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Gubelin H, Osorio JC, Gaggero A, Gubelin W, Aguayo F. Human papillomaviruses in hand squamous cell carcinomas from Chilean patients. Infect Agent Cancer 2024; 19:48. [PMID: 39354509 PMCID: PMC11446095 DOI: 10.1186/s13027-024-00611-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 09/16/2024] [Indexed: 10/03/2024] Open
Abstract
INTRODUCTION Cutaneous squamous cell carcinoma (SCC) accounts for 20% of all skin cancers and its incidence continues to increase globally. It represents 75% of non-melanoma skin cancer (NMSC) mortality. Risk factors include ultraviolet radiation (UVR) exposure, advanced age, chemical exposure, fair skin types, and immunosuppression. While most human papillomavirus (HPV) infections are associated with the development of warts, a subgroup is potentially implicated in the development of cutaneous SCC. The prevalence of alpha, beta, and gamma-HPV in Chilean patients with hand SCCs has not been previously addressed. The objective of this study was to evaluate the presence of HPV and genotyping in hand SCC from Chilean patients. MATERIALS AND METHODS An observational, cross-sectional, descriptive study was conducted. Alpha (α), beta (β) and gamma (γ)-HPV detection was performed by conventional polymerase chain reaction (PCR) in paraffin-embedded tissue samples from 52 patients diagnosed with hand SCC from Santiago, Chile. HPV genotyping was carried out via direct amplicon sequencing by Sanger method. RESULTS The most frequent carcinoma site was the dorsum of the hands (52.5%). α-HPV was not detected in these specimens, whereas β-HPV and γ-HPV were detected in 25% of the analyzed samples. The most frequent genotypes found were β-HPV 100 (38%) and γ-HPV 178 (15%). Additionally, γ-HPV 101, 162, HPV-mSK_016, HPV-mSK_083, HPV-mSK_213 and HPV-mSK249nr genotypes were detected, none of which had been previously described in cutaneous SCC. CONCLUSION β-HPV and γ-HPV are detectable in 25% of hand SCCs from Chilean patients. It is important to conduct prospective studies to better elucidate the role of these viruses in the development of this disease.
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Affiliation(s)
- Hans Gubelin
- Departamento de Dermatología, Universidad de Los Andes, Santiago, Chile
- Centro Médico SkinMed, Santiago, Chile
| | - Julio C Osorio
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad de Tarapacá, Arica, Chile
| | - Aldo Gaggero
- Virology Program, Instituto de Ciencias Biomédicas (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Walter Gubelin
- Departamento de Dermatología, Universidad de Los Andes, Santiago, Chile.
- Centro Médico SkinMed, Santiago, Chile.
| | - Francisco Aguayo
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad de Tarapacá, Arica, Chile.
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Garcia‐Serrano A, Mukhedkar D, Hultin E, Rudsander U, Wettergren Y, Ure AE, Dillner J, Arroyo‐Mühr LS. Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep sequencing. Cancer Med 2023; 12:19291-19300. [PMID: 37641475 PMCID: PMC10557870 DOI: 10.1002/cam4.6483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is known to present a distinct microbiome profile compared to healthy mucosa. Non-targeted deep-sequencing strategies enable nowadays full microbiome characterization up to species level. AIM We aimed to analyze both bacterial and viral communities in CRC using these strategies. MATERIALS & METHODS We analyzed bacterial and viral communities using both DNA and RNA deep-sequencing (Novaseq) in colorectal tissue specimens from 10 CRC patients and 10 matched control patients. Following taxonomy classification using Kraken 2, different metrics for alpha and beta diversities as well as relative and differential abundance were calculated to compare tumoral and healthy samples. RESULTS No viral differences were identified between tissue types, but bacterial species Polynucleobacter necessarius had a highly increased presence for DNA in tumors (p = 0.001). RNA analyses showed that bacterial species Arabia massiliensis had a highly decreased transcription in tumors (p = 0.002) while Fusobacterium nucleatum transcription was highly increased in tumors (p = 0.002). DISCUSSION Sequencing of both DNA and RNA enables a wider perspective of micriobiome profiles. Lack of RNA transcription (Polynucleobacter necessarius) casts doubt on possible role of a microorganism in CRC. The association of F. nucleatum mainly with transcription, may provide further insights on its role in CRC. CONCLUSION Joint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level provided a huge coverage for both bacteria and virus and identifies differential specific bacterial species as tumor associated.
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Affiliation(s)
- Ainhoa Garcia‐Serrano
- Department of Clinical Science, Intervention and Technology (CLINTEC)Karolinska InstitutetStockholmSweden
| | - Dhananjay Mukhedkar
- Department of Clinical Science, Intervention and Technology (CLINTEC)Karolinska InstitutetStockholmSweden
- Hopsworks ABStockholmSweden
| | - Emilie Hultin
- Department of Clinical Science, Intervention and Technology (CLINTEC)Karolinska InstitutetStockholmSweden
| | - Ulla Rudsander
- Department of Clinical Science, Intervention and Technology (CLINTEC)Karolinska InstitutetStockholmSweden
| | - Yvonne Wettergren
- Department of SurgerySahlgrenska University Hospital, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Agustín Enrique Ure
- Department of Clinical Science, Intervention and Technology (CLINTEC)Karolinska InstitutetStockholmSweden
| | - Joakim Dillner
- Department of Clinical Science, Intervention and Technology (CLINTEC)Karolinska InstitutetStockholmSweden
- Center for Cervical Cancer EliminationForskningsgatan F56 Karolinska University Hospital HuddingeStockholmSweden
| | - Laila Sara Arroyo‐Mühr
- Department of Clinical Science, Intervention and Technology (CLINTEC)Karolinska InstitutetStockholmSweden
- Center for Cervical Cancer EliminationForskningsgatan F56 Karolinska University Hospital HuddingeStockholmSweden
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Neyton LPA, Langelier CR, Calfee CS. Metagenomic Sequencing in the ICU for Precision Diagnosis of Critical Infectious Illnesses. Crit Care 2023; 27:90. [PMID: 36941644 PMCID: PMC10027598 DOI: 10.1186/s13054-023-04365-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2023. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2023 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901 .
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Affiliation(s)
- Lucile P A Neyton
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Charles R Langelier
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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Ure A, Mukhedkar D, Arroyo Mühr LS. Using HPV-meta for human papillomavirus RNA quality detection. Sci Rep 2022; 12:13058. [PMID: 35906372 PMCID: PMC9338075 DOI: 10.1038/s41598-022-17318-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
In the era of cervical cancer elimination, accurate and validated pipelines to detect human papillomavirus are essential to elucidate and understand HPV association with human cancers. We aimed to provide an open-source pipeline, "HPV-meta", to detect HPV transcripts in RNA sequencing data, including several steps to warn operators for possible viral contamination. The "HPV-meta" pipeline automatically performs several steps, starting with quality trimming, human genome filtering, HPV detection (blastx), cut-off settlement (10 reads and 690 bp coverage to make an HPV call) and finishing with fasta sequence generation for HPV positive samples. Fasta sequences can then be aligned to assess sequence diversity among HPV positive samples. All RNA sequencing files (n = 10,908) present in the cancer genome atlas (TCGA) were analyzed. "HPV-meta" identified 25 different HPV types being present in 488/10,904 specimens. Validation of results showed 99.98% agreement (10,902/10,904). Multiple alignment from fasta files warned about high sequence identity between several HPV 18 and 38 positive samples, whose contamination had previously been reported. The "HPV-meta" pipeline is a robust and validated pipeline that detects HPV in RNA sequencing data. Obtaining the fasta files enables contamination investigation, a non very rare occurrence in next generation sequencing.
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Affiliation(s)
- Agustin Ure
- Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
| | - Dhananjay Mukhedkar
- Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
- Hopsworks AB, Medborgarplatsen 25, 118 72, Stockholm, Sweden
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Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics. Sci Rep 2021; 11:18852. [PMID: 34552145 PMCID: PMC8458301 DOI: 10.1038/s41598-021-98452-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 09/06/2021] [Indexed: 11/30/2022] Open
Abstract
Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies. We wished to compare DNA and RNA sequencing of bacterial and viral metagenomes and metatranscriptomes in the human cervix. Total nucleic acids from six human cervical samples were subjected to DNA and RNA sequencing. The effect of DNase-treatment before reverse transcription to cDNA were also analyzed. Similarities and differences in the metagenomic findings with the three different sequencing approaches were evaluated. A higher proportion of human sequences were detected by DNA sequencing (93%) compared to RNA sequencing without (76%) and with prior DNase-treatment (11%). On the contrary, bacterial sequences increased 17 and 91 times. However, the number of detected bacterial genera were less by RNA sequencing, suggesting that only a few contribute to most of the bacterial transcripts. The viral sequences were less by RNA sequencing, still twice as many virus genera were detected, including some RNA viruses that were missed by DNA sequencing. Metatranscriptomics of total cDNA provided improved detection of mainly transcribed bacteria and viruses in cervical swabs as well as detection of RNA viruses, compared to metagenomics.
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Arroyo Mühr LS, Hultin E, Dillner J. Transcription of human papillomaviruses in nonmelanoma skin cancers of the immunosuppressed. Int J Cancer 2021; 149:1341-1347. [PMID: 33990956 DOI: 10.1002/ijc.33683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022]
Abstract
Nonmelanoma skin cancer (NMSC) has a greatly increased incidence among the immunosuppressed and the DNA of human papillomavirus (HPV) is commonly found in these tumors. To investigate if there are any actively transcribed HPV infections in these tumors, we identified all skin cancers diagnosed after solid organ transplantation in Sweden during 1964-2011 (n = 7614 NMSCs) and requested the diagnostic tumor blocks from the corresponding pathology archives. For the present study, we selected diagnostic specimens from 345 NMSC and performed whole genome transcriptome analysis using NovaSeq (Illumina), in comparison with three cervical cancers. Although we obtained an abundance of high-quality paired reads per sample (median of 35 million reads), only 15 NMSC specimens contained HPV transcription. Three specimens had transcription of oncogenic anogenital HPVs (HPV16 and 56), six tumors had transcription of HPVs from the beta-2 species (three HPV38, two with HPV23 and one with HPV107) and then there was one observation each of transcription of HPVs 3, 26, 57, 147, 158, 168 and of two nonestablished HPV types belonging to the gamma genus. In conclusion, transcription of specific HPV types can be found in NMSC among the immunosuppressed, but this is not common.
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Affiliation(s)
| | - Emilie Hultin
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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Niu L, Chu X, Jiang Y, Zeng W. HPV infection upregulates the expression of ZNT-1 in condyloma acuminatum. Eur J Histochem 2021; 65. [PMID: 33908744 PMCID: PMC8103779 DOI: 10.4081/ejh.2021.3228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/13/2021] [Indexed: 11/23/2022] Open
Abstract
Condyloma acuminata (CA) are benign anogenital warts caused by human papillomavirus (HPV) infection with a high recurrence rate. Despite its high contagiousness, high recurrence rate and potential for malignant transformation, effective treatments for CA have not yet been developed. Accordingly, it is necessary to clarify the mechanisms underlying CA development. Zinc (Zn) is stably maintained in the weight of human body. Skin is the third most Zn-abundant tissue in the body. Zn is present as a divalent ion (Zn2+) in cells and does not need a redox reaction upon crossing the cellular membrane. Zn transporters (ZnTs; SLC30A) and Irt-like proteins (ZIPs; SLC39A) are involved in Zn2+ efflux and uptake, respectively. ZnT1 is one of the ZnTs, which associates with the development of HPV. However, the role of ZnT1 regulation in the CA caused by HPV infection remains unknown. A multigroup case-control study was designed to investigate the expression and significance of the ZnT1 in patients with CA infected with HPV and in normal vulva controls. ZnT1 was assessed by immunohistochemistry in 44 patients with CA at Zhongnan Hospital of Wuhan University 2019-2020. Samples were analyzed by paraffin embedding and sectioning and hematoxylin-eosin and immunohistochemical staining. Immunohistochemical methods detected specific, dark brown, positive staining of ZnT1 in the keratinocytes of epidermis. We verified that the expression levels of ZnT1 that interact with HPV were upregulated in the CA groups independently of genotype compared with the control group. And then we found that the HPV risk grade in CA patients has a certain correlation with ZnT1 expression. These findings showed that HPV infection upregulated the expression of ZnT1 in CA. Additionally, there were obvious differences in the expression of ZnT1 between the different HPV risk grade infection groups. The higher the HPV risk grade, the stronger the ZNT1 protein expression. This study provided new insights into the sign pathway to HPV infection.
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Affiliation(s)
- Li Niu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan.
| | - Xiaoying Chu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan.
| | - Yaofei Jiang
- Hubei Cancer Clinical Study Centre and Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan.
| | - Wei Zeng
- Hubei Cancer Clinical Study Centre and Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan.
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Arroyo Mühr LS, Dillner J. Author's reply to: Human papillomavirus type 197 is not associated with skin tumors. Int J Cancer 2019; 145:3181. [PMID: 31456228 DOI: 10.1002/ijc.32645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 08/15/2019] [Indexed: 11/12/2022]
Affiliation(s)
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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