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Article: Anatomical landscape of oral squamous cell carcinoma: A single cancer center study in UAE.

Al-Rawi, Natheer H / Hachim, Ibrahim Y / Hachim, Mahmood Y / Salmeh, Abdulrahman / Uthman, Asmaa T / Marei, Hesham

2023 Volume 9, Issue 5, Page(s) e15884

Abstract: Objectives: This study aimed to present demographic and clinicopathological aspects of OSCC identified in Pathology service in the UAE over a 13-year period and compare these findings to a cohort of 523 cases of Head and neck squamous cell carcinoma ... ...

Abstract	Objectives: This study aimed to present demographic and clinicopathological aspects of OSCC identified in Pathology service in the UAE over a 13-year period and compare these findings to a cohort of 523 cases of Head and neck squamous cell carcinoma using the Cancer Genome Atlas's cBioPortal database (http://cbioportal.org). Material and methods: Histological examination of all hematoxylin and eosin-stained slides and assessment of all demographic and clinical information from laboratory records were performed on all OSCC diagnosed between 2005 and 2018. Results: Males made up 71.4% of the sample of 231 OSCCs that were evaluated. The patients' average age was 55.38 years. The two most prevalent afflicted sites were the anterior two-thirds of the tongue (57.6%) and the cheek (28.1%). The most prevalent site among smokers were the floor of mouth, cheek, and jaw bones. There was a link between tumor size and numerous anatomical subsites that was shown to be highly significant. OSCC in the FOM was associated with a 25% mortality rate. Patients with OSCC of the anterior tongue and cheek had the best prognosis, with only 15.7% and 15.3% of patients dying during follow-up. Conclusion: The present investigation found a correlation between the diverse clinicopathological characteristics of the various anatomical subsites in OSCC. Different anatomical subsites also displayed varying degrees of gene mutation.
Language	English
Publishing date	2023-05-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e15884
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Antibody landscapes of SARS-CoV-2 can reveal novel vaccine and diagnostic targets.

Hachim, Asmaa / Kavian, Niloufar / Valkenburg, Sophie A

Current opinion in virology

2021 Volume 50, Page(s) 139–146

Abstract: SARS-CoV-2 virions are composed of structural proteins, but during virus infection, an additional 30 proteins could be expressed according to putative open reading frames (ORFs) of the viral genome. Some of these additional proteins modulate cellular ... ...

Abstract	SARS-CoV-2 virions are composed of structural proteins, but during virus infection, an additional 30 proteins could be expressed according to putative open reading frames (ORFs) of the viral genome. Some of these additional proteins modulate cellular processes through direct interactions, their truncations can affect disease pathogenesis and they can also serve as antigenic targets for more specific serology. In addition to structural proteins, the ORF1a/b polyprotein and accessory proteins can stimulate antibody responses during infection. Antibodies that target non-structural proteins can impact viral infection, through Fc mediated effector functions, through interactions during virus entry, fusion, replication and egress within infected cells. Characterization of the serological responses to additional proteins, provides a snapshot of the 'antibody landscape', which includes the antibody magnitude, antigenic specificity and informs the biological relevance of SARS-CoV-2 proteins.
MeSH term(s)	Antibodies, Viral/blood ; Antibodies, Viral/immunology ; COVID-19/diagnosis ; COVID-19/immunology ; COVID-19/prevention & control ; COVID-19 Vaccines/immunology ; Humans ; SARS-CoV-2/immunology
Chemical Substances	Antibodies, Viral ; COVID-19 Vaccines
Language	English
Publishing date	2021-08-20
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2611378-8
ISSN	1879-6265 ; 1879-6257
ISSN (online)	1879-6265
ISSN	1879-6257
DOI	10.1016/j.coviro.2021.08.006
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Article ; Online: Anatomical landscape of oral squamous cell carcinoma

Natheer H. Al-Rawi / Ibrahim Y. Hachim / Mahmood Y. Hachim / Abdulrahman Salmeh / Asmaa T. Uthman / Hesham Marei

Heliyon, Vol 9, Iss 5, Pp e15884- (2023)

A single cancer center study in UAE

2023

Abstract	Objectives: This study aimed to present demographic and clinicopathological aspects of OSCC identified in Pathology service in the UAE over a 13-year period and compare these findings to a cohort of 523 cases of Head and neck squamous cell carcinoma using the Cancer Genome Atlas's cBioPortal database (http://cbioportal.org). Material and methods: Histological examination of all hematoxylin and eosin-stained slides and assessment of all demographic and clinical information from laboratory records were performed on all OSCC diagnosed between 2005 and 2018. Results: Males made up 71.4% of the sample of 231 OSCCs that were evaluated. The patients' average age was 55.38 years. The two most prevalent afflicted sites were the anterior two-thirds of the tongue (57.6%) and the cheek (28.1%). The most prevalent site among smokers were the floor of mouth, cheek, and jaw bones. There was a link between tumor size and numerous anatomical subsites that was shown to be highly significant. OSCC in the FOM was associated with a 25% mortality rate. Patients with OSCC of the anterior tongue and cheek had the best prognosis, with only 15.7% and 15.3% of patients dying during follow-up. Conclusion: The present investigation found a correlation between the diverse clinicopathological characteristics of the various anatomical subsites in OSCC. Different anatomical subsites also displayed varying degrees of gene mutation.
Keywords	Oral cancer ; Anatomical sites ; Bioportal ; Oral tongue ; Jaw bones ; Base of tongue ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	610
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Anatomical landscape of oral squamous cell carcinoma: A single cancer center study in UAE

Al-Rawi, Natheer H. / Hachim, Ibrahim Y. / Hachim, Mahmood Y. / Salmeh, Abdulrahman / Uthman, Asmaa T. / Marei, Hesham

Heliyon. 2023 May, v. 9, no. 5 p.e15884-

2023

Abstract: This study aimed to present demographic and clinicopathological aspects of OSCC identified in Pathology service in the UAE over a 13-year period and compare these findings to a cohort of 523 cases of Head and neck squamous cell carcinoma using the Cancer ...

Abstract	This study aimed to present demographic and clinicopathological aspects of OSCC identified in Pathology service in the UAE over a 13-year period and compare these findings to a cohort of 523 cases of Head and neck squamous cell carcinoma using the Cancer Genome Atlas's cBioPortal database (http://cbioportal.org). Histological examination of all hematoxylin and eosin-stained slides and assessment of all demographic and clinical information from laboratory records were performed on all OSCC diagnosed between 2005 and 2018. Males made up 71.4% of the sample of 231 OSCCs that were evaluated. The patients' average age was 55.38 years. The two most prevalent afflicted sites were the anterior two-thirds of the tongue (57.6%) and the cheek (28.1%). The most prevalent site among smokers were the floor of mouth, cheek, and jaw bones. There was a link between tumor size and numerous anatomical subsites that was shown to be highly significant. OSCC in the FOM was associated with a 25% mortality rate. Patients with OSCC of the anterior tongue and cheek had the best prognosis, with only 15.7% and 15.3% of patients dying during follow-up. The present investigation found a correlation between the diverse clinicopathological characteristics of the various anatomical subsites in OSCC. Different anatomical subsites also displayed varying degrees of gene mutation.
Keywords	databases ; genes ; head and neck squamous cell carcinoma ; histology ; landscapes ; mortality ; mutation ; prognosis ; squamous cell carcinoma ; tongue ; Oral cancer ; Anatomical sites ; Bioportal ; Oral tongue ; Jaw bones ; Base of tongue ; OSCC
Language	English
Dates of publication	2023-05
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e15884
Database	NAL-Catalogue (AGRICOLA)

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Article: Repeated influenza vaccination provides cumulative protection from distinct H3N2 viruses.

Kavian, Niloufar / Hachim, Asmaa / Cowling, Benjamin J / Valkenburg, Sophie A

Clinical & translational immunology

2021 Volume 10, Issue 6, Page(s) e1297

Abstract: Objectives: Current inactivated influenza vaccines provide suboptimal protection against antigenic drift, and repeated annual vaccinations shape antibody specificity but the effect on protection from infection is not well understood.: Methods: We ... ...

Abstract	Objectives: Current inactivated influenza vaccines provide suboptimal protection against antigenic drift, and repeated annual vaccinations shape antibody specificity but the effect on protection from infection is not well understood. Methods: We studied the effects of cumulative and staggered vaccinations in mice to determine the effect of influenza vaccination on protection from infection and immune quality. Results: We found that the timing of vaccination and antigenic change impacted the quality of immune responses. When mice received two different H3N2 strains (A/Hong Kong/4801/2014 and A/Singapore/INFIMH-16-0019/2016) by staggered timing of vaccination, there were higher H3HA antibody and B-cell memory responses than four cumulative vaccinations or when two vaccinations were successive. Interestingly, after challenge with a lethal-drifted H3N2 virus (A/Hong Kong/1/1968), mice with staggered vaccination were unable to produce high titres of antibodies specific to the challenge strain compared to other vaccination regimens because of high levels of vaccine-specific cross-reactive antibodies. All vaccination regimens resulted in protection, in terms of viral loads and survival, from lethal challenge, while lung IL-6 and inflammation were lowest in staggered or cumulative vaccination groups, indicating further advantage. Conclusion: Our findings help justify influenza vaccination policies that currently recommend repeat vaccination in infants and annual seasonal vaccination, with no evidence for impaired immunity by repeated seasonal vaccination.
Language	English
Publishing date	2021-06-13
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2694482-0
ISSN	2050-0068
ISSN	2050-0068
DOI	10.1002/cti2.1297
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Article ; Online: Postmortem Stability of SARS-CoV-2 in Mouse Lung Tissue.

Valkenburg, Sophie A / Cheng, Samuel M S / Hachim, Asmaa / Peiris, Malik / Nicholls, John

Emerging infectious diseases

2021 Volume 27, Issue 12, Page(s) 3173–3175

Abstract: The infectivity of severe acute respiratory syndrome coronavirus 2 in deceased persons and organisms remains unclear. We studied transgenic K18 hACE2 mice to determine the kinetics of virus infectivity after host death. Five days after death, virus ... ...

Abstract	The infectivity of severe acute respiratory syndrome coronavirus 2 in deceased persons and organisms remains unclear. We studied transgenic K18 hACE2 mice to determine the kinetics of virus infectivity after host death. Five days after death, virus infectivity in the lung declined by >96% and RNA copies declined by 48.2%.
MeSH term(s)	Animals ; COVID-19 ; Disease Models, Animal ; Humans ; Lung ; Mice ; Mice, Transgenic ; SARS-CoV-2
Language	English
Publishing date	2021-09-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2712.211621
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Article ; Online: Vaccination with ADCC activating HA peptide epitopes provides partial protection from influenza infection.

Kavian, Niloufar / Hachim, Asmaa / Poon, Leo L M / Valkenburg, Sophie A

Vaccine

2020 Volume 38, Issue 37, Page(s) 5885–5890

Abstract: Influenza-specific antibody dependent cellular cytotoxicity (ADCC) antibodies have a broad cross reactivity and potential as an immune correlate for universal vaccines. Peptide-mapping for ADCC reactivity of H1-HA and H7-HA proteins from human serum ... ...

Abstract	Influenza-specific antibody dependent cellular cytotoxicity (ADCC) antibodies have a broad cross reactivity and potential as an immune correlate for universal vaccines. Peptide-mapping for ADCC reactivity of H1-HA and H7-HA proteins from human serum samples identified high ADCC-inducing peptides in both the HA1 and HA2 regions. Vaccination of mice with single ADCC-peptides induced ADCC activity leading to partial protection from lethal influenza challenge, with increased survival, reduced viral loads, and reduced activation of NK cells in the lungs. Targeted vaccination strategies to elicit ADCC responses may provide an approach for universal vaccines.
MeSH term(s)	Animals ; Antibodies, Viral ; Antibody-Dependent Cell Cytotoxicity ; Epitopes ; Hemagglutinin Glycoproteins, Influenza Virus ; Influenza A Virus, H1N1 Subtype ; Influenza Vaccines ; Influenza, Human/prevention & control ; Mice ; Peptides ; Vaccination
Chemical Substances	Antibodies, Viral ; Epitopes ; Hemagglutinin Glycoproteins, Influenza Virus ; Influenza Vaccines ; Peptides
Language	English
Publishing date	2020-07-25
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2020.07.008
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Zs.MO 458: Show issues

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Article ; Online: Usp25-Erlin1/2 activity limits cholesterol flux to restrict virus infection.

Teo, Qi Wen / Wong, Ho Him / Heunis, Tiaan / Stancheva, Viktoriya / Hachim, Asmaa / Lv, Huibin / Siu, Lewis / Ho, Julian / Lan, Yun / Mok, Chris Ka Pun / Ulferts, Rachel / Sanyal, Sumana

Developmental cell

2023 Volume 58, Issue 22, Page(s) 2495–2509.e6

Abstract: Reprogramming lipid metabolic pathways is a critical feature of activating immune responses to infection. However, how these reconfigurations occur is poorly understood. Our previous screen to identify cellular deubiquitylases (DUBs) activated during ... ...

Abstract	Reprogramming lipid metabolic pathways is a critical feature of activating immune responses to infection. However, how these reconfigurations occur is poorly understood. Our previous screen to identify cellular deubiquitylases (DUBs) activated during influenza virus infection revealed Usp25 as a prominent hit. Here, we show that Usp25-deleted human lung epithelial A549 cells display a >10-fold increase in pathogenic influenza virus production, which was rescued upon reconstitution with the wild type but not the catalytically deficient (C178S) variant. Proteomic analysis of Usp25 interactors revealed a strong association with Erlin1/2, which we confirmed as its substrate. Newly synthesized Erlin1/2 were degraded in Usp25
MeSH term(s)	Humans ; Lipids ; Lung/metabolism ; Proteomics ; Ubiquitin Thiolesterase/genetics ; Ubiquitin Thiolesterase/metabolism ; Virus Diseases/genetics ; Virus Diseases/metabolism ; Cholesterol/metabolism
Chemical Substances	Lipids ; Ubiquitin Thiolesterase (EC 3.4.19.12) ; USP25 protein, human ; ERLIN1 protein, human ; ERLIN2 protein, human ; Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2023-09-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2023.08.013
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Zs.MG 76: Show issues

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Article: T Cells Targeting SARS-CoV-2: By Infection, Vaccination, and Against Future Variants.

Nguyen, Thi H O / Cohen, Carolyn A / Rowntree, Louise C / Bull, Maireid B / Hachim, Asmaa / Kedzierska, Katherine / Valkenburg, Sophie A

Frontiers in medicine

2021 Volume 8, Page(s) 793102

Abstract: T cell responses are a key cornerstone to viral immunity to drive high-quality antibody responses, establishing memory for recall and for viral clearance. Inefficient recruitment of T cell responses plays a role in the development of severe COVID-19 and ... ...

Abstract	T cell responses are a key cornerstone to viral immunity to drive high-quality antibody responses, establishing memory for recall and for viral clearance. Inefficient recruitment of T cell responses plays a role in the development of severe COVID-19 and is also represented by reduced cellular responses in men, children, and diversity compared with other epitope-specific subsets and available T cell receptor diversity. SARS-CoV-2-specific T cell responses are elicited by multiple vaccine formats and augmented by prior infection for hybrid immunity. Epitope conservation is relatively well-maintained leading to T cell crossreactivity for variants of concern that have diminished serological responses.
Language	English
Publishing date	2021-12-24
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2021.793102
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Article ; Online: Author Correction: Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population.

Nature medicine

2023 Volume 30, Issue 1, Page(s) 305

Language	English
Publishing date	2023-12-30
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-023-02648-2
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