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Article ; Online: Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers

Mayuri Inchanalkar / Sumana Srivatsa / Srikant Ambatipudi / Priyanka G. Bhosale / Asawari Patil / Alejandro A. Schäffer / Niko Beerenwinkel / Manoj B. Mahimkar

Clinical Epigenetics, Vol 15, Iss 1, Pp 1-

2023 Volume 16

Abstract: Abstract Background Gingivobuccal complex oral squamous cell carcinoma (GBC-OSCC) is an aggressive malignancy with high mortality often preceded by premalignant lesions, including leukoplakia. Previous studies have reported genomic drivers in OSCC, but ... ...

Abstract	Abstract Background Gingivobuccal complex oral squamous cell carcinoma (GBC-OSCC) is an aggressive malignancy with high mortality often preceded by premalignant lesions, including leukoplakia. Previous studies have reported genomic drivers in OSCC, but much remains to be elucidated about DNA methylation patterns across different stages of oral carcinogenesis. Results There is a serious lack of biomarkers and clinical application of biomarkers for early detection and prognosis of gingivobuccal complex cancers. Hence, in search of novel biomarkers, we measured genome-wide DNA methylation in 22 normal oral tissues, 22 leukoplakia, and 74 GBC-OSCC tissue samples. Both leukoplakia and GBC-OSCC had distinct methylation profiles as compared to normal oral tissue samples. Aberrant DNA methylation increases during the different stages of oral carcinogenesis, from premalignant lesions to carcinoma. We identified 846 and 5111 differentially methylated promoters in leukoplakia and GBC-OSCC, respectively, with a sizable fraction shared between the two sets. Further, we identified potential biomarkers from integrative analysis in gingivobuccal complex cancers and validated them in an independent cohort. Integration of genome, epigenome, and transcriptome data revealed candidate genes with gene expression synergistically regulated by copy number and DNA methylation changes. Regularised Cox regression identified 32 genes associated with patient survival. In an independent set of samples, we validated eight genes (FAT1, GLDC, HOXB13, CST7, CYB5A, MLLT11, GHR, LY75) from the integrative analysis and 30 genes from previously published reports. Bisulfite pyrosequencing validated GLDC (P = 0.036), HOXB13 (P < 0.0001) promoter hypermethylation, and FAT1 (P < 0.0001) hypomethylation in GBC-OSCC compared to normal controls. Conclusions Our findings identified methylation signatures associated with leukoplakia and gingivobuccal complex cancers. The integrative analysis in GBC-OSCC identified putative biomarkers that enhance ...
Keywords	Leukoplakia ; Gingivobuccal complex cancers ; OSCC ; DNA methylation ; Integrative analysis ; Prognosis ; Medicine ; R ; Genetics ; QH426-470
Subject code	310 ; 570
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Strain level microbial detection and quantification with applications to single cell metagenomics

Kaiyuan Zhu / Alejandro A. Schäffer / Welles Robinson / Junyan Xu / Eytan Ruppin / A. Funda Ergun / Yuzhen Ye / S. Cenk Sahinalp

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 19

Abstract: Here the authors develop CAMMiQ, a combinatorial optimization approach that utilizes variable length, “unique” and “doubly-unique” genomic segments, showing improves identification and quantification of distinct microbes in metagenomic sequence data. ...

Abstract	Here the authors develop CAMMiQ, a combinatorial optimization approach that utilizes variable length, “unique” and “doubly-unique” genomic segments, showing improves identification and quantification of distinct microbes in metagenomic sequence data.
Keywords	Science ; Q
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Large-Scale Study of Antibody Titer Decay following BNT162b2 mRNA Vaccine or SARS-CoV-2 Infection

Ariel Israel / Yotam Shenhar / Ilan Green / Eugene Merzon / Avivit Golan-Cohen / Alejandro A. Schäffer / Eytan Ruppin / Shlomo Vinker / Eli Magen

Vaccines, Vol 10, Iss 64, p

2022 Volume 64

Abstract: Immune protection following either vaccination or infection with SARS-CoV-2 is thought to decrease over time. We designed a retrospective study, conducted at Leumit Health Services in Israel, to determine the kinetics of SARS-CoV-2 IgG antibodies ... ...

Abstract	Immune protection following either vaccination or infection with SARS-CoV-2 is thought to decrease over time. We designed a retrospective study, conducted at Leumit Health Services in Israel, to determine the kinetics of SARS-CoV-2 IgG antibodies following administration of two doses of BNT162b2 vaccine, or SARS-CoV-2 infection in unvaccinated individuals. Antibody titers were measured between 31 January 2021, and 31 July 2021 in two mutually exclusive groups: (i) vaccinated individuals who received two doses of BNT162b2 vaccine and had no history of previous infection with COVID-19 and (ii) SARS-CoV-2 convalescents who had not received the vaccine. A total of 2653 individuals fully vaccinated by two doses of vaccine during the study period and 4361 convalescent patients were included. Higher SARS-CoV-2 IgG antibody titers were observed in vaccinated individuals (median 1581 AU/mL IQR [533.8–5644.6]) after the second vaccination than in convalescent individuals (median 355.3 AU/mL IQR [141.2–998.7]; p < 0.001). In vaccinated subjects, antibody titers decreased by up to 38% each subsequent month while in convalescents they decreased by less than 5% per month. Six months after BNT162b2 vaccination 16.1% subjects had antibody levels below the seropositivity threshold of <50 AU/mL, while only 10.8% of convalescent patients were below <50 AU/mL threshold after 9 months from SARS-CoV-2 infection. This study demonstrates individuals who received the Pfizer-BioNTech mRNA vaccine have different kinetics of antibody levels compared to patients who had been infected with the SARS-CoV-2 virus, with higher initial levels but a much faster exponential decrease in the first group.
Keywords	antibody titer ; BNT162b2 mRNA vaccine ; SARS-CoV-2 infection ; Medicine ; R
Subject code	570
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Clinical and Laboratory Features in the Israeli Population with COVID-19 Infection after Pfizer-BioNTech mRNA Booster Vaccination

Ariel Israel / Eugene Merzon / Yotam Shenhar / Ilan Green / Avivit Golan-Cohen / Alejandro A. Schäffer / Eytan Ruppin / Shlomo Vinker / Eli Magen

Vaccines, Vol 10, Iss 636, p

2022 Volume 636

Abstract: Background: Immune protection following either vaccination or infection with SARS-CoV-2 decreases over time. Objective: We aim to describe clinical and sociodemographic characteristics associated with COVID-19 infection at least 14 days after booster ... ...

Abstract	Background: Immune protection following either vaccination or infection with SARS-CoV-2 decreases over time. Objective: We aim to describe clinical and sociodemographic characteristics associated with COVID-19 infection at least 14 days after booster vaccination in the Israeli population. Methods: We conducted a population-based study among adult members of Leumit Health Services (LHS) in Israel. Nasopharyngeal swabs were examined for SARS-CoV-2 by real-time RT-PCR. The hematological and biochemical parameters in the peripheral blood before booster vaccination were evaluated. Results: Between 1 February 2021 and 30 November 2021, 136,683 individuals in LHS were vaccinated with a booster (third dose) of the BNT162b2 vaccine. Of these, 1171 (0.9%) were diagnosed with COVID-19 by testing positive for SARS-CoV-2 RT-PCR at least >14 days after the booster vaccination. The COVID-19-positive group was characterized by higher rates of chronic kidney disease than the matched COVID-19-negative group (43 (3.7%) vs. 3646 (2.7%); p = 0.039). Anemia, lower peripheral blood lymphocytes, monocytes, basophils, C3 Complement, cholesterol, and prothrombin time were also associated with COVID-19 after booster vaccination. Conclusion: People with chronic kidney disease and anemia should be included in possible future annual SARS-CoV-2 vaccination recommendations.
Keywords	BNT162b2 ; mRNA ; vaccine ; SARS-CoV-2 ; infection ; convalescents ; Medicine ; R
Subject code	630 ; 610
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective

Saba Ahmadi / Pattara Sukprasert / Rahulsimham Vegesna / Sanju Sinha / Fiorella Schischlik / Natalie Artzi / Samir Khuller / Alejandro A. Schäffer / Eytan Ruppin

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 17

Abstract: Intra-tumor heterogeneity is often associated with resistance to targeted therapy, requiring the design of combinatorial therapies. Here, based on tumor single-cell transcriptomic datasets, the authors develop a computational approach to identify optimal ...

Abstract	Intra-tumor heterogeneity is often associated with resistance to targeted therapy, requiring the design of combinatorial therapies. Here, based on tumor single-cell transcriptomic datasets, the authors develop a computational approach to identify optimal combinatorial treatments targeting membrane receptors for cancer therapy.
Keywords	Science ; Q
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: In vitro and in vivo identification of clinically approved drugs that modify ACE2 expression

Sanju Sinha / Kuoyuan Cheng / Alejandro A Schäffer / Kenneth Aldape / Eyal Schiff / Eytan Ruppin

Molecular Systems Biology, Vol 16, Iss 7, Pp n/a-n/a (2020)

2020

Abstract: Abstract The COVID‐19 pandemic caused by SARS‐CoV‐2 has been a global health challenge. Angiotensin‐converting enzyme 2 (ACE2) is the host receptor for SARS‐CoV‐2 entry. Recent studies have suggested that patients with hypertension and diabetes treated ... ...

Abstract	Abstract The COVID‐19 pandemic caused by SARS‐CoV‐2 has been a global health challenge. Angiotensin‐converting enzyme 2 (ACE2) is the host receptor for SARS‐CoV‐2 entry. Recent studies have suggested that patients with hypertension and diabetes treated with ACE inhibitors (ACEIs) or angiotensin receptor blockers have a higher risk of COVID‐19 infection as these drugs could upregulate ACE2, motivating the study of ACE2 modulation by drugs in current clinical use. Here, we mined published datasets to determine the effects of hundreds of clinically approved drugs on ACE2 expression. We find that ACEIs are enriched for ACE2‐upregulating drugs, while antineoplastic agents are enriched for ACE2‐downregulating drugs. Vorinostat and isotretinoin are the top ACE2 up/downregulators, respectively, in cell lines. Dexamethasone, a corticosteroid used in treating severe acute respiratory syndrome and COVID‐19, significantly upregulates ACE2 both in vitro and in vivo. Further top ACE2 regulators in vivo or in primary cells include erlotinib and bleomycin in the lung and vancomycin, cisplatin, and probenecid in the kidney. Our study provides leads for future work studying ACE2 expression modulators.
Keywords	angiotensin I‐converting enzyme 2 ; coronavirus disease 2019 ; dexamethasone ; drug‐modifying ACE2 expression ; severe acute respiratory syndrome coronavirus 2 ; Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A deep learning approach reveals unexplored landscape of viral expression in cancer

Abdurrahman Elbasir / Ying Ye / Daniel E. Schäffer / Xue Hao / Jayamanna Wickramasinghe / Konstantinos Tsingas / Paul M. Lieberman / Qi Long / Quaid Morris / Rugang Zhang / Alejandro A. Schäffer / Noam Auslander

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 12

Abstract: Here, Elbasir et al. develop viRNAtrap, a deep learning approach for detection of viruses from tumor RNA sequencing data, which they showcase on an RNA dataset of different cancer types, revealing tumor expression of divergent viruses that had not been ... ...

Abstract	Here, Elbasir et al. develop viRNAtrap, a deep learning approach for detection of viruses from tumor RNA sequencing data, which they showcase on an RNA dataset of different cancer types, revealing tumor expression of divergent viruses that had not been previously implicated in cancer.
Keywords	Science ; Q
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Quickly identifying identical and closely related subjects in large databases using genotype data.

Yumi Jin / Alejandro A Schäffer / Stephen T Sherry / Michael Feolo

PLoS ONE, Vol 12, Iss 6, p e

2017 Volume 0179106

Abstract: Genome-wide association studies (GWAS) usually rely on the assumption that different samples are not from closely related individuals. Detection of duplicates and close relatives becomes more difficult both statistically and computationally when one ... ...

Abstract	Genome-wide association studies (GWAS) usually rely on the assumption that different samples are not from closely related individuals. Detection of duplicates and close relatives becomes more difficult both statistically and computationally when one wants to combine datasets that may have been genotyped on different platforms. The dbGaP repository at the National Center of Biotechnology Information (NCBI) contains datasets from hundreds of studies with over one million samples. There are many duplicates and closely related individuals both within and across studies from different submitters. Relationships between studies cannot always be identified by the submitters of individual datasets. To aid in curation of dbGaP, we developed a rapid statistical method called Genetic Relationship and Fingerprinting (GRAF) to detect duplicates and closely related samples, even when the sets of genotyped markers differ and the DNA strand orientations are unknown. GRAF extracts genotypes of 10,000 informative and independent SNPs from genotype datasets obtained using different methods, and implements quick algorithms that enable it to find all of the duplicate pairs from more than 880,000 samples within and across dbGaP studies in less than two hours. In addition, GRAF uses two statistical metrics called All Genotype Mismatch Rate (AGMR) and Homozygous Genotype Mismatch Rate (HGMR) to determine subject relationships directly from the observed genotypes, without estimating probabilities of identity by descent (IBD), or kinship coefficients, and compares the predicted relationships with those reported in the pedigree files. We implemented GRAF in a freely available C++ program of the same name. In this paper, we describe the methods in GRAF and validate the usage of GRAF on samples from the dbGaP repository. Other scientists can use GRAF on their own samples and in combination with samples downloaded from dbGaP.
Keywords	Medicine ; R ; Science ; Q
Subject code	020
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The GENDULF algorithm

Noam Auslander / Daniel M Ramos / Ivette Zelaya / Hiren Karathia / Thomas O. Crawford / Alejandro A Schäffer / Charlotte J Sumner / Eytan Ruppin

Molecular Systems Biology, Vol 16, Iss 12, Pp n/a-n/a (2020)

mining transcriptomics to uncover modifier genes for monogenic diseases

2020

Abstract: Abstract Modifier genes are believed to account for the clinical variability observed in many Mendelian disorders, but their identification remains challenging due to the limited availability of genomics data from large patient cohorts. Here, we present ... ...

Abstract	Abstract Modifier genes are believed to account for the clinical variability observed in many Mendelian disorders, but their identification remains challenging due to the limited availability of genomics data from large patient cohorts. Here, we present GENDULF (GENetic moDULators identiFication), one of the first methods to facilitate prediction of disease modifiers using healthy and diseased tissue gene expression data. GENDULF is designed for monogenic diseases in which the mechanism is loss of function leading to reduced expression of the mutated gene. When applied to cystic fibrosis, GENDULF successfully identifies multiple, previously established disease modifiers, including EHF, SLC6A14, and CLCA1. It is then utilized in spinal muscular atrophy (SMA) and predicts U2AF1 as a modifier whose low expression correlates with higher SMN2 pre‐mRNA exon 7 retention. Indeed, knockdown of U2AF1 in SMA patient‐derived cells leads to increased full‐length SMN2 transcript and SMN protein expression. Taking advantage of the increasing availability of transcriptomic data, GENDULF is a novel addition to existing strategies for prediction of genetic disease modifiers, providing insights into disease pathogenesis and uncovering novel therapeutic targets.
Keywords	cystic fibrosis ; digenic inheritance ; gene expression ; modifier gene ; spinal muscular atrophy ; Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: VADR

Alejandro A. Schäffer / Eneida L. Hatcher / Linda Yankie / Lara Shonkwiler / J. Rodney Brister / Ilene Karsch-Mizrachi / Eric P. Nawrocki

BMC Bioinformatics, Vol 21, Iss 1, Pp 1-

validation and annotation of virus sequence submissions to GenBank

2020 Volume 23

Abstract: Abstract Background GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to ... ...

Abstract	Abstract Background GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions. Results We developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available ( https://github.com/nawrockie/vadr ) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Since March 2020, VADR has also been used to check SARS-CoV-2 sequence submissions. Other viruses with high numbers of submissions will be added incrementally. Conclusion VADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the software allow researchers to run the ...
Keywords	Annotation ; Virus ; Alignment ; ncRNA ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	005
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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