Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2300
Nabiha Khan, N. Puri
{"title":"Abstract 2300: Overcoming TKI-resistance in NSCLC using SphK2 inhibitors","authors":"Nabiha Khan, N. Puri","doi":"10.1158/1538-7445.AM2021-2300","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2300","url":null,"abstract":"","PeriodicalId":18754,"journal":{"name":"Molecular and Cellular Biology / Genetics","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78314346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-1936
U. Ray, D. Roy, Ling Jin, P. Thirusangu, J. Staub, Yinan Xiao, V. Shridhar
{"title":"Abstract 1936: Autophagy-dependent therapeutic targeting of group III phospholipase A2 attenuates ovarian cancer metastasis","authors":"U. Ray, D. Roy, Ling Jin, P. Thirusangu, J. Staub, Yinan Xiao, V. Shridhar","doi":"10.1158/1538-7445.AM2021-1936","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-1936","url":null,"abstract":"","PeriodicalId":18754,"journal":{"name":"Molecular and Cellular Biology / Genetics","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78332143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2114
M. Pienkowska, N. Samuel, S. Choufani, Vallijah Subasri, N. Patel, R. Weksberg, Ran Kafri, D. Malkin
Li-Fraumeni syndrome (LFS) is an autosomal dominantly inherited cancer predisposition syndrome associated with germline mutations of the TP53 tumor suppressor gene. TP53 mutation carriers are susceptible to a wide range of cancers that occur at strikingly earlier age of onset than their sporadic counterparts. The lifetime cancer risk in TP53 mutation carriers is estimated to be ~73% for males and approaching 100% in females. Although improved survival outcomes have been demonstrated for carriers undergoing intense clinical surveillance, there is continued interest in identifying new environmental, genetic, and epigenetic risk factors that could improve our ability to predict disease onset and outcome. A number of studies have demonstrated age-associated DNA methylation (DNAm) changes at specific CG dinucleotides and that these changes can be combined into epigenetic age predictors to estimate chronological age. Deviation of chronological and predicted age have been associated with age-associated illnesses such as metabolic disease and cancer. For a given chronological age, older epigenetic age is presumed to indicate poorer health. An epigenetic profile defining the DNA methylation age (DNAm age) of an individual has been suggested to be a biomarker of aging, and thus possibly providing a tool for assessment of health and mortality. Our goal was to test whether DNAm age could be a possible predictor of cancer risk in LFS patients. We applied the DNA age calculator (http://dnamage.genetics.ucla.edu/) (Horvath 2013) to DNA methylation profiles derived from lymphocytes extracted from 157 LFS patients9 blood samples using the Illumina HumanMethylation450 BeadChip. While a correlation of DNAm age and actual age was observed in both ‘normal9 and LFS patients, the latter showed significant deviations (differences between DNAm age and chronological age). Moreover, the extent of deviations seems selectively associated with two distinct age groups (0-5 years and 20-50 years). Remarkably, this bimodal DNAm age profile shows striking resemblance to the epidemiologically characterized age dependency of LFS cancers (Amadou, 2018). Individuals with germline mutant or germline wild-type TP53 and no cancer showed no epigenetic age acceleration whereas individuals who were carriers of mutant TP53 who developed cancer showed accelerated epigenetic aging. Our preliminary results suggest that DNAm age is a dynamic, real-time correlate of patient-specific cancer risk in LFS. Further, the age dependent deviations suggest that the cancer risk profiles derived from Horvath signatures are dynamic and reflect the changes in cancer risk throughout an individual9s lifetime, and could be used as a predictor of cancer onset in TP53 mutation carriers. Citation Format: Malgorzata Pienkowska, Nardin Samuel, Sanaa Choufani, Vallijah Subasri, Nish Patel, Rosanna Weksberg, Ran Kafri, David Malkin. Horvath clock as a predictor of cancer risk in LFS patients [abstract]. In: Proceeding
Li-Fraumeni综合征(LFS)是一种常染色体显性遗传的癌症易感性综合征，与肿瘤抑制基因TP53的种系突变有关。TP53突变携带者易患多种癌症，其发病年龄明显早于散发性癌症携带者。TP53突变携带者的终生癌症风险在男性中估计约为73%，在女性中接近100%。尽管经过严格的临床监测，已经证明携带者的生存结果有所改善，但人们仍对识别新的环境、遗传和表观遗传风险因素感兴趣，这些因素可以提高我们预测疾病发病和预后的能力。许多研究表明，特定CG二核苷酸的年龄相关DNA甲基化(DNAm)变化，这些变化可以结合表观遗传年龄预测因子来估计实足年龄。实际年龄和预测年龄的偏差与年龄相关的疾病，如代谢性疾病和癌症有关。对于给定的实足年龄，表观遗传年龄越大被认为表明健康状况较差。定义个体DNA甲基化年龄(DNAm年龄)的表观遗传谱被认为是衰老的生物标志物，因此可能为评估健康和死亡率提供工具。我们的目标是测试dna年龄是否可以作为LFS患者癌症风险的可能预测因子。我们将DNA年龄计算器(http://dnamage.genetics.ucla.edu/) (Horvath 2013)应用于使用Illumina HumanMethylation450 BeadChip从157例LFS患者血液样本中提取的淋巴细胞的DNA甲基化谱。虽然在正常9和LFS患者中都观察到DNAm年龄与实际年龄的相关性，但后者显示出明显的偏差(DNAm年龄与实足年龄之间的差异)。此外，偏差的程度似乎选择性地与两个不同的年龄组(0-5岁和20-50岁)相关。值得注意的是，这种双峰dna年龄谱与LFS癌症的流行病学特征年龄依赖性惊人相似(Amadou, 2018)。携带种系突变型或种系野生型TP53且未患癌症的个体没有表现出表观遗传年龄加速，而携带突变型TP53并患癌症的个体则表现出加速的表观遗传衰老。我们的初步结果表明，DNAm年龄是LFS患者特异性癌症风险的动态、实时相关性。此外，年龄依赖性偏差表明，来自Horvath特征的癌症风险谱是动态的，反映了个体一生中癌症风险的变化，可以用作TP53突变携带者癌症发病的预测因子。引文格式:Malgorzata Pienkowska, Nardin Samuel, Sanaa Choufani, Vallijah Subasri, Nish Patel, Rosanna Weksberg, Ran Kafri, David Malkin。Horvath时钟作为LFS患者癌症风险的预测因子[摘要]。见:美国癌症研究协会2021年年会论文集;2021年4月10日至15日和5月17日至21日。费城(PA): AACR;癌症杂志，2021;81(13 -增刊):2114。
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Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2139
P. Parrish, James D. Thomas, Shriya Kamlapurkar, R. Bradley, A. Berger
Genome-scale CRISPR-Cas9 screens have enabled the identification of essential genes that can serve as cancer drug targets. However, single-gene knockout screens frequently underestimate the essentiality of paralogs, ancestrally duplicated genes that often functionally compensate for one another9s loss; we have observed this directly in single-gene CRISPR screen data from a lung cancer cell line (P To identify paralog pairs essential for cancer cell survival, we developed a multiplexed CRISPR approach that uses paired guide RNAs to knock out human paralogs individually and in pairs. Our library includes 2,060 paralogs (1,030 pairs); the largest human paralog CRISPR library to date. We screened lung adenocarcinoma (PC9) and cervical carcinoma (HeLa) cell lines to identify synthetic lethal paralogs which have minimal growth effects when targeted individually but whose simultaneous loss leads to severely decreased growth. We found that 128 (16%) of the paralog pairs in our study were synthetic lethal and essential in at least one cell line. Gene set enrichment analysis revealed that our top paralogs are overrepresented in pathways related to cell cycle regulation, protein secretion, DNA repair, and PI3K-AKT signaling (FDR q-value We validated our screen results using in vitro competition assays and DepMap CRISPR data analysis. For known synthetic lethal paralogs MAGOH and MAGOHB, competition assay data confirmed significantly reduced growth in the dual gene knockout condition versus single-gene knockouts (P Our studies point to a number of novel synthetic lethal paralogs that could serve as lung cancer drug targets. These paralogs could be targeted alone or in combination with existing therapies to suppress lung cancer growth and prevent acquired drug resistance. Paralog synthetic lethal therapies could make a major impact on clinical care by improving patient outcomes. Citation Format: Phoebe C. Parrish, James D. Thomas, Shriya Kamlapurkar, Robert K. Bradley, Alice H. Berger. Enabling cancer drug target discovery through genome-scale identification of synthetic lethal paralog pairs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2139.
基因组规模的CRISPR-Cas9筛选已经能够识别出可以作为癌症药物靶点的必要基因。然而，单基因敲除筛选经常低估了同源基因的重要性，即祖先复制的基因经常在功能上弥补彼此的损失;我们已经在肺癌细胞系的单基因CRISPR筛选数据中直接观察到这一点(P)。为了鉴定对癌细胞存活至关重要的平行对，我们开发了一种多路CRISPR方法，该方法使用成对的引导rna来单独或成对地敲除人类的平行对。我们的库包括2,060个类似物(1,030对);迄今为止最大的人类平行CRISPR库。我们筛选肺腺癌(PC9)和宫颈癌(HeLa)细胞系，以确定合成致死性同源物，这些同源物在单独靶向时具有最小的生长效应，但同时丢失会导致生长严重下降。我们发现，在我们的研究中，128对(16%)平行蛋白对至少一种细胞系具有合成致死性和必需性。基因集富集分析显示，我们的顶级相似基因在细胞周期调节、蛋白质分泌、DNA修复和PI3K-AKT信号通路(FDR q值)相关的途径中被过度代表。我们使用体外竞争分析和DepMap CRISPR数据分析验证了我们的筛选结果。对于已知的合成致死性类似物MAGOH和MAGOHB，竞争分析数据证实，与单基因敲除相比，双基因敲除条件下的生长显著降低(P)。我们的研究指出，一些新的合成致死性类似物可能作为肺癌药物靶点。这些类似物可以单独靶向或与现有疗法联合抑制肺癌生长和预防获得性耐药。平行合成致死疗法可以通过改善患者预后对临床护理产生重大影响。引用格式:Phoebe C. Parrish, James D. Thomas, Shriya Kamlapurkar, Robert K. Bradley, Alice H. Berger。通过基因组尺度合成致死平行对的鉴定实现癌症药物靶点发现[摘要]。见:美国癌症研究协会2021年年会论文集;2021年4月10日至15日和5月17日至21日。费城(PA): AACR;癌症杂志，2021;81(13 -增刊):2139。
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Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2181
M. Greene, Peter Abraham, E. Lipke, P. Kuhlers
{"title":"Abstract 2181: Obesity and the consensus molecular subtypes of colorectal cancer","authors":"M. Greene, Peter Abraham, E. Lipke, P. Kuhlers","doi":"10.1158/1538-7445.AM2021-2181","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2181","url":null,"abstract":"","PeriodicalId":18754,"journal":{"name":"Molecular and Cellular Biology / Genetics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73030967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-1983
A. E. Gulec, Hepsen H. Husnugil, Goksu Oral, Ilir Sheraj, Sreeparna Banerjee
{"title":"Abstract 1983: Investigation of the effects of nutrient restriction on endolysosomal signaling in colorectal cancer (CRC) cells","authors":"A. E. Gulec, Hepsen H. Husnugil, Goksu Oral, Ilir Sheraj, Sreeparna Banerjee","doi":"10.1158/1538-7445.AM2021-1983","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-1983","url":null,"abstract":"","PeriodicalId":18754,"journal":{"name":"Molecular and Cellular Biology / Genetics","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74239230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2094
K. Hamada, Ying Tian, Mao Fujimoto, Takahashi Yoriko, T. Kohno, K. Tsuta, Shun-ichi Watanabe, Teruhiko Yoshida, H. Asamura, Y. Kanai, Eri Arai
The aim of this study was to clarify correlations between epigenomic and genomic alterations during multistage lung adenocarcinogenesis. Single-CpG resolution genome-wide DNA methylation analysis with the Infinium HumanMethylation27 BeadChip was performed using 162 paired samples of non-cancerous lung tissue (N) and corresponding tumorous tissue (T) from patients with lung adenocarcinomas. Correlations between DNA methylation data on the one hand and clinicopathological parameters and genomic driver mutations, i.e. mutations of EGFR, KRAS, BRAF, and HER2 and fusion involving ALK, RET, and ROS1, were examined. In N samples, which were considered to be at precancerous stages, DNA methylation levels in 12,629 probes were significantly correlated with recurrence-free survival. DNA methylation profiles at the precancerous N stages may determine the prognostic outcome. Principal component analysis revealed that distinct DNA methylation profiles at the precancerous N stage tended not to induce specific genomic driver mutations. Most of the genes showing significant DNA methylation alterations during transition from N to T were shared by two or more driver aberration groups, indicating that, in general, each driver mutation does not induce a specific DNA methylation profile. Commonly shared DNA methylation alterations which could potentially result in expression abnormalities were enriched among transcriptional factors. In contrast, only 67 genes showed EGFR mutation-specific or “pan-negative”-specific DNA methylation alterations. Among the 67 genes, most of the DNA methylation alterations were correlated with clinicopathological parameters reflecting tumor aggressiveness. We further focused on the ZNF132 gene, for which DNA hypermethylation had been observed only in the “pan-negative”-type lung adenocarcinomas and was significantly correlated with their vascular invasion. 5-aza-29-deoxycytidine treatment restored the expression levels of ZNF132 mRNA in lung adenocarcinoma cell lines, indicating that ZNF132 had been silenced due to DNA hypermethylation. Knockdown of ZNF132 using siRNA transfection led to increased cell migration ability, rather than increased cell growth or reduced apoptosis. We concluded that DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of “pan-negative”-type lung adenocarcinomas. In addition, DNA methylation alterations at the precancerous stage may determine tumor aggressiveness, and such alterations that accumulate after driver mutation may additionally modify clinicopathological features through alterations of gene expression. Citation Format: Kenichi Hamada, Ying Tian, Mao Fujimoto, Takahashi Yoriko, Takashi Kohno, Koji Tsuta, Shun-ichi Watanabe, Teruhiko Yoshida, Hisao Asamura, Yae Kanai, Eri Arai. Correaltions between genome-wide DNA methylation profiles and genomic driver aberrations during multistage lung adenocaricinogenesis [abstract]. In: Proceedings of the American Associati
{"title":"Abstract 2094: Correaltions between genome-wide DNA methylation profiles and genomic driver aberrations during multistage lung adenocaricinogenesis","authors":"K. Hamada, Ying Tian, Mao Fujimoto, Takahashi Yoriko, T. Kohno, K. Tsuta, Shun-ichi Watanabe, Teruhiko Yoshida, H. Asamura, Y. Kanai, Eri Arai","doi":"10.1158/1538-7445.AM2021-2094","DOIUrl":"https://doi.org/10.1158/1538-7445.AM2021-2094","url":null,"abstract":"The aim of this study was to clarify correlations between epigenomic and genomic alterations during multistage lung adenocarcinogenesis. Single-CpG resolution genome-wide DNA methylation analysis with the Infinium HumanMethylation27 BeadChip was performed using 162 paired samples of non-cancerous lung tissue (N) and corresponding tumorous tissue (T) from patients with lung adenocarcinomas. Correlations between DNA methylation data on the one hand and clinicopathological parameters and genomic driver mutations, i.e. mutations of EGFR, KRAS, BRAF, and HER2 and fusion involving ALK, RET, and ROS1, were examined. In N samples, which were considered to be at precancerous stages, DNA methylation levels in 12,629 probes were significantly correlated with recurrence-free survival. DNA methylation profiles at the precancerous N stages may determine the prognostic outcome. Principal component analysis revealed that distinct DNA methylation profiles at the precancerous N stage tended not to induce specific genomic driver mutations. Most of the genes showing significant DNA methylation alterations during transition from N to T were shared by two or more driver aberration groups, indicating that, in general, each driver mutation does not induce a specific DNA methylation profile. Commonly shared DNA methylation alterations which could potentially result in expression abnormalities were enriched among transcriptional factors. In contrast, only 67 genes showed EGFR mutation-specific or “pan-negative”-specific DNA methylation alterations. Among the 67 genes, most of the DNA methylation alterations were correlated with clinicopathological parameters reflecting tumor aggressiveness. We further focused on the ZNF132 gene, for which DNA hypermethylation had been observed only in the “pan-negative”-type lung adenocarcinomas and was significantly correlated with their vascular invasion. 5-aza-29-deoxycytidine treatment restored the expression levels of ZNF132 mRNA in lung adenocarcinoma cell lines, indicating that ZNF132 had been silenced due to DNA hypermethylation. Knockdown of ZNF132 using siRNA transfection led to increased cell migration ability, rather than increased cell growth or reduced apoptosis. We concluded that DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of “pan-negative”-type lung adenocarcinomas. In addition, DNA methylation alterations at the precancerous stage may determine tumor aggressiveness, and such alterations that accumulate after driver mutation may additionally modify clinicopathological features through alterations of gene expression. Citation Format: Kenichi Hamada, Ying Tian, Mao Fujimoto, Takahashi Yoriko, Takashi Kohno, Koji Tsuta, Shun-ichi Watanabe, Teruhiko Yoshida, Hisao Asamura, Yae Kanai, Eri Arai. Correaltions between genome-wide DNA methylation profiles and genomic driver aberrations during multistage lung adenocaricinogenesis [abstract]. In: Proceedings of the American Associati","PeriodicalId":18754,"journal":{"name":"Molecular and Cellular Biology / Genetics","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72811388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-01DOI: 10.1158/1538-7445.AM2021-2388
A. Uboveja, Y. K. Satija, F. Siraj, Chanchal Bareja, D. Saluja
p73 is a member of the p53 tumor suppressor family and exerts its tumor suppressor functions by suppressing metastasis. It is increasingly evident that long noncoding RNAs (lncRNAs) play a significant role in tumor suppression. The present study is aimed to identify novel lncRNAs that play a role in p73-mediated suppression of metastasis in colorectal cancer cells. Transcriptome analysis was performed to detect the differentially expressed lncRNAs in presence and absence of p73. Out of these, FER1L4 lncRNA was found to be significantly induced in a p73-dependent manner. p73 binding to FER1L4 promoter was confirmed through bioinformatic analysis, luciferase reporter, ChIP and site-directed mutagenesis assays. Knockdown of FER1L4 and p73 significantly increased the invasion and migration rate of colorectal cancer cells as confirmed by wound-healing assay. Knockdown of FER1L4 decreased the expression of E-cadherin and increased the expression of prominent EMT markers such as N-cadherin, Snail, Vimentin and Fibronectin. FER1L4 causes a G2/M cell cycle arrest in a p73-dependent manner in HCT116p53-/-p73+/+ cells and upon FER1L4kd, normal cell cycle progression was observed. Annexin V/PI and TUNEL apoptosis assays revealed that FER1L4 induced apoptosis in HCT116p53-/-p73+/+ cells with increase in time-dependent treatment of etoposide and FER1L4kd inhibited apoptosis even in the presence of p73. The protein expression level of pro-apoptotic genes such as Bad, Bax, Bik, Bim, BID, Bak and PUMA decreased upon FER1L4kd and p73kd, confirming that FER1L4 plays a role in p73 mediated apoptosis and cell cycle arrest. FER1L4 also sponges the expression of miR-1273g-3p, thus inhibiting its oncogenic role. RNA-In situ hybridization (RNA-ISH) confirmed the decreased expression of p73 and FER1L4 mRNA in 30 human metastatic CRC tissues as compared to 30 human non-metastatic CRC tissues. Taken together, we provide conclusive proof that p73 exerts its anti-metastatic function by inducing the expression of lncRNA FER1L4 in response to genotoxic stress. Citation Format: Apoorva Uboveja, Yatendra Kumar Satija, Fouzia Siraj, Chanchal Bareja, Daman Saluja. p73 - lncRNA Fer1l4 axis plays a critical role in suppression of cancer cell migration, invasion and metastasis in a p73-dependent manner via inhibition of miR-1273g-3p [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2388.
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