1
|
Schepps S, Xu J, Yang H, Mandel J, Mehta J, Tolotta J, Baker N, Tekmen V, Nikbakht N, Fortina P, Fuentes I, LaFleur B, Cho RJ, South AP. Skin in the game: a review of single-cell and spatial transcriptomics in dermatological research. Clin Chem Lab Med 2024; 0:cclm-2023-1245. [PMID: 38656304 DOI: 10.1515/cclm-2023-1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/29/2024] [Indexed: 04/26/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) are two emerging research technologies that uniquely characterize gene expression microenvironments on a cellular or subcellular level. The skin, a clinically accessible tissue composed of diverse, essential cell populations, serves as an ideal target for these high-resolution investigative approaches. Using these tools, researchers are assembling a compendium of data and discoveries in healthy skin as well as a range of dermatologic pathophysiologies, including atopic dermatitis, psoriasis, and cutaneous malignancies. The ongoing advancement of single-cell approaches, coupled with anticipated decreases in cost with increased adoption, will reshape dermatologic research, profoundly influencing disease characterization, prognosis, and ultimately clinical practice.
Collapse
Affiliation(s)
- Samuel Schepps
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Jonathan Xu
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Henry Yang
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Jenna Mandel
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Jaanvi Mehta
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Julianna Tolotta
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Nicole Baker
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Volkan Tekmen
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Neda Nikbakht
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
- Department of Pharmacology, Physiology and Cancer Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Paolo Fortina
- Department of Pharmacology, Physiology and Cancer Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
| | - Ignacia Fuentes
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Directora de Investigación Fundación DEBRA Chile, Santiago, Chile
| | - Bonnie LaFleur
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
- R. Ken Coit College of Pharmacy, University of Arizona, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Raymond J Cho
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
- Department of Dermatology, University of San Francisco, San Francisco, CA, USA
| | - Andrew P South
- Department of Pharmacology, Physiology and Cancer Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
| |
Collapse
|
2
|
Rajpar I, Kumar G, Fortina P, Tomlinson RE. Toll-like receptor 4 signaling in osteoblasts is required for load-induced bone formation in mice. iScience 2023; 26:106304. [PMID: 36950122 PMCID: PMC10025993 DOI: 10.1016/j.isci.2023.106304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/06/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
In mature bone, NGF is produced by osteoblasts following mechanical loading and signals through resident sensory nerves expressing its high affinity receptor, neurotrophic tyrosine kinase receptor type 1 (TrkA), to support bone formation. Here, we investigated whether osteoblastic expression of Toll-like receptor 4 (TLR4), a key receptor in the NF-κB signaling pathway, is required to initiate NGF-TrkA signaling required for load-induced bone formation. Although Tlr4 conditional knockout mice have normal skeletal mass and strength in adulthood, the loss of TLR4 signaling significantly reduced lamellar bone formation following loading. Inhibition of TLR4 signaling reduced Ngf expression in primary osteoblasts and RNA sequencing of bones from Tlr4 conditional knockout mice and wild-type littermates revealed dysregulated inflammatory signaling three days after osteogenic mechanical loading. In total, our study reveals an important role for osteoblastic TLR4 in the skeletal adaptation of bone to mechanical forces.
Collapse
Affiliation(s)
- Ibtesam Rajpar
- Department of Orthopaedic Surgery, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gaurav Kumar
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Paolo Fortina
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ryan E. Tomlinson
- Department of Orthopaedic Surgery, Thomas Jefferson University, Philadelphia, PA, USA
- Corresponding author
| |
Collapse
|
3
|
Rasouli J, Casella G, Zhang W, Xiao D, Kumar G, Fortina P, Zhang GX, Ciric B, Rostami A. Transcription Factor RUNX3 Mediates Plasticity of ThGM Cells Toward Th1 Phenotype. Front Immunol 2022; 13:912583. [PMID: 35860266 PMCID: PMC9289370 DOI: 10.3389/fimmu.2022.912583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
GM-CSF-producing T helper (Th) cells play a crucial role in the pathogenesis of autoimmune diseases such as multiple sclerosis (MS). Recent studies have identified a distinct population of GM-CSF-producing Th cells, named ThGM cells, that also express cytokines TNF, IL-2, and IL-3, but lack expression of master transcription factors (TF) and signature cytokines of commonly recognized Th cell lineages. ThGM cells are highly encephalitogenic in a mouse model of MS, experimental autoimmune encephalomyelitis (EAE). Similar to Th17 cells, in response to IL-12, ThGM cells upregulate expression of T-bet and IFN-γ and switch their phenotype to Th1. Here we show that in addition to T-bet, TF RUNX3 also contributes to the Th1 switch of ThGM cells. T-bet-deficient ThGM cells in the CNS of mice with EAE had low expression of RUNX3, and knockdown of RUNX3 expression in ThGM cells abrogated the Th1-inducing effect of IL-12. Comparison of ThGM and Th1 cell transcriptomes showed that ThGM cells expressed a set of TFs known to inhibit the development of other Th lineages. Lack of expression of lineage-specific cytokines and TFs by ThGM cells, together with expression of TFs that inhibit the development of other Th lineages, suggests that ThGM cells are a non-polarized subset of Th cells with lineage characteristics.
Collapse
Affiliation(s)
- Javad Rasouli
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Giacomo Casella
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Weifeng Zhang
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Dan Xiao
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Gaurav Kumar
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Paolo Fortina
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, United States
- Department of Translation and Precision Medicine, Sapienza University, Rome, Italy
| | - Guang-Xian Zhang
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Bogoljub Ciric
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Abdolmohamad Rostami
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
- *Correspondence: Abdolmohamad Rostami,
| |
Collapse
|
4
|
Saeidian AH, Youssefian L, Huang CY, Palizban F, Naji M, Saffarian Z, Mahmoudi H, Goodarzi A, Sotoudeh S, Vahidnezhad F, Amani M, Tavakoli N, Ajami A, Mozafarpoor S, Teimoorian M, Dorgaleleh S, Shokri S, Shenagari M, Abedi N, Zeinali S, Fortina P, Béziat V, Jouanguy E, Casanova JL, Uitto J, Vahidnezhad H. Whole-transcriptome sequencing-based concomitant detection of viral and human genetic determinants of cutaneous lesions. JCI Insight 2022; 7:156021. [PMID: 35316210 PMCID: PMC9089792 DOI: 10.1172/jci.insight.156021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Severe viral infections of the skin can occur in patients with inborn errors of immunity (IEI). We report an all-in-one whole-transcriptome sequencing–based method by RNA-Seq on a single skin biopsy for concomitantly identifying the cutaneous virome and the underlying IEI. Skin biopsies were obtained from healthy and lesional skin from patients with cutaneous infections suspected to be of viral origin. RNA-Seq was utilized as the first-tier strategy for unbiased human genome-wide rare variant detection. Reads unaligned to the human genome were utilized for the exploration of 926 viruses in a viral genome catalog. In 9 families studied, the patients carried pathogenic variants in 6 human IEI genes, including IL2RG, WAS, CIB1, STK4, GATA2, and DOCK8. Gene expression profiling also confirmed pathogenicity of the human variants and permitted genome-wide homozygosity mapping, which assisted in identification of candidate genes in consanguineous families. This automated, online, all-in-one computational pipeline, called VirPy, enables simultaneous detection of the viral triggers and the human genetic variants underlying skin lesions in patients with suspected IEI and viral dermatosis.
Collapse
Affiliation(s)
- Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson Univerrsity, Philadelphia, United States of America
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, United States of America
| | - Charles Y Huang
- Department of Dermatology and Cutaneous Biology, Jefferson Medical College,Thomas Jefferson University, Philadelphia, United States of America
| | - Fahimeh Palizban
- Laboratory and Complex Biological Systems and Bioinformactics, University of Tehran, Tehran, Iran (Islamic Republic of)
| | - Mahtab Naji
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, United States of America
| | - Zahra Saffarian
- Imam Khomeini Hospaital, Tehran University of Medical Sciences, Tehran, Iran (Islamic Republic of)
| | - Hamidreza Mahmoudi
- Department of Dermatology, Tehran University of Medical Sciences, Tehran, Iran (Islamic Republic of)
| | - Azadeh Goodarzi
- Department of Dermatology, Iran University of Medical Sciences, Tehran, Iran (Islamic Republic of)
| | - Soheila Sotoudeh
- Department of Dermatology, Tehran University of Medical Sciences, Tehran, Iran (Islamic Republic of)
| | - Fatemeh Vahidnezhad
- UCSC Silicon Valley Extension, University of California, Santa Cruz, United States of America
| | - Maliheh Amani
- Department of Dermatology, Gonabad University of Medical Sciences, Gonabad, Iran (Islamic Republic of)
| | - Narjes Tavakoli
- Nobel Laboratory, Isfahan University of Medical Sciences, Isfahan Province, Iran (Islamic Republic of)
| | - Ali Ajami
- Nobel Laboratory, Isfahan University of Medical Sciences, Isfahan Province, Iran (Islamic Republic of)
| | - Samaneh Mozafarpoor
- Department of Dermatology, Skin Disease and Leishmaniasis Research Center, Isfahan University of Medical Sciences, Isfahan Province, Iran (Islamic Republic of)
| | - Mehrdad Teimoorian
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran (Islamic Republic of)
| | - Saeed Dorgaleleh
- Student Research Committee, Golestan University of Medical Sciences, Gorgan, Iran (Islamic Republic of)
| | - Sima Shokri
- Department of Allergy and Clinical Immunology, Iran University of Medical Sciences, Tehran, Iran (Islamic Republic of)
| | - Mohammad Shenagari
- Department of Microbiology, Guilan University of Medical Sciences, Rasht, Iran (Islamic Republic of)
| | - Nima Abedi
- Bioinformatics Department, University of Tehran, Tehran, Iran (Islamic Republic of)
| | - Sirous Zeinali
- Kawsar Human Genetics Research Center, Tehran, Iran (Islamic Republic of)
| | - Paolo Fortina
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, United States of America
| | - Vivien Béziat
- Human Genetics of Infectious Diseases Laboratory, Imagine Institute - INSERM U1163 (ex U980), Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, United States of America
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockfeller University, New York, United States of America
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson Univerrsity, Philadelphia, United States of America
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson Univerrsity, Philadelphia, United States of America
| |
Collapse
|
5
|
Dasgeb B, Pajouhanfar S, Jazayeri A, Schoenberg E, Kumar G, Fortina P, Berger AC, Uitto J. Novel PTCH1 and concurrent TP53 mutations in four patients with numerous non-syndromic basal cell carcinomas: The paradigm of oncogenic synergy. Exp Dermatol 2021; 31:736-742. [PMID: 34862824 DOI: 10.1111/exd.14510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022]
Abstract
There has been a significant increase in basal cell carcinoma (BCC) incidence, the most common cancer in humans and the age of presentation with the first diagnosis of BCC has decreased in past decades. In this study, we investigated the possibility of genetic markers that can lead to earlier and closer observation of patients at high risk for development of multiple BCCs. The overall goal is to decrease the morbidity and the economic burden of diagnosis and treatment of recurring and/or advanced BCCs. Four patients with numerous BCCs, some of them exceptionally large, were included in this study. A sample of representative BCCs, normal non-sun-exposed skin and blood samples were obtained from each patient. Whole-exome sequencing of DNA was conducted on all samples, and a series of bioinformatics filtering was performed to identify potentially pathogenic sequence variants. The analysis of the data resulted in detection of oncogenic mutations in PTCH1, two of which being novel, and concurrent mutations in TP53 in BCC tumours of all four patients. Such mutations may explain the numerous and postexcision recurring nature of the BCCs of exceptionally large size observed in all these patients, and they can be suggested to serve as a genetic marker for high-risk patients for early detection, prognostication and close follow-up.
Collapse
Affiliation(s)
- Bahar Dasgeb
- Department of Surgical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Sara Pajouhanfar
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Ali Jazayeri
- College of Computing & Informatics, Drexel University, Philadelphia, Pennsylvania, USA
| | - Elizabeth Schoenberg
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Gaurav Kumar
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Paolo Fortina
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Adam C Berger
- Department of Surgical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
6
|
Saeidian AH, Youssefian L, Huang J, Touati A, Vahidnezhad H, Kowal L, Caffet M, Wurst T, Singh J, Snook AE, Ryu E, Fortina P, Terry SF, Schoenecker JG, Uitto J, Li Q. Genetic heterogeneity of heritable ectopic mineralization disorders in a large international cohort. Genet Med 2021; 24:75-86. [PMID: 34906475 DOI: 10.1016/j.gim.2021.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/17/2021] [Accepted: 08/16/2021] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Heritable ectopic mineralization disorders comprise a group of conditions with a broad range of clinical manifestations in nonskeletal connective tissues. We report the genetic findings from a large international cohort of 478 patients afflicted with ectopic mineralization. METHODS Sequence variations were identified using a next-generation sequencing panel consisting of 29 genes reported in association with ectopic mineralization. The pathogenicity of select splicing and missense variants was analyzed in experimental systems in vitro and in vivo. RESULTS A total of 872 variants of unknown significance as well as likely pathogenic and pathogenic variants were disclosed in 25 genes. A total of 159 distinct variants were identified in 425 patients in ABCC6, the gene responsible for pseudoxanthoma elasticum, a heritable multisystem ectopic mineralization disorder. The interpretation of variant pathogenicity relying on bioinformatic predictions did not provide a consensus. Our in vitro and in vivo functional assessment of 14 ABCC6 variants highlighted this dilemma and provided unambiguous interpretations to their pathogenicity. CONCLUSION The results expand the ABCC6 variant repertoire, shed new light on the genetic heterogeneity of heritable ectopic mineralization disorders, and provide evidence that functional characterization in appropriate experimental systems is necessary to determine the pathogenicity of genetic variants.
Collapse
Affiliation(s)
- Amir Hossein Saeidian
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA; Department of Dermatology & Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA; Genetics, Genomics & Cancer Biology PhD Program, College of Life Sciences, Thomas Jefferson University, Philadelphia, PA
| | - Leila Youssefian
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA; Department of Dermatology & Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Jianhe Huang
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA; Department of Dermatology & Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA; PXE International Center of Excellence in Research & Clinical Care, Thomas Jefferson University, Philadelphia, PA
| | - Andrew Touati
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA; Department of Dermatology & Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Hassan Vahidnezhad
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA; Department of Dermatology & Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Luke Kowal
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA
| | | | | | - Jagmohan Singh
- Department of Pharmacology & Experimental Therapeutics, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, PA
| | - Adam E Snook
- Department of Pharmacology & Experimental Therapeutics, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, PA
| | - Ellen Ryu
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | | | - Jonathan G Schoenecker
- Department of Orthopedics and Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, TN
| | - Jouni Uitto
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA; Department of Dermatology & Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA; PXE International Center of Excellence in Research & Clinical Care, Thomas Jefferson University, Philadelphia, PA
| | - Qiaoli Li
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA; Department of Dermatology & Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA; PXE International Center of Excellence in Research & Clinical Care, Thomas Jefferson University, Philadelphia, PA.
| |
Collapse
|
7
|
Capparelli C, Purwin TJ, Tiago M, Wilski N, Pomante D, Glasheen M, Rosenbaum S, Nguyen MQ, Cai W, Zheng R, Kumar G, Chervoneva I, Shimada A, Snook AE, Fortina P, Xu X, Hookim K, Cukierman E, Davies MA, Herlyn M, Aplin AE. Abstract 40: Targeting SOX10-deficient cells to reduce resistance to targeted therapy in melanoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Intratumoral heterogeneity and cellular plasticity enable tumors to alter phenotypes and adapt to foreign microenvironments and resist targeted inhibitors. While the ability to switch between phenotypic states has been broadly characterized, the key mechanisms that underlie tumor plasticity remain poorly understood. We studied the neural crest lineage transcription factor, SOX10, in the context of cutaneous melanoma and resistance to targeted therapies. SOX10 is heterogeneously expressed in melanoma samples. Using bio-informatics as well as in vivo and 3D in vitro melanoma models, SOX10 loss was sufficient to induce an invasive but slow proliferating phenotype in vitro and in vivo that was associated with expression of a mesenchymal gene set. Interestingly, while SOX10 knockout initially induced a targeted inhibitor tolerant state, longer exposure of co-mixed populations of SOX10 proficient and SOX10 deficient to targeted therapy drives the clonal selection of SOX10 knockout cells. Furthermore, cell lines generated from xenograft tumors that have acquired resistance to either vemurafenib, paradox-breaking BRAFi or the combination of BRAFi + MEKi showed dramatically reduced SOX10 expression compared to their parental counterparts. Altogether these data suggest that acquired resistant clones may arise from drug tolerant persister cells. As a strategy to selectively target this invasive, drug-tolerant SOX10-deficient sub-population, we screened a drug compound library and identified a class of cIAP1/2 inhibitors to be synthetically lethal for SOX10-deficient cells. Our preliminary data suggest that birinapant can delay or prevent resistance to BRAFi/MEKi in vivo. Together, these data suggest that SOX10 mediates phenotypic switching in cutaneous melanoma and enables tumor adaptation to altered microenvironments and drug treatments which could be targeted using cIAP1/2 inhibitors.
Citation Format: Claudia Capparelli, Timothy J. Purwin, Manoela Tiago, Nicole Wilski, Danielle Pomante, McKenna Glasheen, Sheera Rosenbaum, Mai Q. Nguyen, Weijia Cai, Richard Zheng, Gaurav Kumar, Inna Chervoneva, Ayako Shimada, Adam E. Snook, Paolo Fortina, Xiaowei Xu, Kim Hookim, Edna Cukierman, Michael A. Davies, Meenhard Herlyn, Andrew E. Aplin. Targeting SOX10-deficient cells to reduce resistance to targeted therapy in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 40.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Weijia Cai
- 1Thomas Jefferson University, Philadelphia, PA
| | | | | | | | | | | | | | - Xiaowei Xu
- 2University of Pennsylvania, Philadelphia, Pennsylvania, Philadelphia, PA
| | - Kim Hookim
- 1Thomas Jefferson University, Philadelphia, PA
| | | | | | | | | |
Collapse
|
8
|
Rasouli J, Casella G, Ishikawa LLW, Thome R, Boehm A, Ertel A, Melo-Silva CR, Mari ER, Porazzi P, Zhang W, Xiao D, Sigal LJ, Fortina P, Zhang GX, Rostami A, Ciric B. IFN-β Acts on Monocytes to Ameliorate CNS Autoimmunity by Inhibiting Proinflammatory Cross-Talk Between Monocytes and Th Cells. Front Immunol 2021; 12:679498. [PMID: 34149716 PMCID: PMC8213026 DOI: 10.3389/fimmu.2021.679498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/12/2021] [Indexed: 01/18/2023] Open
Abstract
IFN-β has been the treatment for multiple sclerosis (MS) for almost three decades, but understanding the mechanisms underlying its beneficial effects remains incomplete. We have shown that MS patients have increased numbers of GM-CSF+ Th cells in circulation, and that IFN-β therapy reduces their numbers. GM-CSF expression by myelin-specific Th cells is essential for the development of experimental autoimmune encephalomyelitis (EAE), an animal model of MS. These findings suggested that IFN-β therapy may function via suppression of GM-CSF production by Th cells. In the current study, we elucidated a feedback loop between monocytes and Th cells that amplifies autoimmune neuroinflammation, and found that IFN-β therapy ameliorates central nervous system (CNS) autoimmunity by inhibiting this proinflammatory loop. IFN-β suppressed GM-CSF production in Th cells indirectly by acting on monocytes, and IFN-β signaling in monocytes was required for EAE suppression. IFN-β increased IL-10 expression by monocytes, and IL-10 was required for the suppressive effects of IFN-β. IFN-β treatment suppressed IL-1β expression by monocytes in the CNS of mice with EAE. GM-CSF from Th cells induced IL-1β production by monocytes, and, in a positive feedback loop, IL-1β augmented GM-CSF production by Th cells. In addition to GM-CSF, TNF and FASL expression by Th cells was also necessary for IL-1β production by monocyte. IFN-β inhibited GM-CSF, TNF, and FASL expression by Th cells to suppress IL-1β secretion by monocytes. Overall, our study describes a positive feedback loop involving several Th cell- and monocyte-derived molecules, and IFN-β actions on monocytes disrupting this proinflammatory loop.
Collapse
MESH Headings
- Animals
- Antigen-Presenting Cells/immunology
- Antigen-Presenting Cells/metabolism
- Autoimmunity/drug effects
- Cell Communication/genetics
- Cell Communication/immunology
- Cytokines/metabolism
- Disease Models, Animal
- Disease Susceptibility/immunology
- Encephalomyelitis, Autoimmune, Experimental/etiology
- Encephalomyelitis, Autoimmune, Experimental/metabolism
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Granulocyte-Macrophage Colony-Stimulating Factor/biosynthesis
- Interferon-beta/metabolism
- Interferon-beta/pharmacology
- Mice
- Mice, Knockout
- Monocytes/drug effects
- Monocytes/immunology
- Monocytes/metabolism
- T-Lymphocytes, Helper-Inducer/drug effects
- T-Lymphocytes, Helper-Inducer/immunology
- T-Lymphocytes, Helper-Inducer/metabolism
Collapse
Affiliation(s)
- Javad Rasouli
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Giacomo Casella
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | | | - Rodolfo Thome
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Alexandra Boehm
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Adam Ertel
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Carolina R. Melo-Silva
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Elisabeth R. Mari
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Patrizia Porazzi
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Weifeng Zhang
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Dan Xiao
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Luis J. Sigal
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Paolo Fortina
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, United States
- Department of Translation and Precision Medicine, Sapienza University, Rome, Italy
| | - Guang-Xian Zhang
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Abdolmohamad Rostami
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Bogoljub Ciric
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| |
Collapse
|
9
|
Youssefian L, Saeidian AH, Palizban F, Bagherieh A, Abdollahimajd F, Sotoudeh S, Mozafari N, Farahani RA, Mahmoudi H, Babashah S, Zabihi M, Zeinali S, Fortina P, Salas-Alanis JC, South AP, Vahidnezhad H, Uitto J. Whole-Transcriptome Analysis by RNA Sequencing for Genetic Diagnosis of Mendelian Skin Disorders in the Context of Consanguinity. Clin Chem 2021; 67:876-888. [PMID: 33969388 DOI: 10.1093/clinchem/hvab042] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Among the approximately 8000 Mendelian disorders, >1000 have cutaneous manifestations. In many of these conditions, the underlying mutated genes have been identified by DNA-based techniques which, however, can overlook certain types of mutations, such as exonic-synonymous and deep-intronic sequence variants. Whole-transcriptome sequencing by RNA sequencing (RNA-seq) can identify such mutations and provide information about their consequences. METHODS We analyzed the whole transcriptome of 40 families with different types of Mendelian skin disorders with extensive genetic heterogeneity. The RNA-seq data were examined for variant detection and prioritization, pathogenicity confirmation, RNA expression profiling, and genome-wide homozygosity mapping in the case of consanguineous families. Among the families examined, RNA-seq was able to provide information complementary to DNA-based analyses for exonic and intronic sequence variants with aberrant splicing. In addition, we tested the possibility of using RNA-seq as the first-tier strategy for unbiased genome-wide mutation screening without information from DNA analysis. RESULTS We found pathogenic mutations in 35 families (88%) with RNA-seq in combination with other next-generation sequencing methods, and we successfully prioritized variants and found the culprit genes. In addition, as a novel concept, we propose a pipeline that increases the yield of variant calling from RNA-seq by concurrent use of genome and transcriptome references in parallel. CONCLUSIONS Our results suggest that "clinical RNA-seq" could serve as a primary approach for mutation detection in inherited diseases, particularly in consanguineous families, provided that tissues and cells expressing the relevant genes are available for analysis.
Collapse
Affiliation(s)
- Leila Youssefian
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Amir Hossein Saeidian
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Fahimeh Palizban
- Laboratory of Complex Biological Systems and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Atefeh Bagherieh
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Nikoo Mozafari
- Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rahele A Farahani
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | | | - Paolo Fortina
- Cancer Genomics and Bioinformatics, Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Translation and Precision Medicine, Sapienza University, Rome, Italy
| | | | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hassan Vahidnezhad
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jouni Uitto
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
10
|
Youssefian L, Saeidian A, Fortina P, South A, Uitto J, Vahidnezhad H. 184 Whole-transcriptome analysis by RNA-Seq for genetic diagnosis of Mendelian skin disorders in the context of consanguinity. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.02.204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
11
|
Rasouli J, Casella G, Yoshimura S, Zhang W, Xiao D, Garifallou J, Gonzalez MV, Wiedeman A, Kus A, Mari ER, Fortina P, Hakonarson H, Long SA, Zhang GX, Ciric B, Rostami A. A distinct GM-CSF + T helper cell subset requires T-bet to adopt a T H1 phenotype and promote neuroinflammation. Sci Immunol 2020; 5:5/52/eaba9953. [PMID: 33097590 DOI: 10.1126/sciimmunol.aba9953] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022]
Abstract
Elevation of granulocyte-macrophage colony-stimulating factor (GM-CSF)-producing T helper (TH) cells has been associated with several autoimmune diseases, suggesting a potential role in the pathogenesis of autoimmunity. However, the identity of GM-CSF-producing TH cells has not been closely examined. Using single-cell RNA sequencing and high-dimensional single-cell mass cytometry, we identified eight populations of antigen-experienced CD45RA-CD4+ T cells in blood of healthy individuals including a population of GM-CSF-producing cells, known as THGM, that lacked expression of signature transcription factors and cytokines of established TH lineages. Using GM-CSF-reporter/fate reporter mice, we show that THGM cells are present in the periphery and central nervous system in a mouse model of experimental autoimmune encephalomyelitis. In addition to GM-CSF, human and mouse THGM cells also expressed IL-2, tumor necrosis factor (TNF), IL-3, and CCL20. THGM cells maintained their phenotype through several cycles of activation but up-regulated expression of T-bet and interferon-γ (IFN-γ) upon exposure to IL-12 in vitro and in the central nervous system of mice with autoimmune neuroinflammation. Although T-bet was not required for the development of THGM cells, it was essential for their encephalitogenicity. These findings demonstrate that THGM cells constitute a distinct population of TH cells with lineage characteristics that are poised to adopt a TH1 phenotype and promote neuroinflammation.
Collapse
Affiliation(s)
- Javad Rasouli
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, Pennsylvania, PA, USA
| | - Giacomo Casella
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Satoshi Yoshimura
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Weifeng Zhang
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Dan Xiao
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA
| | - James Garifallou
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael V Gonzalez
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alice Wiedeman
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Anna Kus
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Elisabeth R Mari
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Paolo Fortina
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Translation and Precision Medicine, Sapienza University, Rome, Italy
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - S Alice Long
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Guang-Xian Zhang
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Bogoljub Ciric
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA
| | | |
Collapse
|
12
|
Kumar G, Kelly M, Fortina P, Ertel A. Abstract 5469: iCVA- A knowledge-based cancer variation annotation application. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A typical genomic sequencing experiment results in a long list of statistically significant variant candidates among protein-coding genes without any unifying biological theme. This leads to a daunting task of identifying the causal variants and genes to accurately diagnose the disease for clinical or research utility. While a number of downstream tools exist to aid in cancer genome annotation and interpretation, including Clinical Interpretations of Variants in Cancer (CIViC), ClinGen, Database of Curated Mutations (DoCM), Oncotator, and Variant Interpretation for Cancer (VIC), these only provide selective information (somatic/germline/gene-variant specific) or are time/resource consuming. To address this challenge, we developed a software called iCVA using the following methodology: 1) we obtained a priori defined gene sets for different cancer-inducing mechanisms such as pro-oncogenesis, tumor-suppression, DNA repair, angiogenesis, inflammation, metabolism, hypoxia, cell cycle and immune system. 2) genomic variation data were integrated from 1000 Genome, Exome Sequencing Project, Exome Aggregation Consortium (ExAC), ClinVar, dbSNP, GNOMAD, The Cancer Genome Atlas (TCGA), the Catalogue of Somatic Mutations in Cancer (COSMIC) and the International Cancer Gene Census (ICGC), and re-classified into a consensus classification according to ACMG guidelines. 3) Finally, we devised a reporting system to process mutation data from a sequencing experiment to utilize the harmonized pathway and mutational information integrated in a local database to identify and classify cancer-specific gene mutations. The iCVA reporting system classifies mutations as germline or somatic and then sub-classifies these into different cancer-specific mechanisms, including those known to be targetable through existing therapies. To our knowledge, iCVA is the first tool to provide a comprehensive report on cancer variants in a simplified and faster manner, to accelerate the genomic characterization of cancer samples analyzed by high-throughput DNA sequencing.
Citation Format: Gaurav Kumar, Melanie Kelly, Paolo Fortina, Adam Ertel. iCVA- A knowledge-based cancer variation annotation application [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5469.
Collapse
Affiliation(s)
| | | | | | - Adam Ertel
- Sidney Kimmel Cancer Center, Philadelphia, PA
| |
Collapse
|
13
|
Kricka LJ, Polevikov S, Park JY, Fortina P, Bernardini S, Satchkov D, Kolesov V, Grishkov M. Artificial Intelligence-Powered Search Tools and Resources in the Fight Against COVID-19. EJIFCC 2020; 31:106-116. [PMID: 32549878 PMCID: PMC7294813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Emerging technologies are set to play an important role in our response to the COVID-19 pandemic. This paper explores three prominent initiatives: COVID-19 focused datasets (e.g., CORD-19); Artificial intelligence-powered search tools (e.g., WellAI, SciSight); and contact tracing based on mobile communication technology. We believe that increasing awareness of these tools will be important in future research into the disease, COVID-19, and the virus, SARS-CoV-2.
Collapse
Affiliation(s)
- Larry J. Kricka
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Philadelphia, PA, USA, Member of I FCC Emerging Technology Division,Corresponding author: Larry J. Kricka, DPhil, FRCPath Department of Pathology and Laboratory Medicine University of Pennsylvania Medical Center Philadelphia, PA 19108 USA E-mail:
| | | | - Jason Y. Park
- Department of Pathology and the Eugene McDermott Center for Human Growth and Development, Children’s Medical Center, and University of Texas Southwestern Medical School, USA, Member of I FCC Emerging Technology Division
| | - Paolo Fortina
- Cancer Genomics and Bioinformatics, Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA, Department of Translational and Precision Medicine, University La Sapienza, Rome, Italy, Member of I FCC Emerging Technology Division
| | - Sergio Bernardini
- Department of Experimental Medicine, University Tor Vergata, Rome, Italy, Member of I FCC Emerging Technology Division
| | | | | | | |
Collapse
|
14
|
Quaglia F, Krishn SR, Daaboul GG, Sarker S, Pippa R, Domingo-Domenech J, Kumar G, Fortina P, McCue P, Kelly WK, Beltran H, Liu Q, Languino LR. Small extracellular vesicles modulated by αVβ3 integrin induce neuroendocrine differentiation in recipient cancer cells. J Extracell Vesicles 2020; 9:1761072. [PMID: 32922691 PMCID: PMC7448905 DOI: 10.1080/20013078.2020.1761072] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The ability of small extracellular vesicles (sEVs) to reprogram cancer cells is well established. However, the specific sEV components able to mediate aberrant effects in cancer cells have not been characterized. Integrins are major players in mediating sEV functions. We have previously reported that the αVβ3 integrin is detected in sEVs of prostate cancer (PrCa) cells and transferred into recipient cells. Here, we investigate whether sEVs from αVβ3-expressing cells affect tumour growth differently than sEVs from control cells that do not express αVβ3. We compared the ability of sEVs to stimulate tumour growth, using sEVs isolated from PrCa C4-2B cells by iodixanol density gradient and characterized with immunoblotting, nanoparticle tracking analysis, immunocapturing and single vesicle analysis. We incubated PrCa cells with sEVs and injected them subcutaneously into nude mice to measure in vivo tumour growth or analysed in vitro their anchorage-independent growth. Our results demonstrate that a single treatment with sEVs shed from C4-2B cells that express αVβ3, but not from control cells, stimulates tumour growth and induces differentiation of PrCa cells towards a neuroendocrine phenotype, as quantified by increased levels of neuroendocrine markers. In conclusion, the expression of αVβ3 integrin generates sEVs capable of reprogramming cells towards an aggressive phenotype.
Collapse
Affiliation(s)
- Fabio Quaglia
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Shiv Ram Krishn
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - George G Daaboul
- Department of Research and Development, NanoView Biosciences, Boston, MA, USA
| | - Srawasti Sarker
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Raffaella Pippa
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Gaurav Kumar
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Paolo Fortina
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Peter McCue
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA, USA
| | - William K Kelly
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Qin Liu
- Molecular and Cellular Oncogenesis Program, the Wistar Institute, Philadelphia, PA, USA
| | - Lucia R Languino
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
15
|
De Dominici M, Porazzi P, Xiao Y, Chao A, Tang HY, Kumar G, Fortina P, Spinelli O, Rambaldi A, Peterson LF, Petruk S, Barletta C, Mazo A, Cingolani G, Salvino JM, Calabretta B. Selective inhibition of Ph-positive ALL cell growth through kinase-dependent and -independent effects by CDK6-specific PROTACs. Blood 2020; 135:1560-1573. [PMID: 32040545 PMCID: PMC7193186 DOI: 10.1182/blood.2019003604] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022] Open
Abstract
Expression of the cell cycle regulatory gene CDK6 is required for Philadelphia-positive (Ph+) acute lymphoblastic leukemia (ALL) cell growth, whereas expression of the closely related CDK4 protein is dispensable. Moreover, CDK6 silencing is more effective than treatment with the dual CDK4/6 inhibitor palbociclib in suppressing Ph+ ALL in mice, suggesting that the growth-promoting effects of CDK6 are, in part, kinase-independent in Ph+ ALL. Accordingly, we developed CDK4/6-targeted proteolysis-targeting chimeras (PROTACs) that inhibit CDK6 enzymatic activity in vitro, promote the rapid and preferential degradation of CDK6 over CDK4 in Ph+ ALL cells, and markedly suppress S-phase cells concomitant with inhibition of CDK6-regulated phospho-RB and FOXM1 expression. No such effects were observed in CD34+ normal hematopoietic progenitors, although CDK6 was efficiently degraded. Treatment with the CDK6-degrading PROTAC YX-2-107 markedly suppressed leukemia burden in mice injected with de novo or tyrosine kinase inhibitor-resistant primary Ph+ ALL cells, and this effect was comparable or superior to that of the CDK4/6 enzymatic inhibitor palbociclib. These studies provide "proof of principle" that targeting CDK6 with PROTACs that inhibit its enzymatic activity and promote its degradation represents an effective strategy to exploit the "CDK6 dependence" of Ph+ ALL and, perhaps, of other hematologic malignancies. Moreover, they suggest that treatment of Ph+ ALL with CDK6-selective PROTACs would spare a high proportion of normal hematopoietic progenitors, preventing the neutropenia induced by treatment with dual CDK4/6 inhibitors.
Collapse
Affiliation(s)
- Marco De Dominici
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | | | | | - Gaurav Kumar
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Orietta Spinelli
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Alessandro Rambaldi
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
- Department of Oncology and Hematology-Oncology, Università Statale Milano, Milan, Italy
| | - Luke F Peterson
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI; and
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Camilla Barletta
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | | | - Bruno Calabretta
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| |
Collapse
|
16
|
Upton K, Modi A, Patel K, Kendsersky NM, Conkrite KL, Sussman RT, Way GP, Adams RN, Sacks GI, Fortina P, Diskin SJ, Maris JM, Rokita JL. Epigenomic profiling of neuroblastoma cell lines. Sci Data 2020; 7:116. [PMID: 32286315 PMCID: PMC7156688 DOI: 10.1038/s41597-020-0458-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/12/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma.
Collapse
Affiliation(s)
- Kristen Upton
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Apexa Modi
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Khushbu Patel
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Nathan M Kendsersky
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Karina L Conkrite
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Robyn T Sussman
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Gregory P Way
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rebecca N Adams
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania, 19107, USA
| | - Gregory I Sacks
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Paolo Fortina
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania, 19107, USA
| | - Sharon J Diskin
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.
| | - Jo Lynne Rokita
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.
| |
Collapse
|
17
|
Kumar G, Ertel A, Feldman G, Kupper J, Fortina P. iSeqQC: a tool for expression-based quality control in RNA sequencing. BMC Bioinformatics 2020; 21:56. [PMID: 32054449 PMCID: PMC7020508 DOI: 10.1186/s12859-020-3399-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/07/2020] [Indexed: 12/17/2022] Open
Abstract
Background Quality Control in any high-throughput sequencing technology is a critical step, which if overlooked can compromise an experiment and the resulting conclusions. A number of methods exist to identify biases during sequencing or alignment, yet not many tools exist to interpret biases due to outliers. Results Hence, we developed iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers. It can be utilized through command-line (Github: https://github.com/gkumar09/iSeqQC) or web-interface (http://cancerwebpa.jefferson.edu/iSeqQC). A local shiny installation can also be obtained from github (https://github.com/gkumar09/iSeqQC). Conclusion iSeqQC is a fast, light-weight, expression-based QC tool that detects outliers by implementing various statistical approaches.
Collapse
Affiliation(s)
- Gaurav Kumar
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Department of Cancer Biology, BLSB 1009, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA-19107, USA.
| | - Adam Ertel
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Department of Cancer Biology, BLSB 1009, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA-19107, USA
| | - George Feldman
- Department of Orthopedic Research, Thomas Jefferson University, Philadelphia, PA, USA
| | - Joan Kupper
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Department of Cancer Biology, BLSB 1009, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA-19107, USA
| | - Paolo Fortina
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Department of Cancer Biology, BLSB 1009, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA-19107, USA
| |
Collapse
|
18
|
Meyer LK, Huang BJ, Delgado-Martin C, Roy RP, Hechmer A, Wandler AM, Vincent TL, Fortina P, Olshen AB, Wood BL, Horton TM, Shannon KM, Teachey DT, Hermiston ML. Glucocorticoids paradoxically facilitate steroid resistance in T cell acute lymphoblastic leukemias and thymocytes. J Clin Invest 2020; 130:863-876. [PMID: 31687977 PMCID: PMC6994137 DOI: 10.1172/jci130189] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/30/2019] [Indexed: 12/24/2022] Open
Abstract
Glucocorticoids (GCs) are a central component of therapy for patients with T cell acute lymphoblastic leukemia (T-ALL), and although resistance to GCs is a strong negative prognostic indicator in T-ALL, the mechanisms of GC resistance remain poorly understood. Using diagnostic samples from patients enrolled in the frontline Children's Oncology Group (COG) T-ALL clinical trial AALL1231, we demonstrated that one-third of primary T-ALLs were resistant to GCs when cells were cultured in the presence of IL-7, a cytokine that is critical for normal T cell function and that plays a well-established role in leukemogenesis. We demonstrated that in these T-ALLs and in distinct populations of normal developing thymocytes, GCs paradoxically induced their own resistance by promoting upregulation of IL-7 receptor (IL-7R) expression. In the presence of IL-7, this augmented downstream signal transduction, resulting in increased STAT5 transcriptional output and upregulation of the prosurvival protein BCL-2. Taken together, we showed that IL-7 mediates an intrinsic and physiologic mechanism of GC resistance in normal thymocyte development that is retained during leukemogenesis in a subset of T-ALLs and is reversible with targeted inhibition of the IL-7R/JAK/STAT5/BCL-2 axis.
Collapse
Affiliation(s)
- Lauren K. Meyer
- Department of Pediatrics, UCSF, San Francisco, California, USA
| | | | | | - Ritu P. Roy
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Aaron Hechmer
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | | | - Tiffaney L. Vincent
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paolo Fortina
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Adam B. Olshen
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | - Brent L. Wood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Terzah M. Horton
- Texas Children’s Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Kevin M. Shannon
- Department of Pediatrics, UCSF, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - David T. Teachey
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michelle L. Hermiston
- Department of Pediatrics, UCSF, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| |
Collapse
|
19
|
Simonneau C, Yang J, Kong X, Kilker R, Edelstein L, Fortina P, Londin E, Horowitz A. Validation of a Miniaturized Permeability Assay Compatible with CRISPR-Mediated Genome-Wide Screen. Sci Rep 2019; 9:14238. [PMID: 31578372 PMCID: PMC6775082 DOI: 10.1038/s41598-019-50588-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/11/2019] [Indexed: 12/28/2022] Open
Abstract
The impermeability of the luminal endothelial cell monolayer is crucial for the normal performance of the vascular and lymphatic systems. A key to this function is the integrity of the monolayer's intercellular junctions. The known repertoire of junction-regulating genes is incomplete. Current permeability assays are incompatible with high-throughput genome-wide screens that could identify these genes. To overcome these limitations, we designed a new permeability assay that consists of cell monolayers grown on ~150 μm microcarriers (MCs). Each MC functions as a miniature individual assay of permeability (MAP). We demonstrate that false-positive results can be minimized, and that MAP sensitivity to thrombin-induced increase in monolayer permeability is similar to the sensitivity of impedance measurement. We validated the assay by showing that the expression of single guide RNAs (sgRNAs) that target genes encoding known thrombin signaling proteins blocks effectively thrombin-induced junction disassembly, and that MAPs carrying such cells can be separated effectively by fluorescence-assisted sorting from those that carry cells expressing non-targeting sgRNAs. These results indicate that MAPs are suitable for high-throughput experimentation and for genome-wide screens for genes that mediate the disruptive effect of thrombin on endothelial cell junctions.
Collapse
Affiliation(s)
- Claire Simonneau
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Roche Innovation Center Basel, Zürich, Switzerland
| | - Junning Yang
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Xianguo Kong
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Robert Kilker
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Leonard Edelstein
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Paolo Fortina
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | | |
Collapse
|
20
|
Greaves RF, Bernardini S, Ferrari M, Fortina P, Gouget B, Gruson D, Lang T, Loh TP, Morris HA, Park JY, Roessler M, Yin P, Kricka LJ. Key questions about the future of laboratory medicine in the next decade of the 21st century: A report from the IFCC-Emerging Technologies Division. Clin Chim Acta 2019; 495:570-589. [DOI: 10.1016/j.cca.2019.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 12/21/2022]
|
21
|
Fortina P. High-throughput technologies for gathering data. Clin Chim Acta 2019. [DOI: 10.1016/j.cca.2019.03.1487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
22
|
Youssefian L, Vahidnezhad H, Yousefi M, Saeidian AH, Azizpour A, Touati A, Nikbakht N, Hesari KK, Adib-Sereshki MM, Zeinali S, Mansoori B, Jazayeri A, Karamzadeh R, Fortina P, Jouanguy E, Casanova JL, Uitto J. Inherited Interleukin 2-Inducible T-Cell (ITK) Kinase Deficiency in Siblings With Epidermodysplasia Verruciformis and Hodgkin Lymphoma. Clin Infect Dis 2019; 68:1938-1941. [PMID: 30778533 PMCID: PMC7317279 DOI: 10.1093/cid/ciy942] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 02/04/2023] Open
Abstract
Biallelic mutations in the ITK gene cause a T-cell primary immunodeficiency with Epstein-Barr virus (EBV)-lymphoproliferative disorders. We describe a novel association of a homozygous ITK mutation with β-human papillomavirus (HPV)-positive epidermodysplasia verruciformis. Thus, loss of function in ITK can result in broad dysregulation of T-cell responses to oncogenic viruses, including β-HPV and EBV.
Collapse
Affiliation(s)
- Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Iran
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
- Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran
| | - Mehdi Yousefi
- Department of Immunology, Faculty of Medicine, Tehran University of Medical Sciences, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tehran University of Medical Sciences, Iran
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Arghavan Azizpour
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Iran
| | - Andrew Touati
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
- Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Neda Nikbakht
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Kambiz Kamyab- Hesari
- Department of Pathology, Razi Hospital, Tehran University of Medical Sciences, Tehran
| | - Mohammad Mahdi Adib-Sereshki
- Gastrointestinal and Liver Diseases Research Center, Firoozgar Hospital, Iran University of Medical Sciences, Tehran
| | - Sirous Zeinali
- Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran
- Kawsar Human Genetics Research Center, Tehran
| | - Behzad Mansoori
- Immunology Research Center, Tehran
- Student Research Committee, Tabriz University of Medical Sciences, Iran
| | - Ali Jazayeri
- Department of Information Science, College of Computing and Informatics, Drexel University, Philadelphia, Pennsylvania
| | - Razieh Karamzadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research, Tehran, Iran
| | - Paolo Fortina
- Cancer Genomics and Bioinformatics, Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Emmanuelle Jouanguy
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, France
- Imagine Institute, Paris Descartes University, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, France
- Imagine Institute, Paris Descartes University, France
- Howard Hughes Medical Institute, New York, New York
- Pediatric Hematology and Immunology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| |
Collapse
|
23
|
Abstract
BACKGROUND Single-cell genomics is an approach to investigate cell heterogeneity and to identify new molecular features correlated with clinical outcomes. This approach allows identification of the complexity of cell diversity in a sample without the loss of information that occurs when multicellular or bulk tissue samples are analyzed. CONTENT The first single-cell RNA-sequencing study was published in 2009, and since then many more studies and single-cell sequencing methods have been published. These studies have had a major impact on several fields, including microbiology, neurobiology, cancer, and developmental biology. Recently, improvements in reliability and the development of commercial single-cell isolation platforms are opening the potential of this technology to the clinical laboratory. SUMMARY In this review we provide an overview of the current state of single-cell genomics. We describe opportunities in clinical research and medical applications.
Collapse
Affiliation(s)
- Carmela Paolillo
- Division of Precision and Computational Diagnostics, Department of Clinical Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA; .,Department of Molecular Medicine, Sapienza University, Rome, Italy
| |
Collapse
|
24
|
Totaro A, Gasparini P, Estivill X, Volpini V, Castellvi-Bel S, Govea N, Mila M, Della Monica M, Ventruto V, De Benedetto M, Stanziale P, Zelante L, Mansfield E, Sandkuijl L, Surrey S, Fortina P. Linkage of DFNB1 to Non-Syndromic Neurosensory Autosomal-Recessive Deafness in Mediterranean Families. Eur J Hum Genet 2019. [DOI: 10.1159/000484738] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
25
|
Youssefian L, Vahidnezhad H, Saeidian AH, Touati A, Sotoudeh S, Mahmoudi H, Mansouri P, Daneshpazhooh M, Aghazadeh N, Hesari KK, Basiri M, Londin E, Kumar G, Zeinali S, Fortina P, Uitto J. Autosomal recessive congenital ichthyosis: Genomic landscape and phenotypic spectrum in a cohort of 125 consanguineous families. Hum Mutat 2019; 40:288-298. [PMID: 30578701 DOI: 10.1002/humu.23695] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/31/2018] [Accepted: 11/13/2018] [Indexed: 11/06/2022]
Abstract
Autosomal recessive congenital ichthyosis (ARCI), a phenotypically heterogeneous group of non-syndromic Mendelian disorders of keratinization, is caused by mutations in as many as 13 distinct genes. We examined a cohort of 125 consanguineous families with ARCI for underlying genetic mutations. The patients' DNA was analyzed with a gene-targeted next generation sequencing panel comprising 38 ichthyosis associated genes. The interpretations of results of genomic data were assisted by genome-wide homozygosity mapping and transcriptome sequencing. Sequence data analysis identified biallelic mutations in 106 families out of a total of 125 (85%), most of them (102, 96.2%) being homozygous, reflecting consanguinity in these families. Among the 85 distinct mutations in 10 different genes, 45 (53%) were previously unreported. Phenotype-genotype correlations allowed assignment of specific genes in the majority of the families to a specific subtype of ARCI, lamellar ichthyosis (LI) versus congenital ichthyosiform erythroderma (CIE). Interestingly, mutations in several genes could give rise to an overlapping phenotype consistent with either LI or CIE. Also, this is the third report for SDR9C7 and SULT2B1, and fourth report for CERS3 mutations. Direct comparison of our results with previously published regional cohorts highlights the global mutation landscape of ARCI, however, population specific differences were noted.
Collapse
Affiliation(s)
- Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Andrew Touati
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Drexel University College of Medicine, Philadelphia, PA, USA
| | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Pediatric Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvin Mansouri
- Skin and Stem Cell Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Daneshpazhooh
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Nessa Aghazadeh
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Kambiz Kamyab Hesari
- Pathology Department, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Basiri
- School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Sciences, Yazd, Iran
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gaurav Kumar
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sirous Zeinali
- Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran.,Kawsar Human Genetics Research Center, Tehran, Iran
| | - Paolo Fortina
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.,Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
26
|
Youssefian L, Vahidnezhad H, Saeidian AH, Mahmoudi H, Karamzadeh R, Kariminejad A, Huang J, Li L, Jannace TF, Fortina P, Zeinali S, White TW, Uitto J. A novel autosomal recessive GJB2-associated disorder: Ichthyosis follicularis, bilateral severe sensorineural hearing loss, and punctate palmoplantar keratoderma. Hum Mutat 2018; 40:217-229. [PMID: 30431684 DOI: 10.1002/humu.23686] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 11/07/2022]
Abstract
Ichthyosis follicularis, a distinct cutaneous entity reported in combination with atrichia, and photophobia has been associated with mutations in MBTPS2. We sought the genetic cause of a novel syndrome of ichthyosis follicularis, bilateral severe sensorineural hearing loss and punctate palmoplantar keratoderma in two families. We performed whole exome sequencing on three patients from two families. The pathogenicity and consequences of mutations were studied in the Xenopus oocyte expression system and by molecular modeling analysis. Compound heterozygous mutations in the GJB2 gene were discovered: a pathogenic c.526A>G; p.Asn176Asp, and a common frameshift mutation, c.35delG; p.Gly12Valfs*2. The p.Asn176Asp missense mutation was demonstrated to significantly reduce the cell-cell gap junction channel activity and increase the nonjunctional hemichannel activity in the Xenopus oocyte expression system. Molecular modeling analyses of the mutant Cx26 protein revealed significant changes in the structural characteristics and electrostatic potential of the Cx26, either in hemichannel or gap junction conformation. Thus, association of a new syndrome of an autosomal recessive disorder of ichthyosis follicularis, bilateral severe sensorineural hearing loss and punctate palmoplantar keratoderma with mutations in GJB2, expands the phenotypic spectrum of the GJB2-associated disorders. The findings attest to the complexity of the clinical consequences of different mutations in GJB2.
Collapse
Affiliation(s)
- Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
- Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Razieh Karamzadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Jianhe Huang
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Leping Li
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Thomas F Jannace
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Sirous Zeinali
- Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Thomas W White
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
27
|
Tricoci P, Neely M, Whitley MJ, Edelstein LC, Simon LM, Shaw C, Fortina P, Moliterno DJ, Armstrong PW, Aylward P, White H, Van de Werf F, Jennings LK, Wallentin L, Held C, Harrington RA, Mahaffey KW, Bray PF. Effects of genetic variation in protease activated receptor 4 after an acute coronary syndrome: Analysis from the TRACER trial. Blood Cells Mol Dis 2018; 72:37-43. [PMID: 30055940 DOI: 10.1016/j.bcmd.2018.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 01/05/2023]
Abstract
Variation in platelet response to thrombin may affect the safety and efficacy of PAR antagonism. The Thr120 variant of the common single nucleotide polymorphism (SNP) rs773902 in the protease-activated receptor (PAR) 4 gene is associated with higher platelet aggregation compared to the Ala120 variant. We investigated the relationship between the rs773902 SNP with major bleeding and ischemic events, safety, and efficacy of PAR1 inhibition in 6177 NSTE ACS patients in the TRACER trial. There was a lower rate of GUSTO moderate/severe bleeding in patients with the Thr120 variant. The difference was driven by a lower rate in the smaller homozygous group (recessive model, HR 0.13 [0.02-0.92] P = 0.042). No significant differences were observed in the ischemic outcomes. The excess in bleeding observed with PAR1 inhibition was attenuated in patients with the Thr120 variant, but the interactions were not statistically significant. In summary, lower major bleeding rates were observed in the overall TRACER cohort with the hyperreactive PAR4 Thr120 variant. The increase in bleeding with vorapaxar was attenuated with the Thr120 variant, but we could not demonstrate an interaction with PAR1 inhibition. These findings warrant further exploration, including those of African ancestry where the A allele (Thr120) frequency is ~65%.
Collapse
Affiliation(s)
| | - Megan Neely
- Duke Clinical Research Institute, Duke University, Durham, NC, USA
| | - Michael J Whitley
- The Cardeza Foundation for Hematologic Research and the Department of Medicine, Thomas Jefferson University, Sidney Kimmel Medical College, Philadelphia, PA, USA
| | - Leonard C Edelstein
- The Cardeza Foundation for Hematologic Research and the Department of Medicine, Thomas Jefferson University, Sidney Kimmel Medical College, Philadelphia, PA, USA
| | - Lukas M Simon
- Department of Human & Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chad Shaw
- Department of Human & Molecular Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Statistics, Rice University, Houston, TX, USA
| | - Paolo Fortina
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - David J Moliterno
- Gill Heart Institute and Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY, USA
| | | | - Philip Aylward
- Division of Medicine, Cardiac & Critical Care Services, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Harvey White
- Green Lane Cardiovascular Service, Auckland City Hospital, Auckland, New Zealand
| | - Frans Van de Werf
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Lisa K Jennings
- CirQuest Labs, LLC, and University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lars Wallentin
- Department of Medical Sciences, Uppsala Clinical Research Center, Uppsala, Sweden
| | - Claes Held
- Department of Medical Sciences, Uppsala Clinical Research Center, Uppsala, Sweden
| | | | | | - Paul F Bray
- Division of Hematology and Hematologic Malignancies in the Department of Internal Medicine and the Molecular Medicine Program, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
28
|
Youssefian L, Vahidnezhad H, Saeidian A, Zeinali S, Sotoudeh S, Mahmoudi H, Mansouri P, Daneshpazhooh M, Fortina P, Uitto J. 820 Customized gene-targeted next generation sequencing panel identifies a spectrum of mutations in consanguineous families affected by ichthyoses. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
29
|
Wang G, Gormley M, Qiao J, Zhao Q, Wang M, Di Sante G, Deng S, Dong L, Pestell T, Ju X, Casimiro MC, Addya S, Fortina P, Tozeren A, Li Q, Yu Z, Pestell RG. Cyclin D1-mediated microRNA expression signature predicts breast cancer outcome. Am J Cancer Res 2018; 8:2251-2263. [PMID: 29721077 PMCID: PMC5928887 DOI: 10.7150/thno.23877] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/25/2017] [Indexed: 01/03/2023] Open
Abstract
Background: Genetic classification of breast cancer based on the coding mRNA suggests the evolution of distinct subtypes. Whether the non-coding genome is altered concordantly with the coding genome and the mechanism by which the cell cycle directly controls the non-coding genome is poorly understood. Methods: Herein, the miRNA signature maintained by endogenous cyclin D1 in human breast cancer cells was defined. In order to determine the clinical significance of the cyclin D1-mediated miRNA signature, we defined a miRNA expression superset from 459 breast cancer samples. We compared the coding and non-coding genome of breast cancer subtypes. Results: Hierarchical clustering of human breast cancers defined four distinct miRNA clusters (G1-G4) associated with distinguishable relapse-free survival by Kaplan-Meier analysis. The cyclin D1-regulated miRNA signature included several oncomirs, was conserved in multiple breast cancer cell lines, was associated with the G2 tumor miRNA cluster, ERα+ status, better outcome and activation of the Wnt pathway. The coding and non-coding genome were discordant within breast cancer subtypes. Seed elements for cyclin D1-regulated miRNA were identified in 63 genes of the Wnt signaling pathway including DKK. Cyclin D1 restrained DKK1 via the 3'UTR. In vivo studies using inducible transgenics confirmed cyclin D1 induces Wnt-dependent gene expression. Conclusion: The non-coding genome defines breast cancer subtypes that are discordant with their coding genome subtype suggesting distinct evolutionary drivers within the tumors. Cyclin D1 orchestrates expression of a miRNA signature that induces Wnt/β-catenin signaling, therefore cyclin D1 serves both upstream and downstream of Wnt/β-catenin signaling.
Collapse
|
30
|
Lu H, Bowler N, Harshyne LA, Craig Hooper D, Krishn SR, Kurtoglu S, Fedele C, Liu Q, Tang HY, Kossenkov AV, Kelly WK, Wang K, Kean RB, Weinreb PH, Yu L, Dutta A, Fortina P, Ertel A, Stanczak M, Forsberg F, Gabrilovich DI, Speicher DW, Altieri DC, Languino LR. Exosomal αvβ6 integrin is required for monocyte M2 polarization in prostate cancer. Matrix Biol 2018. [PMID: 29530483 DOI: 10.1016/j.matbio.2018.03.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Therapeutic approaches aimed at curing prostate cancer are only partially successful given the occurrence of highly metastatic resistant phenotypes that frequently develop in response to therapies. Recently, we have described αvβ6, a surface receptor of the integrin family as a novel therapeutic target for prostate cancer; this epithelial-specific molecule is an ideal target since, unlike other integrins, it is found in different types of cancer but not in normal tissues. We describe a novel αvβ6-mediated signaling pathway that has profound effects on the microenvironment. We show that αvβ6 is transferred from cancer cells to monocytes, including β6-null monocytes, by exosomes and that monocytes from prostate cancer patients, but not from healthy volunteers, express αvβ6. Cancer cell exosomes, purified via density gradients, promote M2 polarization, whereas αvβ6 down-regulation in exosomes inhibits M2 polarization in recipient monocytes. Also, as evaluated by our proteomic analysis, αvβ6 down-regulation causes a significant increase in donor cancer cells, and their exosomes, of two molecules that have a tumor suppressive role, STAT1 and MX1/2. Finally, using the Ptenpc-/- prostate cancer mouse model, which carries a prostate epithelial-specific Pten deletion, we demonstrate that αvβ6 inhibition in vivo causes up-regulation of STAT1 in cancer cells. Our results provide evidence of a novel mechanism that regulates M2 polarization and prostate cancer progression through transfer of αvβ6 from cancer cells to monocytes through exosomes.
Collapse
Affiliation(s)
- Huimin Lu
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Nicholas Bowler
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Larry A Harshyne
- Department of Neurological Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - D Craig Hooper
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Neurological Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Shiv Ram Krishn
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Senem Kurtoglu
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Carmine Fedele
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Qin Liu
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA, USA
| | - Hsin-Yao Tang
- Center for Systems and Computational Biology, Wistar Institute, Philadelphia, PA, USA
| | - Andrew V Kossenkov
- Center for Systems and Computational Biology, Wistar Institute, Philadelphia, PA, USA
| | - William K Kelly
- Departments of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kerith Wang
- Departments of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Rhonda B Kean
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Neurological Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | | | - Lei Yu
- Flow Cytometry Core Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Anindita Dutta
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Adam Ertel
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Maria Stanczak
- Department of Radiology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Flemming Forsberg
- Department of Radiology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Dmitry I Gabrilovich
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Immunology, Microenvironment and Metastasis Program, Wistar Institute, Philadelphia, PA, USA
| | - David W Speicher
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA, USA; Center for Systems and Computational Biology, Wistar Institute, Philadelphia, PA, USA
| | - Dario C Altieri
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Immunology, Microenvironment and Metastasis Program, Wistar Institute, Philadelphia, PA, USA
| | - Lucia R Languino
- Prostate Cancer Discovery and Development Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
| |
Collapse
|
31
|
Sponziello M, Benvenuti S, Gentile A, Pecce V, Rosignolo F, Virzì AR, Milan M, Comoglio PM, Londin E, Fortina P, Barnabei A, Appetecchia M, Marandino F, Russo D, Filetti S, Durante C, Verrienti A. Whole exome sequencing identifies a germline MET mutation in two siblings with hereditary wild-type RET medullary thyroid cancer. Hum Mutat 2017; 39:371-377. [PMID: 29219214 DOI: 10.1002/humu.23378] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 11/12/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022]
Abstract
Whole exome sequencing (WES) was used to investigate two Italian siblings with wild-type RET genotype, who developed medullary thyroid cancers (MTCs) and, later, primary prostate and breast cancers, respectively. The proband's MTC harbored a p.Met918Thr RET mutation; his sister's MTC was RET/RAS wild-type. Both siblings had a germline mutation (p.Arg417Gln) in the extracellular Sema domain of the proto-oncogene MET. Experiments involving ectopic expression of MET p.Arg417Gln in MET-negative T47D breast cancer cells documented the mutant receptor's functionality and its ability to enhance cell migration and invasion. Our findings highlight a possible link between MET germline mutations and MTCs and suggest that MET p. Arg417Gln may promote an invasive malignant phenotype. The possibility that MTC can be driven/co-driven by a MET mutation has potential management implications, since the tyrosine-kinase inhibitor cabozantinib-approved for treating advanced MTCs-is a specific MET inhibitor.
Collapse
Affiliation(s)
- Marialuisa Sponziello
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy
| | - Silvia Benvenuti
- Molecular Therapeutics and Exploratory Research, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy
| | - Alessandra Gentile
- Molecular Therapeutics and Exploratory Research, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy
| | - Valeria Pecce
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy
| | - Francesca Rosignolo
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy
| | - Anna Rita Virzì
- Molecular Therapeutics and Exploratory Research, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy.,Department of Oncology, University of Turin, Candiolo, Italy
| | - Melissa Milan
- Molecular Therapeutics and Exploratory Research, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy.,Department of Medical Oncology, Catholic University of the Sacred Heart, Rome, Italy
| | - Paolo M Comoglio
- Molecular Therapeutics and Exploratory Research, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Paolo Fortina
- Cancer Genomics Laboratory, Sidney Kimmel Cancer Center, Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Agnese Barnabei
- Unit of Endocrinology, Regina Elena National Cancer Institute, Rome, Italy
| | | | | | - Diego Russo
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Sebastiano Filetti
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy
| | - Cosimo Durante
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy
| | - Antonella Verrienti
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
32
|
Santacroce R, Bossone A, Brancaccio V, Fortina P, Margaglione M. In the Presence of other Inherited or Acquired High-risk Situations, the FV Cambridge Mutation May Be an Additional Thrombophilic Risk Factor, through Its Effect on APC Sensitivity. Thromb Haemost 2017. [DOI: 10.1055/s-0037-1613951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
33
|
De Dominici M, Porazzi P, Soliera AR, Mariani SA, Addya S, Fortina P, Peterson LF, Spinelli O, Rambaldi A, Martinelli G, Ferrari A, Iacobucci I, Calabretta B. Targeting CDK6 and BCL2 Exploits the "MYB Addiction" of Ph + Acute Lymphoblastic Leukemia. Cancer Res 2017; 78:1097-1109. [PMID: 29233926 DOI: 10.1158/0008-5472.can-17-2644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/25/2017] [Accepted: 12/08/2017] [Indexed: 01/09/2023]
Abstract
Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL) is currently treated with BCR-ABL1 tyrosine kinase inhibitors (TKI) in combination with chemotherapy. However, most patients develop resistance to TKI through BCR-ABL1-dependent and -independent mechanisms. Newly developed TKI can target Ph+ ALL cells with BCR-ABL1-dependent resistance; however, overcoming BCR-ABL1-independent mechanisms of resistance remains challenging because transcription factors, which are difficult to inhibit, are often involved. We show here that (i) the growth of Ph+ ALL cell lines and primary cells is highly dependent on MYB-mediated transcriptional upregulation of CDK6, cyclin D3, and BCL2, and (ii) restoring their expression in MYB-silenced Ph+ ALL cells rescues their impaired proliferation and survival. Levels of MYB and CDK6 were highly correlated in adult Ph+ ALL (P = 0.00008). Moreover, Ph+ ALL cells exhibited a specific requirement for CDK6 but not CDK4 expression, most likely because, in these cells, CDK6 was predominantly localized in the nucleus, whereas CDK4 was almost exclusively cytoplasmic. Consistent with their essential role in Ph+ ALL, pharmacologic inhibition of CDK6 and BCL2 markedly suppressed proliferation, colony formation, and survival of Ph+ ALL cells ex vivo and in mice. In summary, these findings provide a proof-of-principle, rational strategy to target the MYB "addiction" of Ph+ ALL.Significance: MYB blockade can suppress Philadelphia chromosome-positive leukemia in mice, suggesting that this therapeutic strategy may be useful in patients who develop resistance to imatinib and other TKIs used to treat this disease. Cancer Res; 78(4); 1097-109. ©2017 AACR.
Collapse
Affiliation(s)
- Marco De Dominici
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Angela Rachele Soliera
- Department of Diagnostic, Clinical Medicine and Public Health, University of Modena, Modena, Italy
| | - Samanta A Mariani
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Sankar Addya
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Luke F Peterson
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Orietta Spinelli
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Alessandro Rambaldi
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Giovanni Martinelli
- Department of Hematology and Istituto L. and E. Seragnoli, University of Bologna, Bologna, Italy
| | - Anna Ferrari
- Department of Hematology and Istituto L. and E. Seragnoli, University of Bologna, Bologna, Italy
| | - Ilaria Iacobucci
- Department of Hematology and Istituto L. and E. Seragnoli, University of Bologna, Bologna, Italy
| | - Bruno Calabretta
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
| |
Collapse
|
34
|
Kudaravalli R, Tidd T, Pinotti M, Ratti A, Santacroce R, Margaglione M, Dallapiccola B, Bernardi F, Fortina P, Devoto M, Pollak E. Polymorphic Changes in the 5’ Flanking Region of Factor VII Have a Combined Effect on Promoter Strength. Thromb Haemost 2017. [DOI: 10.1055/s-0037-1613299] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
SummaryPolymorphic differences in the 5’ flanking region of the gene encoding procoagulant protein Factor VII (FVII) are associated with variations in FVII coagulant activity (FVII:C) and FVII antigen (FVII:Ag) levels. A decanucleotide insert polymorphism (CCTATATCCT) at 323 bp upstream of the start site of translation correlates with a decrease of approximately 20% FVII:C levels per allele containing this insert. However, linkage disequilibrium of the decanucleotide polymorphism with two single nucleotide polymorphisms (SNPs) at –122 and –401 have made it difficult to pinpoint the functional role, if any, of these genetic changes in lowering FVII levels. In vitro reporter gene studies in HepG2 cells analyzing the 8 possible combinations of polymorphic sites at –401, –323, and –122 reveal the necessity of the presence of the three concurrent polymorphic changes to maximally decrease promoter strength. In addition, these in vitro results are supported by in vivo studies in 89 individuals of African heritage, 34% of whom display a new haplotype that shows the polymorphic changes at -323 and -401 but lacks the change at -122.
Collapse
|
35
|
Harenza JL, Diamond MA, Adams RN, Song MM, Davidson HL, Hart LS, Dent MH, Fortina P, Reynolds CP, Maris JM. Corrigendum: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines. Sci Data 2017; 4:170183. [PMID: 29206221 PMCID: PMC5716011 DOI: 10.1038/sdata.2017.183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This corrects the article DOI: 10.1038/sdata.2017.33.
Collapse
|
36
|
Vahidnezhad H, Youssefian L, Saeidian AH, Mahmoudi H, Touati A, Abiri M, Kajbafzadeh AM, Aristodemou S, Liu L, McGrath JA, Ertel A, Londin E, Kariminejad A, Zeinali S, Fortina P, Uitto J. Recessive mutation in tetraspanin CD151 causes Kindler syndrome-like epidermolysis bullosa with multi-systemic manifestations including nephropathy. Matrix Biol 2017; 66:22-33. [PMID: 29138120 DOI: 10.1016/j.matbio.2017.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/03/2017] [Accepted: 11/03/2017] [Indexed: 01/05/2023]
Abstract
Epidermolysis bullosa (EB) is caused by mutations in as many as 19 distinct genes. We have developed a next-generation sequencing (NGS) panel targeting genes known to be mutated in skin fragility disorders, including tetraspanin CD151 expressed in keratinocytes at the dermal-epidermal junction. The NGS panel was applied to a cohort of 92 consanguineous families of unknown subtype of EB. In one family, a homozygous donor splice site mutation in CD151 (NM_139029; c.351+2T>C) at the exon 5/intron 5 border was identified, and RT-PCR and whole transcriptome analysis by RNA-seq confirmed deletion of the entire exon 5 encoding 25 amino acids. Immunofluorescence of proband's skin and Western blot of skin proteins with a monoclonal antibody revealed complete absence of CD151. Transmission electron microscopy showed intracellular disruption and cell-cell dysadhesion of keratinocytes in the lower epidermis. Clinical examination of the 33-year old proband, initially diagnosed as Kindler syndrome, revealed widespread blistering, particularly on pretibial areas, poikiloderma, nail dystrophy, loss of teeth, early onset alopecia, and esophageal webbing and strictures. The patient also had history of nephropathy with proteinuria. Collectively, the results suggest that biallelic loss-of-function mutations in CD151 underlie an autosomal recessive mechano-bullous disease with systemic features. Thus, CD151 should be considered as the 20th causative, EB-associated gene.
Collapse
Affiliation(s)
- Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Andrew Touati
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Drexel University College of Medicine, Philadelphia, PA, USA
| | - Maryam Abiri
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Abdol-Mohammad Kajbafzadeh
- Pediatric Urology Research Center, Department of Urology, Children's Hospital Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Lu Liu
- Viapath, St Thomas' Hospital, London, UK
| | - John A McGrath
- Department of Medical and Molecular Genetics, St. John's Institute of Dermatology, King's College London (Guy's Campus), London, UK
| | - Adam Ertel
- Computational Medicine Center, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Sirous Zeinali
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Paolo Fortina
- Computational Medicine Center, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA; Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA.
| |
Collapse
|
37
|
Uitto J, Youssefian L, Saeidian A, Mahmoudi H, Touati A, McGrath J, Zeinali S, Fortina P, Vahidnezhad H. 176 A distinct cutaneous blistering phenotype with multi-system manifestations caused by a mutation in CD151, the 20th causative gene in epidermolysis bullosa. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
38
|
Touati A, Vahidnezhad H, Youssefian L, Saeidian A, Zahabiyon M, Sotoudeh S, Barzegar M, Zeinali S, Fortina P, Uitto J. LB970 ABHD5, the gene associated with Chanarin-Dorfman syndrome, can contribute to non-alcoholic fatty liver disease and dyslipidemia in mutation carriers. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
39
|
Youssefian L, Vahidnezhad H, Saeidian AH, Sotoudeh S, Mahmoudi H, Daneshpazhooh M, Aghazadeh N, Adams R, Ghanadan A, Zeinali S, Fortina P, Uitto J. Autosomal recessive congenital ichthyosis: CERS3 mutations identified by a next generation sequencing panel targeting ichthyosis genes. Eur J Hum Genet 2017; 25:1282-1285. [PMID: 28875980 DOI: 10.1038/ejhg.2017.137] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/24/2017] [Accepted: 08/01/2017] [Indexed: 01/06/2023] Open
Abstract
There are at least 38 mutant genes known to be associated with the ichthyosis phenotypes, and autosomal recessive congenital ichthyosis (ARCI) is a specific subgroup caused by mutations in 13 different genes. Mutations in some of these genes, such as CERS3 with only two previous reports, are rare. In this study, we identified mutations in candidate genes in consanguineous families with ARCI with a next generation sequencing (NGS) array that incorporates 38 ichthyosis associated genes. We applied this sequencing array to DNA from 140 ichthyosis families with high prevalence of consanguinity. Among these patients we identified six distinct, previously unreported mutations in CERS3 in six Iranian families. These mutations in each family co-segregated with the ichthyosis phenotype. The patients demonstrated collodion membrane at birth, acrogeria, generalized scaling, and hyperlinearity of the palms and soles. The presence of a significant percentage of CERS3 mutations in our cohort depicts a marked difference between the etiology of ichthyoses in genetically poorly characterized regions and well-characterized western populations. Also, it shows that rare alleles are more prevalent in the gene pool of consanguineous populations and emphasizes the importance of these population studies for better understanding of ichthyosis pathogenesis.
Collapse
Affiliation(s)
- Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Mahmoudi
- Department of Dermatology and Dermatopathology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Daneshpazhooh
- Department of Dermatology and Dermatopathology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Nessa Aghazadeh
- Department of Dermatology and Dermatopathology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Rebecca Adams
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alireza Ghanadan
- Department of Dermatology and Dermatopathology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pathology, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Kawsar Human Genetics Research Center, Tehran, Iran
| | - Paolo Fortina
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.,Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
40
|
Vahidnezhad H, Youssefian L, Saeidian AH, Touati A, Sotoudeh S, Abiri M, Barzegar M, Aghazadeh N, Mahmoudi H, Norouz-Zadeh S, Hamid M, Zahabiyon M, Bagherian H, Zeinali S, Fortina P, Uitto J. Multigene Next-Generation Sequencing Panel Identifies Pathogenic Variants in Patients with Unknown Subtype of Epidermolysis Bullosa: Subclassification with Prognostic Implications. J Invest Dermatol 2017; 137:2649-2652. [PMID: 28830826 DOI: 10.1016/j.jid.2017.07.830] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/12/2017] [Accepted: 07/28/2017] [Indexed: 11/20/2022]
Affiliation(s)
- Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Andrew Touati
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Abiri
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Kawsar Human Genetics Research Center, Tehran, Iran
| | | | - Nessa Aghazadeh
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sara Norouz-Zadeh
- Kawsar Human Genetics Research Center, Tehran, Iran; Department of Biology, Islamic Azad University, Arsanjan Branch, Arsanjan, Iran
| | - Mohammad Hamid
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mahla Zahabiyon
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | | | - Sirous Zeinali
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran; Kawsar Human Genetics Research Center, Tehran, Iran
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
| |
Collapse
|
41
|
Paolillo C, Mu Z, Rossi G, Schiewer MJ, Nguyen T, Austin L, Capoluongo E, Knudsen K, Cristofanilli M, Fortina P. Detection of Activating Estrogen Receptor Gene ( ESR1) Mutations in Single Circulating Tumor Cells. Clin Cancer Res 2017; 23:6086-6093. [PMID: 28679775 DOI: 10.1158/1078-0432.ccr-17-1173] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/20/2017] [Accepted: 06/30/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Early detection is essential for treatment plans before onset of metastatic disease. Our purpose was to demonstrate feasibility to detect and monitor estrogen receptor 1 (ESR1) gene mutations at the single circulating tumor cell (CTC) level in metastatic breast cancer (MBC).Experimental Design: We used a CTC molecular characterization approach to investigate heterogeneity of 14 hotspot mutations in ESR1 and their correlation with endocrine resistance. Combining the CellSearch and DEPArray technologies allowed recovery of 71 single CTCs and 12 WBC from 3 ER-positive MBC patients. Forty CTCs and 12 WBC were subjected to whole genome amplification by MALBAC and Sanger sequencing.Results: Among 3 selected patients, 2 had an ESR1 mutation (Y537). One showed two different ESR1 variants in a single CTC and another showed loss of heterozygosity. All mutations were detected in matched cell-free DNA (cfDNA). Furthermore, one had 2 serial blood samples analyzed and showed changes in both cfDNA and CTCs with emergence of mutations in ESR1 (Y537S and T570I), which has not been reported previously.Conclusions: CTCs are easily accessible biomarkers to monitor and better personalize management of patients with previously demonstrated ER-MBC who are progressing on endocrine therapy. We showed that single CTC analysis can yield important information on clonal heterogeneity and can be a source of discovery of novel and potential driver mutations. Finally, we also validate a workflow for liquid biopsy that will facilitate early detection of ESR1 mutations, the emergence of endocrine resistance and the choice of further target therapy. Clin Cancer Res; 23(20); 6086-93. ©2017 AACR.
Collapse
Affiliation(s)
- Carmela Paolillo
- Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia Pennsylvania.,Institute of Biochemistry and Clinical Biochemistry, Laboratory of Clinical Molecular and Personalized Diagnostics, Catholic University of the Sacred Heart, Rome, Italy
| | - Zhaomei Mu
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Giovanna Rossi
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Matthew J Schiewer
- Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia Pennsylvania
| | - Thomas Nguyen
- Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia Pennsylvania
| | - Laura Austin
- Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia Pennsylvania
| | - Ettore Capoluongo
- Institute of Biochemistry and Clinical Biochemistry, Laboratory of Clinical Molecular and Personalized Diagnostics, Catholic University of the Sacred Heart, Rome, Italy
| | - Karen Knudsen
- Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia Pennsylvania
| | - Massimo Cristofanilli
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia Pennsylvania. .,Department of Molecular Medicine, Sapienza University, Rome, Italy
| |
Collapse
|
42
|
Kageyama K, Ohara M, Saito K, Ozaki S, Terai M, Mastrangelo MJ, Fortina P, Aplin AE, Sato T. Establishment of an orthotopic patient-derived xenograft mouse model using uveal melanoma hepatic metastasis. J Transl Med 2017. [PMID: 28645290 PMCID: PMC5481921 DOI: 10.1186/s12967-017-1247-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Background Metastatic uveal melanoma is a highly fatal disease; most patients die from their hepatic metastasis within 1 year. A major drawback in the development of new treatments for metastatic uveal melanoma is the difficulty in obtaining appropriate cell lines and the lack of appropriate animal models. Patient-derived xenograft (PDX) tumor models, bearing ectopically implanted tumors at a subcutaneous site, have been developed. However, these ectopically implanted PDX models have obstacles to translational research, including a low engraftment rate, slow tumor growth, and biological changes after multiple passages due to the different microenvironment. To overcome these limitations, we developed a new method to directly transplant biopsy specimens to the liver of immunocompromised mice. Results By using two metastatic uveal melanoma cell lines, we demonstrated that the liver provides a more suitable microenvironment for tumor growth compared to subcutaneous sites and that surgical orthotopic implantation (SOI) of tumor pieces allows the creation of a liver tumor in immunocompromised mice. Subsequently, 10 of 12 hepatic metastasis specimens from patients were successfully xenografted into the immunocompromised mice (83.3% success rate) using SOI, including 8 of 10 needle biopsy specimens (80%). Additionally, four cryopreserved PDX tumors were re-implanted to new mice and re-establishment of PDX tumors was confirmed in all four mice. The serially passaged xenograft tumors as well as the re-implanted tumors after cryopreservation were similar to the original patient tumors in histologic, genomic, and proteomic expression profiles. CT imaging was effective for detecting and monitoring PDX tumors in the liver of living mice. The expression of Ki67 in original patient tumors was a predictive factor for implanted tumor growth and the success of serial passages in PDX mice. Conclusions Surgical orthotopic implantation of hepatic metastasis from uveal melanoma is highly successful in the establishment of orthotopic PDX models, enhancing their practical utility for research applications. By using CT scan, tumor growth can be monitored, which is beneficial to evaluate treatment effects in interventional studies. Electronic supplementary material The online version of this article (doi:10.1186/s12967-017-1247-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ken Kageyama
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA, 19107, USA.,Department of Radiology, Osaka City University, 1-4-3 Asahimachi Abenoku, Osaka, Osaka, 545-8585, Japan
| | - Masahiro Ohara
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA, 19107, USA
| | - Kengo Saito
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA, 19107, USA
| | - Shinji Ozaki
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA, 19107, USA.,Department of Surgery, National Hospital Organization, Kure Medical Center/Chugoku Cancer Center, 3-1 Aoyamacho Kure, Hiroshima, 737-0023, Japan
| | - Mizue Terai
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA, 19107, USA
| | - Michael J Mastrangelo
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA, 19107, USA
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA, 19107, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA, 19107, USA
| | - Takami Sato
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA, 19107, USA.
| |
Collapse
|
43
|
Uitto J, Youssefian L, Vahidnezhad H, Saeidian A, Sotoudeh S, Aghazadeh N, Daneshpazhooh M, Mahmoudi H, Ertel A, Fortina P, Kamyab-Hesari K, Zeinali S. 511 Autosomal recessive congenital ichthyosis: CERS3 mutations identified by a next generation sequencing array targeting ichthyosis genes. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
44
|
Saeidian A, Youssefian L, Vahidnezhad H, Zeinali S, Daneshpazhooh M, Hamid M, Ertel A, Fortina P, Uitto J. 509 Disease-targeted next generation sequencing identifies mutations in patients with epidermolysis bullosa. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
45
|
Harenza JL, Diamond MA, Adams RN, Song MM, Davidson HL, Hart LS, Dent MH, Fortina P, Reynolds CP, Maris JM. Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines. Sci Data 2017; 4:170033. [PMID: 28350380 PMCID: PMC5369315 DOI: 10.1038/sdata.2017.33] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/07/2017] [Indexed: 11/09/2022] Open
Abstract
Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or mRNA expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. These data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (e.g., MYCN amplification status, ALK mutation status, chromosome arm 1p, 11q and/or 17q status, sensitivity to pharmacologic perturbation). Additionally, we designed this experiment to enable structural variant and/or long-noncoding RNA analysis across these cell lines. Finally, as more DNase/ATAC and histone/transcription factor ChIP sequencing is performed in these cell lines, our RNA-Seq data will be an important complement to inform transcriptional targets as well as regulatory (enhancer or repressor) elements in neuroblastoma.
Collapse
Affiliation(s)
- Jo Lynne Harenza
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Maura A Diamond
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Rebecca N Adams
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania 19107, USA
| | - Michael M Song
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, Texas 79430, USA
| | - Heather L Davidson
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, Texas 79430, USA
| | - Lori S Hart
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Maiah H Dent
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Paolo Fortina
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania 19107, USA
| | - C Patrick Reynolds
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, Texas 79430, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
46
|
Vahidnezhad H, Youssefian L, Zeinali S, Saeidian AH, Sotoudeh S, Mozafari N, Abiri M, Kajbafzadeh AM, Barzegar M, Ertel A, Fortina P, Uitto J. Dystrophic Epidermolysis Bullosa: COL7A1 Mutation Landscape in a Multi-Ethnic Cohort of 152 Extended Families with High Degree of Customary Consanguineous Marriages. J Invest Dermatol 2017; 137:660-669. [DOI: 10.1016/j.jid.2016.10.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 12/11/2022]
|
47
|
Vahidnezhad H, Youssefian L, Saeidian AH, Zeinali S, Mansouri P, Sotoudeh S, Barzegar M, Mohammadi-Asl J, Karamzadeh R, Abiri M, McCormick K, Fortina P, Uitto J. Gene-Targeted Next Generation Sequencing Identifies PNPLA1 Mutations in Patients with a Phenotypic Spectrum of Autosomal Recessive Congenital Ichthyosis: The Impact of Consanguinity. J Invest Dermatol 2016; 137:678-685. [PMID: 27884779 DOI: 10.1016/j.jid.2016.11.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/25/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
Abstract
Autosomal recessive congenital ichthyosis is a heterogeneous group of disorders associated with mutations in at least nine distinct genes. To ascertain the molecular basis of ichthyosis patients in Iran, a country of approximately 80 million people with a high prevalence of customary consanguineous marriages, we have developed a gene-targeted next generation sequencing array consisting of 38 genes reported in association with ichthyosis phenotypes. In a subset of nine extended consanguineous families, we found homozygous missense mutations in the PNPLA1 gene, six of them being distinct and, to our knowledge, previously unpublished. This gene encodes an enzyme with lipid hydrolase activity, important for development and maintenance of the barrier function of the epidermis. These six mutations, as well as four previously published mutations, reside exclusively within the patatin-like subdomain of PNPLA1 containing the catalytic site. The mutations clustered around the active center of the enzyme or resided at the surface of the protein possibly involved in the protein-protein interactions. Clinical features of the patients showed considerable intra- and interfamilial heterogeneity. Knowledge of the specific mutations allows identification of heterozygous carriers, assisting in genetic counseling, prenatal testing, and preimplantation genetic diagnosis in extended families at risk of recurrence of this disorder, the incidence of which is significantly increased in consanguineous marriages.
Collapse
Affiliation(s)
- Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sirous Zeinali
- Biotechnology Research Center, Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran; Kawsar Human Genetics Research Center, Tehran, Iran
| | - Parvin Mansouri
- Skin and Stem Cell Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Javad Mohammadi-Asl
- Department of Genetics, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Razieh Karamzadeh
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Department of Molecular Systems Biology, Cell Sciences Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Maryam Abiri
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Kevin McCormick
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Paolo Fortina
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
| |
Collapse
|
48
|
Mu Z, Benali-Furet N, Uzan G, Znaty A, Ye Z, Paolillo C, Wang C, Austin L, Rossi G, Fortina P, Yang H, Cristofanilli M. Detection and Characterization of Circulating Tumor Associated Cells in Metastatic Breast Cancer. Int J Mol Sci 2016; 17:ijms17101665. [PMID: 27706044 PMCID: PMC5085698 DOI: 10.3390/ijms17101665] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 01/06/2023] Open
Abstract
The availability of blood-based diagnostic testing using a non-invasive technique holds promise for real-time monitoring of disease progression and treatment selection. Circulating tumor cells (CTCs) have been used as a prognostic biomarker for the metastatic breast cancer (MBC). The molecular characterization of CTCs is fundamental to the phenotypic identification of malignant cells and description of the relevant genetic alterations that may change according to disease progression and therapy resistance. However, the molecular characterization of CTCs remains a challenge because of the rarity and heterogeneity of CTCs and technological difficulties in the enrichment, isolation and molecular characterization of CTCs. In this pilot study, we evaluated circulating tumor associated cells in one blood draw by size exclusion technology and cytological analysis. Among 30 prospectively enrolled MBC patients, CTCs, circulating tumor cell clusters (CTC clusters), CTCs of epithelial-mesenchymal transition (EMT) and cancer associated macrophage-like cells (CAMLs) were detected and analyzed. For molecular characterization of CTCs, size-exclusion method for CTC enrichment was tested in combination with DEPArray™ technology, which allows the recovery of single CTCs or pools of CTCs as a pure CTC sample for mutation analysis. Genomic mutations of TP53 and ESR1 were analyzed by targeted sequencing on isolated 7 CTCs from a patient with MBC. The results of genomic analysis showed heterozygous TP53 R248W mutation from one single CTC and pools of three CTCs, and homozygous TP53 R248W mutation from one single CTC and pools of two CTCs. Wild-type ESR1 was detected in the same isolated CTCs. The results of this study reveal that size-exclusion method can be used to enrich and identify circulating tumor associated cells, and enriched CTCs were characterized for genetic alterations in MBC patients, respectively.
Collapse
Affiliation(s)
- Zhaomei Mu
- Department of Medicine-Hematology and Oncology, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | | | | | | | - Zhong Ye
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Carmela Paolillo
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Chun Wang
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Laura Austin
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Giovanna Rossi
- Department of Medicine-Hematology and Oncology, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
- Department of Molecular Medicine, University of Rome "Sapienza", Rome 00185, Italy.
| | - Hushan Yang
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Massimo Cristofanilli
- Department of Medicine-Hematology and Oncology, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|
49
|
Vozikis A, Cooper DN, Mitropoulou C, Kambouris ME, Brand A, Dolzan V, Fortina P, Innocenti F, Lee MTM, Leyens L, Macek Jr M, Al-Mulla F, Prainsack B, Squassina A, Taruscio D, van Schaik RH, Vayena E, Williams MS, Patrinos GP. Test Pricing and Reimbursement in Genomic Medicine: Towards a General Strategy. Public Health Genomics 2016; 19:352-363. [DOI: 10.1159/000449152] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/16/2016] [Indexed: 11/19/2022] Open
|
50
|
Paolillo C, Londin E, Fortina P. Next generation sequencing in cancer: opportunities and challenges for precision cancer medicine. Scand J Clin Lab Invest Suppl 2016; 245:S84-91. [PMID: 27542004 DOI: 10.1080/00365513.2016.1210331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Over the past decade, testing the genes of patients and their specific cancer types has become standardized practice in medical oncology since somatic mutations, changes in gene expression and epigenetic modifications are all hallmarks of cancer. However, while cancer genetic assessment has been limited to single biomarkers to guide the use of therapies, improvements in nucleic acid sequencing technologies and implementation of different genome analysis tools have enabled clinicians to detect these genomic alterations and identify functional and disease-associated genomic variants. Next-generation sequencing (NGS) technologies have provided clues about therapeutic targets and genomic markers for novel clinical applications when standard therapy has failed. While Sanger sequencing, an accurate and sensitive approach, allows for the identification of potential novel variants, it is however limited by the single amplicon being interrogated. Similarly, quantitative and qualitative profiling of gene expression changes also represents a challenge for the cancer field. Both RT-PCR and microarrays are efficient approaches, but are limited to the genes present on the array or being assayed. This leaves vast swaths of the transcriptome, including non-coding RNAs and other features, unexplored. With the advent of the ability to collect and analyze genomic sequence data in a timely fashion and at an ever-decreasing cost, many of these limitations have been overcome and are being incorporated into cancer research and diagnostics giving patients and clinicians new hope for targeted and personalized treatment. Below we highlight the various applications of next-generation sequencing in precision cancer medicine.
Collapse
Affiliation(s)
- Carmela Paolillo
- a Department of Cancer Biology , Sidney Kimmel Medical College , Philadelphia , PA , USA
| | - Eric Londin
- b Computational Medicine Center , Thomas Jefferson University , Philadelphia , PA , USA
| | - Paolo Fortina
- a Department of Cancer Biology , Sidney Kimmel Medical College , Philadelphia , PA , USA
| |
Collapse
|