Evidence map›Paper›PMID 39123171›Full record

ArticleBMC medical genomics2024

Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing.

Perihan Hamdy Kassem, Iman Fawzy Montasser, Ramy Mohamed Mahmoud, Rasha Ahmed Ghorab, Dina A AbdelHakam, Marium El Sayed Ahmad Fathi, Marwa A Abdel Wahed, Khaled Mohey, Mariam Ibrahim, Mohamed El Hadidi and 6 more

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Article in BMC medical genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors.

Perihan Hamdy KassemClinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Iman Fawzy MontasserTropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt. imanfawzy2@gmail.com.
Ramy Mohamed MahmoudClinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Rasha Ahmed GhorabClinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Dina A AbdelHakamClinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Marium El Sayed Ahmad FathiClinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Marwa A Abdel WahedClinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Khaled MoheyClinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Mariam IbrahimPathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Mohamed El HadidiInstitute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham Dubai Campus, Dubai, United Arab Emirates.
Yasmine M MasssoudTropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Manar SalahTropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Arwa AbugableSchool of Biosciences, University of Sheffield, Sheffield, UK.
Mohamad BahaaHepato-Pancreatico-Biliary Surgery Department and liver Transplantation, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Sherif El KhamisySchool of Biosciences, University of Sheffield, Sheffield, UK.
Mahmoud El MeteiniHepato-Pancreatico-Biliary Surgery Department and liver Transplantation, Faculty of Medicine, Ain Shams University, Cairo, Egypt.

Funding

Science and Technology Development Fund Basic and Applied Research Grant Call 7 (BARG Call 7, Project ID:38229).
6 · The paper itself

Abstract

backgroundHepatocellular carcinoma (HCC) is the most common primary liver cancer. Chronic hepatitis and liver cirrhosis lead to accumulation of genetic alterations driving HCC pathogenesis. This study is designed to explore genomic landscape of HCC in Egyptian patients by whole exome sequencing.

methodsWhole exome sequencing using Ion Torrent was done on 13 HCC patients, who underwent surgical intervention (7 patients underwent living donor liver transplantation (LDLT) and 6 patients had surgical resection}.

resultsMutational signature was mostly S1, S5, S6, and S12 in HCC. Analysis of highly mutated genes in both HCC and Non-HCC revealed the presence of highly mutated genes in HCC (AHNAK2, MUC6, MUC16, TTN, ZNF17, FLG, MUC12, OBSCN, PDE4DIP, MUC5b, and HYDIN). Among the 26 significantly mutated HCC genes-identified across 10 genome sequencing studies-in addition to TCGA, APOB and RP1L1 showed the highest number of mutations in both HCC and Non-HCC tissues. Tier 1, Tier 2 variants in TCGA SMGs in HCC and Non-HCC (TP53, PIK3CA, CDKN2A, and BAP1). Cancer Genome Landscape analysis revealed Tier 1 and Tier 2 variants in HCC (MSH2) and in Non-HCC (KMT2D and ATM). For KEGG analysis, the significantly annotated clusters in HCC were Notch signaling, Wnt signaling, PI3K-AKT pathway, Hippo signaling, Apelin signaling, Hedgehog (Hh) signaling, and MAPK signaling, in addition to ECM-receptor interaction, focal adhesion, and calcium signaling. Tier 1 and Tier 2 variants KIT, KMT2D, NOTCH1, KMT2C, PIK3CA, KIT, SMARCA4, ATM, PTEN, MSH2, and PTCH1 were low frequency variants in both HCC and Non-HCC.

conclusionOur results are in accordance with previous studies in HCC regarding highly mutated genes, TCGA and specifically enriched pathways in HCC. Analysis for clinical interpretation of variants revealed the presence of Tier 1 and Tier 2 variants that represent potential clinically actionable targets. The use of sequencing techniques to detect structural variants and novel techniques as single cell sequencing together with multiomics transcriptomics, metagenomics will integrate the molecular pathogenesis of HCC in Egyptian patients.

Indexed as

Carcinoma, HepatocellularExome SequencingLiver NeoplasmsMutationAdultEgyptFemaleGenomicsHumansMaleMiddle AgedHepatocelleular carcinoma (HCC)Living Donor Liver Transplantation (LDLT)Mutational signatureWhole exome sequencing

Identifiers

PMID39123171
PMCPMC11311965

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.