Integrative analysis reveals early epigenetic alterations in high-grade serous ovarian carcinomas

Machino Hidenori,Dozen Ai,Konaka Mariko,Komatsu Masaaki,Nakamura Kohei,Ikawa Noriko,Shozu Kanto,Asada Ken,Kaneko Syuzo,Yoshida Hiroshi,Kato Tomoyasu,Nakayama Kentaro,Saloura Vassiliki,Kyo Satoru,Hamam 생화학분자생물학회 2023 Experimental and molecular medicine Vol.55 No.-

High-grade serous ovarian carcinoma (HGSOC) is the most lethal gynecological malignancy. To date, the profiles of gene mutations and copy number alterations in HGSOC have been well characterized. However, the patterns of epigenetic alterations and transcription factor dysregulation in HGSOC have not yet been fully elucidated. In this study, we performed integrative omics analyses of a series of stepwise HGSOC model cells originating from human fallopian tube secretory epithelial cells (HFTSECs) to investigate early epigenetic alterations in HGSOC tumorigenesis. Assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) methods were used to analyze HGSOC samples. Additionally, protein expression changes in target genes were confirmed using normal HFTSECs, serous tubal intraepithelial carcinomas (STICs), and HGSOC tissues. Transcription factor motif analysis revealed that the DNA-binding activity of the AP-1 complex and GATA family proteins was dysregulated during early tumorigenesis. The protein expression levels of JUN and FOSL2 were increased, and those of GATA6 and DAB2 were decreased in STIC lesions, which were associated with epithelial-mesenchymal transition (EMT) and proteasome downregulation. The genomic region around the FRA16D site, containing a cadherin cluster region, was epigenetically suppressed by oncogenic signaling. Proteasome inhibition caused the upregulation of chemokine genes, which may facilitate immune evasion during HGSOC tumorigenesis. Importantly, MEK inhibitor treatment reversed these oncogenic alterations, indicating its clinical effectiveness in a subgroup of patients with HGSOC. This result suggests that MEK inhibitor therapy may be an effective treatment option for chemotherapy-resistant HGSOC.

Loss of Autophagy Diminishes Pancreatic β Cell Mass and Function with Resultant Hyperglycemia

Jung, Hye Seung,Chung, Kun Wook,Won Kim, Jeong,Kim, Jin,Komatsu, Masaaki,Tanaka, Keiji,Nguyen, Yen Hoang,Kang, Tong Mook,Yoon, Kun-Ho,Kim, Ji-Won,Jeong, Yeon Taek,Han, Myoung Sook,Lee, Moon-Kyu,Kim, K Elsevier 2008 Cell metabolism Vol.8 No.4

<P><B>Summary</B></P><P>Autophagy is a cellular degradation-recycling system for aggregated proteins and damaged organelles. Although dysregulated autophagy is implicated in various diseases including neurodegeneration, its role in pancreatic β cells and glucose homeostasis has not been described. We produced mice with β cell-specific deletion of <I>Atg7</I> (<I>autophagy-related 7</I>). <I>Atg7</I> mutant mice showed impaired glucose tolerance and decreased serum insulin level. β cell mass and pancreatic insulin content were reduced because of increased apoptosis and decreased proliferation of β cells. Physiological studies showed reduced basal and glucose-stimulated insulin secretion and impaired glucose-induced cytosolic Ca<SUP>2+</SUP> transients in autophagy-deficient β cells. Morphologic analysis revealed accumulation of ubiquitinated protein aggregates colocalized with p62, which was accompanied by mitochondrial swelling, endoplasmic reticulum distension, and vacuolar changes in β cells. These results suggest that autophagy is necessary to maintain structure, mass and function of pancreatic β cells, and its impairment causes insulin deficiency and hyperglycemia because of abnormal turnover and function of cellular organelles.</P>

Mitochondrial Complexes I and II Are More Susceptible to Autophagy Deficiency in Mouse β-Cells

Kim, Min Joo,Choi, Ok Kyong,Chae, Kyung Sil,Kim, Min Kyeong,Kim, Jung Hee,Komatsu, Masaaki,Tanaka, Keiji,Lee, Hakmo,Chung, Sung Soo,Kwak, Soo Heon,Cho, Young Min,Park, Kyong Soo,Jung, Hye Seung Korean Endocrine Society 2015 Endocrinology and metabolism Vol.30 No.1

<P><B>Background</B></P><P>Damaged mitochondria are removed by autophagy. Therefore, impairment of autophagy induces the accumulation of damaged mitochondria and mitochondrial dysfunction in most mammalian cells. Here, we investigated mitochondrial function and the expression of mitochondrial complexes in autophagy-related 7 (<I>Atg7</I>)-deficient β-cells.</P><P><B>Methods</B></P><P>To evaluate the effect of autophagy deficiency on mitochondrial function in pancreatic β-cells, we isolated islets from <I>Atg7</I><SUP>F/F</SUP>:RIP-<I>Cre</I>+ mice and wild-type littermates. Oxygen consumption rate and intracellular adenosine 5'-triphosphate (ATP) content were measured. The expression of mitochondrial complex genes in <I>Atg7</I>-deficient islets and in β-TC6 cells transfected with si<I>Atg7</I> was measured by quantitative real-time polymerase chain reaction.</P><P><B>Results</B></P><P>Baseline oxygen consumption rate of <I>Atg7</I>-deficient islets was significantly lower than that of control islets (<I>P</I><0.05). Intracellular ATP content of <I>Atg7</I>-deficient islets during glucose stimulation was also significantly lower than that of control islets (<I>P</I><0.05). By Oxygraph-2k analysis, mitochondrial respiration in <I>Atg7</I>-deficient islets was significantly decreased overall, although state 3 respiration and responses to antimycin A were unaffected. The mRNA levels of mitochondrial complexes I, II, III, and V in <I>Atg7</I>-deficient islets were significantly lower than in control islets (<I>P</I><0.05). Down-regulation of <I>Atg7</I> in β-TC6 cells also reduced the expression of complexes I and II, with marginal significance (<I>P</I><0.1).</P><P><B>Conclusion</B></P><P>Impairment of autophagy in pancreatic β-cells suppressed the expression of some mitochondrial respiratory complexes, and may contribute to mitochondrial dysfunction. Among the complexes, I and II seem to be most vulnerable to autophagy deficiency.</P>

Advances in cancer DNA methylation analysis with methPLIER: use of non-negative matrix factorization and knowledge-based constraints to enhance biological interpretability

Takasawa Ken,Asada Ken,Kaneko Syuzo,Shiraishi Kouya,Machino Hidenori,Takahashi Satoshi,Shinkai Norio,Kouno Nobuji,Kobayashi Kazuma,Komatsu Masaaki,Mizuno Takaaki,Okubo Yu,Mukai Masami,Yoshida Tatsuya 생화학분자생물학회 2024 Experimental and molecular medicine Vol.56 No.-

DNA methylation is an epigenetic modification that results in dynamic changes during ontogenesis and cell differentiation. DNA methylation patterns regulate gene expression and have been widely researched. While tools for DNA methylation analysis have been developed, most of them have focused on intergroup comparative analysis within a dataset; therefore, it is difficult to conduct cross-dataset studies, such as rare disease studies or cross-institutional studies. This study describes a novel method for DNA methylation analysis, namely, methPLIER, which enables interdataset comparative analyses. methPLIER combines Pathway Level Information Extractor (PLIER), which is a non-negative matrix factorization (NMF) method, with regularization by a knowledge matrix and transfer learning. methPLIER can be used to perform intersample and interdataset comparative analysis based on latent feature matrices, which are obtained via matrix factorization of large-scale data, and factor-loading matrices, which are obtained through matrix factorization of the data to be analyzed. We used methPLIER to analyze a lung cancer dataset and confirmed that the data decomposition reflected sample characteristics for recurrence-free survival. Moreover, methPLIER can analyze data obtained via different preprocessing methods, thereby reducing distributional bias among datasets due to preprocessing. Furthermore, methPLIER can be employed for comparative analyses of methylation data obtained from different platforms, thereby reducing bias in data distribution due to platform differences. methPLIER is expected to facilitate cross-sectional DNA methylation data analysis and enhance DNA methylation data resources.

Role of hypothalamic proopiomelanocortin neuron autophagy in the control of appetite and leptin response.

Quan, Wenying,Kim, Hyun-Kyong,Moon, Eun-Yi,Kim, Su Sung,Choi, Cheol Soo,Komatsu, Masaaki,Jeong, Yeon Taek,Lee, Moon-Kyu,Kim, Kwang-Won,Kim, Min-Seon,Lee, Myung-Shik Association for the Study of Internal Secretions 2012 Endocrinology Vol.153 No.4

<P>Autophagy is a catabolic cellular process involving the degradation of the cell's own components. Although the role of autophagy of diverse tissues in body metabolism has been investigated, the importance of autophagy in hypothalamic proopiomelanocortin (POMC) neurons, key regulators of energy balance, has not been addressed. The role of autophagy in leptin sensitivity that is critical for the control of body weight and appetite has also not been investigated. We produced mice with specific deletion of autophagy-related 7 (Atg7), an essential autophagy gene, in hypothalamic POMC neurons (Atg7(δPOMC) mice). Atg7 expression was deficient in the arcuate nucleus of the hypothalamus of Atg7(δPOMC) mice. p62, a specific substrate of autophagy, accumulated in the hypothalamus of Atg7(δPOMC) mice, which colocalized with ubiquitin. Atg7(δPOMC) mice had increased body weight due to increased food intake and decreased energy expenditure. Atg7(δPOMC) mice were not more prone to diet-induced obesity compared with control mice but more susceptible to hyperglycemia after high-fat diet. The ability of leptin to suppress fasting-elicited hyperphagia and weight gain during refeeding was attenuated in Atg7(δPOMC) mice. Deficient autophagy did not significantly affect POMC neuron number but impaired leptin-induced signal transducer and activation of transcription 3 activation. Our findings indicate a critical role for autophagy of POMC neurons in the control of energy homeostasis and leptin signaling.</P>

Persistent activation of Nrf2 through p62 in hepatocellular carcinoma cells

Inami, Yoshihiro,Waguri, Satoshi,Sakamoto, Ayako,Kouno, Tsuguka,Nakada, Kazuto,Hino, Okio,Watanabe, Sumio,Ando, Jin,Iwadate, Manabu,Yamamoto, Masayuki,Lee, Myung-Shik,Tanaka, Keiji,Komatsu, Masaaki The Rockefeller University Press 2011 The Journal of cell biology Vol.193 No.2

<P>Suppression of autophagy is always accompanied by marked accumulation of p62, a selective autophagy substrate. Because p62 interacts with the Nrf2-binding site on Keap1, which is a Cullin 3–based ubiquitin ligase adapter protein, autophagy deficiency causes competitive inhibition of the Nrf2–Keap1 interaction, resulting in stabilization of Nrf2 followed by transcriptional activation of Nrf2 target genes. Herein, we show that liver-specific autophagy-deficient mice harbor adenomas linked to both the formation of p62- and Keap1-positive cellular aggregates and induction of Nrf2 targets. Importantly, similar aggregates were identified in more than 25% of human hepatocellular carcinomas (HCC), and induction of Nrf2 target genes was recognized in most of these tumors. Gene targeting of <I>p62</I> in an HCC cell line markedly abrogates the anchorage-independent growth, whereas forced expression of p62, but not a Keap1 interaction-defective mutant, resulted in recovery of the growth defect. These results indicate the involvement of persistent activation of Nrf2 through the accumulation of p62 in hepatoma development.</P>

Modification of ASC1 by UFM1 Is Crucial for ERα Transactivation and Breast Cancer Development

Yoo, Hee Min,Kang, Sung Hwan,Kim, Jae Yeon,Lee, Joo Eun,Seong, Min Woo,Lee, Seong Won,Ka, Seung Hyeun,Sou, Yu-Shin,Komatsu, Masaaki,Tanaka, Keiji,Lee, Soon Tae,Noh, Dong Young,Baek, Sung Hee,Jeon, You Elsevier 2014 Molecular cell Vol.56 No.2

<P><B>Summary</B></P> <P>Biological roles for UFM1, a ubiquitin-like protein, are largely unknown, and therefore we screened for targets of ufmylation. Here we show that ufmylation of the nuclear receptor coactivator ASC1 is a key step for ERα transactivation in response to 17β-estradiol (E<SUB>2</SUB>). In the absence of E<SUB>2</SUB>, the UFM1-specific protease UfSP2 was bound to ASC1, which maintains ASC1 in a nonufmylated state. In the presence of E<SUB>2</SUB>, ERα bound ASC1 and displaced UfSP2, leading to ASC1 ufmylation. Polyufmylation of ASC1 enhanced association of p300, SRC1, and ASC1 at promoters of ERα target genes. ASC1 overexpression or UfSP2 knockdown promoted ERα-mediated tumor formation in vivo, which could be abrogated by treatment with the anti-breast cancer drug tamoxifen. In contrast, expression of ufmylation-deficient ASC1 mutant or knockdown of the UFM1-activating E1 enzyme UBA5 prevented tumor growth. These findings establish a role for ASC1 ufmylation in breast cancer development by promoting ERα transactivation.</P> <P><B>Highlights</B></P> <P> <UL> <LI> 17β-estradiol induces ASC1 modification by poly-UFM1 chains (ufmylation) </LI> <LI> Poly-UFM1 chains recruit ASC1, p300, and SRC1 to the promoters of ERα target genes </LI> <LI> ASC1 ufmylation promotes cell growth and tumor formation by ERα transactivation </LI> <LI> ASC1 ufmylation plays a crucial role in development of ERα-positive breast cancer </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>

Amyloidogenic peptide oligomer accumulation in autophagy-deficient β cells induces diabetes.

Kim, Jinyoung,Cheon, Hwanju,Jeong, Yeon Taek,Quan, Wenying,Kim, Kook Hwan,Cho, Jae Min,Lim, Yu-Mi,Oh, Seung Hoon,Jin, Sang-Man,Kim, Jae Hyeon,Lee, Moon-Kyu,Kim, Sunshin,Komatsu, Masaaki,Kang, Sang-Woo American Society for Clinical Investigation 2014 The Journal of clinical investigation Vol.124 No.8

<P>Islet amyloid accumulation is a hallmark of human type 2 diabetes (T2D). In contrast to human islet amyloid polypeptide (hIAPP), murine islet amyloid polypeptide (mIAPP) does not exhibit amyloidogenic propensity. Because autophagy is important in the clearance of amyloid-like proteins, we studied transgenic mice with β cell-specific expression of hIAPP to evaluate the contribution of autophagy in T2D-associated accumulation of hIAPP. In mice with β cell-specific expression of hIAPP, a deficiency in autophagy resulted in development of overt diabetes, which was not observed in mice expressing hIAPP alone or lacking autophagy alone. Furthermore, lack of autophagy in hIAPP-expressing animals resulted in hIAPP oligomer and amyloid accumulation in pancreatic islets, leading to increased death and decreased mass of β cells. Expression of hIAPP in purified monkey islet cells or a murine β cell line resulted in pro-hIAPP dimer formation, while dimer formation was absent or reduced dramatically in cells expressing either nonamyloidogenic mIAPP or nonfibrillar mutant hIAPP. In autophagy-deficient cells, accumulation of pro-hIAPP dimers increased markedly, and pro-hIAPP trimers were detected in the detergent-insoluble fraction. Enhancement of autophagy improved the metabolic profile of hIAPP-expressing mice fed a high-fat diet. These results suggest that autophagy promotes clearance of amyloidogenic hIAPP, autophagy deficiency exacerbates pathogenesis of human T2D, and autophagy enhancers have therapeutic potential for islet amyloid accumulation-associated human T2D.</P>