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Lee SM, Loo C, Prasasya R, Bartolomei M, Kohli R, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. Nucleic Acids Res 2024; 52:e38. [PMID: 38407446 PMCID: PMC11040145 DOI: 10.1093/nar/gkae127] [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: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection P-value calculation achieved higher sensitivities for low-input datasets and was validated in over 100 000 public diverse methylome profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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Affiliation(s)
- Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi D Prasasya
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Jackson JT, Nutt SL, McCormack MP. The Haematopoietically-expressed homeobox transcription factor: roles in development, physiology and disease. Front Immunol 2023; 14:1197490. [PMID: 37398663 PMCID: PMC10313424 DOI: 10.3389/fimmu.2023.1197490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
The Haematopoietically expressed homeobox transcription factor (Hhex) is a transcriptional repressor that is of fundamental importance across species, as evident by its evolutionary conservation spanning fish, amphibians, birds, mice and humans. Indeed, Hhex maintains its vital functions throughout the lifespan of the organism, beginning in the oocyte, through fundamental stages of embryogenesis in the foregut endoderm. The endodermal development driven by Hhex gives rise to endocrine organs such as the pancreas in a process which is likely linked to its role as a risk factor in diabetes and pancreatic disorders. Hhex is also required for the normal development of the bile duct and liver, the latter also importantly being the initial site of haematopoiesis. These haematopoietic origins are governed by Hhex, leading to its crucial later roles in definitive haematopoietic stem cell (HSC) self-renewal, lymphopoiesis and haematological malignancy. Hhex is also necessary for the developing forebrain and thyroid gland, with this reliance on Hhex evident in its role in endocrine disorders later in life including a potential role in Alzheimer's disease. Thus, the roles of Hhex in embryological development throughout evolution appear to be linked to its later roles in a variety of disease processes.
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Affiliation(s)
- Jacob T. Jackson
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Stephen L. Nutt
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Matthew P. McCormack
- The Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
- iCamuno Biotherapeutics, Melbourne, VIC, Australia
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3
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Du S, Zhu C, Ren X, Chen X, Cui X, Guan S. Regulation of secretory pathway kinase or kinase-like proteins in human cancers. Front Immunol 2023; 14:942849. [PMID: 36825005 PMCID: PMC9941534 DOI: 10.3389/fimmu.2023.942849] [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: 05/13/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Secretory pathway kinase or kinase-like proteins (SPKKPs) are effective in the lumen of the endoplasmic reticulum (ER), Golgi apparatus (GA), and extracellular space. These proteins are involved in secretory signaling pathways and are distinctive from typical protein kinases. Various reports have shown that SPKKPs regulate the tumorigenesis and progression of human cancer via the phosphorylation of various substrates, which is essential in physiological and pathological processes. Emerging evidence has revealed that the expression of SPKKPs in human cancers is regulated by multiple factors. This review summarizes the current understanding of the contribution of SPKKPs in tumorigenesis and the progression of immunity. With the epidemic trend of immunotherapy, targeting SPKKPs may be a novel approach to anticancer therapy. This study briefly discusses the recent advances regarding SPKKPs.
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Affiliation(s)
- Shaonan Du
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Xiaolin Ren
- Department of Neurosurgery, Shenyang Red Cross Hospital, Shenyang, China
| | - Xin Chen
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiao Cui
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Shu Guan
- Department of Surgical Oncology and Breast Surgery, The First Hospital of China Medical University, Shenyang, China
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4
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Nirgude S, Desai S, Choudhary B. Genome-wide differential DNA methylation analysis of MDA-MB-231 breast cancer cells treated with curcumin derivatives, ST08 and ST09. BMC Genomics 2022; 23:807. [PMID: 36474139 PMCID: PMC9727864 DOI: 10.1186/s12864-022-09041-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 10/17/2022] [Indexed: 12/12/2022] Open
Abstract
ST08 and ST09 are potent curcumin derivatives with antiproliferative, apoptotic, and migrastatic properties. Both ST08 and ST09 exhibit in vitro and in vivo anticancer properties. As reported earlier, these derivatives were highly cytotoxic towards MDA-MB-231 triple-negative breast cancer cells with IC50 values in the nanomolar (40-80nM) range.In this study,we performed whole-genome bisulfite sequencing(WGBS) of untreated (control), ST08 and ST09 (treated) triple-negative breast cancer cell line MDA-MB-231 to unravel epigenetic changes induced by the drug. We identified differentially methylated sites (DMSs) enriched in promoter regions across the genome. Analysis of the CpG island promoter methylation identified 12 genes common to both drugs, and 50% of them are known to be methylated in patient samples that were hypomethylated by drugs belonging to the homeobox family transcription factors.Methylation analysis of the gene body revealed 910 and 952 genes to be hypermethylatedin ST08 and ST09 treated MDA-MB-231 cells respectively. Correlation of the gene body hypermethylation with expression revealed CACNAH1 to be upregulated in ST08 treatment and CDH23 upregulation in ST09.Further, integrated analysis of the WGBS with RNA-seq identified uniquely altered pathways - ST08 altered ECM pathway, and ST09 cell cycle, indicating drug-specific signatures.
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Affiliation(s)
- Snehal Nirgude
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Electronic city phase 1, 560100 Bangalore, India ,grid.239552.a0000 0001 0680 8770Working at Division of Human Genetics, Children’s Hospital of Philadelphia, 19104 Philadelphia, PA USA
| | - Sagar Desai
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Electronic city phase 1, 560100 Bangalore, India
| | - Bibha Choudhary
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Electronic city phase 1, 560100 Bangalore, India
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5
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Vicente ALSA, Novoloaca A, Cahais V, Awada Z, Cuenin C, Spitz N, Carvalho AL, Evangelista AF, Crovador CS, Reis RM, Herceg Z, de Lima Vazquez V, Ghantous A. Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure. Nat Commun 2022; 13:4115. [PMID: 35840550 PMCID: PMC9287446 DOI: 10.1038/s41467-022-31488-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 06/16/2022] [Indexed: 11/08/2022] Open
Abstract
Ultraviolet radiation (UV) is causally linked to cutaneous melanoma, yet the underlying epigenetic mechanisms, known as molecular sensors of exposure, have not been characterized in clinical biospecimens. Here, we integrate clinical, epigenome (DNA methylome), genome and transcriptome profiling of 112 cutaneous melanoma from two multi-ethnic cohorts. We identify UV-related alterations in regulatory regions and immunological pathways, with multi-OMICs cancer driver potential affecting patient survival. TAPBP, the top gene, is critically involved in immune function and encompasses several UV-altered methylation sites that were validated by targeted sequencing, providing cost-effective opportunities for clinical application. The DNA methylome also reveals non UV-related aberrations underlying pathological differences between the cutaneous and 17 acral melanomas. Unsupervised epigenomic mapping demonstrated that non UV-mutant cutaneous melanoma more closely resembles acral rather than UV-exposed cutaneous melanoma, with the latter showing better patient prognosis than the other two forms. These gene-environment interactions reveal translationally impactful mechanisms in melanomagenesis.
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Affiliation(s)
- Anna Luiza Silva Almeida Vicente
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France.
| | - Alexei Novoloaca
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Zainab Awada
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Natália Spitz
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- Early Detection Prevention and Infections Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Camila Souza Crovador
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Vinicius de Lima Vazquez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- Department of Surgery-Melanoma and Sarcoma, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France.
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6
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Ahuja G, Kim JH, Tran JF, Nnorom S, Ali A, Ibrahim M, Okoye GA, Shokrani B, Dunmore-Griffith J, Geter K, Frederick WAI, Wilson L. Metastatic Acral lentiginous melanoma: A case report and review. J Natl Med Assoc 2022; 114:290-294. [PMID: 35221075 DOI: 10.1016/j.jnma.2022.01.011] [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: 09/25/2021] [Revised: 01/20/2022] [Accepted: 01/31/2022] [Indexed: 12/01/2022]
Abstract
Of the four subtypes of cutaneous melanoma, acral lentiginous melanoma (ALM) is atypical in its presentation. ALM is a rare melanoma subtype that presents on the volar surfaces of the hand and foot. The difficulty of making an early diagnosis of ALM is highlighted by the case seen in our institution. The dire prognosis associated with ALM is postulated to be not only related to its destructive nature, but also due to a lack of patient awareness and vigilance, inadequate physician awareness, and disparity in healthcare access. We present this as a unique account of an ALM lesion in a 76 year old African-American male presenting originally in the left foot that went misdiagnosed for several years. The original lesion was considered to be an ulcerating left great toe lesion with signs typical of osteomyelitis. These clinical findings were corroborated by radiological x-ray evidence. Upon amputation and biopsy for suspected worsening osteomyelitis five years later, the pathological diagnosis of melanoma was finally made.
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Affiliation(s)
- Geeta Ahuja
- Howard University College of Medicine, Washington, DC, United States.
| | - Jae Ho Kim
- Howard University College of Medicine, Washington, DC, United States
| | | | - Siobhan Nnorom
- Department of Surgical Outcomes, Howard University Hospital, Washington, DC, United States
| | - Ahmed Ali
- Department of Hematology and Oncology, Howard University Hospital, Washington, DC, United States
| | - Mohammed Ibrahim
- Department of Internal Medicine, Howard University Hospital, Washington, DC, United States
| | - Ginette A Okoye
- Department of Dermatology, Howard University Hospital, Washington, DC, United States
| | - Babak Shokrani
- Department of Pathology, Howard University Hospital, Washington, DC, United States
| | | | - Kirk Geter
- Department of Surgical Outcomes, Howard University Hospital, Washington, DC, United States
| | - Wayne A I Frederick
- Howard University College of Medicine, Washington, DC, United States; Division of Surgical Oncology, Dept. of Surgery, Howard University Hospital, Washington, DC, United States
| | - Lori Wilson
- Howard University College of Medicine, Washington, DC, United States; Division of Surgical Oncology, Dept. of Surgery, Howard University Hospital, Washington, DC, United States
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7
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Yue Z, Cao M, Hong A, Zhang Q, Zhang G, Jin Z, Zhao L, Wang Q, Fang F, Wang Y, Sun J. m 6A Methyltransferase METTL3 Promotes the Progression of Primary Acral Melanoma via Mediating TXNDC5 Methylation. Front Oncol 2022; 11:770325. [PMID: 35117988 PMCID: PMC8804213 DOI: 10.3389/fonc.2021.770325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
m6A modification is one of the most important post-transcriptional modifications in RNA and plays an important role in promoting translation or decay of RNAs. The role of m6A modifications has been highlighted by increasing evidence in various cancers, which, however, is rarely explored in acral melanoma. Here, we demonstrated that m6A level was highly elevated in acral melanoma tissues, along with the expression of METTL3, one of the most important m6A methyltransferase. Besides, higher expression of METTL3 messenger RNA (mRNA) correlated with a higher stage in primary acral melanoma patients. Knockdown of METTL3 decreased global m6A level in melanoma cells. Furthermore, METTL3 knockdown suppressed the proliferation, migration, and invasion of melanoma cells. In METTL3 knockdown xenograft mouse models, we observed decreased volumes and weights of melanoma tissues. Mechanistically, we found that METTL3 regulates certain m6A-methylated transcripts, thioredoxin domain containing protein 5 (TXNDC5), with the confirmation of RNA-seq, MeRIP-seq, and Western blot. These data suggest that METTL3 may play a key role in the progression of acral melanoma, and targeting the m6A dependent-METTL3 signaling pathway may serve as a promising therapeutic strategy for management of patients of acral melanomas.
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Affiliation(s)
- Zhanghui Yue
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Meng Cao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Anlan Hong
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Qian Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Guoqiang Zhang
- Department of Dermatology, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhibin Jin
- Department of Ultrasound, Nanjing Drum Tower Hospital, Nanjing, China
| | - Liang Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Qiang Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Fang Fang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Yan Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Jianfang Sun
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
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8
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Bernardes SS, Ferreira I, Elder DE, Nobre AB, Martínez‐Said H, Adams DJ, Robles‐Espinoza CD, Possik PA. More than just acral melanoma: the controversies of defining the disease. J Pathol Clin Res 2021; 7:531-541. [PMID: 34213090 PMCID: PMC8503895 DOI: 10.1002/cjp2.233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 01/17/2023]
Abstract
Acral melanoma (AM) is a malignant cutaneous melanocytic tumour specifically located on the palms, soles, and nail apparatus, which are areas of glabrous (hairless) skin. Acral lentiginous melanoma, a subtype of AM, represents a histopathological subtype diagnosis of cutaneous melanoma with unique morphological and structural features. Despite clear definitions, the misuse of these terms and the inconsistency in reporting the histopathological features of AM cases have become a major obstacle to the study of the disease. In this review, we discuss the epidemiology, histopathological features, prognosis, and genetic profile of AM, highlighting the differences observed when histopathological subtypes are considered. The increasing global effort to characterise AM cases from ethnically diverse populations would benefit greatly from a more consistent classification of the disease.
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Affiliation(s)
- Sara S Bernardes
- Program of Immunology and Tumour BiologyBrazilian National Cancer InstituteRio de JaneiroBrazil
- Tissue Microenvironment Laboratory, Department of General PathologyFederal University of Minas GeraisBelo HorizonteBrazil
| | - Ingrid Ferreira
- Experimental Cancer GeneticsWellcome Sanger InstituteHinxtonUK
- Université Libre de BruxellesBrusselsBelgium
| | - David E Elder
- Division of Anatomic PathologyHospital of the University of PennsylvaniaPhiladelphiaPAUSA
| | - Aretha B Nobre
- Division of PathologyBrazilian National Cancer InstituteRio de JaneiroBrazil
- Serviço de Patologia, Maternidade EscolaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Héctor Martínez‐Said
- Servicio de Piel y Partes BlandasInstituto Nacional de CancerologíaCiudad de MéxicoMexico
| | - David J Adams
- Experimental Cancer GeneticsWellcome Sanger InstituteHinxtonUK
| | - Carla Daniela Robles‐Espinoza
- Experimental Cancer GeneticsWellcome Sanger InstituteHinxtonUK
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de MéxicoSantiago de QuerétaroMexico
| | - Patricia A Possik
- Program of Immunology and Tumour BiologyBrazilian National Cancer InstituteRio de JaneiroBrazil
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9
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Sliz E, Huilaja L, Pasanen A, Laisk T, Reimann E, Mägi R, Hannula-Jouppi K, Peltonen S, Salmi T, Koulu L, Tasanen K, Kettunen J. Uniting biobank resources reveals novel genetic pathways modulating susceptibility for atopic dermatitis. J Allergy Clin Immunol 2021; 149:1105-1112.e9. [PMID: 34454985 DOI: 10.1016/j.jaci.2021.07.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/08/2021] [Accepted: 07/20/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is a common chronic inflammatory skin disease with high heritability. Previous genome-wide association studies have identified several loci predisposing to AD. These findings explain approximately 30% of the variance in AD susceptibility, suggesting that further work is required to fully understand the genetic underpinnings. OBJECTIVE We sought to gain additional understanding of the genetic contribution to AD risk by using biobank resources. METHODS We completed a genome-wide meta-analysis of AD in 796,661 individuals (Ncases = 22,474) from the FinnGen study, the Estonian Biobank, and the UK Biobank. We further performed downstream in silico analyses to characterize the risk variants at the novel loci. RESULTS We report 30 loci associating with AD (P < 5 × 10-8), 5 of which are novel. In 2 of the novel loci, we identified missense mutations with deleterious predictions in desmocollin 1 and serpin family B member 7, genes encoding proteins crucial to epidermal strength and integrity. CONCLUSIONS These findings elucidate novel genetic pathways involved in AD pathophysiology. The likely involvement of desmocollin 1 and serpin family B member 7 in AD pathogenesis may offer opportunities for the development of novel treatment strategies for AD in the future.
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Affiliation(s)
- Eeva Sliz
- Center for Life Course Health Research, Faculty of Medicine, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Laura Huilaja
- Department of Dermatology, PEDEGO Research Unit, Medical Research Center Oulu, Oulu, Finland; University Hospital and University of Oulu, Oulu, Finland
| | - Anu Pasanen
- Department of Dermatology, PEDEGO Research Unit, Medical Research Center Oulu, Oulu, Finland; University Hospital and University of Oulu, Oulu, Finland; PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ene Reimann
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | | | - Katariina Hannula-Jouppi
- Department of Dermatology and Allergology, ERN-Skin Center, University of Helsinki, Helsinki, Finland; Helsinki University Central Hospital, Helsinki, Finland; Folkhälsan Research Center, Helsinki, Finland; Research Programs Unit, Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Sirkku Peltonen
- Department of Dermatology and Venereology, University of Turku, Turku, Finland; Department of Dermatology, Turku University Hospital, Turku, Finland; Department of Dermatology and Venereology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Dermatology and Venereology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Teea Salmi
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Department of Dermatology, Tampere University Hospital, Tampere, Finland
| | - Leena Koulu
- Department of Dermatology and Venereology, University of Turku, Turku, Finland; Department of Dermatology, Turku University Hospital, Turku, Finland
| | - Kaisa Tasanen
- Department of Dermatology, PEDEGO Research Unit, Medical Research Center Oulu, Oulu, Finland; University Hospital and University of Oulu, Oulu, Finland
| | - Johannes Kettunen
- Center for Life Course Health Research, Faculty of Medicine, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
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10
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A four-gene signature predicts survival and anti-CTLA4 immunotherapeutic responses based on immune classification of melanoma. Commun Biol 2021; 4:383. [PMID: 33753855 PMCID: PMC7985195 DOI: 10.1038/s42003-021-01911-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
Cutaneous melanoma is the most malignant skin cancer. Biomarkers for stratifying patients at initial diagnosis and informing clinical decisions are highly sought after. Here we classified melanoma patients into three immune subtypes by single-sample gene-set enrichment analysis. We further identified a four-gene tumor immune-relevant (TIR) signature that was significantly associated with the overall survival of melanoma patients in The Cancer Genome Atlas cohort and in an independent validation cohort. Moreover, when applied to melanoma patients treated with the CTLA4 antibody, ipilimumab, the TIR signature could predict the response to ipilimumab and the survival. Notably, the predictive power of the TIR signature was higher than that of other biomarkers. The genes in this signature, SEL1L3, HAPLN3, BST2, and IFITM1, may be functionally involved in melanoma progression and immune response. These findings suggest that this four-gene signature has potential use in prognosis, risk assessment, and prediction of anti-CTLA4 response in melanoma patients. Ying Mei et al. identify a four-gene tumor immune-relevant signature that predicts the overall survival of melanoma patients and their response to the CTLA4 antibody ipilimumab. This study suggests a potential utility of this four-gene signature in prognosis, risk assessment, and prediction of anti-CTLA4 response in melanoma patients.
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11
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Hu B, Wei Q, Zhou C, Ju M, Wang L, Chen L, Li Z, Wei M, He M, Zhao L. Analysis of immune subtypes based on immunogenomic profiling identifies prognostic signature for cutaneous melanoma. Int Immunopharmacol 2020; 89:107162. [PMID: 33168410 DOI: 10.1016/j.intimp.2020.107162] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022]
Abstract
Skin cutaneous melanoma (SKCM) is the most invasive form of skin cancer with poor prognosis. Growing evidence has demonstrated that tumor immune microenvironment plays a key contributing role in tumorigenesis and predicting clinical outcomes. The aim of this study was to recognize immune classification and a reliable prognostic signature for patients with SKCM. By using single-sample gene set enrichment (ssGSEA) and hierarchical clustering analyses, we evaluated the immune infiltration landscape of SKCM afflicted patients from The Cancer Genome Atlas (TCGA) dataset and named two SKCM subtypes: Immunity-high and Immunity-low. The Immunity-high subgroup was characterized by up-regulation of immune response and favorable survival probability. Seven candidate small molecule drugs which potentially reverse SKCM immune status were identified by using Connectivity map (CMap) database. A prognostic five-immune-associated gene (IAG) signature consisting IFITM1, TNFSF13B, APOBEC3G, CCL8 and KLRK1 with high predictive value was established using the LASSO Cox regression analysis in training set, and validated in testing set as well as Gene Expression Omnibus (GEO) external validation cohort (P < 0.05). Lower tumor purity and active immune-related signaling pathways were obviously presented in low-risk group. Furthermore, a novel composite nomogram based upon the five-IAG signature and other clinical parameters was built with excellent calibration curves. Collectively, comprehensively characterizing the SKCM subtypes based upon immune microenvironment landscape and development of a survival-related IAG signature may provide a promising avenue for improving individualized treatment design and prognosis prediction for patients with SKCM.
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Affiliation(s)
- Baohui Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Qian Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Chenyi Zhou
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Mingyi Ju
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Lin Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Lianze Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Zinan Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China.
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province 110122, China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, China Medical University, Shenyang, Liaoning Province 110122, China.
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12
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Ramani NS, Aung PP, Gu J, Sfamenos S, Sdringola-Maranga C, Nagarajan P, Tetzlaff MT, Curry JL, Ivan D, Diab A, Prieto VG, Hwu WJ, Torres-Cabala CA. TERT amplification but not activation of canonical Wnt/β-catenin pathway is involved in acral lentiginous melanoma progression to metastasis. Mod Pathol 2020; 33:2067-2074. [PMID: 32404956 DOI: 10.1038/s41379-020-0565-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 01/10/2023]
Abstract
Acral lentiginous melanoma (ALM) is a rare tumor that occurs on non-sun exposed skin areas of the hands and feet. Reports suggest that ALM exhibits poor prognosis, although mechanisms driving this remain poorly understood. Alterations in TERT and the Wnt/β-catenin (Wnt) pathway have been suggested to correlate with prognosis of ALM. Thus, immunohistochemical expression of β-catenin and LEF1 along with TERT amplification by FISH was investigated in 34 primary ALMs, 20 metastatic ALMs, 10 primary non-ALMs, and 15 acral nevi. Foot/toe was the most common primary tumor location (85%) for ALM. TERT amplification was detected in 6 of 28 (21.4%) primary ALM, 2 of 8 (25%) primary non-ALM, and 8 of 18 (44.4%) metastatic ALM, the latter showing significantly higher frequency compared with primary melanomas (P = 0.043). Most metastatic ALMs positive for TERT amplification lacked BRAF V600E (87.5%). Cytoplasmic and nonnuclear expression of β-catenin was variably detected in all cases. Metastatic ALM revealed lower expression of β-catenin compared with primary ALM (P = 0.017). No differences in LEF1 expression were detected among the groups; however, acral nevi showed decreased labeling with dermal descent, in contrast to melanoma. No molecular-genetic alteration correlated with prognosis. TERT amplification by FISH is a frequent finding in primary ALM and appears to increase in metastatic tumors, suggesting a role in tumor progression to metastasis. Although TERT amplification has been reported to be infrequent in primary non-ALM, it showed comparable frequency with ALM in our series. Our immunohistochemical findings are not fully supportive of activation of either canonical or noncanonical Wnt cascades in ALM. TERT amplification by FISH and LEF1 immunohistochemistry may help in the differential diagnosis between primary ALM and acral nevus. TERT amplification appears to be a promising target for therapy in patients with metastatic ALM.
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Affiliation(s)
- Nisha S Ramani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Phyu P Aung
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jun Gu
- Cytogenetics Training Laboratory, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven Sfamenos
- Cytogenetics Training Laboratory, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chiara Sdringola-Maranga
- Cytogenetics Training Laboratory, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priyardhisini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Molecular Translational Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan L Curry
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Doina Ivan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adi Diab
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Victor G Prieto
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wen-Jen Hwu
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlos A Torres-Cabala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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