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Chronic infection of hepatitis B virus (HBV) is the major cause of hepatocellular carcinoma (HCC). Notably, 90% of HBV-positive HCC cases exhibit detectable HBV integrations, hinting at the potential early entanglement of these viral integrations in tumorigenesis and their subsequent oncogenic implications. Nevertheless, the precise chronology of integration events during HCC tumorigenesis, alongside their sequential structural patterns, has remained elusive thus far. In this study, we applied whole-genome sequencing to multiple biopsies extracted from six HBV-positive HCC cases. Through this approach, we identified point mutations and viral integrations, offering a blueprint for the intricate tumor phylogeny of these samples. The emergent narrative paints a rich tapestry of diverse evolutionary trajectories characterizing the analyzed tumors. We uncovered oncogenic integration events in some samples that appear to happen before and during the initiation stage of tumor development based on their locations in reconstituted trajectories. Furthermore, we conducted additional long-read sequencing of selected samples and unveiled integration-bridged chromosome rearrangements and tandem repeats of the HBV sequence within integrations. In summary, this study revealed premalignant oncogenic and sequential complex integrations and highlighted the contributions of HBV integrations to HCC development and genome instability.

End-stage kidney disease represents irreversible kidney failure. Dialysis and transplantation, two main treatment options currently available, present various drawbacks and complications. Innovative cell-based therapies, such as a bioartificial kidney, have not reached the clinic yet, mostly due to safety and/or functional issues. Here, we assessed the safety of conditionally immortalized proximal tubule epithelial cells (ciPTECs) for bioartificial kidney application, by using in vitro assays and athymic nude rats. We demonstrate that these cells do not possess key properties of oncogenically transformed cells, including anchorage-independent growth, lack of contact inhibition and apoptosis-resistance. In late-passage cells we did observe complex chromosomal abnormalities favoring near-tetraploidy, indicating chromosomal instability. However, time-lapse imaging of ciPTEC-OAT1, confined to a 3D extracellular matrix (ECM)-based environment, revealed that the cells were largely non-invasive. Furthermore, we determined the viral integration sites of SV40 Large T antigen (SV40T), human telomerase (hTERT) and OAT1 (SLC22A6), the transgenes used for immortalization and cell function enhancement. All integrations sites were found to be located in the intronic regions of endogenous genes. Among these genes, early endosome antigen 1 (EEA1) involved in endocytosis, and BCL2 Like 1 (BCL2L1) known for its role in regulating apoptosis, were identified. Nevertheless, both gene products appeared to be functionally intact. Finally, after subcutaneous injection in athymic nude rats we show that ciPTEC-OAT1 lack tumorigenic and oncogenic effects in vivo, confirming the in vitro findings. Taken together, this study lays an important foundation towards bioartificial kidney (BAK) development by confirming the safety of the cell line intended for incorporation.

[Background] The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the unintentional activation of oncogenes that can result in cancer. Therefore, the analysis of integration sites of retroviral vectors is a crucial step in developing safer vectors for therapeutic use., [Results] Here we present VISMapper, a vector integration site analysis web server, to analyze next-generation sequencing data for retroviral vector integration sites. VISMapper can be found at: http://vismapper.babelomics.org ., [Conclusions] Because it uses novel mapping algorithms VISMapper is remarkably faster than previous available programs. It also provides a useful graphical interface to analyze the integration sites found in the genomic context.

Cervical cancer is the second most prevalent cancer worldwide and is the second leading cause of cancer deaths in women. Persistent infection with high-risk human papillomaviruses (HPVs) types are the causative agents of cervical cancer, since 99% of tumors are positive for HPV DNA, HPV is a necessary cause of invasive cervical cancer worldwide. One of the key events of HPV-induced carcinogenesis is the integration of the HPV genome into a host chromosome, related with precancerous lesions progression. Integration follows a more specific pattern with respect to the HPV genome, expression of the viral E6 and E7 genes is consistently maintained, whereas other positions of the viral DNA are deleted or their expression is disturbed, like E2 gene. Loss of expression of the HPV E2 transcriptional repressor is significant and may be critical for malignant progression, as it may result in increased HPV E6 and E7 expression. The HPV E6 and E7 oncoproteins inactivate the p53 and pRB tumor suppressors; expression of high-risk HPV E6/E7 oncogenes provides a subset of the minimally required carcinogenic hits for full transformation of human epithelial cells. There is also evidence for deregulated HPV-16 E6-E7 mRNA stability after integration and specific alterations of host cellular gene expression have been detected upon HPV genome integration. Currently, integration of HPV is considered to be an important genetic alteration for the progression of intraepithelial lesions to invasive disease with potential clinical applications like mark tumour progression and diagnostic tool., El cáncer de cuello uterino (CCU) constituye un problema generalizado de salud que ocupa el segundo lugar a nivel mundial entre las neoplasias malignas de la mujer. Las infecciones persistentes con virus del papiloma humano (VPH) de alto riesgo son reconocidas actualmente como un factor necesario en el desarrollo de CCU y sus lesiones precursoras. Uno de los procesos que parece estar más involucrado en el origen de las células malignas, es el evento de integración del virus al genoma del huésped, relacionado también con la progresión de lesiones preinvasivas y el mantenimiento del fenotipo transformado. Estos eventos de integración, especialmente de VPH tipo 16 se dan en secuencias específicas del genoma viral, principalmente en su región E1/E2, interrumpiendo la secuencia y permitiendo que exista desregulación de las actividades de transcripción, conduciendo a la sobreexpresión de las oncoproteínas virales E6 y E7 que normalmente inactivan genes supresores de tumores, como p53 y pRb, responsables del control en importantes puntos de chequeo del ciclo celular. Actualmente el proceso de integración viral, es considerado como una alteración genética importante que caracteriza las displasias malignas, con potenciales aplicaciones como marcador de progresión de lesiones precursoras y herramienta de diagnóstico.

Active transport of proteins and mRNAs between the nucleus and cytoplasm is a major process in eukaryotic cells. Recently, factors that recognize transport substrates and mediate nuclear import or export have been characterized, revealing interactions that target substrates to the nuclear pore complexes, through which translocation occurs. In the first half of the report, nuclear import of the human immunodeficiency virus 1 (HIV-1) preintegration complex (PIC) is discussed. The second half describes recent information on the mechanistic details of nuclear export of viral mRNA so-called Revdependent trans-activation of viral genes.

Active transport of proteins and mRNAs between the nucleus and cytoplasm is a major process in eukaryotic cells. Recently, factors that recognize transport substrates and mediate nuclear import or export have been characterized, revealing interactions that target substrates to the nuclear pore complexes, through which translocation occurs. In the first half of the report, nuclear import of the human immunodeficiency virus 1 (HIV-1) preintegration complex (PIC) is discussed. The second half describes recent information on the mechanistic details of nuclear export of viral mRNA so-called Revdependent trans-activation of viral genes.