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Borowczyk M, Sypniewski M, Szyda J, Braszka M, Ziemnicka K, Ruchała M, Oszywa M, Król ZJ, Dobosz P. Genetic predisposition to differentiated thyroid cancer in the Polish population. Pol Arch Intern Med 2024; 134:16654. [PMID: 38165228 DOI: 10.20452/pamw.16654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
INTRODUCTION Genome sequencing technologies reveal molecular mechanisms of differentiated thyroid cancer (DTC). Unlike somatic mutation analysis from thyroidectomy samples, germline mutations showing genetic susceptibility to DTC are less understood. OBJECTIVES The study aimed to assess the prevalence of germline mutations predisposing to DTC in a cohort of Polish individuals based on their whole genome sequencing data. PATIENTS AND METHODS We analyzed sequencing data from 1076 unrelated individuals totaling over 1018 billion read pairs and yielding an average 35.26 × read depth per genome, released openly for academic and clinical research as the Thousand Polish Genomes database (https://1000polishgenomes.com). The list of genes chosen for further analysis was based on the review of previous studies. RESULTS The cohort contained 104 variants located within the coding and noncoding DNA sequences of 90 genes selected by ClinVar classification as pathogenic and potentially pathogenic. The frequency of variants in the Polish cohort was compared with the frequency estimated for the non‑Finnish European population obtained from the gnomAD database (gnomad.broadinstitute.org). Significant differences in variant frequency were found for the APC, ARSB, ATM, BRCA1, CHEK2, DICER1, GPD1L, INSR, KCNJ10, MYH9, PALB2, PLCB1, PLEKHG5, PTEN, RET, SEC23B, SERPINA1, SLC26A4, SMAD3, STK11, TERT, TOE1, and WRN genes. CONCLUSIONS Even though the Polish population is genetically similar to the other European populations, there are significant differences in variant frequencies contributing to the disease development and progression, such as those in the RET, CHEK2, BRCA1, SLC26A4, or TERT genes. Further studies are needed to identify genomic variants associated directly with DTC.
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Chowaniec H, Ślubowska A, Mroczek M, Borowczyk M, Braszka M, Dworacki G, Dobosz P, Wichtowski M. New hopes for the breast cancer treatment: perspectives on the oncolytic virus therapy. Front Immunol 2024; 15:1375433. [PMID: 38576614 PMCID: PMC10991781 DOI: 10.3389/fimmu.2024.1375433] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
Oncolytic virus (OV) therapy has emerged as a promising frontier in cancer treatment, especially for solid tumours. While immunotherapies like immune checkpoint inhibitors and CAR-T cells have demonstrated impressive results, their limitations in inducing complete tumour regression have spurred researchers to explore new approaches targeting tumours resistant to current immunotherapies. OVs, both natural and genetically engineered, selectively replicate within cancer cells, inducing their lysis while sparing normal tissues. Recent advancements in clinical research and genetic engineering have enabled the development of targeted viruses that modify the tumour microenvironment, triggering anti-tumour immune responses and exhibiting synergistic effects with other cancer therapies. Several OVs have been studied for breast cancer treatment, including adenovirus, protoparvovirus, vaccinia virus, reovirus, and herpes simplex virus type I (HSV-1). These viruses have been modified or engineered to enhance their tumour-selective replication, reduce toxicity, and improve oncolytic properties.Newer generations of OVs, such as Oncoviron and Delta-24-RGD adenovirus, exhibit heightened replication selectivity and enhanced anticancer effects, particularly in breast cancer models. Clinical trials have explored the efficacy and safety of various OVs in treating different cancers, including melanoma, nasopharyngeal carcinoma, head and neck cancer, and gynecologic malignancies. Notably, Talimogene laherparepvec (T-VEC) and Oncorine have. been approved for advanced melanoma and nasopharyngeal carcinoma, respectively. However, adverse effects have been reported in some cases, including flu-like symptoms and rare instances of severe complications such as fistula formation. Although no OV has been approved specifically for breast cancer treatment, ongoing preclinical clinical trials focus on four groups of viruses. While mild adverse effects like low-grade fever and nausea have been observed, the effectiveness of OV monotherapy in breast cancer remains insufficient. Combination strategies integrating OVs with chemotherapy, radiotherapy, or immunotherapy, show promise in improving therapeutic outcomes. Oncolytic virus therapy holds substantial potential in breast cancer treatment, demonstrating safety in trials. Multi-approach strategies combining OVs with conventional therapies exhibit more promising therapeutic effects than monotherapy, signalling a hopeful future for OV-based breast cancer treatments.
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Affiliation(s)
- Hanna Chowaniec
- Department of Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Antonina Ślubowska
- Department of Biostatistics and Research Methodology, Faculty of Medicine, Collegium Medicum, Cardinal Stefan Wyszynski University of Warsaw, Warsaw, Poland
| | - Magdalena Mroczek
- Department of Neurology, University Hospital Basel, Univeristy of Basel, Basel, Switzerland
| | - Martyna Borowczyk
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Małgorzata Braszka
- Faculty of Medical Sciences, University College London Medical School, London, United Kingdom
| | - Grzegorz Dworacki
- Department of Immunology, Poznan University of Medical Sciences, Poznan, Poland
- Chair of Patomorphology and Clinical Immunology, Poznań University of Medical Sciences, Poznan, Poland
| | - Paula Dobosz
- University Centre of Cancer Diagnostics, Poznan University of Medical Sciences, Poznan, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Mateusz Wichtowski
- Surgical Oncology Clinic, Institute of Oncology, Poznan University of Medical Sciences, Poznan, Poland
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Kalyta K, Stelmaszczyk W, Szczęśniak D, Kotuła L, Dobosz P, Mroczek M. The Spectrum of the Heterozygous Effect in Biallelic Mendelian Diseases-The Symptomatic Heterozygote Issue. Genes (Basel) 2023; 14:1562. [PMID: 37628614 PMCID: PMC10454578 DOI: 10.3390/genes14081562] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Heterozygous carriers of pathogenic/likely pathogenic variants in autosomal recessive disorders seem to be asymptomatic. However, in recent years, an increasing number of case reports have suggested that mild and unspecific symptoms can occur in some heterozygotes, as symptomatic heterozygotes have been identified across different disease types, including neurological, neuromuscular, hematological, and pulmonary diseases. The symptoms are usually milder in heterozygotes than in biallelic variants and occur "later in life". The status of symptomatic heterozygotes as separate entities is often disputed, and alternative diagnoses are considered. Indeed, often only a thin line exists between dual, dominant, and recessive modes of inheritance and symptomatic heterozygosity. Interestingly, recent population studies have found global disease effects in heterozygous carriers of some genetic variants. What makes the few heterozygotes symptomatic, while the majority show no symptoms? The molecular basis of this phenomenon is still unknown. Possible explanations include undiscovered deep-splicing variants, genetic and environmental modifiers, digenic/oligogenic inheritance, skewed methylation patterns, and mutational burden. Symptomatic heterozygotes are rarely reported in the literature, mainly because most did not undergo the complete diagnostic procedure, so alternative diagnoses could not be conclusively excluded. However, despite the increasing accessibility to high-throughput technologies, there still seems to be a small group of patients with mild symptoms and just one variant of autosomes in biallelic diseases. Here, we present some examples, the current state of knowledge, and possible explanations for this phenomenon, and thus argue against the existing dominant/recessive classification.
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Affiliation(s)
- Kateryna Kalyta
- School of Life Sciences, FHNW—University of Applied Sciences, 4132 Muttenz, Switzerland;
| | - Weronika Stelmaszczyk
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK;
| | - Dominika Szczęśniak
- Institute of Psychiatry and Neurology in Warsaw, Genetics Department, 02-957 Warsaw, Poland;
| | - Lidia Kotuła
- Department of Genetics, Medical University, 20-080 Lublin, Poland;
| | - Paula Dobosz
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland;
| | - Magdalena Mroczek
- University Hospital Basel, University of Basel, 4031 Basel, Switzerland
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Mroczek M, Liu J, Sypniewski M, Pieńkowski T, Itrych B, Stojak J, Pronobis-Szczylik B, Stępień M, Kaja E, Dąbrowski M, Suchocki T, Wojtaszewska M, Zawadzki P, Mach A, Sztromwasser P, Król ZJ, Szyda J, Dobosz P. The cancer-risk variant frequency among Polish population reported by the first national whole-genome sequencing study. Front Oncol 2023; 13:1045817. [PMID: 36845707 PMCID: PMC9950741 DOI: 10.3389/fonc.2023.1045817] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Introduction Population-based cancer screening has raised many controversies in recent years, not only regarding the costs but also regarding the ethical nature and issues related to variant interpretation. Nowadays, genetic cancer screening standards are different in every country and usually encompass only individuals with a personal or family history of relevant cancer. Methods Here we performed a broad genetic screening for cancer-related rare germline variants on population data from the Thousand Polish Genomes database based on 1076 Polish unrelated individuals that underwent whole genome sequencing (WGS). Results We identified 19 551 rare variants in 806 genes related to oncological diseases, among them 89% have been located in non-coding regions. The combined BRCA1/BRCA2 pathogenic/likely pathogenic according to ClinVar allele frequency in the unselected population of 1076 Poles was 0.42%, corresponding to nine carriers. Discussion Altogether, on the population level, we found especially problematic the assessment of the pathogenicity of variants and the relation of ACMG guidelines to the population frequency. Some of the variants may be overinterpreted as disease-causing due to their rarity or lack of annotation in the databases. On the other hand, some relevant variants may have been overseen given that there is little pooled population whole genome data on oncology. Before population WGS screening will become a standard, further studies are needed to assess the frequency of the variants suspected to be pathogenic on the population level and with reporting of likely benign variants.
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Affiliation(s)
- Magdalena Mroczek
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland,*Correspondence: Magdalena Mroczek,
| | - Jakub Liu
- Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Mateusz Sypniewski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Tadeusz Pieńkowski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland,Postgraduate Medical Education Center, Warsaw, Poland
| | - Bartosz Itrych
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Joanna Stojak
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland,Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Science, Jastrzębiec, Poland
| | | | - Maria Stępień
- Department of Sports Medicine, Doctoral School, Medical University of Lublin, Lublin, Poland
| | - Elżbieta Kaja
- Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Tomasz Suchocki
- Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,National Research Institute of Animal Production, Balice, Poland
| | - Marzena Wojtaszewska
- Department of Haematology, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszów, Rzeszów, Poland,Department of Haematology, Frederic Chopin Provincial Specialist Hospital, Rzeszów, Poland
| | | | - Anna Mach
- Department of Psychiatry, Medical University of Warsaw, Warsaw, Poland
| | | | - Zbigniew J. Król
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Joanna Szyda
- Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,National Research Institute of Animal Production, Balice, Poland
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
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Sypniewski M, Kresa D, Dobosz P, Topolski P, Kotuła L, Sztromwasser P, Mroczek M. Population WGS-based spinal muscular atrophy carrier screening in a cohort of 1076 healthy Polish individuals. J Appl Genet 2023; 64:135-139. [PMID: 36417168 DOI: 10.1007/s13353-022-00737-5] [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: 08/24/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Spinal muscular atrophy is a severe neuromuscular disorder with an autosomal recessive inheritance pattern. The disease-causing gene is SMN1, and its paralogue, SMN2, is a disease course modifier. Both genes SMN1 and SMN2 show over 99.9% sequence identity and a high rate of crossing over in the genomic region. Due to this reason, SMN1/SMN2 is usually excluded from the whole-genome sequencing (WGS) analysis and investigated with traditional methods, such as MLPA and qPCR. Recently, novel bioinformatic algorithms dedicated to analyzing this particular genomic region have been developed. Here, we analyze the SMN1/SMN2 genomic region with a dedicated program, SMNCopyNumberCaller. We report a similar prevalence of SMN1 gene deletion carrier status (1 per 41 people) to published data from the Polish population (1 per 35 people). Additionally, SMNCopyNumberCaller can identify SMN2 CNVs and SMN2Δ7-8 present in 153 healthy Polish individuals. Two other programs for the CNV analysis in standard genomic regions were not able to provide reliable results. Using WGS-based tools for SMN1/2 genomic region analysis is not only an efficient method in terms of time but will also enable more complex analysis such screening for markers related with a silent carrier status and identification of further genetic modifiers. Although still an experimental method, soon WGS-based SMN1/SMN2 carrier identification may become a standard method for patients screened with WGS for other purposes.
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Affiliation(s)
- Mateusz Sypniewski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507, Warsaw, Poland
| | - Dominika Kresa
- Faculty of Bioscience Engineering, KU Leuven, Louvain, Belgium
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507, Warsaw, Poland
| | - Piotr Topolski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507, Warsaw, Poland
| | - Lidia Kotuła
- Zakład Genetyki Klinicznej, Uniwersytet Medyczny w Lublinie, Lublin, Poland
| | | | - Magdalena Mroczek
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People With Rare Diseases, 8952, Schlieren-Zurich, Switzerland.
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Liu J, Mroczek M, Mach A, Stępień M, Aplas A, Pronobis-Szczylik B, Bukowski S, Mielczarek M, Gajewska E, Topolski P, Król ZJ, Szyda J, Dobosz P. Genetics, Genomics and Emerging Molecular Therapies of Pancreatic Cancer. Cancers (Basel) 2023; 15:cancers15030779. [PMID: 36765737 PMCID: PMC9913594 DOI: 10.3390/cancers15030779] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 02/01/2023] Open
Abstract
The number of cases of pancreatic cancers in 2019 in Poland was 3852 (approx. 2% of all cancers). The course of the disease is very fast, and the average survival time from the diagnosis is 6 months. Only <2% of patients live for 5 years from the diagnosis, 8% live for 2 years, and almost half live for only about 3 months. A family predisposition to pancreatic cancer occurs in about 10% of cases. Several oncogenes in which somatic changes lead to the development of tumours, including genes BRCA1/2 and PALB2, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1, are involved in pancreatic cancer. Between 4% and 10% of individuals with pancreatic cancer will have a mutation in one of these genes. Six percent of patients with pancreatic cancer have NTRK pathogenic fusion. The pathogenesis of pancreatic cancer can in many cases be characterised by homologous recombination deficiency (HRD)-cell inability to effectively repair DNA. It is estimated that from 24% to as many as 44% of pancreatic cancers show HRD. The most common cause of HRD are inactivating mutations in the genes regulating this DNA repair system, mainly BRCA1 and BRCA2, but also PALB2, RAD51C and several dozen others.
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Affiliation(s)
- Jakub Liu
- Biostatistics Group, Wroclaw University of Environmental and Life Sciences, 51-631 Wroclaw, Poland
| | - Magdalena Mroczek
- Centre for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Wagistrasse 25, 8952 Schlieren, Switzerland
| | - Anna Mach
- Department of Psychiatry, Medical University of Warsaw, 00-665 Warsaw, Poland
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Maria Stępień
- Department of Infectious Diseases, Doctoral School, Medical University of Lublin, 20-059 Lublin, Poland
- Correspondence: (M.S.); (P.D.)
| | - Angelika Aplas
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Bartosz Pronobis-Szczylik
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Szymon Bukowski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Magda Mielczarek
- Biostatistics Group, Wroclaw University of Environmental and Life Sciences, 51-631 Wroclaw, Poland
- National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
| | - Ewelina Gajewska
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Piotr Topolski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Zbigniew J. Król
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Joanna Szyda
- Biostatistics Group, Wroclaw University of Environmental and Life Sciences, 51-631 Wroclaw, Poland
- National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
- Correspondence: (M.S.); (P.D.)
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Słomian D, Szyda J, Dobosz P, Stojak J, Michalska-Foryszewska A, Sypniewski M, Liu J, Kotlarz K, Suchocki T, Mroczek M, Stępień M, Sztromwasser P, Król ZJ. Better safe than sorry-Whole-genome sequencing indicates that missense variants are significant in susceptibility to COVID-19. PLoS One 2023; 18:e0279356. [PMID: 36662838 PMCID: PMC9858061 DOI: 10.1371/journal.pone.0279356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/06/2022] [Indexed: 01/22/2023] Open
Abstract
Undoubtedly, genetic factors play an important role in susceptibility and resistance to COVID-19. In this study, we conducted the GWAS analysis. Out of 15,489,173 SNPs, we identified 18,191 significant SNPs for severe and 11,799 SNPs for resistant phenotype, showing that a great number of loci were significant in different COVID-19 representations. The majority of variants were synonymous (60.56% for severe, 58.46% for resistant phenotype) or located in introns (55.77% for severe, 59.83% for resistant phenotype). We identified the most significant SNPs for a severe outcome (in AJAP1 intron) and for COVID resistance (in FIG4 intron). We found no missense variants with a potential causal function on resistance to COVID-19; however, two missense variants were determined as significant a severe phenotype (in PM20D1 and LRP4 exons). None of the aforementioned SNPs and missense variants found in this study have been previously associated with COVID-19.
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Affiliation(s)
- Dawid Słomian
- National Research Institute of Animal Production, Balice, Poland
| | - Joanna Szyda
- National Research Institute of Animal Production, Balice, Poland
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
- Department of Haematology, Transplantation and Internal Medicine, University Clinical Centre of the Medical University of Warsaw, Warsaw, Poland
| | - Joanna Stojak
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Magdalenka, Poland
| | | | - Mateusz Sypniewski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
- Department of Genetics and Animal Breedings, Poznan University of Life Sciences, Poznan, Poland
| | - Jakub Liu
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Krzysztof Kotlarz
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Tomasz Suchocki
- National Research Institute of Animal Production, Balice, Poland
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Magdalena Mroczek
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - Maria Stępień
- Department of Infectious Diseases, Doctoral School, Medical University of Lublin, Lublin, Poland
| | | | - Zbigniew J. Król
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
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8
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Borowczyk M, Dobosz P, Szczepanek-Parulska E, Budny B, Dębicki S, Filipowicz D, Wrotkowska E, Oszywa M, Verburg FA, Janicka-Jedyńska M, Ziemnicka K, Ruchała M. Follicular Thyroid Adenoma and Follicular Thyroid Carcinoma-A Common or Distinct Background? Loss of Heterozygosity in Comprehensive Microarray Study. Cancers (Basel) 2023; 15:cancers15030638. [PMID: 36765597 PMCID: PMC9913827 DOI: 10.3390/cancers15030638] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Pre- and postsurgical differentiation between follicular thyroid adenoma (FTA) and follicular thyroid cancer (FTC) represents a significant diagnostic challenge. Furthermore, it remains unclear whether they share a common or distinct background and what the mechanisms underlying follicular thyroid lesions malignancy are. The study aimed to compare FTA and FTC by the comprehensive microarray and to identify recurrent regions of loss of heterozygosity (LOH). We analyzed formalin-fixed paraffin-embedded (FFPE) samples acquired from 32 Caucasian patients diagnosed with FTA (16) and FTC (16). We used the OncoScan™ microarray assay (Affymetrix, USA), using highly multiplexed molecular inversion probes for single nucleotide polymorphism (SNP). The total number of LOH was higher in FTC compared with FTA (18 vs. 15). The most common LOH present in 21 cases, in both FTA (10 cases) and FTC (11 cases), was 16p12.1, which encompasses many cancer-related genes, such as TP53, and was followed by 3p21.31. The only LOH present exclusively in FTA patients (56% vs. 0%) was 11p11.2-p11.12. The alteration which tended to be detected more often in FTC (6 vs. 1 in FTA) was 12q24.11-q24.13 overlapping FOXN4, MYL2, PTPN11 genes. FTA and FTC may share a common genetic background, even though differentiating rearrangements may also be detected.
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Affiliation(s)
- Martyna Borowczyk
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
- Department of Medical Simulation, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Correspondence: ; Tel.: +48-512131285
| | - Paula Dobosz
- Department of Genetics and Genomics, Central Clinical Hospital of the Ministry of Interior Affairs and Administration, 02-507 Warsaw, Poland
| | - Ewelina Szczepanek-Parulska
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Bartłomiej Budny
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Szymon Dębicki
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Dorota Filipowicz
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Elżbieta Wrotkowska
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Michalina Oszywa
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Frederik A. Verburg
- Department of Radiology and Nuclear Medicine, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | | | - Katarzyna Ziemnicka
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Marek Ruchała
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
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Sypniewski M, Król ZJ, Szyda J, Kaja E, Mroczek M, Suchocki T, Lejman A, Stępień M, Topolski P, Dąbrowski M, Kotlarz K, Aplas A, Wasiak M, Wojtaszewska M, Zawadzki P, Pawlak A, Gil R, Dobosz P, Stojak J. Gene Variants Related to Cardiovascular and Pulmonary Diseases May Correlate with Severe Outcome of COVID-19. Int J Mol Sci 2022; 23:ijms23158696. [PMID: 35955824 PMCID: PMC9369343 DOI: 10.3390/ijms23158696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/11/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 01/25/2023] Open
Abstract
Background: Severe outcomes of COVID-19 account for up to 15% of all cases. The study aims to check if any gene variants related to cardiovascular (CVD) and pulmonary diseases (PD) are correlated with a severe outcome of COVID-19 in a Polish cohort of COVID-19 patients. Methods: In this study, a subset of 747 samples from unrelated individuals collected across Poland in 2020 and 2021 was used and whole-genome sequencing was performed. Results: The GWAS analysis of SNPs and short indels located in genes related to CVD identified one variant significant in COVID-19 severe outcome in the HADHA gene, while for the PD gene panel, we found two significant variants in the DRC1 gene. In this study, both potentially protective and risk variants were identified, of which variants in the HADHA gene deserve the most attention. Conclusions: This is the first study reporting the association between the HADHA and DRC1 genetic variants and COVID-19 severe outcome based on the cohort WGS analysis. Although all the identified variants are localised in introns, they may be correlated and therefore inherited along with other risk variants, potentially causative to severe outcome of COVID-19 but not discovered yet.
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Affiliation(s)
- Mateusz Sypniewski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637 Poznan, Poland
| | - Zbigniew J. Król
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Joanna Szyda
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, 51-631 Wrocław, Poland
- National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
| | - Elżbieta Kaja
- Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Magdalena Mroczek
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, 8952 Schlieren-Zurich, Switzerland
| | - Tomasz Suchocki
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, 51-631 Wrocław, Poland
- National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
| | - Adrian Lejman
- MNM Bioscience Inc., 1 Broadway, Cambridge, MA 02142, USA
| | - Maria Stępień
- Department of Infectious Diseases, Doctoral School, Medical University of Lublin, 20-059 Lublin, Poland
| | - Piotr Topolski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | | | - Krzysztof Kotlarz
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, 51-631 Wrocław, Poland
| | - Angelika Aplas
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Michał Wasiak
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Marzena Wojtaszewska
- Department of Hematology, Frederic Chopin Provincial Teaching Hospital No. 1 in Rzeszow, 35-055 Rzeszow, Poland
| | - Paweł Zawadzki
- MNM Bioscience Inc., 1 Broadway, Cambridge, MA 02142, USA
| | - Agnieszka Pawlak
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Robert Gil
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
- Correspondence: (P.D.); (J.S.)
| | - Joanna Stojak
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
- Correspondence: (P.D.); (J.S.)
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10
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Mroczek M, Inashkina I, Stavusis J, Zayakin P, Khrunin A, Micule I, Kenina V, Zdanovica A, Zídková J, Fajkusová L, Limborska S, van der Kooi AJ, Brusse E, Leonardis L, Maver A, Pajusalu S, Õunap K, Puusepp S, Dobosz P, Sypniewski M, Burnyte B, Lace B. CAPN3 c.1746-20C>G variant is hypomorphic for LGMD R1 calpain 3-related. Hum Mutat 2022; 43:1347-1353. [PMID: 35731190 DOI: 10.1002/humu.24421] [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: 12/10/2021] [Revised: 05/07/2022] [Accepted: 06/02/2022] [Indexed: 11/08/2022]
Abstract
The investigated intronic CAPN3 variant NM_000070.3:c.1746-20C>G occurs in the Central and Eastern Europe with a frequency of >1% and there are conflicting interpretations on its pathogenicity. We collected data on 14 patients carrying the CAPN3 c.1746-20C>G variant in trans position with another CAPN3 pathogenic/likely pathogenic variant. The patients compound heterozygous for the CAPN3 c.1746-20C>G variant presented a phenotype consistent with calpainopathy of mild/medium severity. This variant is most frequent in the North/West regions of Russia and may originate from that area. Molecular studies revealed that different splicing isoforms are produced in the muscle. We hypothesize that c.1746-20C>G is a hypomorphic variant with a reduction of RNA and protein expression and only individuals having a higher ratio of abnormal isoforms are affected. Reclassification of the CAPN3 variant c.1746-20C>G from variant with a conflicting interpretation of pathogenicity to hypomorphic variant explains many unidentified cases of limb girdle muscular dystrophy R1 calpain 3-related in Eastern and Central Europe.
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Affiliation(s)
- Magdalena Mroczek
- Department of Neurology and Neurophysiology, Balgrist University Hospital, University of Zurich, Zürich, Switzerland
| | | | | | | | - Andrey Khrunin
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ieva Micule
- Biomedical Research and Study Center, Riga, Latvia
| | - Victorija Kenina
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia.,Rare Disease Center, Riga East Clinical University Hospital, Riga, Latvia
| | | | - Jana Zídková
- Centre of Molecular Biology And Genetics, University Hospital, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology And Genetics, University Hospital, Brno, Czech Republic
| | - Svetlana Limborska
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Anneke J van der Kooi
- Department of Neurology, Amsterdam University Medical Centre, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Esther Brusse
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Lea Leonardis
- Department of Neurology, University Medical Centre Ljubljana, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Sanna Puusepp
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Paula Dobosz
- MNM Diagnostics Sp. z o.o., Poznań, Poland.,Department of Hematology, Transplantation and Internal Medicine, University Clinical Center of the Medical University of Warsaw, Warsaw, Poland.,Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | | | - Birute Burnyte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Baiba Lace
- Biomedical Research and Study Center, Riga, Latvia.,Medical Genetics Clinic, Children's Clinical University Hospital, Riga, Latvia
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11
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Dobosz P, Stempor PA, Ramírez Moreno M, Bulgakova NA. Transcriptional and post-transcriptional regulation of checkpoint genes on the tumour side of the immunological synapse. Heredity (Edinb) 2022; 129:64-74. [PMID: 35459932 PMCID: PMC9273643 DOI: 10.1038/s41437-022-00533-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/20/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023] Open
Abstract
Cancer is a disease of the genome, therefore, its development has a clear Mendelian component, demonstrated by well-studied genes such as BRCA1 and BRCA2 in breast cancer risk. However, it is known that a single genetic variant is not enough for cancer to develop leading to the theory of multistage carcinogenesis. In many cases, it is a sequence of events, acquired somatic mutations, or simply polygenic components with strong epigenetic effects, such as in the case of brain tumours. The expression of many genes is the product of the complex interplay between several factors, including the organism’s genotype (in most cases Mendelian-inherited), genetic instability, epigenetic factors (non-Mendelian-inherited) as well as the immune response of the host, to name just a few. In recent years the importance of the immune system has been elevated, especially in the light of the immune checkpoint genes discovery and the subsequent development of their inhibitors. As the expression of these genes normally suppresses self-immunoreactivity, their expression by tumour cells prevents the elimination of the tumour by the immune system. These discoveries led to the rapid growth of the field of immuno-oncology that offers new possibilities of long-lasting and effective treatment options. Here we discuss the recent advances in the understanding of the key mechanisms controlling the expression of immune checkpoint genes in tumour cells.
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Affiliation(s)
- Paula Dobosz
- Central Clinical Hospital of the Ministry of Interior Affairs and Administration in Warsaw, Warsaw, Poland
| | | | - Miguel Ramírez Moreno
- School of Biosciences and Bateson Centre, The University of Sheffield, Sheffield, UK
| | - Natalia A Bulgakova
- School of Biosciences and Bateson Centre, The University of Sheffield, Sheffield, UK.
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12
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Król ZJ, Dorobek M, Dąbrowski M, Zielińska-Turek J, Mruk B, Walecki J, Sklinda K, Gil R, Pawlak A, Wojtaszewska M, Lejman A, Dobosz P, Zawadzki P, Pawłowska A, Szczepaniak M, Król D, Zaczyński A, Wierzba W. SARS-CoV-2 infection activating a novel variant of the NOTCH3 gene and subsequently causing development of CADASIL. Arch Med Sci 2022; 19:1781-1794. [PMID: 38058732 PMCID: PMC10696999 DOI: 10.5114/aoms/146978] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/27/2022] [Indexed: 12/08/2023] Open
Abstract
Introduction In the following study we describe the diagnostic process and further case analysis of a 30-year-old woman admitted with typical COVID-19 symptoms, who subsequently developed additional symptoms suggesting cerebral autosomal dominant arteriopathy with sub-cortical infarcts and leukoencephalopathy (CADASIL). Material and methods Other than the standard diagnostic procedures, whole genome sequencing (WGS) was used, which led to following findings. A new variant of the NOTCH3 gene, which led to CADASIL-like symptoms, was found, and it had been most likely activated by the SARS-CoV-2 infection. This novel variant in NOTCH3 has not been found in existing databases and has never been mentioned in research concerning CADASIL before. Results Furthermore, after subjecting the patient's close relatives to WGS it was found that no other examined person demonstrated the same genetic mutation. Conclusions It seems therefore that the new variant of NOTCH3 is of de novo origin in the patient's genome. Additionally, the relatively early onset of CADASIL and the unexpectedly severe COVID-19 infection suggest that the two occurred simultaneously: the infection with SARS-CoV-2 accelerated development of CADASIL symptoms and the unusual variant of the NOTCH3 gene contributed to the more severe course of COVID-19.
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Affiliation(s)
- Zbigniew J. Król
- Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Małgorzata Dorobek
- Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | | | | | - Bartosz Mruk
- Department of Radiology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Jerzy Walecki
- Department of Radiology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Katarzyna Sklinda
- Department of Radiology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Robert Gil
- Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Agnieszka Pawlak
- Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | | | | | | | | | - Aneta Pawłowska
- Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Michał Szczepaniak
- Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Dorota Król
- Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Artur Zaczyński
- Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Waldemar Wierzba
- Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
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13
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Gadot M, Gal M, Dobosz P, Dotan Z, Ramon J, Berger R, Avni D, Fridman E, Leibowitz R. Associations between T cell infiltration, T cell receptor clonality, histology and recurrence in renal cell carcinoma. Clin Exp Immunol 2021; 205:160-168. [PMID: 33899933 DOI: 10.1111/cei.13608] [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: 08/30/2020] [Revised: 03/14/2021] [Accepted: 03/28/2021] [Indexed: 11/29/2022] Open
Abstract
Renal cell carcinoma (RCC) is comprised of clear-cell (ccRCC) and non-clear-cell (nccRCC) tumors. Despite definitive surgical resection in localized disease, recurrence often occurs. A commercial method based on a multiplex polymerase chain reaction (PCR) assay exclusively targets rearranged T cell receptor (TCR) genes to generate high-throughput sequencing-based data, allowing characterization of the immune repertoire within tumors. In this study we performed a retrospective analysis on archived tumor samples from patients with recurring versus non-recurring T3 ccRCC and on samples from early nccRCC versus ccRCC. Following genomic DNA extraction and multiplex PCR, the fraction of T cells within tumors, the number of unique receptors ('richness') and their relative abundances ('clonality') were calculated. Statistical significance and correlations were calculated using Student's t-test and Spearman's rho, respectively. Average fraction and clonality of T cells in tumors from non-recurring patients was 2.5- and 4.3-fold higher than in recurring patients (P = 0.025 and P = 0.043, respectively). A significant positive correlation was found between T cell fraction and clonality (Spearman's rho = 0.78, P = 0.008). The average fraction of T cells in ccRCC tumors was 2.8-fold higher than in nccRCC tumors (P = 0.015). Clonality and estimated richness were similar between ccRCC and nccRCC tumors. In summary, recurrence of ccRCC is associated with a lower fraction and clonality of T cells within tumors; nccRCC tumors are more 'deserted' than ccRCC, but similar in their ability to generate a clonal T cell repertoire. Our work suggests associations between the characteristics of T cell infiltrate, histology and tumor recurrence.
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Affiliation(s)
- Moran Gadot
- Oncology Institute, Sheba Medical Center, Tel-Hashomer, Israel
| | - Mordechay Gal
- Faculty of Life Science, Bar Ilan University, Ramat-Gan, Israel
| | - Paula Dobosz
- Department of Hematology, Oncology and Internal Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Zohar Dotan
- Department of Urology, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel
| | - Jacob Ramon
- Department of Urology, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel
| | - Raanan Berger
- Oncology Institute, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel
| | - Dror Avni
- Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel.,Laboratory of Molecular Cell Biology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Eduard Fridman
- Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel.,Pathology Institute, Sheba Medical Center, Tel-Hashomer, Israel
| | - Raya Leibowitz
- Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel.,Oncology Institute, Shamir Medical Center, Zerifin, Israel
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14
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Stempor PA, Avni D, Leibowitz R, Sidi Y, Stępień M, Dzieciątkowski T, Dobosz P. Comprehensive Analysis of Correlations in the Expression of miRNA Genes and Immune Checkpoint Genes in Bladder Cancer Cells. Int J Mol Sci 2021; 22:2553. [PMID: 33806327 PMCID: PMC7961343 DOI: 10.3390/ijms22052553] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Personalised medicine is the future and hope for many patients, including those with cancers. Early detection, as well as rapid, well-selected treatment, are key factors leading to a good prognosis. MicroRNA mediated gene regulation is a promising area of development for new diagnostic and therapeutic methods, crucial for better prospects for patients. Bladder cancer is a frequent neoplasm, with high lethality and lacking modern, advanced therapeutic modalities, such as immunotherapy. MicroRNAs are involved in bladder cancer pathogenesis, proliferation, control and response to treatment, which we summarise in this perspective in response to lack of recent review publications in this field. We further performed a correlation-based analysis of microRNA and gene expression data in bladder cancer (BLCA) TCGA dataset. We identified 27 microRNAs hits with opposite expression profiles to genes involved in immune response in bladder cancer, and 24 microRNAs hits with similar expression profiles. We discuss previous studies linking the functions of these microRNAs to bladder cancer and assess if they are good candidates for personalised medicine therapeutics and diagnostics. The discussed functions include regulation of gene expression, interplay with transcription factors, response to treatment, apoptosis, cell proliferation and angiogenesis, initiation and development of cancer, genome instability and tumour-associated inflammatory reaction.
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Affiliation(s)
- Przemysław A. Stempor
- SmartImmune Ltd, Accelerate Cambridge, University of Cambridge Judge Business School, Cambridge CB4 1EE, UK;
| | - Dror Avni
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashome 52621, Israel;
| | - Raya Leibowitz
- Oncology Institute, Shamir Medical Center, Be’er Yaakov, Tel Hashome 52621, Israel;
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Yechezkel Sidi
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Maria Stępień
- Faculty of Medicine, Medical University of Lublin, 20-059 Lublin, Poland;
| | | | - Paula Dobosz
- Department of Hematology, Transplantationand Internal Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
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15
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Dobosz P, Stempor PA, Roszik J, Herman A, Layani A, Berger R, Avni D, Sidi Y, Leibowitz-Amit R. Checkpoint Genes at the Cancer Side of the Immunological Synapse in Bladder Cancer. Transl Oncol 2020; 13:193-200. [PMID: 31869744 PMCID: PMC6931203 DOI: 10.1016/j.tranon.2019.10.018] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/30/2019] [Accepted: 10/31/2019] [Indexed: 12/27/2022] Open
Abstract
Immune checkpoint inhibitors have revolutionized cancer therapy, but not all cancers respond to the currently available drugs, and even within cancers considered responsive to such modality, response rates range between 15 and 40%, depending on the cancer type, the line of treatment, and yet unknown clinical/molecular factors. Coordinated expression of checkpoint proteins was shown to occur on T cells, probably allowing fine-tuning of the signal transmitted to the cell. We performed a bioinformatic analysis of the expression of putative checkpoint mRNAs at the cancer side of the immunological synapse from the bladder cancer tumorgenome atlas (TCGA) database. Fifteen mRNAs, corresponding to both coinhibitory and costimulatory checkpoints, were shown to be expressed above a designated threshold. Of these, seven mRNAs were found to be coexpressed: CD277, PD-1L, CD48, CD86, galectin-9, TNFRSF14 (HVEM), and CD40. The expression of 2 of these mRNAs-BTN3A1 (CD277) and TNFRSF14 (HVEM)-was positively correlated with overall survival in the TCGA database. All these seven mRNA share putative binding sites of a few transcription factors (TFs). Of these, the expression of the TF BACH-2 was positively correlated with the expression of checkpoint mRNAs from the network. This suggests a joint transcriptional regulation on the expression of checkpoint mRNAs at the bladder tumor side of the immunological synapse.
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Affiliation(s)
- Paula Dobosz
- Oncology Institute and Cancer Research Centre, Sheba Medical Centre Hospital, Tel Hashomer, Ramat Gan, Israel
| | - Przemysław A Stempor
- School of Life Sciences, Gurdon Institute, Department of Genetics, Tennis Court Rd, Cambridge, UK; The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Centre, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Centre, USA
| | - Amir Herman
- Orthopedic Department, Assuta Medical Center, Ashdod, Israel
| | - Adi Layani
- Oncology Institute and Cancer Research Centre, Sheba Medical Centre Hospital, Tel Hashomer, Ramat Gan, Israel
| | - Raanan Berger
- Oncology Institute and Cancer Research Centre, Sheba Medical Centre Hospital, Tel Hashomer, Ramat Gan, Israel; Oncology Department, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror Avni
- Oncology Institute and Cancer Research Centre, Sheba Medical Centre Hospital, Tel Hashomer, Ramat Gan, Israel
| | - Yechezkel Sidi
- Oncology Institute and Cancer Research Centre, Sheba Medical Centre Hospital, Tel Hashomer, Ramat Gan, Israel; Oncology Department, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raya Leibowitz-Amit
- Oncology Institute and Cancer Research Centre, Sheba Medical Centre Hospital, Tel Hashomer, Ramat Gan, Israel; Oncology Department, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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16
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Abstract
Immunotherapy is often perceived as a relatively recent advance. In reality, however, one should be looking for the beginnings of cancer immunotherapy under different names as far as in the Antiquity. The first scientific attempts to modulate patients' immune systems to cure cancer can be attributed to two German physicians, Fehleisen and Busch, who independently noticed significant tumor regression after erysipelas infection. The next significant advances came from William Bradley Coley who is known today as the Father of Immunotherapy. It was Coley who first attempted to harness the immune system for treating bone cancer in 1891. His achievements were largely unnoticed for over fifty years, and several seminal discoveries in the field of Immunology, such as the existence of T cells and their crucial role in immunity in 1967, stepped up the research toward cancer immunotherapy known today. The following paper tracks cancer immunotherapy from its known beginnings up until recent events, including the 2018 Nobel Prize award to James Allison and Tasuku Honjo for their meticulous work on checkpoint molecules as potential therapeutic targets. That work has led to the successful development of new checkpoint inhibitors, CAR T-cells and oncolytic viruses and the pace of such advances brings the highest hope for the future of cancer treatment.
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Affiliation(s)
- Paula Dobosz
- Department of Hematology, Oncology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Dzieciątkowski
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
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17
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Roszik J, Markovits E, Dobosz P, Layani A, Slabodnik-Kaner K, Baruch EN, Ben-Betzalel G, Grimm E, Berger R, Sidi Y, Schachter J, Shapira-Frommer R, Avni D, Markel G, Leibowitz-Amit R. TNFSF4 (OX40L) expression and survival in locally advanced and metastatic melanoma. Cancer Immunol Immunother 2019; 68:1493-1500. [PMID: 31501955 DOI: 10.1007/s00262-019-02382-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 01/21/2019] [Accepted: 08/20/2019] [Indexed: 01/16/2023]
Abstract
Immunotherapy with checkpoint inhibitors revolutionized melanoma treatment in both the adjuvant and metastatic setting, yet not all metastatic patients respond, and metastatic disease still often recurs among immunotherapy-treated patients with locally advanced disease. TNFSF4 is a co-stimulatory checkpoint protein expressed by several types of immune and non-immune cells, and was shown in the past to enhance the anti-neoplastic activity of T cells. Here, we assessed its expression in melanoma and its association with outcome in locally advanced and metastatic disease. We used publicly available data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE), and RNA sequencing data from anti-PD1-treated patients at Sheba medical center. TNFSF4 mRNA is expressed in melanoma cell lines and melanoma samples, including those with low lymphocytic infiltrates, and is not associated with the ulceration status of the primary tumor. Low expression of TNFSF4 mRNA is associated with worse prognosis in all melanoma patients and in the cohorts of stage III and stage IIIc-IV patients. Low expression of TNFSF4 mRNAs is also associated with worse prognosis in the subgroup of patients with low lymphocytic infiltrates, suggesting that tumoral TNFSF4 is associated with outcome. TNFSF4 expression was not correlated with the expression of other known checkpoint mRNAs. Last, metastatic patients with TNFSF4 mRNA expression within the lowest quartile have significantly worse outcome on anti-PD1 treatment, and a significantly lower response rate to these agents. Our current work points to TNFSF4 expression in melanoma as a potential determinant of prognosis, and warrants further translational and clinical research.
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Affiliation(s)
- Jason Roszik
- Departments of Melanoma Medical Oncology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Ettai Markovits
- Ella Lemelbaum Institute for Immuno-Oncology, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel.,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Paula Dobosz
- Lab of Molecular Cancer Research, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel
| | - Adi Layani
- Lab of Molecular Cancer Research, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel
| | - Keren Slabodnik-Kaner
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel.,Lab of Molecular Cancer Research, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel
| | - Erez N Baruch
- Ella Lemelbaum Institute for Immuno-Oncology, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel.,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Guy Ben-Betzalel
- Ella Lemelbaum Institute for Immuno-Oncology, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel
| | - Elizabeth Grimm
- Departments of Melanoma Medical Oncology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Raanan Berger
- Department of Oncology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel.,Division of Oncology, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel.,Oncology Institute and Cancer Research Center, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel
| | - Yehezkel Sidi
- Lab of Molecular Cancer Research, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel
| | - Jacob Schachter
- Ella Lemelbaum Institute for Immuno-Oncology, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel.,Department of Oncology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Ronnie Shapira-Frommer
- Ella Lemelbaum Institute for Immuno-Oncology, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel
| | - Dror Avni
- Lab of Molecular Cancer Research, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel
| | - Gal Markel
- Ella Lemelbaum Institute for Immuno-Oncology, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel. .,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel.
| | - Raya Leibowitz-Amit
- Department of Oncology, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel. .,Division of Oncology, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel. .,Oncology Institute and Cancer Research Center, Sheba Medical Center-Tel Hashomer, 2 Sheba Road, 5266202, Ramat Gan, Israel.
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Sokola M, Malec K, Brzewski P, Dobosz P. The use of CO 2 laser in skin complications following BAHA implantation: our experience in the eight patients. Clin Otolaryngol 2017; 42:1403-1406. [PMID: 28544707 DOI: 10.1111/coa.12907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2017] [Indexed: 11/30/2022]
Affiliation(s)
- M Sokola
- Department of Otolaryngology, Head and Neck Surgery, 5th Military Hospital with Polyclinic, Krakow, Poland
| | - K Malec
- Department of Otolaryngology, Head and Neck Surgery, 5th Military Hospital with Polyclinic, Krakow, Poland
| | - P Brzewski
- Department of Dermatology, Jagiellonian University Medical College, Krakow, Poland
| | - P Dobosz
- Department of Otolaryngology, Head and Neck Surgery, 5th Military Hospital with Polyclinic, Krakow, Poland
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Dobosz P, Morais S, Puchades R, Maquieira A. Nanogold bioconjugates for direct and sensitive multiplexed immunosensing. Biosens Bioelectron 2015; 69:294-300. [PMID: 25771301 DOI: 10.1016/j.bios.2015.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 12/24/2014] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 02/05/2023]
Abstract
The use of nanogold bioconjugates for direct detection of the antibody-antigen immunoreaction is addressed. The integration of gold nanoparticles tracers as signal generators in microarray immunosensing and compact disc detection technique show important advantages to reach sensitive, selective, high throughput, reliable and cost-effective assays. For that, a thorough study of the performances of the size of spherical nanogold particles and coating density was developed. The size of the nanoparticle determines the optimal antibody dilution, being the smaller particles the best performing ones. Enhancement effect of lower size is also studied. The gold labeling method do not affects the recognition capability of the labeled proteins. As a proof of concept, the nanoconjugates were used for the simultaneous and direct determination of small molecules. Employing nanogold bioconjugates as recognition labels resulted in robust and reliable assays, reaching a sensitivity of 0.03 and 1.3μg/L for sulfasalazine and atrazine, respectively. This shows that the use of nanogold bioconjugates for direct immunosensing is very competitive, achieving highly sensitive and reproducible assays (RSD<10%). This approach would simultaneously determine both small and large molecular size targets, in different formats, using the same detection mode what paves the way for many other applications in different scenarios.
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Affiliation(s)
- P Dobosz
- Instituto Interuniversitario de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46071 Valencia, Spain
| | - S Morais
- Instituto Interuniversitario de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46071 Valencia, Spain
| | - R Puchades
- Instituto Interuniversitario de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46071 Valencia, Spain
| | - A Maquieira
- Instituto Interuniversitario de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46071 Valencia, Spain.
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Abstract
The broad clinical utilization of the internal thoracic artery (ITA), including the role of its branches in supplying circulation to the sternum, requires explicit anatomic knowledge of this vessel. Fifty-six ITAs (28 right, 28 left) were dissected from their point of origins after injection with a mixture of contrast medium and latex after perfusion with saline and immersion in 4% formaldehyde. All ITA branches were studied according to their course, size, and distribution within intercostal spaces with the aid of an operating microscope. The branches were divided in two main groups: proper (solitary) branches and common trunks. The proper branches consisted of four types: sternal, perforating, intercostal, and mediastinal. The four types of common trunks were: sternal/perforating, sternal/intercostal, perforating/intercostal, sternal/perforating/intercostal. Points of most frequent origin from main trunk of the vessel were established for each type. Mean external diameter of proper branches was 0.72 mm and common trunks was 1.06 mm. Mean length of common trunks was 3.0 mm. Those parameters (adequate diameter and length) allow for ligation of the common trunks close to the ITA so that their points of division can be preserved. This fact is crucial for creation of collateral blood supply to the sternum after bilateral ITA mobilizations.
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Affiliation(s)
- K Pietrasik
- Department of Anatomy, University Medical School of Warsaw, Warsaw, Poland.
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