• Humans
• Altitude
• Neoplasms/genetics
• Neoplasms/pathology
• Adaptation, Physiological/genetics
• Hypoxia/genetics

• Financial support for the Center of Excellence Severo Ochoa (CEX2020-001024-S/AEI/10.13039/501100011 State Agency for Research
• #PID2023-151388OB-I00 Ministerio de Ciencia, Innovación y Universidades (MCIU)
• European Union (ERDF/ESF)-A way to build Europe and Fundació Enric Masip.
• #CA264248 Neuroendocrine Tumor Research Foundation (NETRF)
• R01 GM114102 NIGMS NIH HHS
• Paradifference Foundation (The Paradifference foundation)
• #PI20/00895 Instituto de Salud Carlos III (ISCIII)
• COST Action CA20122 Harmonisation European Cooperation in Science and Technology (COST)
• Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)
• Centres de Recerca de Catalunya (CERCA)
• R01 CA264248 NCI NIH HHS
• #91430 Pheipas Patients Association
• #GM114102 National Institute of Health
• #PI20/01754 Instituto de Salud Carlos III (ISCIII)
• Startup grant for VHIO's Biomarkers and Clonal Dynamics Laboratory Fundación Fero (Fundació Fero)
• For providing Institutional research facilities and equipment Fundación Cellex (Cellex Foundation)
• CAIMI-I Fundación BBVA (FBBVA)
• Miguel Servet #CP17/00199 Instituto de Salud Carlos III (ISCIII)
• European Union (ERDF/ESF)—A way to build Europe and Fundació Enric Masip.

• Humans
• Genomic Instability
• Neoplasms/genetics
• Neoplasms/pathology
• Tumor Hypoxia/genetics
• Tumor Microenvironment/genetics
• Animals
• Mutation

• software
• data mining

• Humans
• Single-Cell Analysis/methods
• Colorectal Neoplasms/genetics
• Transcriptome
• Computational Biology/methods
• Lupus Erythematosus, Systemic/genetics
• Gene Expression Profiling/methods
• Sequence Analysis, RNA/methods

• DNA damage and repair
• Hypoxia
• genomic instability
• non-coding RNAs
• phenotypes
• tumor hypoxia
• tumor microenvironment

• Humans
• RNA, Long Noncoding/genetics
• Gene Expression Regulation, Neoplastic
• Neoplasms/genetics
• Neoplasms/metabolism
• RNA, Untranslated/genetics
• Hypoxia/genetics
• DNA Damage/genetics
• Cell Hypoxia/genetics
• Genomic Instability
• Hypoxia-Inducible Factor 1, alpha Subunit/genetics
• Tumor Microenvironment/genetics

Tumour hypoxia is a known and extensively researched phenomenon that occurs in both solid and haematological malignancies. As cancer cells proliferate, demand for oxygen can outstrip supply reducing tumour oxygenation. In solid tumours this is contributed to by disorganized blood vessel development. Tumour hypoxia is associated with resistance to treatment, more aggressive disease behaviour and an increased likelihood of metastatic progression. It can be measured using both invasive and non-invasive methods to varying degrees of accuracy. The presence of hypoxia stimulates a complex cellular network of downstream factors including Hypoxia Inducible Factor 1 (HIF1), C-X-C motif chemokine 4 (CXCR4) and Hypoxia‐inducible glycolytic enzyme hexokinase‐2 (HK2) amongst many others. They work by affecting different mechanisms including influencing angiogenesis, treatment resistance, immune surveillance and the ability to metastasize all of which contribute to a more aggressive disease pattern. Tumour hypoxia has been correlated with poorer outcomes and worse prognosis in patients. The correlation between hypoxic microenvironments and poor prognosis has led to an interest in trying to therapeutically target this phenomenon. Various methods have been used to target hypoxic microenvironments. Hypoxia-activated prodrugs (HAPs) are drugs that are only activated within hypoxic environments and these agents have been subject to investigation in several clinical trials. Drugs that target downstream factors of hypoxic environments including HIF inhibitors, mammalian target of rapamycin (mTOR) inhibitors and vascular endothelial growth factor (anti-VEGF) therapies are also in development and being used in combination in clinical trials. Despite promising pre-clinical data, clinical trials of hypoxia targeting strategies have proven challenging. Further understanding of the effect of hypoxia and related molecular mechanisms in human rather than animal models is required to guide novel therapeutic strategies and future trial design. This review will discuss the currently available methods of hypoxia targeting and assessments that may be considered in planning future clinical trials. It will also outline key trials to date in both the solid and haemato-oncology treatment spheres and discuss the limitations that may have impacted on clinical success to date.

• Cancer
• Haematological
• Hypoxia
• Solid tumours

• gastric cancer
• hallmarks of cancer
• hypoxia
• hypoxia-inducible factor-1α

While studies on embryonic stem cells have been actively conducted, little is known about the epigenetic mechanisms in human embryonic stem cells (hESCs) in extended culture systems. Here, we investigated whether CpG island (CGI) methylation patterns of 24 tumor suppressor genes could be maintained during extended hESC cultures. In total, 10 hESC lines were analyzed. For each cell line, genomic DNA was extracted from early and late passages of cell cultures. CGI methylation levels of 24 tumor suppressor genes were analyzed using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), pyrosequencing, and real-time polymerase chain reaction (PCR). Different CGI methylation patterns of CASP8, FHIT, and CHFR genes were identified in between early and late passages in some hESC lines. CGI methylation levels of CASP8 significantly increased at late passage in CHA-36, CHA-40, and CHA-42 cell lines compared to those at early passage. The CGI methylation of the FHIT gene was higher at late passage than at early passage in CHA-15, CHA-31, CHA-32, and iPS (FS)-1 cell lines but decreased at the late passage in CHA-20 and H1 cell lines. Different CGI methylation patterns were detected for the CHFR gene only in iPS (FS)-1, and the level significantly increased at late passage. Thus, our findings show that CGI methylation patterns could be altered during prolonged ESC cultures and examining these epigenetic changes is important to assess the maintenance, differentiation, and clinical usage of stem cells.

• HIF-1α
• MSI-H
• MSI-L
• colorectal cancer (CRC)
• microsatellite instability (MSI)

• cancer
• computational biology and bioinformatics
• immunology
• risk factors

• Acute kidney injury
• Autophagy
• Hypoxic mesenchymal stem cells
• Ischemia-reperfusion injury

Glioblastoma, a grade IV astrocytoma, has a poor survival rate in part due to ineffective treatment options available. These tumours are heterogeneous with areas of low oxygen levels, termed hypoxic regions. Many intra-cellular signalling pathways, including DNA repair, can be altered by hypoxia. Since DNA damage induction and subsequent activation of DNA repair mechanisms is the cornerstone of glioblastoma treatment, alterations to DNA repair mechanisms could have a direct influence on treatment success. Our aim was to elucidate the impact of chronic hypoxia on DNA repair gene expression in a range of glioblastoma cell lines. We adopted a NanoString transcriptomic approach to examine the expression of 180 DNA repair-related genes in four classical glioblastoma cell lines (U87-MG, U251-MG, D566-MG, T98G) exposed to 5 days of normoxia (21% O₂), moderate (1% O₂) or severe (0.1% O₂) hypoxia. We observed altered gene expression in several DNA repair pathways including homologous recombination repair, non-homologous end-joining and mismatch repair, with hypoxia primarily resulting in downregulation of gene expression. The extent of gene expression changes was dependent on hypoxic severity. Some, but not all, of these downregulations were directly under the control of HIF activity. For example, the downregulation of LIG4, a key component of non-homologous end-joining, was reversed upon inhibition of the hypoxia-inducible factor (HIF). In contrast, the downregulation of the mismatch repair gene, PMS2, was not affected by HIF inhibition. This suggests that numerous molecular mechanisms lead to hypoxia-induced reprogramming of the transcriptional landscape of DNA repair. Whilst the global impact of hypoxia on DNA repair gene expression is likely to lead to genomic instability, tumorigenesis and reduced sensitivity to anti-cancer treatment, treatment re-sensitising might require additional approaches to a simple HIF inhibition.

• DNA Ligase IV
• DNA repair
• Glioblastoma
• HIF inhibition
• Hypoxia
• Mismatch repair
• NanoString
• Non-homologous end-joining
• PMS2

• Hif1
• reactive oxygen species
• spermatogonia

• Cancer
• Radiotherapy

• hypoxia
• immunogenic cell death
• therapeutics
• tumor microenvironment

• B-Lymphocytes/immunology
• Cell Death/immunology
• Cell Hypoxia
• Dendritic Cells/immunology
• Humans
• Immunotherapy/methods
• Killer Cells, Natural/immunology
• Macrophages/immunology
• Neoplasms/immunology
• Neoplasms/pathology
• Neoplasms/therapy
• Signal Transduction/genetics
• T-Lymphocytes/immunology
• Transcription Factors/metabolism
• Tumor Microenvironment/immunology

• CIHR

• DNA methylation
• IPF
• MeCP2
• epigenetic regulation
• fibrosis
• human lung fibroblast
• α-SMA

Genomic instability is an essential feature of cancer cells. The somatic mutation theory suggests that along with inherited ones, the changes in DNA caused by environmental factors may cause cancer. Although approximately 50–60 mutations per tumor are observed in established cancer tissue, it is known that not all of these mutations occur at the beginning of carcinogenesis but also occur later in the disease progression. The high frequency of somatic mutations referring to genomic instability contributes to the intratumoral genetic heterogeneity and treatment resistance. The contribution of the tumor microenvironment to the mutations observed following the acquirement of essential malignant characteristics of a cancer cell is one of the topics that have been extensively investigated in recent years. The frequency of mutations in hematologic tumors is generally less than solid tumors. Although it is a hematologic tumor, multiple myeloma is more similar to solid tumors in terms of the high number of chromosomal abnormalities and genetic heterogeneity. In multiple myeloma, bone marrow microenvironment also plays a role in genomic instability that occurs in the very early stages of the disease. In this review, we will briefly summarize the role of the tumor microenvironment and bone marrow microenvironment in the genomic instability seen in solid tumors and multiple myeloma.

• bone marrow
• cancer
• genomic instability
• multiple myeloma
• tumor microenvironment

Ten years after the initial generation of induced pluripotent stem cells (hiPSCs) from human tissues, their potential is no longer questioned, with over 15000 publications listed on PubMed, covering various fields of research; including disease modeling, cell therapy strategies, pharmacology/toxicology screening and 3D organoid systems. However, despite evidences that the presence of mutations in hiPSCs should be a concern, publications addressing genomic integrity of these cells represent less than 1% of the literature. After a first overview of the mutation types currently reported in hiPSCs, including karyotype abnormalities, copy number variations, single point mutation as well as uniparental disomy, this review will discuss the impact of reprogramming parameters such as starting cell type and reprogramming method on the maintenance of the cellular genomic integrity. Then, a specific focus will be placed on culture conditions and subsequent differentiation protocols and how their may also trigger genomic aberrations within the cell population of interest. Finally, in a last section, the impact of genomic alterations on the possible usages of hiPSCs and their derivatives will also be exemplified and discussed. We will also discuss which techniques or combination of techniques should be used to screen for genomic abnormalities with a particular focus on the necessary quality controls and the potential alternatives.

• Induced pluripotent stem cells
• Genomic integrity
• Mutations
• Karyotype
• Differentiation
• Cell therapy
• Quality control
• Reprogramming

• DNA damage and repair
• Disease
• Gene Therapy
• Stem cells

• Cancer-associated fibroblasts
• Lung adenocarcinoma
• Podoplanin
• Single nucleotide variants

• Adenocarcinoma/genetics
• Adenocarcinoma/metabolism
• Adenocarcinoma/pathology
• Adult
• Aged
• Aged, 80 and over
• Cancer-Associated Fibroblasts/metabolism
• Female
• Humans
• Kaplan-Meier Estimate
• Lung Neoplasms/genetics
• Lung Neoplasms/metabolism
• Lung Neoplasms/pathology
• Lymphatic Metastasis
• Male
• Membrane Glycoproteins/metabolism
• Middle Aged
• Multivariate Analysis
• Mutation
• Polymorphism, Single Nucleotide
• Prognosis
• Tumor Microenvironment/genetics
• Exome Sequencing

• 25-A-6 and 28-A-9 National Cancer Center Research and Development Fund

Spinal cord injury (SCI) suffers from a lack of effective therapeutic strategies. We have previously shown that individual therapeutic strategies, transplantation of ependymal stem/progenitor cells of the spinal cord after injury (epSPCi) or FM19G11 pharmacological treatment, induce moderate functional recovery after SCI. Here, the combination of treatments has been assayed for functional and histological analysis. Immediately after severe SCI, one million epSPCi were intramedullary injected, and the FM19G11 compound or dimethyl sulfoxide (DMSO) (as the vehicle control) was administrated via intrathecal catheterization. The combination of treatments, epSPCi and FM19G11, improves locomotor tasks compared to the control group, but did not significantly improve the Basso, Beattie, Bresnahan (BBB) scores for locomotor analysis in comparison with the individual treatments. However, the histological analysis of the spinal cord tissues, two months after SCI and treatments, demonstrated that when we treat the animals with both epSPCi and FM19G11, an improved environment for neuronal preservation was generated by reduction of the glial scar extension. The combinatorial treatment also contributes to enhancing the oligodendrocyte precursor cells by inducing the expression of Olig1 in vivo. These results suggest that a combination of therapies may be an exciting new therapeutic treatment for more efficient neuronal activity recovery after severe SCI.

• FM19G11
• axon growth
• ependymal progenitor stem cells
• locomotion
• neuronal regeneration
• oligodendrogenesis
• spinal cord injury

• epirubicin
• gastric cancer
• oxaliplatin and 5-fluorouracil chemotherapy
• single nucleotide polymorphism
• survival
• treatment response

• Adipose-derived stromal cell
• Bone marrow-mesenchymal stromal/stem cell
• DNA repair
• Hypoxia
• Long-term culture

• Cancer
• DNA repair
• fractionation
• hypofractionation
• normal tissues
• radiotherapy

• Biomarkers, Tumor/metabolism
• DNA Repair
• Dose Fractionation, Radiation
• Humans
• Neoplasms/radiotherapy
• Radiation Tolerance/genetics

• 19727 Cancer Research UK
• G9600656 Medical Research Council

• Nuclear blebs
• high glucoose
• hypoxia
• ischemia
• mesenchymal stem cells
• micronuclei

• DNA damage response
• DNA repair
• Gene regulation
• Gene silencing
• Genetic instability
• Hypoxia
• Post-translational modifications
• Replication stress
• Tumor microenvironment

DNA mismatch repair (MMR) function is critical for correcting errors coincident with polymerase-driven DNA replication, and its proteins are frequent targets for inactivation (germline or somatic), generating a hypermutable tumor that drives cancer progression. The biomarker for defective DNA MMR is microsatellite instability-high (MSI-H), observed in ~15% of colorectal cancers, and defined by mono- and dinucleotide microsatellite frameshift mutations. MSI-H is highly correlated with loss of MMR protein expression, is commonly diploid, is often located in the right side of the colon, prognosticates good patient outcome, and predicts poor efficacy with 5-fluorouracil treatment. Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) is another form of MSI at tetranucleotide repeats that has been observed in multiple cancers, but its etiology and clinical relevance to patient care has only been recently illuminated. Specifically, EMAST is an acquired somatic defect observed in up to 60% of colorectal cancers and caused by unique dysfunction of the DNA MMR protein MSH3 (and its DNA MMR complex MutSβ, a heterodimer of MSH2-MSH3), and in particular a loss-of-function phenotype due to a reversible shift from its normal nuclear location into the cytosol in response to oxidative stress and the pro-inflammatory cytokine interleukin-6. Tumor hypoxia may also be a contributor. Patients with EMAST colorectal cancers show diminished prognosis compared to patients without the presence of EMAST in their cancer. In addition to defective DNA MMR recognized by tetranucleotide (and di- and tri-nucleotide) frameshifts, loss of MSH3 also contributes to homologous recombination-mediated repair of DNA double stranded breaks, indicating the MSH3 dysfunction is a complex defect for cancer cells that generates not only EMAST but also may contribute to chromosomal instability and aneuploidy. Areas for future investigation for this most common DNA MMR defect among colorectal cancers include relationships between EMAST and chemotherapy response, patient outcome with aneuploid changes in colorectal cancers, target gene mutation analysis, and mechanisms related to inflammation-induced compartmentalization and inactivation for MSH3.

Hypoxic niches help maintain mesenchymal stromal cell properties, and their amplification under hypoxia sustains their immature state. However, how MSCs maintain their genomic integrity in this context remains elusive, since hypoxia may prevent proper DNA repair by downregulating expression of BRCA1 and RAD51. Here, we find that the ING1b tumor suppressor accumulates in adipose-derived stromal cells (ADSCs) upon genotoxic stress, owing to SUMOylation on K193 that is mediated by the E3 small ubiquitin-like modifier (SUMO) ligase protein inhibitor of activated STAT protein γ (PIAS4). We demonstrate that ING1b finely regulates the hypoxic response by triggering HIF1α proteasomal degradation. On the contrary, when mutated on its SUMOylation site, ING1b failed to efficiently decrease HIF1α levels. Consistently, we observed that the adipocyte differentiation, generally described to be downregulated by hypoxia, was highly dependent on ING1b expression, during the early days of this process. Accordingly, contrary to what was observed with HIF1α, the absence of ING1b impeded the adipogenic induction under hypoxic conditions. These data indicate that ING1b contributes to adipogenic induction in adipose-derived stromal cells, and thus hinders the phenotype maintenance of ADSCs.

• Cell Hypoxia/drug effects
• Cell Hypoxia/genetics
• Cell Line, Tumor
• Cell Survival/drug effects
• Colorectal Neoplasms/enzymology
• Colorectal Neoplasms/genetics
• Colorectal Neoplasms/pathology
• DNA Glycosylases/metabolism
• DNA Repair/drug effects
• DNA Repair/genetics
• Down-Regulation/genetics
• Gene Expression Regulation, Neoplastic/drug effects
• Humans
• Hydrogen Peroxide/pharmacology
• Methyl Methanesulfonate/pharmacology
• Mutation/genetics
• Phenotype
• Protein Biosynthesis/drug effects
• RNA, Messenger/genetics
• RNA, Messenger/metabolism

• Aged
• Aged, 80 and over
• Animals
• Biomarkers/metabolism
• Combined Modality Therapy
• Disease Models, Animal
• Female
• Gene Expression Profiling
• Histone Deacetylase Inhibitors/metabolism
• Humans
• Hydroxamic Acids/metabolism
• Hydroxamic Acids/pharmacology
• Leukocytes, Mononuclear/drug effects
• Male
• Mice
• Mice, Inbred BALB C
• Microarray Analysis
• Middle Aged
• Pelvic Neoplasms/drug therapy
• Pelvic Neoplasms/radiotherapy
• Radiation-Sensitizing Agents/pharmacology
• Reverse Transcriptase Polymerase Chain Reaction
• Statistics, Nonparametric
• Time Factors
• Vorinostat

Jumonji domain-containing protein 2B (JMJD2B), directly targeted by hypoxia-inducible factor 1α, maintains the histone methylation balance important for the transcriptional activation of many oncogenes. Jumonji domain-containing protein 2B has been implicated in colorectal cancer (CRC) progression; however, the mechanism remains unclear.

Immunofluorescence and western blotting detected phosphorylated histone H2AX, characteristic of double-strand breaks, and comet assay was used to investigate DNA damage, in CRC cells after JMJD2B small interfering RNA (siRNA) transfection. We assessed the resulting in vitro responses, that is, cell cycle progression, apoptosis, and senescence coupled with JMJD2B silencing-induced DNA damage, studying the regulatory role of signal transducers and activators of transcription 3 (STAT3). The JMJD2B silencing anti-cancer effect was determined using an in vivo CRC xenograft model.

Jumonji domain-containing protein 2B knockdown induced DNA damage via ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related pathway activation, resulting in cell cycle arrest, apoptosis, and senescence in both normoxia and hypoxia. Signal transducers and activators of transcription 3 suppression by JMJD2B silencing enhanced DNA damage. Intratumoural injection of JMJD2B siRNA suppressed tumour growth in vivo and activated the DNA damage response (DDR).

Jumonji domain-containing protein 2B has an essential role in cancer cell survival and tumour growth via DDR mediation, which STAT3 partially regulates, suggesting that JMJD2B is a potential anti-cancer target.

• Deferoxamine
• dental pulp cells
• hypoxia-inducible factors-1α
• repair ability

Previous reports have demonstrated that human embryonic stem cells (hESCs) tend to develop genomic alterations and progress to a malignant state during long-term in vitro culture. This raises concerns of the clinical safety in using cultured hESCs. However, transformed hESCs might serve as an excellent model to determine the process of embryonic stem cell transition. In this study, ITRAQ-based tandem mass spectrometry was used to quantify normal and aberrant karyotypic hESCs proteins from simple to more complex karyotypic abnormalities. We identified and quantified 2583 proteins, and found that the expression levels of 316 proteins that represented at least 23 functional molecular groups were significantly different in both normal and abnormal hESCs. Dysregulated protein expression in epigenetic regulation was further verified in six pairs of hESC lines in early and late passage. In summary, this study is the first large-scale quantitative proteomic analysis of the malignant transformation of aberrant karyotypic hESCs. The data generated should serve as a useful reference of stem cell-derived tumor progression. Increased expression of both HDAC2 and CTNNB1 are detected as early as the pre-neoplastic stage, and might serve as prognostic markers in the malignant transformation of hESCs.

• Animals
• Blotting, Western
• Cell Line
• Cell Transformation, Neoplastic/genetics
• Cell Transformation, Neoplastic/pathology
• Cluster Analysis
• DNA Copy Number Variations/genetics
• Embryonic Stem Cells/metabolism
• Epigenesis, Genetic
• Gene Expression Profiling
• Humans
• Isotope Labeling
• Karyotyping
• Mass Spectrometry
• Mice
• Molecular Sequence Annotation
• Neoplasm Proteins/genetics
• Neoplasm Proteins/metabolism
• Proteome/metabolism
• Proteomics
• Real-Time Polymerase Chain Reaction
• Reproducibility of Results
• Transcriptome/genetics

Sub-regions of hypoxia exist within all tumors and the presence of intratumoral hypoxia has an adverse impact on patient prognosis. Tumor hypoxia can increase metastatic capacity and lead to resistance to chemotherapy and radiotherapy. Hypoxia also leads to altered transcription and translation of a number of DNA damage response and repair genes. This can lead to inhibition of recombination-mediated repair of DNA double-strand breaks. Hypoxia can also increase the rate of mutation. Therefore, tumor cell adaptation to the hypoxic microenvironment can drive genetic instability and malignant progression. In this review, we focus on hypoxia-mediated genetic instability in the context of aberrant DNA damage signaling and DNA repair. Additionally, we discuss potential therapeutic approaches to specifically target repair-deficient hypoxic tumor cells.

In this paper we propose a chemical physics mechanism for the initiation of the glycolytic switch commonly known as the Warburg hypothesis, whereby glycolytic activity terminating in lactate continues even in well-oxygenated cells. We show that this may result in cancer via mitotic failure, recasting the current conception of the Warburg effect as a metabolic dysregulation consequent to cancer, to a biophysical defect that may contribute to cancer initiation.

Our model is based on analogs of thermodynamic concepts that tie non-equilibrium fluid dynamics ultimately to metabolic imbalance, disrupted microtubule dynamics, and finally, genomic instability, from which cancers can arise. Specifically, we discuss how an analog of non-equilibrium Rayleigh-Benard convection can result in glycolytic oscillations and cause a cell to become locked into a higher-entropy state characteristic of cancer.

A quantitative model is presented that attributes the well-known Warburg effect to a biophysical mechanism driven by a convective disturbance in the cell. Contrary to current understanding, this effect may precipitate cancer development, rather than follow from it, providing new insights into carcinogenesis, cancer treatment, and prevention.

• dna mismatch repair
• hereditary non-polyposis colorectal carcinoma
• immunohistochemistry
• lynch syndrome
• microsatellite instability

• Antineoplastic Agents
• Cell Migration Assays/methods
• Cell Movement/physiology
• Drug Discovery
• Extracellular Matrix
• Humans
• Neoplasm Invasiveness
• Neoplasm Metastasis/pathology
• Neoplasms/pathology
• Neovascularization, Pathologic
• Signal Transduction
• Tumor Cells, Cultured
• Tumor Microenvironment

• 11566 Cancer Research UK
• G1000121/1 National Centre for the Replacement, Refinement and Reduction of Animals in Research
• C309/A8274 Cancer Research UK

• hif
• modulation
• pharmacology

• DNA/metabolism
• Epigenesis, Genetic
• Humans
• Hypoxia-Inducible Factor 1/antagonists & inhibitors
• Hypoxia-Inducible Factor 1/genetics
• Hypoxia-Inducible Factor 1/metabolism
• Protein Binding
• Transcription, Genetic
• Transcriptional Activation

Hypoxia is an integral part of tumorigenesis and contributes extensively to the neoplastic phenotype including drug resistance and genomic instability. It has also been reported that hypoxia results in global demethylation. Because a majority of the cytosine-phosphate-guanine (CpG) islands are found within the repeat elements of DNA, and are usually methylated under normoxic conditions, we suggested that retrotransposable Alu or short interspersed nuclear elements (SINEs) which show altered methylation and associated changes of gene expression during hypoxia, could be associated with genomic instability. U87MG glioblastoma cells were cultured in 0.1% O₂ for 6 weeks and compared with cells cultured in 21% O₂ for the same duration. Real-time PCR analysis showed a significant increase in SINE and reverse transcriptase coding long interspersed nuclear element (LINE) transcripts during hypoxia. Sequencing of bisulphite treated DNA as well as the Combined Bisulfite Restriction Analysis (COBRA) assay showed that the SINE loci studied underwent significant hypomethylation though there was patchy hypermethylation at a few sites. The inter-alu PCR profile of DNA from cells cultured under 6-week hypoxia, its 4-week revert back to normoxia and 6-week normoxia showed several changes in the band pattern indicating increased alu mediated genomic alteration. Our results show that aberrant methylation leading to increased transcription of SINE and reverse transcriptase associated LINE elements could lead to increased genomic instability in hypoxia. This might be a cause of genetic heterogeneity in tumours especially in variegated hypoxic environment and lead to a development of foci of more aggressive tumour cells.