), a leukemic variant of CTCL, lacks highly consistent phenotypic and genetic markers that may be leveraged to prevent the delay in diagnosis experienced by most patients with CTCL and could be useful for optimal treatment selection. Using single-cell mRNA and T-cell receptor sequencing of peripheral blood immune cells in SS, we extensively mapped the transcriptomic variations of nearly 50 000 T cells of both malignant and nonmalignant origins. We identified potential diverging SS cell populations, including quiescent and proliferative populations shared across multiple patients. In particular, the expression of AIRE was the most highly upregulated gene in our analysis, and AIRE protein expression could be observed over a variety of CTCLs. Furthermore, within a single patient, we were able to characterize differences in cell populations by comparing malignant T cells over the course of treatment with histone deacetylase inhibition and photopheresis. New cellular clusters after progression of the therapy notably exhibited increased expression of the transcriptional factor FOXP3, a master regulator of regulatory T-cell function, raising the potential implication of an evolving mechanism of immune evasion.
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Affiliation(s)
- Nicholas Borcherding
- Department of Pathology, University of Iowa, Iowa City, IA
- Department of Pathology and Immunology, Washington University, St. Louis, MO
| | | | | | - Luana S. Ortolan
- Department of Dermatology, University of Iowa, Iowa City, IA
- Seattle Children’s Research Institute, Seattle, WA
| | | | | | - Vincent Liu
- Department of Pathology, University of Iowa, Iowa City, IA
- Department of Dermatology, University of Iowa, Iowa City, IA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
| | - Brian K. Link
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Department of Internal Medicine, University of Iowa, Iowa City, IA
| | | | - Ali Jabbari
- Department of Pathology, University of Iowa, Iowa City, IA
- Department of Dermatology, University of Iowa, Iowa City, IA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Iowa City Veterans Affairs Medical Center, Iowa City, IA
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4
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Licht P, Mailänder V. Transcriptional Heterogeneity and the Microbiome of Cutaneous T-Cell Lymphoma. Cells 2022; 11:cells11030328. [PMID: 35159138 PMCID: PMC8834405 DOI: 10.3390/cells11030328] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/31/2021] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Cutaneous T-Cell Lymphomas (CTCL) presents with substantial clinical variability and transcriptional heterogeneity. In the recent years, several studies paved the way to elucidate aetiology and pathogenesis of CTCL using sequencing methods. Several T-cell subtypes were suggested as the source of disease thereby explaining clinical and transcriptional heterogeneity of CTCL entities. Several differentially expressed pathways could explain disease progression. However, exogenous triggers in the skin microenvironment also seem to affect CTCL status. Especially Staphylococcus aureus was shown to contribute to disease progression. Only little is known about the complex microbiome patterns involved in CTCL and how microbial shifts might impact this malignancy. Nevertheless, first hints indicate that the microbiome might at least in part explain transcriptional heterogeneity and that microbial approaches could serve in diagnosis and prognosis. Shaping the microbiome could be a treatment option to maintain stable disease. Here, we review current knowledge of transcriptional heterogeneity of and microbial influences on CTCL. We discuss potential benefits of microbial applications and microbial directed therapies to aid patients with CTCL burden.
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Affiliation(s)
- Philipp Licht
- Dermatology Clinic, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131 Mainz, Germany;
| | - Volker Mailänder
- Dermatology Clinic, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131 Mainz, Germany;
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Correspondence:
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5
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Jiang TT, Kruglov O, Lin GHY, Minic A, Jordan K, Uger RA, Wong M, Shou Y, Akilov OE. Clinical Response to Anti-CD47 Immunotherapy Is Associated with Rapid Reduction of Exhausted Bystander CD4 + BTLA + T Cells in Tumor Microenvironment of Mycosis Fungoides. Cancers (Basel) 2021; 13:cancers13235982. [PMID: 34885092 PMCID: PMC8656720 DOI: 10.3390/cancers13235982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 02/08/2023] Open
Abstract
Simple Summary The identification of the events that accompany cancer progression is essential for developing new therapies. We have used mycosis fungoides, the most common type of cutaneous lymphoma, as a model for our study. We have shown that cancer progression is accompanied by the expansion of exhausted immune cells around malignant cells. Those exhausted cells prevent immune activation, blocking cancer clearance by the immune system. Furthermore, we have demonstrated that novel anti-CD47 immunotherapy with mycosis fungoides leads to the reduction of exhausted T cells accompanied by the expansion of NK and CD8+ T cells. These therapeutic benefits of CD47 blockade were further facilitated by interferon-α, which stimulates cytotoxic cells. Thus, we showed that CD47 might serve as an effective therapeutic target in treating mycosis fungoides. Abstract Cancer progression in mycosis fungoides, the most common form of cutaneous T-cell lymphoma, occurs in a predictable, sequential pattern that starts from patches and that evolves to plaques and later to tumors. Therefore, unlocking the relationship between the microarchitecture of mycosis fungoides and the clinical counterparts of that microstructure represents important steps for the design of targeted therapies. Using multispectral fluorescent imaging, we show that the progression of mycosis fungoides from plaque to tumor parallels the cutaneous expansion of the malignant CD4+ T cells that express TOX. The density of exhausted BTLA+ CD4+ T cells around malignant CD4+TOX+ cells was higher in tumors than it was in plaques, suggesting that undesired safeguards are in place within the tumor microenvironment that prevent immune activation and subsequent cancer eradication. Overriding the CD47 checkpoint with an intralesional SIRPαFc fusion decoy receptor induced the resolution of mycosis fungoides in patients that paralleled an amplified expansion of NK and CD8+ T cells in addition to a reduction of the exhausted BTLA+ CD4+ T cells that were engaged in promiscuous intercellular interactions. These therapeutic benefits of the CD47 blockade were further unleashed by adjuvant interferon-α, which stimulates cytotoxic cells, underscoring the importance of an inflamed microenvironment in facilitating the response to immunotherapy. Collectively, these findings support CD47 as a therapeutic target in treating mycosis fungoides and demonstrate a synergistic role of interferon-α in exploiting these clinical benefits.
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Affiliation(s)
- Tony T. Jiang
- Cutaneous Lymphoma Program, Department of Dermatology, University of Pittsburgh, Pittsburgh, PA 15261, USA; (T.T.J.); (O.K.)
| | - Oleg Kruglov
- Cutaneous Lymphoma Program, Department of Dermatology, University of Pittsburgh, Pittsburgh, PA 15261, USA; (T.T.J.); (O.K.)
| | - Gloria H. Y. Lin
- Trillium Therapeutics Inc., Mississauga, ON L5L 1J9, Canada; (G.H.Y.L.); (R.A.U.); (M.W.); (Y.S.)
| | - Angela Minic
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO 80045, USA; (A.M.); (K.J.)
| | - Kimberly Jordan
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO 80045, USA; (A.M.); (K.J.)
| | - Robert A. Uger
- Trillium Therapeutics Inc., Mississauga, ON L5L 1J9, Canada; (G.H.Y.L.); (R.A.U.); (M.W.); (Y.S.)
| | - Mark Wong
- Trillium Therapeutics Inc., Mississauga, ON L5L 1J9, Canada; (G.H.Y.L.); (R.A.U.); (M.W.); (Y.S.)
| | - Yaping Shou
- Trillium Therapeutics Inc., Mississauga, ON L5L 1J9, Canada; (G.H.Y.L.); (R.A.U.); (M.W.); (Y.S.)
| | - Oleg E. Akilov
- Cutaneous Lymphoma Program, Department of Dermatology, University of Pittsburgh, Pittsburgh, PA 15261, USA; (T.T.J.); (O.K.)
- Correspondence: ; Tel.: +1-412-648-9982
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6
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Litvinov IV, Xie P, Gunn S, Sasseville D, Lefrançois P. The transcriptional landscape analysis of basal cell carcinomas reveals novel signalling pathways and actionable targets. Life Sci Alliance 2021; 4:4/7/e202000651. [PMID: 33972406 PMCID: PMC8200290 DOI: 10.26508/lsa.202000651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 12/19/2022] Open
Abstract
Basal cell carcinoma (BCC) is the most common skin cancer and human malignancy. By analyzing BCC RNA sequencing data according to clinically important features, we identified novel differentially regulated genes and new targetable pathways. Several biomarkers were validated in patient-derived BCC samples. Basal cell carcinoma (BCC) is the most common skin cancer and human malignancy. Although most BCCs are easily managed, some are aggressive locally, require Mohs micrographic surgery, or can even metastasize. In the latter, resistance to Sonic Hedgehog inhibitors may occur. Despite their frequent occurrence in clinical practice, their transcriptional landscape remains poorly understood. By analyzing BCC RNA sequencing data according to clinically important features (all BCCs versus normal skin, high-risk versus low-risk BCCs based solely on histopathological subtypes with aggressive features, advanced versus non-advanced BCCs, and vismodegib-resistant versus vismodegib-sensitive tumors), we have identified novel differentially regulated genes and new targetable pathways implicated in BCC tumorigenesis. Pathways as diverse as IL-17, TLR, Akt/PI3K, cadherins, integrins, PDGF, and Wnt/β-catenin are promising therapeutic avenues for local and systemic agents in managing this common malignancy, including through drug re-purposing of existing medications. We experimentally validated several of these targets as biomarkers in our patient-derived cohort of primary BCC tumors.
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Affiliation(s)
- Ivan V Litvinov
- Division of Dermatology, Department of Medicine, McGill University, Montreal, Canada
| | - Pingxing Xie
- Division of Dermatology, Department of Medicine, McGill University, Montreal, Canada
| | - Scott Gunn
- Division of Dermatology, Department of Medicine, McGill University, Montreal, Canada
| | - Denis Sasseville
- Division of Dermatology, Department of Medicine, McGill University, Montreal, Canada
| | - Philippe Lefrançois
- Division of Dermatology, Department of Medicine, McGill University, Montreal, Canada
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7
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Single-Cell Heterogeneity of Cutaneous T-Cell Lymphomas Revealed Using RNA-Seq Technologies. Cancers (Basel) 2020; 12:cancers12082129. [PMID: 32751918 PMCID: PMC7464763 DOI: 10.3390/cancers12082129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/16/2020] [Accepted: 07/29/2020] [Indexed: 01/04/2023] Open
Abstract
Cutaneous T-cell lymphomas (CTCLs) represent a large, heterogeneous group of non-Hodgkin lymphomas that primarily affect the skin. Among multiple CTCL variants, the most prevalent types are mycosis fungoides (MF) and Sézary syndrome (SS). In the past decade, the molecular genetics of CTCL have been the target of intense study, increasing the knowledge of CTCL genomic alterations, discovering novel biomarkers, and potential targets for patient-specific therapy. However, the detailed pathogenesis of CTCL development still needs to be discovered. This review aims to summarize the novel insights into molecular heterogeneity of malignant cells using high-throughput technologies, such as RNA sequencing and single-cell RNA sequencing, which might be useful to identify tumour-specific molecular signatures and, therefore, offer guidance for therapy, diagnosis, and prognosis of CTCL.
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8
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Hypopigmented Mycosis Fungoides: Loss of Pigmentation Reflects Antitumor Immune Response in Young Patients. Cancers (Basel) 2020; 12:cancers12082007. [PMID: 32707930 PMCID: PMC7465783 DOI: 10.3390/cancers12082007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022] Open
Abstract
Hypopigmented mycosis fungoides (HMF) is a form of cutaneous T-cell lymphoma (CTCL), a heterogeneous group of extranodal non-Hodgkin's lymphomas. HMF has a unique set of defining features that include light colored to achromic lesions, a predilection for darker skin phototypes, an early onset of disease, and predominance of CD8+ T-cells, among others. In the current review, we detail the known pathways of molecular pathogenesis for this lymphoma and posit that an active Th1/cytotoxic antitumor immune response in part explains why this variant is primarily seen in children/adolescents and young adults, who do not exhibit signs of immunosenescence. As a result of this potent cytotoxic response, HMF patients experience mostly favorable overall prognosis, while hypopigmentation may in fact represent a useful surrogate marker of cytotoxic immunity targeting the malignant cells. Understanding the molecular processes behind the specific features that define HMF may lead to improved diagnostic accuracy, personalized prognosis by risk stratification, and improved management of HMF. Moreover, improving our knowledge of HMF may aid our further understanding of other cutaneous lymphomas.
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9
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Cattelan L, Ghazawi FM, Le M, Savin E, Zubarev A, Lagacé F, Sasseville D, Waschke K, Litvinov IV. Investigating epidemiologic trends and the geographic distribution of patients with anal squamous cell carcinoma throughout Canada. Curr Oncol 2020; 27:e294-e306. [PMID: 32669936 PMCID: PMC7339845 DOI: 10.3747/co.27.6061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Anal cancer is a rare disease, constituting 0.5% of new cancer cases in the United States. The most common subtype is squamous cell carcinoma (scc). Studies in several developed nations have reported on an increasing incidence of anal cancer in recent decades, and various risk factors pertaining to the pathogenesis of the disease have been identified, including infection with the human papillomavirus, tobacco use, and immunosuppression. The epidemiology and distribution of anal scc throughout Canada remain poorly understood, however. Methods Using 3 population-based cancer registries, a retrospective analysis of demographic data across Canada for 1992-2010 was performed. The incidence and mortality for anal scc was examined at the levels of provinces, cities, and the forward sortation area (FSA) component (first 3 characters) of postal codes. Results During 1992-2010, 3720 individuals were diagnosed with anal scc in Canada; 64% were women. The overall national incidence rate was 6.3 cases per million population per year, with an average age at diagnosis of 60.4 years. The incidence increased over time, with significantly higher incidence rates documented in British Columbia and Nova Scotia (9.3 cases per million population each). Closer examination revealed clustering of cases in various urban centres and self-identified lgbtq communities in Toronto, Montreal, and Vancouver. Discussion This study provides, for the first time, a comprehensive analysis of the burden of anal scc in Canada, identifying susceptible populations and shedding light onto novel avenues of research to lower the incidence of anal cancer throughout the country.
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Affiliation(s)
- L Cattelan
- Department of Medicine, McGill University, Montreal, QC
| | - F M Ghazawi
- Division of Dermatology, University of Ottawa, Ottawa, ON
| | - M Le
- Division of Dermatology, McGill University, Montreal, QC
| | - E Savin
- Division of Dermatology, McGill University, Montreal, QC
| | - A Zubarev
- Division of Dermatology, McGill University, Montreal, QC
| | - F Lagacé
- Department of Medicine, McGill University, Montreal, QC
| | - D Sasseville
- Division of Dermatology, McGill University, Montreal, QC
| | - K Waschke
- Division of Gastroenterology, McGill University, Montreal, QC
| | - I V Litvinov
- Division of Dermatology, McGill University, Montreal, QC
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10
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Ghazawi FM, Lu J, Savin E, Zubarev A, Chauvin P, Sasseville D, Zeitouni A, Litvinov IV. Epidemiology and Patient Distribution of Oral Cavity and Oropharyngeal SCC in Canada. J Cutan Med Surg 2020; 24:340-349. [PMID: 32238063 DOI: 10.1177/1203475420915448] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Oral cavity cancers (OCCs) and oropharyngeal cancers (OPCs) continue to be a major source of morbidity and mortality worldwide requiring the shared effort of numerous specialists. Tobacco and alcohol consumption have long been identified as risk factors for both OCC and OPC. In addition, human papilloma virus (HPV) is gaining its position as the main causal agent for OPC. OBJECTIVE The objective of this study is to analyze the epidemiology of OCC and OPC in Canada. METHODS Data pertaining to the year of diagnosis, the patient's sex, age at the time of diagnosis, province/territory, city and postal code of oral cavity, and oropharyngeal malignancies diagnosed during 1992-2010 were extracted from the Canadian Cancer Registry and Le Registre Québécois du Cancer. RESULTS In total, 21 685 OCC cases and 15 965 OPC cases were identified from 1992 to 2010. Of those, 84.97% were oral cavity squamous cell carcinomas (SCCs), 88.10% were oropharyngeal SCCs, and both had a significant male predominance. While oral cavity SCC incidence stabilized over the study period, oropharyngeal SCC continued to increase. Oral cavity SCC incidence increased with age, while oropharyngeal SCC incidence peaked in the 50- to 59-year age group. Detailed geographic distribution analysis of patients at the provincial/territorial, city, and postal code levels identified several patient clusters. CONCLUSIONS This work highlights important epidemiological differences in trends between oral and oropharyngeal cancers, identifies high-incidence postal codes for each malignancy, and correlates incidence/mortality with known risk factors including alcohol/tobacco use and HPV infections, therefore providing a comprehensive understanding of epidemiology for these cancers in Canada.
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Affiliation(s)
| | - Jessica Lu
- 507266 Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Evgeny Savin
- 5620 Division of Dermatology, McGill University, Montreal, QC, Canada
| | - Andrei Zubarev
- 5620 Division of Dermatology, McGill University, Montreal, QC, Canada
| | - Peter Chauvin
- 507266 Faculty of Dentistry, McGill University, Montreal, QC, Canada
| | - Denis Sasseville
- 5620 Division of Dermatology, McGill University, Montreal, QC, Canada
| | - Anthony Zeitouni
- 507266 Department of Otolaryngology-Head and Neck Surgery, McGill University, Montreal, QC, Canada
| | - Ivan V Litvinov
- 5620 Division of Dermatology, McGill University, Montreal, QC, Canada
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11
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Gomolin A, Netchiporouk E, Gniadecki R, Litvinov IV. Artificial Intelligence Applications in Dermatology: Where Do We Stand? Front Med (Lausanne) 2020; 7:100. [PMID: 32296706 PMCID: PMC7136423 DOI: 10.3389/fmed.2020.00100] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/05/2020] [Indexed: 12/17/2022] Open
Abstract
Artificial intelligence (AI) has become a progressively prevalent Research Topic in medicine and is increasingly being applied to dermatology. There is a need to understand this technology's progress to help guide and shape the future for medical care providers and recipients. We reviewed the literature to evaluate the types of publications on the subject, the specific dermatological topics addressed by AI, and the most challenging barriers to its implementation. A substantial number of original articles and commentaries have been published to date and only few detailed reviews exist. Most AI applications focus on differentiating between benign and malignant skin lesions, however; others exist pertaining to ulcers, inflammatory skin diseases, allergen exposure, dermatopathology, and gene expression profiling. Applications commonly analyze and classify images, however, other tools such as risk assessment calculators are becoming increasingly available. Although many applications are technologically feasible, important implementation barriers have been identified including systematic biases, difficulty of standardization, interpretability, and acceptance by physicians and patients alike. This review provides insight into future research needs and possibilities. There is a strong need for clinical investigation in dermatology providing evidence of success overcoming the identified barriers. With these research goals in mind, an appropriate role for AI in dermatology may be achieved in not so distant future.
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Affiliation(s)
- Arieh Gomolin
- Division of Dermatology, McGill University Health Centre, Montreal, QC, Canada
| | - Elena Netchiporouk
- Division of Dermatology, McGill University Health Centre, Montreal, QC, Canada
| | - Robert Gniadecki
- Division of Dermatology, University of Alberta, Edmonton, AB, Canada
| | - Ivan V Litvinov
- Division of Dermatology, McGill University Health Centre, Montreal, QC, Canada
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12
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Borcherding N, Voigt AP, Liu V, Link BK, Zhang W, Jabbari A. Single-Cell Profiling of Cutaneous T-Cell Lymphoma Reveals Underlying Heterogeneity Associated with Disease Progression. Clin Cancer Res 2019; 25:2996-3005. [PMID: 30718356 PMCID: PMC6659117 DOI: 10.1158/1078-0432.ccr-18-3309] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/07/2018] [Accepted: 01/25/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Cutaneous T-cell lymphomas (CTCL), encompassing a spectrum of T-cell lymphoproliferative disorders involving the skin, have collectively increased in incidence over the last 40 years. Sézary syndrome is an aggressive form of CTCL characterized by significant presence of malignant cells in both the blood and skin. The guarded prognosis for Sézary syndrome reflects a lack of reliably effective therapy, due, in part, to an incomplete understanding of disease pathogenesis. EXPERIMENTAL DESIGN Using single-cell sequencing of RNA and the machine-learning reverse graph embedding approach in the Monocle package, we defined a model featuring distinct transcriptomic states within Sézary syndrome. Gene expression used to differentiate the unique transcriptional states were further used to develop a boosted tree classification for early versus late CTCL disease. RESULTS Our analysis showed the involvement of FOXP3 + malignant T cells during clonal evolution, transitioning from FOXP3 + T cells to GATA3 + or IKZF2 + (HELIOS) tumor cells. Transcriptomic diversities in a clonal tumor can be used to predict disease stage, and we were able to characterize a gene signature that predicts disease stage with close to 80% accuracy. FOXP3 was found to be the most important factor to predict early disease in CTCL, along with another 19 genes used to predict CTCL stage. CONCLUSIONS This work offers insight into the heterogeneity of Sézary syndrome, providing better understanding of the transcriptomic diversities within a clonal tumor. This transcriptional heterogeneity can predict tumor stage and thereby offer guidance for therapy.
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Affiliation(s)
- Nicholas Borcherding
- Department of Pathology, University of Iowa, College of Medicine, Iowa City, Iowa
- Cancer Biology Graduate Program, University of Iowa, College of Medicine, Iowa City, Iowa
- Medical Scientist Training Program, University of Iowa, College of Medicine, Iowa City, Iowa
- Holden Comprehensive Cancer Center, University of Iowa, College of Medicine, Iowa City, Iowa
| | - Andrew P Voigt
- Medical Scientist Training Program, University of Iowa, College of Medicine, Iowa City, Iowa
| | - Vincent Liu
- Department of Pathology, University of Iowa, College of Medicine, Iowa City, Iowa
- Holden Comprehensive Cancer Center, University of Iowa, College of Medicine, Iowa City, Iowa
- Department of Dermatology, University of Iowa, College of Medicine, Iowa City, Iowa
| | - Brian K Link
- Holden Comprehensive Cancer Center, University of Iowa, College of Medicine, Iowa City, Iowa
- Department of Internal Medicine, University of Iowa, College of Medicine, Iowa City, Iowa
| | - Weizhou Zhang
- Department of Pathology, University of Iowa, College of Medicine, Iowa City, Iowa
- Cancer Biology Graduate Program, University of Iowa, College of Medicine, Iowa City, Iowa
- Medical Scientist Training Program, University of Iowa, College of Medicine, Iowa City, Iowa
- Holden Comprehensive Cancer Center, University of Iowa, College of Medicine, Iowa City, Iowa
- Interdisciplinary Program in Immunology, University of Iowa, College of Medicine, Iowa City, Iowa
| | - Ali Jabbari
- Cancer Biology Graduate Program, University of Iowa, College of Medicine, Iowa City, Iowa.
- Medical Scientist Training Program, University of Iowa, College of Medicine, Iowa City, Iowa
- Holden Comprehensive Cancer Center, University of Iowa, College of Medicine, Iowa City, Iowa
- Department of Dermatology, University of Iowa, College of Medicine, Iowa City, Iowa
- Interdisciplinary Program in Immunology, University of Iowa, College of Medicine, Iowa City, Iowa
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13
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Tsang M, Gantchev J, Netchiporouk E, Moreau L, Ghazawi FM, Glassman S, Sasseville D, Litvinov IV. A study of meiomitosis and novel pathways of genomic instability in cutaneous T-cell lymphomas (CTCL). Oncotarget 2018; 9:37647-37661. [PMID: 30701021 PMCID: PMC6340880 DOI: 10.18632/oncotarget.26479] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022] Open
Abstract
Genomic instability is a hallmark of cancer and an enabling factor for genetic alterations that drive cancer development and progression. The clashing of mitosis and aberrantly expressed meiosis machineries, which may contribute to genomic instability, has been coined cancer “meiomitosis”. LINE-1 retrotransposition, a process active in germ cells, acts outside of the meiotic machinery to create DNA double strand breaks (DNA DSBs) and has played an important role in the evolution of the human genome. We have previously demonstrated that in CTCL several cancer testis/meiotic genes are expressed. Furthermore, this cancer exhibits extensive and ongoing chromosomal/microsatellite instability. In this study we analyzed immortalized patient-derived cells and primary CTCL patient samples using RT-PCR, western blotting and confocal microscopy and found that proteins critically involved in meiosis and LINE-1 retrotransposition are expressed and are associated with chromosomal instability and DNA DSB formation. Using cell cycle synchronization, we show G1/S phase-transition-specific expression of meiosis proteins. Using the Alu retrotransposition assay, we demonstrate the functional activity of LINE-1 retrotransposon in CTCL. Histone acetyltransferase inhibition results in downregulation of the ectopic germ cell programs and concomitant decrease in DNA DSBs foci formation. Notably, LINE-1 and meiosis genes were expressed across a panel of other solid tumor cell lines. Taken together, our results indicate that malignant cells in culture undergo “cancer meiomitosis” rather than the classic mitosis division. The ectopic expression of meiosis genes and reactivation of LINE-1 may be contributing to genomic instability and represent novel targets for immunotherapy in this and other cancers.
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Affiliation(s)
- Matthew Tsang
- Division of Dermatology, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada
| | - Jennifer Gantchev
- Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Elena Netchiporouk
- Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Linda Moreau
- Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Feras M Ghazawi
- Division of Dermatology, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada
| | - Steven Glassman
- Division of Dermatology, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada
| | - Denis Sasseville
- Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Ivan V Litvinov
- Division of Dermatology, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada.,Division of Dermatology, McGill University, Montréal, Québec H4A 3J1, Canada
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14
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Lefrançois P, Xie P, Wang L, Tetzlaff MT, Moreau L, Watters AK, Netchiporouk E, Provost N, Gilbert M, Ni X, Sasseville D, Wheeler DA, Duvic M, Litvinov IV. Gene expression profiling and immune cell-type deconvolution highlight robust disease progression and survival markers in multiple cohorts of CTCL patients. Oncoimmunology 2018; 7:e1467856. [PMID: 30221071 DOI: 10.1080/2162402x.2018.1467856] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/14/2018] [Accepted: 04/16/2018] [Indexed: 02/01/2023] Open
Abstract
CTCL follows different courses depending on the clinical stage at the time of diagnosis. Patients with early stage Mycosis Fungoides (MF) variant of CTCL may experience an indolent course over decades, whereas patients with advanced MF and Sézary Syndrome (SS) disease at diagnosis, often succumb within 5 years. Even within early stage CTCL/MF, a minority of patients will progress to more advanced stages. We recently generated RNA sequencing data on 284 CTCL-relevant genes for 157 patients and identified differentially expressed genes across stages I-IV. In this study, we aim to validate robust molecular markers linked to disease progression and survival. We performed multiple hypothesis testing-corrected analysis of variance (ANOVA) on the expression of individual genes across all CTCL samples and early stage (≤IIA) CTCL/MF patients. We used in silico immune cell-type deconvolution from gene expression data to estimate immune cell populations. Based on the analysis of all CTCL samples, we identified TOX, FYB, and CD52 as predictors of disease progression and poor survival. Among early stage (≤IIA) CTCL/MF patients, these 3 genes, along with CCR4, were valuable to predict disease progression. We validated these 4 genes in 3 independent, external Sézary Syndrome patient cohorts with RNA-Sequencing data. In silico immune cell-type deconvolution revealed that neutrophil infiltration in early stage MF conveyed a higher risk for disease progression. Also, NK cell infiltration in late stage MF/SS correlated with improved survival. TOX, FYB, CCR4 and CD52 are robust disease progression and decreased survival biomarkers in CTCL.
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Affiliation(s)
- Philippe Lefrançois
- Division of Dermatology, McGill University Health Centre, Montreal, QC, Canada
| | - Pingxing Xie
- Division of Dermatology, McGill University Health Centre, Montreal, QC, Canada
| | - Linghua Wang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael T Tetzlaff
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linda Moreau
- Division of Dermatology, McGill University Health Centre, Montreal, QC, Canada
| | - Andrew K Watters
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Elena Netchiporouk
- Division of Dermatology, McGill University Health Centre, Montreal, QC, Canada
| | - Nathalie Provost
- Division of Dermatology, Université de Montréal, Montréal, QC, Canada
| | - Martin Gilbert
- Division of Dermatology, Université Laval, Québec, QC, Canada
| | - Xiao Ni
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Denis Sasseville
- Division of Dermatology, McGill University Health Centre, Montreal, QC, Canada
| | - David A Wheeler
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Madeleine Duvic
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ivan V Litvinov
- Division of Dermatology, McGill University Health Centre, Montreal, QC, Canada.,Division of Dermatology, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
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