Huang, Shengbing

Abstract Objective. Four-dimensional CT (4DCT) enables visualization of dynamic wrist joint pathology but may be compromised by motion artifacts. Deep learning (DL)-assisted motion correction has the potential to enhance wrist 4DCT quality, but model development is hindered by scarce training data. To address this, we developed a model-based motion simulation framework that generated realistic 4DCT data with paired static ground truth images to demonstrate wrist motion correction using a physics-informed DL model trained with simulated data. Approach. Wrist motion was simulated by synchronizing rotational and translational movements of carpal bones and connective tissues. Elastic deformation guided by analytically-derived motion vector fields was applied to static wrist scans at neutral positions to create artifact-free images at multiple angular positions. Virtual motion-corrupted 4DCT images were produced via forward projection and reconstruction with synchronized gantry and wrist motion. Experimental data from 4DCT cadaver scans were collected to validate simulation quality. Low-intensity region score (LIRS), positivity, and entropy were used to assess simulated motion artifacts. A physics-informed motion correction network was adapted exclusively using simulated training data and subsequently deployed on simulated, real cadaveric, and in vivo 4DCT scans. LIRS and structural similarity index (SSIM) were used to evaluate motion correction quality. Wilcoxon signed-rank tests were conducted ( α = 0.05). Results. The simulation method created realistic motion artifacts compared to real scan reference ( p > 0.05). Motion artifacts were effectively mitigated across testing cases demonstrating generalizability. In simulated scans, LIRS improved from 0.55 ± 0.12–0.75 ± 0.04 and SSIM from 0.87 ± 0.08–0.95 ± 0.03 at bone regions (each p < 0.01). In experimental cadaveric scans, LIRS improved from 0.05 ± 0.01–0.31 ± 0.17 in marker regions and from 0.58 ± 0.19–0.77 ± 0.14 in bone regions (each p < 0.01). Significance. Our simulation method facilitates training DL-assisted motion correction algorithms by providing high-quality training data, effectively supporting 4DCT image quality enhancement.

Abstract Resistance to chemotherapy remains a major obstacle to improving outcomes of cancer treatment. Recent data suggest intrinsic functions of immune checkpoint proteins, including PD-L1, that may be distinct from their immunoregulatory roles. We found that colorectal cancer (CRC) cells with mutant BRAF(V600E) or KRASalleles show increased PD-L1 transcripts and expression of cell surface PD-L1 protein compared to those with wild-type copies. Furthermore, ectopic expression of BRAFV600E or mutant KRAS induced PD-L1 whose upregulation was attenuated by inhibition of RAS-RAF-MEK-ERK signaling. Combined knockdown of MEK/ERK effectors c-JUN and YAP markedly reduced PD-L1. Knockout of PD-L1 in RKO cells resulted in a reduction in chemotherapy-induced DNA double strand breaks (pH2AX) and caspase-3 cleavage compared to parental cells. Results were confirmed in PD-L1 knockout MC38 murine CRC cells where re-expression of PD-L1, but not its deletion mutants, was shown to induced pH2AX and apoptosis. In cells with knockout of PD-L1, reductions in p-AKT and the BH3-only proteins BIM and BIK were observed that could be restored by re-expression of PD-L1. Treatment of cells with an anti-PD-L1 antibody reduced p-AKT, BIM and BIK, and also attenuated chemotherapy-induced apoptosis. Re-expression of BIM in PD-L1 knockout cells restored apoptosis. Murine tumor xenografts generated from cells with knockout of PD-L1 displayed resistance to oxaliplatin-induced tumor regression compared to tumors derived from parental cells. Using TCGA datasets, human CRCs with high vs low PD-L1 mRNA levels were significantly associated with better survival. In summary, we identified a non-immune function of tumor cell-intrinsic PD-L1 that upregulates BH3-only proteins BIM and BIK to promote apoptosis, thereby suggesting its potential as a predictive biomarker. Citation Format: Daofu Feng, Krishnendu Pal, Debabrata Mukhopadhyay, Xin Liu, Haidong Dong, Shengbing Huang, Frank A. Sinicrope. Tumor intrinsic PD-L1 is mediated by BRAFV600E and can regulate drug-induced apoptosis in human colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 705.

Abstract Background. Mutation of the BRAF(V600E) oncogene occurs in ~8% of human colorectal cancers (CRC) and its inhibition is associated with treatment resistance that is due, in part, to paradoxical re-activation of MEK/ERK signaling. Recently, pathway analysis identified cyclin-dependent kinase 1 (CDK1) upregulation in a subset of human BRAFV600E CRCs. We determined whether CDK1 antagonism can enhance the efficacy of MEK inhibition in BRAFV600E CRC cell lines. Methods. Manipulation of gene expression was achieved by siRNA and/or ectopic expression, or using isogenic cell pairs. Cells were treated with the CDK1 selective inhibitor RO-3306 or dinaciclib (CDK1,2,5,9 inhibitor) alone or combined with the MEK inhibitor cobimetinib. Apoptosis was quantified by Annexin V staining with flow cytometry; apoptotic signaling was analyzed by immunoblotting of caspase-8 phosphorylation and caspase cleavage. Long-term cell survival was evaluated by clonogenic assay. In vivo efficacy of the drug combination was determined in a murine flank xenograft model. Results. BRAFV600E CRC cell lines expressed CDK1 whose siRNA knockdown or pharmacological inhibition by RO-3306 or dinaciclib was shown to sensitize them to apoptosis (annexin V labeling). The combination of RO-3306 or dinaciclib with cobimetinib cooperatively enhanced apoptosis and reduced clonogenic survival compared to drug monotherapy. Cells isogenic or ectopic for BRAFV600E displayed apoptosis resistance to CDK inhibitors, as did cells with ectopic expression of constitutively active MEK. CDK1 inhibition by RO-3306 or dinaciclib induced a caspase-8-dependent apoptosis shown by caspase-8 restoration in deficient NB7 cells that enhanced dinaciclib-induced caspase-3 cleavage. Furthermore, CDK inhibitors suppressed procaspase-8 phosphorylation at S387 shown by drug withdrawal that restored phospho-S387 and increased cell mitosis. In a CRC xenograft model, dinaciclib plus cobimetinib produced significantly greater tumor growth inhibition in association with a caspase-dependent apoptosis than did either drug alone. Analysis of TCGA datasets revealed overexpression of CDK1 in human CRCs compared to normal colonic tissue. An inverse relationship existed between expression of CDK1 and the cell cycle inhibitor p16. In CRC cells, ectopic p16 was shown to downregulate CDK1 expression. In conclusion, our data establish CDK1 as a novel mediator of apoptosis resistance in BRAFV600E CRC cells lines whose combined targeting with CDK and MEK/ERK inhibitors may represent an effective therapeutic strategy. Citation Format: Peng Zhang, Hisato Kawakami, Weizhen Liu, Xiangyu Zeng, Klaus Stebhardt, Kaixiong Tao, Shengbing Huang, Frank A. Sinicrope. Targeting CDK1 and MEK/ERK overcomes apoptosis resistance in BRAFV600E human colorectal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2336.

Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome data, which contain a vast number of zeros due to the physical absence or under-sampling of the microbes. Normalization methods that specifically address the zero-inflation remain largely undeveloped. Here we propose geometric mean of pairwise ratios—a simple but effective normalization method—for zero-inflated sequencing data such as microbiome data. Simulation studies and real datasets analyses demonstrate that the proposed method is more robust than competing methods, leading to more powerful detection of differentially abundant taxa and higher reproducibility of the relative abundances of taxa.

Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome data, which contain a vast number of zeros due to the physical absence or under-sampling of the microbes. Normalization methods that specifically address the zero inflation remain largely undeveloped. Here we propose GMPR - a simple but effective normalization method - for zero-inflated sequencing data such as microbiome data. Simulation studies and real datasets analyses demonstrate that the proposed method is more robust than competing methods, leading to more powerful detection of differentially abundant taxa and higher reproducibility of the relative abundances of taxa.

Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome data, which contain a vast number of zeros due to the physical absence or under-sampling of the microbes. Normalization methods that specifically address the zero inflation remain largely undeveloped. Here we propose GMPR - a simple but effective normalization method - for zero-inflated sequencing data such as microbiome data. Simulation studies and real datasets analyses demonstrate that the proposed method is more robust than competing methods, leading to more powerful detection of differentially abundant taxa and higher reproducibility of the relative abundances of taxa.

Abstract The BRAFV600E mutation occurs in approximately 8% of human colorectal cancers and is associated with therapeutic resistance that is due, in part, to reactivation of MEK/ERK signaling cascade. Recently, pathway analysis identified cyclin-dependent kinase 1 (CDK1) upregulation in a subset of human BRAFV600E colorectal cancers. Therefore, it was determined whether CDK1 antagonism enhances the efficacy of MEK inhibition in BRAFV600E colorectal cancer cells. BRAFV600E colorectal cancer cell lines expressing CDK1 were sensitized to apoptosis upon siRNA knockdown or small-molecule inhibition with RO-3306 (CDK1 inhibitor) or dinaciclib (CDK1, 2, 5, 9 inhibitors). Combination of RO-3306 or dinaciclib with cobimetinib (MEK inhibitor) cooperatively enhanced apoptosis and reduced clonogenic survival versus monotherapy. Cells isogenic or ectopic for BRAFV600E displayed resistance to CDK1 inhibitors, as did cells with ectopic expression of constitutively active MEK. CDK1 inhibitors induced a CASP8-dependent apoptosis shown by caspase-8 restoration in deficient NB7 cells that enhanced dinaciclib-induced CASP3 cleavage. CDK inhibitors suppressed pro-CASP8 phosphorylation at S387, as shown by drug withdrawal, which restored p-S387 and increased mitosis. In a colorectal cancer xenograft model, dinaciclib plus cobimetinib produced significantly greater tumor growth inhibition in association with a caspase-dependent apoptosis versus either drug alone. The Cancer Genome Atlas (TCGA) transcriptomic dataset revealed overexpression of CDK1 in human colorectal cancers versus normal colon. Together, these data establish CDK1 as a novel mediator of apoptosis resistance in BRAFV600E colorectal cancers whose combined targeting with a MEK/ERK inhibitor represents an effective therapeutic strategy. Implications: CDK1 is a novel mediator of apoptosis resistance in BRAFV600E colorectal cancers whose dual targeting with a MEK inhibitor may be therapeutically effective. Mol Cancer Res; 16(3); 378–89. ©2017 AACR.

Abstract BRAFV600E mutation occurs in ~10% of human colorectal cancers (CRC) where it is associated with treatment resistance and poor prognosis. Data from TCGA and a clinical trial cohort identified a distinct subset of BRAF mutant colon cancers with deregulation of the cell cycle and overexpression of CDK1 (Barras D, et al, Clin Cancer Res. 2016). We tested the hypothesis that CDK1 inhibition can enhance apoptosis in BRAFV600E CRC cells. Since BRAF mutant cells show p-ERK activation, combined inhibition of CDK1 and MEK/ERK was evaluated. Using isogenic colon cancer cells, BRAF mutant alleles were shown to confer resistance to the CDK1 inhibitor, R0-3306, in a gene dose-dependent manner that was associated with reduced cleavage of caspase-3 and downstream PARP, and decreased pH2AX (DNA fragmentation marker). Ectopic BRAFV600E or constitutively active MEK mutant also conferred resistance to R0-3306. CDK1 siRNA was shown to increase cobimetinib-induced apoptosis, including annexin V labeling, and increased pH2AX. Furthermore, ERK siRNA or cobimetinib treatment attenuated CDK1 protein expression and increased R0-3306-induced pH2Ax. Moreover, treatment with R0-3306 plus cobimetinib significantly enhanced a caspase-dependent apoptosis and markedly reduced colony formation vs either drug alone in two CRC cell lines. Caspase-3 cleavage by R0-3306 + cobimetinib was dependent upon caspase-8. Mechanistically, CDK1 inhibition by R0-3306 suppressed the phosphorylation of procaspase-8 at Ser-387 shown by R0-3306 withdrawal which restored p-C8-S387 coincident with expression of the mitotic marker, pH3S10. In conclusion, inhibition of CDK1 can significantly augment apoptosis induction by MEK/ERK inhibition in BRAFV600E CRC cells, suggesting a novel therapeutic strategy to overcome mutant BRAF-mediated resistance. Apoptosis induction by CDK1 inhibitor (R0-3306) ± MEK/ERK inhibitor cobimetinibTreatmentTreatmentTreatementTreatmentCRC cell linesDMSOR0-3306 (5 µM)cobimetinib (5 µM)combinationAnnexin V+ (%)RKO13.43 ± 1.4132.55 ± 2.9315.04 ± 0.2652.72 ± 3.16Annexin V+ (%)HT-2911.22 ± 1.8442.44 ± 2.7025.29 ± 0.1665.62 ± 4.11 Citation Format: Hisato Kawakami, Shengbing Huang, Frank A. Sinicrope. Targeting CDK1 and MEK/ERK overcome mutant BRAF-mediated apoptosis resistance in human colorectal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2173. doi:10.1158/1538-7445.AM2017-2173

603 Background: Oncogenic BRAFV600E mutations activate MAP kinase signaling and are associated with treatment resistance and poor prognosis in patients with colorectal cancer (CRC). In BRAFV600E mutant CRCs, treatment failure may be related to BRAFV600E-mediated apoptosis resistance that occurs by an as yet undefined mechanism. Methods: BRAF isogenic RKO CRC cells and RKO, HT29, WiDr cell lines were treated with cobimetinib ± the small molecule MCL-1 inhibitor, A-1210477. Apoptosis was measured by Annexin V staining and caspase cleavage. Gene knockdown or overexpression was achieved by lentivirus; ERK siRNA was utilized. Competitive RT-PCR was performed for MCL-1 mRNA expression. HT-29 cells with control or MCL-1 shRNA were xenografted into SCID mice, treated with cobimetinib or vehicle, and tumor volume was measured. Results: We found that BRAFV600E can upregulate anti-apoptotic MCL-1 in a gene dose-dependent manner using CRC cell lines isogenic for BRAF. BRAFV600E-induced MCL-1 upregulation was confirmed by ectopic BRAFV600E expression that activated MEK/ERK signaling to phosphorylate (MCL-1Thr163) and stabilize MCL-1. Upregulation of MCL-1 was mediated by MEK/ERK shown by ERK siRNA that suppressed MCL-1. Stabilization of MCL-1 by phosphorylation was shown by a phosphorylation-mimicking mutant and an unphosphorylated MCL-1 mutant that decreased or increased MCL-1 protein turnover, respectively.MEK /ERK inhibition by cobimetinib suppressed MCL-1 expression/phosphorylation and induced pro-apoptotic BIM to a greater extent than did vemurafenib in BRAFV600E cell lines. MCL-1 knockdown vs control shRNA significantly enhanced cobimetinib-induced apoptosis in vitro and in HT29 colon cancer xenografts. A-1210477 also enhanced cobimetinib-induced apoptosis in vitrothat was due to disruption of the interaction of MCL-1 with pro-apoptotic BAK and BIM. Knockdown of BIM attenuated BAX, but not BAK, activation by cobimetinib plus A-1210477. Conclusions: BRAFV600E-mediated MEK/ERK activation can upregulate MCL-1 by phosphorylation/stabilization to confer apoptosis resistance that can be reversed by MCL-1 antagonism.

492 Background: Beclin 1 interacts with its cofactor UVRAG to promote autophagy, a cellular degradation process induced by cellular stress. While cells with defective autophagy are prone to genomic instability, it is unknown whether Beclin 1 and/or UVRAG can regulate DNA damage/repair. Methods: Colorectal cancer cell lines (HT-29, DLD1) with Beclin 1 or UVRAG siRNA were irradiated ± 5-FU. DNA damage (pATM, pH2Ax, 53BP1, RAD51), cell death (annexin V, caspase-3, clonogenic survival), and centrosome number (γ-tubulin staining), were determined. Beclin 1 protein expression was analyzed in pretreatment endoscopic biopsies from 96 rectal carcinoma patients who received radiation + 5-FU followed by surgery. Results: Beclin 1 or UVRAG knockdown was shown to enhance DNA double-strand breaks (DSBs) and cell death induced by radiation ± 5-FU. Suppression of either gene increased the percentage of irradiated cells with nuclear foci expressing 53BP1 (nonhomologous end joining), but not RAD51 (homologous recombination). Beclin 1 was shown to regulate UVRAG, and a UVRAG deletion mutant defective in Beclin 1 binding decreased protection against radiation-induced DSBs. Knockdown of Beclin 1 or UVRAG increased centrosome number in irradiated cells. While autophagy inhibition by ATG5 or LC3 siRNA enhanced radiation-induced DSBs, they did not alter centrosome number suggesting independence from autophagy. In rectal carcinomas, high vs low level Beclin 1 expression was detected in 56 (58.3%) and 40 (41.7%) tumors, respectively. Pre-treatment Beclin 1 was not associated with clinicopathological variables. However, high vs low Beclin 1 predicted a significantly reduced pathological response (macroscopic vs. microscopic or no residual tumor) to chemoradiation (high: 14.2% vs. low: 40%; p = 0.017). High vs low Beclin 1 was independently associated with poorer overall survival (HR, 4.30; 95% CI, 1.42-16.47; p = 0.009). Conclusions: Beclin 1 and UVRAG confer protection against radiation-induced DNA damage and maintain centrosome stability. The ability of Beclin 1 overexpression to confer resistance to chemoradiation, suggests its potential utility as a predictive biomarker in rectal cancer.