Development of a multigenomic liquid biopsy (PROSTest) for prostate cancer in whole blood

INTRODUCTION

We describe the development of a molecular assay from publicly available tumor tissue mRNA databases using machine learning and present preliminary evidence of functionality as a diagnostic and monitoring tool for prostate cancer (PCa) in whole blood.

MATERIALS AND METHODS

We assessed 1055 PCas (public microarray data sets) to identify putative mRNA biomarkers. Specificity was confirmed against 32 different solid and hematological cancers from The Cancer Genome Atlas (n = 10,990). This defined a 27-gene panel which was validated by qPCR in 50 histologically confirmed PCa surgical specimens and matched blood. An ensemble classifier (Random Forest, Support Vector Machines, XGBoost) was trained in age-matched PCas (n = 294), and in 72 controls and 64 BPH. Classifier performance was validated in two independent sets (n = 263 PCas; n = 99 controls). We assessed the panel as a postoperative disease monitor in a radical prostatectomy cohort (RPC: n = 47).

RESULTS

A PCa-specific 27-gene panel was identified. Matched blood and tumor gene expression levels were concordant (r = 0.72, p < 0.0001). The ensemble classifier ("PROSTest") was scaled 0%-100% and the industry-standard operating point of ≥50% used to define a PCa. Using this, the PROSTest exhibited an 85% sensitivity and 95% specificity for PCa versus controls. In two independent sets, the metrics were 92%-95% sensitivity and 100% specificity. In the RPCs (n = 47), PROSTest scores decreased from 72% ± 7% to 33% ± 16% (p < 0.0001, Mann-Whitney test). PROSTest was 26% ± 8% in 37 with normal postoperative PSA levels (<0.1 ng/mL). In 10 with elevated postoperative PSA, PROSTest was 60% ± 4%.

CONCLUSION

A 27-gene whole blood signature for PCa is concordant with tissue mRNA levels. Measuring blood expression provides a minimally invasive genomic tool that may facilitate prostate cancer management.

Accelerating Patterned Vascularization Using Granular Hydrogel Scaffolds and Surgical Micropuncture

Bulk hydrogel scaffolds are common in reconstructive surgery. They allow for the staged repair of soft tissue loss by providing a base for revascularization. Unfortunately, they are limited by both slow and random vascularization, which may manifest as treatment failure or suboptimal repair. Rapidly inducing patterned vascularization within biomaterials has profound translational implications for current clinical treatment paradigms and the scaleup of regenerative engineering platforms. To address this long-standing challenge, a novel microsurgical approach and granular hydrogel scaffold (GHS) technology are co-developed to hasten and pattern microvascular network formation. In surgical micropuncture (MP), targeted recipient blood vessels are perforated using a microneedle to accelerate cell extravasation and angiogenic outgrowth. By combining MP with an adjacent GHS with precisely tailored void space architecture, microvascular pattern formation as assessed by density, diameter, length, and intercapillary distance is rapidly guided. This work opens new translational opportunities for microvascular engineering, advancing reconstructive surgery, and regenerative medicine.

Vascular persistence following precision micropuncture

OBJECTIVE

The success of engineered tissues continues to be limited by time to vascularization and perfusion. Recently, we described a simple microsurgical approach, termed micropuncture (MP), which could be used to rapidly vascularize an adjacently placed scaffold from the recipient macrovasculature. Here we studied the long-term persistence of the MP-induced microvasculature.

METHODS

Segmental 60 μm diameter MPs were created in the recipient rat femoral artery and vein followed by coverage with a simple Type 1 collagen scaffold. The recipient vasculature and scaffold were then wrapped en bloc with a silicone sheet to isolate intrinsic vascularization. Scaffolds were harvested at 28 days post-implantation for detailed analysis, including using a novel artificial intelligence (AI) approach.

RESULTS

MP scaffolds demonstrated a sustained increase of vascular density compared to internal non-MP control scaffolds (p < 0.05) secondary to increases in both vessel diameters (p < 0.05) and branch counts (p < 0.05). MP scaffolds also demonstrated statistically significant increases in red blood cell (RBC) perfused lumens.

CONCLUSIONS

This study further highlights that the intrinsic MP-induced vasculature continues to persist long-term. Its combination of rapid and stable angiogenesis represents a novel surgical platform for engineered scaffold and graft perfusion.

AATF inhibition exerts antiangiogenic effects against human hepatocellular carcinoma

Background and aims

Angiogenesis is a key factor in the growth and metastasis of hepatic tumors and thus a potential therapeutic target in hepatocellular carcinoma (HCC). In this study, we aim to identify the key role of apoptosis antagonizing transcription factor (AATF) in tumor angiogenesis and its underlying mechanisms in HCC.

Methods

HCC tissues were analyzed for AATF expression by qRT-PCR and immunohistochemistry. Stable clones of control and AATF knockdown (KD) were established in human HCC cells. The effect of AATF inhibition on the angiogenic processes was determined by proliferation, invasion, migration, chick chorioallantoic membrane (CAM) assay, zymography, and immunoblotting techniques.

Results

We identified high levels of AATF in human HCC tissues compared to adjacent normal liver tissues, and the expression was found to be correlated with the stages and tumor grades of HCC. Inhibiting AATF in QGY-7703 cells resulted in higher levels of pigment epithelium-derived factor (PEDF) than controls due to decreased matric metalloproteinase activity. Conditioned media from AATF KD cells inhibited the proliferation, migration, and invasion of human umbilical vein endothelial cells as well as the vascularization of the chick chorioallantoic membrane. Furthermore, the VEGF-mediated downstream signaling pathway responsible for endothelial cell survival and vascular permeability, cell proliferation, and migration favoring angiogenesis was suppressed by AATF inhibition. Notably, PEDF inhibition effectively reversed the anti-angiogenic effect of AATF KD.

Conclusion

Our study reports the first evidence that the therapeutic strategy based on the inhibition of AATF to disrupt tumor angiogenesis may serve as a promising approach for HCC treatment.

Mesenchymal Stem Cell-Derived Extracellular Vesicles for Therapeutic Use and in Bioengineering Applications

Extracellular vesicles (EVs) are small lipid bilayer-delimited particles that are naturally released from cells into body fluids, and therefore can travel and convey regulatory functions in the distal parts of the body. EVs can transmit paracrine signaling by carrying over cytokines, chemokines, growth factors, interleukins (ILs), transcription factors, and nucleic acids such as DNA, mRNAs, microRNAs, piRNAs, lncRNAs, sn/snoRNAs, mtRNAs and circRNAs; these EVs travel to predecided destinations to perform their functions. While mesenchymal stem cells (MSCs) have been shown to improve healing and facilitate treatments of various diseases, the allogenic use of these cells is often accompanied by serious adverse effects after transplantation. MSC-produced EVs are less immunogenic and can serve as an alternative to cellular therapies by transmitting signaling or delivering biomaterials to diseased areas of the body. This review article is focused on understanding the properties of EVs derived from different types of MSCs and MSC-EV-based therapeutic options. The potential of modern technologies such as 3D bioprinting to advance EV-based therapies is also discussed.

Abstract 2291: microRNA/mRNA integrated analysis of multiple myeloma transcriptomics

Myeloma is plasma cell disorder, mostly effects adults over 60 years. Non-coding RNAs are emerging field and play vital role in development of disease. Major non-coding RNAs are miRNAs, lncRNAs, circRNAs and sn/snoRNAs. We analyzed restricted and publically available RNA-seq and small RNA-seq data sets for biomarkers identification and their involvement in myeloma. We obtained restricted data from “BluePrint”, which contains 11 myeloma plasma cells and 4 normal tonsil plasma cells (EGAS00001001110). We identified 1534 genes are differentially regulated (2-fold cut-off, &gt;10-FC 218 genes). Top 10 upregulated genes were: EDNRB (1246-FC), SCUBE1 (737-FC), MC4R (691-FC), NDNF (601-FC), PTGS2 (567-FC), GPRC5D (531-FC), MFAP3L (467-FC), CCND1 (381-FC), CXCL12 (344-FC) and BTBD3 (326-FC) ; top 10 downregulated were: EBF1 (-111-FC), HLA-DRB1(-133-FC), CPXM1 (-171-FC), LOC642131 (-171-FC), IGHV1OR15-3 (-171-FC), HLA-DRB5 (-204-FC), PRAMENP (-210-FC), DTX1 (-220-FC), CD22 (-337-FC) and RFTN1 (-356-FC). Publically available small RNA-seq data downloaded and analyzed for miRNAs, lncRNAs, circRNAs and sn/snoRNAs which contains 3 healthy donor’s plasma cells and 3 newly diagnosed myeloma patient plasma cells (PRJNA377345). We used mirDIP portal to analyze miRNA and mRNA differentially expressed data, predicated from more than 13 databases showed major role of miR-152-3p (targets 28 mRNAs), miR-93-5p (targets 19 mRNAs), miR-301a-3p (targets 13 mRNAs), miR-29c-3p (targets 12 mRNAs), and miR-144-3p (targets 9 mRNAs). Integrated analysis can provide valuable information from the transcriptomics data and effect of miRNAs on mRNAs.

Citation Format: Srinivas V. Koduru. microRNA/mRNA integrated analysis of multiple myeloma transcriptomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2291.

Regenerative Engineering: Current Applications and Future Perspectives

Many pathologies, congenital defects, and traumatic injuries are untreatable by conventional pharmacologic or surgical interventions. Regenerative engineering represents an ever-growing interdisciplinary field aimed at creating biological replacements for injured tissues and dysfunctional organs. The need for bioengineered replacement parts is ubiquitous among all surgical disciplines. However, to date, clinical translation has been limited to thin, small, and/or acellular structures. Development of thicker tissues continues to be limited by vascularization and other impediments. Nevertheless, currently available materials, methods, and technologies serve as robust platforms for more complex tissue fabrication in the future. This review article highlights the current methodologies, clinical achievements, tenacious barriers, and future perspectives of regenerative engineering.

Navigating the Genomic Landscape of Human Adipose Stem Cell-Derived β-Cells

Diabetes is a pandemic manifested through glucose dysregulation mediated by inadequate insulin secretion by beta cells. A beta cell replacement strategy would transform the treatment paradigm from pharmacologic glucose modulation to a genuine cure. Stem cells have emerged as a potential source for beta cell (β-cell) engineering. The detailed generation of functional β-cells from both embryonic and induced pluripotent stem cells has recently been described. Adult stem cells, including adipose derived, may also offer a therapeutic approach, but remain ill defined. In our study, we performed an in-depth assessment of insulin-producing beta cells generated from human adipose, irrespective of donor patient age, gender, and health status. Cellular transformation was confirmed using flow cytometry and single-cell imaging. Insulin secretion was observed with glucose stimulation and abrogated following palmitate exposure, a common free fatty acid implicated in human beta cell dysfunction. We used next-generation sequencing to explore gene expression changes before and after differentiation of patient-matched samples, which revealed more than 5,000 genes enriched. Adipose-derived beta cells displayed comparable gene expression to native β-cells. Pathway analysis demonstrated relevance to stem cell differentiation and pancreatic developmental processes, which are vital to cellular function, structural development, and regulation. We conclude that the functions associated with adipose derived beta cells are mediated through relevant changes in the transcriptome, which resemble those seen in native β-cell morphogenesis and maturation. Therefore, they may represent a viable option for the clinical translation of stem cell-based therapies in diabetes.

Induction of scaffold angiogenesis by recipient vasculature precision micropuncture

The success of engineered tissues continues to be limited by time to vascularization and perfusion. Here, we studied the effects of precision injury to a recipient macrovasculature in promoting neovessel formation in an adjacently placed scaffold. Segmental 60 μm diameter micropunctures (MP) were created in the recipient rat femoral artery and vein followed by coverage with a simple collagen scaffold. Scaffolds were harvested at 24, 48, 72, and 96 h post-implantation for detailed analysis. Those placed on top of an MP segment showed an earlier and more robust cellular infiltration, including both endothelial cells (CD31) and macrophages (F4/80), compared to internal non-micropunctured control limbs (p < 0.05). At the 96-hour timepoint, MP scaffolds demonstrated an increase in physiologic perfusion (p < 0.003) and a 2.5-fold increase in capillary network formation (p < 0.001). These were attributed to an overall upsurge in small vessel quantity. Furthermore, MP positioned scaffolds demonstrated significant increases in many modulators of angiogenesis, including VEGFR2 and Tie-2 despite a decrease in HIF-1α at all timepoints. This study highlights a novel microsurgical approach that can be used to rapidly vascularize or inosculate contiguously placed scaffolds and grafts. Thereby, offering an easily translatable route towards the creation of thicker and more clinically relevant engineered tissues.

Identification of a Metabolic, Transcriptomic, and Molecular Signature of Patatin-Like Phospholipase Domain Containing 3-Mediated Acceleration of Steatohepatitis

BACKGROUND AND AIMS

The mechanisms by which the I148M mutant variant of the patatin-like phospholipase domain-containing 3 (PNPLA3^I148M ) drives development of nonalcoholic steatohepatitis (NASH) are not known. The aim of this study was to obtain insights on mechanisms underlying PNPLA3^I148M -induced acceleration of NASH.

APPROACH AND RESULTS

Hepatocyte-specific overexpression of empty vector (luciferase), human wild-type PNPLA3, or PNPLA3^I148M was achieved using adeno-associated virus 8 in a diet-induced mouse model of nonalcoholic fatty liver disease followed by chow diet or high-fat Western diet with ad libitum administration of sugar in drinking water (WDSW) for 8 weeks. Under WDSW, PNPLA3^I148M overexpression accelerated steatohepatitis with increased steatosis, inflammation ballooning, and fibrosis (P < 0.001 versus other groups for all). Silencing PNPLA3^I148M after its initial overexpression abrogated these findings. PNPLA3^I148M caused 22:6n3 docosahexanoic acid depletion and increased ceramides under WDSW in addition to increasing triglycerides and diglycerides, especially enriched with unsaturated fatty acids. It also increased oxidative stress and endoplasmic reticulum stress. Increased total ceramides was associated with signature of transducer and activator of transcription 3 (STAT3) activation with downstream activation of multiple immune-inflammatory pathways at a transcriptomic level by network analyses. Silencing PNPLA3^I148M reversed STAT3 activation. Conditioned media from HepG2 cells overexpressing PNPLA3^I148M increased procollagen mRNA expression in LX2 cells; this was abrogated by hepatocyte STAT3 inhibition.

CONCLUSIONS

Under WDSW, PNPLA3^I148M overexpression promotes steatosis and NASH by metabolic reprogramming characterized by increased triglycerides and diglycerides, n3 polyunsaturated fatty acid depletion, and increased ceramides with resultant STAT3 phosphorylation and downstream inflammatory pathway activation driving increased stellate cell fibrogenic activity.

Hybrid Bioprinting of Zonally Stratified Human Articular Cartilage Using Scaffold-Free Tissue Strands as Building Blocks

The heterogeneous and anisotropic articular cartilage is generally studied as a layered structure of "zones" with unique composition and architecture, which is difficult to recapitulate using current approaches. A novel hybrid bioprinting strategy is presented here to generate zonally stratified cartilage. Scaffold-free tissue strands (TSs) are made of human adipose-derived stem cells (ADSCs) or predifferentiated ADSCs. Cartilage TSs with predifferentiated ADSCs exhibit improved mechanical properties and upregulated expression of cartilage-specific markers at both transcription and protein levels as compared to TSs with ADSCs being differentiated in the form of strands and TSs of nontransfected ADSCs. Using the novel hybrid approach integrating new aspiration-assisted and extrusion-based bioprinting techniques, the bioprinting of zonally stratified cartilage with vertically aligned TSs at the bottom zone and horizontally aligned TSs at the superficial zone is demonstrated, in which collagen fibers are aligned with designated orientation in each zone imitating the anatomical regions and matrix orientation of native articular cartilage. In addition, mechanical testing study reveals a compression modulus of ≈1.1 MPa, which is similar to that of human articular cartilage. The prominent findings highlight the potential of this novel bioprinting approach for building biologically, mechanically, and histologically relevant cartilage for tissue engineering purposes.

Differentiation of Adipose Tissue-Derived CD34+/CD31- Cells into Endothelial Cells In Vitro

In this study, CD34+/CD31- progenitor cells were isolated from the stromal vascular fraction (SVF) of adipose tissue using magnetic activated cell sorting. The endothelial differentiation capability of these cells in vitro was evaluated by culturing them in vascular endothelial growth factor (VEGF) induced medium for 14 days. Viability, proliferation, differentiation and tube formation of these cells were evaluated. Cell viability study revealed that both undifferentiated and endothelial differentiated cells remained healthy for 14 days. However, the proliferation rate was higher in undifferentiated cells compared to endothelial differentiated ones. Upregulation of endothelial characteristic genes (Von Willebrand Factor (vWF) and VE Cadherin) was observed in 2D culture. However, PECAM (CD31) was only found to be upregulated after the cells had formed tube-like structures in 3D Matrigel culture. These results indicate that adipose derived CD34+/CD31- cells when cultured in VEGF induced medium, are capable differentiation into endothelial-like lineages. Tube formation of the cells started 3h after seeding the cells on Matrigel and formed more stable and connected network 24 h post seeding in presence of VEGF.

Bioprinting functional tissues

Despite the numerous lives that have been saved since the first successful procedure in 1954, organ transplant has several shortcomings which prevent it from becoming a more comprehensive solution for medical care than it is today. There is a considerable shortage of organ donors, leading to patient death in many cases. In addition, patients require lifelong immunosuppression to prevent graft rejection postoperatively. With such issues in mind, recent research has focused on possible solutions for the lack of access to donor organs and rejections, with the possibility of using the patient's own cells and tissues for treatment showing enormous potential. Three-dimensional (3D) bioprinting is a rapidly emerging technology, which holds great promise for fabrication of functional tissues and organs. Bioprinting offers the means of utilizing a patient's cells to design and fabricate constructs for replacement of diseased tissues and organs. It enables the precise positioning of cells and biologics in an automated and high throughput manner. Several studies have shown the promise of 3D bioprinting. However, many problems must be overcome before the generation of functional tissues with biologically-relevant scale is possible. Specific focus on the functionality of bioprinted tissues is required prior to clinical translation. In this perspective, this paper discusses the challenges of functionalization of bioprinted tissue under eight dimensions: biomimicry, cell density, vascularization, innervation, heterogeneity, engraftment, mechanics, and tissue-specific function, and strives to inform the reader with directions in bioprinting complex and volumetric tissues. STATEMENT OF SIGNIFICANCE: With thousands of patients dying each year waiting for an organ transplant, bioprinted tissues and organs show the potential to eliminate this ever-increasing organ shortage crisis. However, this potential can only be realized by better understanding the functionality of the organ and developing the ability to translate this to the bioprinting methodologies. Considering the rate at which the field is currently expanding, it is reasonable to expect bioprinting to become an integral component of regenerative medicine. For this purpose, this paper discusses several factors that are critical for printing functional tissues including cell density, vascularization, innervation, heterogeneity, engraftment, mechanics, and tissue-specific function, and inform the reader with future directions in bioprinting complex and volumetric tissues.

The contribution of cross-talk between the cell-surface proteins CD36 and CD47-TSP-1 in osteoclast formation and function

Antibody-mediated blockade of cluster of differentiation 47 (CD47)-thrombospondin-1 (TSP-1) interactions blocks osteoclast formation in vitro and attenuates parathyroid hormone (PTH)-induced hypercalcemia in vivo in mice. Hypercalcemia in this model reflects increased bone resorption. TSP-1 has two cell-associated binding partners, CD47 and CD36. The roles of these two molecules in mediating the effects of TSP1 in osteoclasts are unclear. Osteoclast formation was attenuated but not absent when preosteoclasts isolated from CD47^-/- mice were cocultured with WT osteoblasts. Suppressing CD36 in osteoclast progenitors also attenuated osteoclast formation. The hypercalcemic response to a PTH infusion was blunted in CD47^-/-/CD36^-/- (double knockout (DKO)) female mice but not CD47^-/- mice or CD36^-/- animals, supporting a role for both CD47 and CD36 in mediating this effect. Consistent with this, DKO osteoclasts had impaired resorptive activity when analyzed in vitro Inhibition of nitric oxide (NO) signaling is known to promote osteoclastogenesis, and TSP-1 suppresses NO production and signaling. An anti-TSP-1 antibody increased NO production in osteoclasts, and the inhibitory effect of anti-TSP-1 on osteoclastogenesis was completely rescued by l-nitroarginine methyl ester (l-NAME), a competitive NO synthase inhibitor. Supportive of an important role for CD36 in mediating the pro-osteoclastogenic effects of TSP-1, engaging CD36 with a synthetic agonist, p907, suppressed NO production in anti-TSP-1-treated cultures, allowing osteoclast maturation to occur. These results establish that CD36 and CD47 both participate in mediating the actions of TSP-1 in osteoclasts and establish a physiologically relevant cross-talk in bone tissue between these two molecules.

Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs

Hepatocellular carcinoma (HCC) was the fifth leading cause of cancer death in men and eighth leading cause of death in women in the United States in 2017. In our study, we sought to identify sncRNAs in various stages of development of HCC. We obtained publicly available small RNA-seq data derived from patients with cirrhosis (n = 14), low-grade dysplastic nodules (LGDN, n = 9), high grade dysplastic nodules (HGDN, n = 6), early hepatocellular carcinoma (eHCC, n = 6), and advanced hepatocellular carcinoma (HCC, n = 20), along with healthy liver tissue samples (n = 9). All samples were analyzed for various types of non-coding RNAs using PartekFlow software. We remapped small RNA-seq to miRBase to obtain differential expressions of miRNAs and found 87 in cirrhosis, 106 in LGDN, 59 in HGDN, 80 in eHCC, and 133 in HCC. Pathway analysis of miRNAs obtained from diseased samples compared to normal samples showed signaling pathways in the microRNA dependent EMT, CD44, and others. Additionally, we analyzed the data sets for piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs. We validated the in silico data using human HCC samples with NanoString miRNA global expression. Our results suggest that publically available data is a valuable resource for sncRNA identification in HCC progression (FDR set to <0.05 for all samples) and that a data mining approach is useful for biomarker development.

Small Non-coding RNA Abundance in Adrenocortical Carcinoma: A Footprint of a Rare Cancer

BACKGROUND: Adrenocortical carcinoma (ACC) is a relatively rare, but aggressive type of cancer, which affects both children and adults. OBJECTIVE: Small non-coding RNAs (sncRNAs) play important roles and may serve as biomarkers for disease diagnosis, prognosis and treatment. METHODS: In our study, we sought to identify sncRNAs associated with malignant adrenal tumors. We obtained publicly available, small RNA sequencing data derived from 45 ACC and 30 benign tumors arising from the cortex of the adrenal gland, adrenocortical adenomas (ACA), and compared their sncRNA expression profiles. RESULTS: First, we remapped small RNA-seq to miRBase version 21 to check expression of miRNAs and found 147 miRNAs were aberrantly expressed (p<0.05) in ACC samples compared to ACA samples. Pathway analysis of differentially expressed miRNAs revealed p53 signaling pathways to be profoundly affected in ACC samples. Further examination for other types of small RNAs revealed 16 piRNAs, 48 lncRNAs and 19 sn/snoRNAs identified in ACC samples. Conclusions: Our data analysis suggests that publically available resources can be mined for biomarker development and improvements in-patient care; however, further research must be performed to correlate tumor grade with gene expression.

Abstract 3490: Interrogation of small RNA-seq data for small noncoding RNA in human colon cancer

Genomic analysis of the human transcriptome has been made possible only in last decade by next generation sequencing (NGS). Recent advancements in NGS has further allowed us to look into small non-coding RNAs (sncRNAs) such as microRNAs (miRNAs), Piwi-interacting-RNAs (piRNAs), long non-coding RNAs (lncRNAs) & small nuclear/nucleolar RNAs (sn/snoRNAs). Recently, the roles of sncRNAs in biological processes have been implicated in biomarker development for diagnosis, prognosis &therapy. In the present study, 50 colon cancer patient’s small RNA sequencing raw data was downloaded from NIH bioproject (PRJNA266667; 7 TNM stage II & 43 TNM stage III) which contained 27 female & 23 male samples. 24 samples had metachronous metastasis (MM) & 26 non-metachronous metastasis (NMM). The small RNA-seq data was analyzed using PartekFlow. In depth analysis showed aberrant expression of 48 miRNAs (all upregulated) in TNM-III vs TNM-II specimens & 20 miRNAs (17 upregulated & 3 downregulated) in MM vs NMM. Further investigation of dysregulated miRNA through pathway analysis confirmed that the majority of the miRNAs were involved in cancer signaling pathways. Analysis of piRNA found unusual expression of 60 piRNAs (57 upregulated & 3 downregulated) in TNM-III vs TNM-II & 31 piRNAs (28 upregulated & 3 downregulated) in MM vs NMM. Further analysis of long non-coding RNAs, we found 77 lncRNAs were significantly expressed in TNM-III vs TNM-II &18 lncRNAs in MM vs NMM. We also, investigated small nuclear/nucleolar RNAs (sn/snoRNAs), miscRNAs & mtRNAs, we identified 37 snRNAs, 105 snoRNAs, 28 miscRNAs & 5 mtRNAs in TNM-III vs TNM-II whereas 2 snRNAs, 11 snoRNAs, 57 miscRNAs & 8 mtRNAs in MM vs NMM were identified. In summary, our comprehensive analysis on publicly available small RNA-seq data identified multiple small non-coding RNAs that need to be further explored for their use in the prognosis, diagnosis & therapy of colon cancer.

Citation Format: Srinivas V. Koduru, Angelique Nyinawabera, Dino J. Ravnic, Amit K. Tiwari. Interrogation of small RNA-seq data for small noncoding RNA in human colon cancer [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 3490. doi:10.1158/1538-7445.AM2017-3490

Abstract 3489: Noncoding RNA distribution in clear cell renal cell cancer: small RNA-seq data

Small noncoding RNAs (sncRNAs) play pivotal roles in biological processes and may prove to be a tool in cancer diagnosis, prognosis, and treatment. Noncoding RNAs such as microRNAs (miRNAs), piwi-interacting-RNAs (piRNAs), long noncoding RNA (lncRNAs) and small nuclear/nucleolar RNAs (sn/snoRNAs) have recently been investigated to identify their role in cancer. Approximately 62,700 new cases of kidney cancer are expected each year in the United States leading to 14,240 deaths, with rates rising over the past 20 years. Nearly 90% of all kidney cancers will be renal cell carcinoma, of which 70% will be a clear cell renal cell carcinoma (ccRCC) subtype. When detected early most cases can be treated effectively, however there is a lack of early detection tests. We sought to identify molecular markers for early detection and diagnosis. We downloaded publically available (NIH bioproject PRJNA162397) ccRCC small RNA sequence raw data for noncoding RNA analysis. 22 ccRCC and 11 non-tumor renal cortex patient samples were evaluated. Data was analyzed by PartekFlow software. sRNA-seq data was annotated to miRNAs with 69 miRNAs aberrantly expressed in ccRCC with 37 being upregulated (top five: miR-122, miR-210, miR155, miR-224 and miR-21) and 32 being downregulated (top five: miR-200c, miR-502, miR-20b, miR10a and miR-204). Utilizing MetaCore software for pathway analysis the majority of expressed miRNAs were involved in metabolism related signaling pathways. Examining data for piRNAs revealed 22 which were significantly expressed (8 upregulated and 14 downregulated). Investigation of lncRNAs revealed 15 to be downregulated and 27 upregulated. We also uncovered 2 mitochondrial rRNAs, 10 miscRNAs, 1 snRNA, 7 snoRNAs, and 5 rRNAs in ccRCC samples. Our comprehensive analysis of publically available small RNA-seq data identified numerous sncRNAs associated with ccRCC. Pending further validation, they may prove useful as early detection biomarkers in this common cancer.

Citation Format: Srinivas V. Koduru, Dino J. Ravnic. Noncoding RNA distribution in clear cell renal cell cancer: small RNA-seq data [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 3489. doi:10.1158/1538-7445.AM2017-3489

Abstract 4447: Analysis of small RNA-seq data for differential expression of small noncoding RNAs in human colorectal cancer

Background: Cancer is a major cause of deaths worldwide, despite improved healthcare and technologies. Recent advancements in genome sequencing have led to the rapid study of the whole transcriptome and small RNAs with their biological functions. Non-coding RNAs (ncRNAs) play an important role in biological processes that greatly impact biomarker development for diagnosis, prognosis, and therapy. Non-coding RNAs such as microRNAs (miRNA), Piwi-interacting-RNAs (piRNAs), small nuclear/nucleolar RNAs (sn/snoRNAs) have recently been studied to understand their biology and pathology.

Results: In the present study, we used eight matched colorectal patient tissue samples (benign, tumor, and metastasis) small RNA sequencing data remapped for various small RNA annotation. We identified aberrant expression of 13 miRs in tumor and metastasis specimens [tumor vs benign group (19 miRs) and metastasis vs benign group (38 miRs)] of which five were upregulated, and eight were downregulated, during disease progression. We also investigated pathway analysis on abbarent expression of miRNAs, which showed majority of miRs involved in the colon other types of cancers. Further analysis of piRNAs revealed that six piRNAs in tumor vs benign and 24 in metastasis vs benign samples (commonly in both groups, only two piRNAs). Additionally, we examined other types of small RNAs [sn/snoRNAs, mt_rRNA, misc_RNA, nonsense mediated decay (NMD) and rRNA], we identified 15 in tumor vs benign and 104 metastasis vs benign and only four in commonly expressed.

Conclusion: In summary, our results identified multiple sncRNAs during colorectal cancer progression which needs to be further validated and can be used for prognosis, diagnosis, and therapeutic potentials.

Citation Format: Srinivas V. Koduru, Amit K. Tiwari, Sprague W. Hazard, Milind K. Mahajan, Dino J. Ravnic. Analysis of small RNA-seq data for differential expression of small noncoding RNAs in human colorectal cancer [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 4447. doi:10.1158/1538-7445.AM2017-4447

Abstract 3499: Differentially expressed small noncoding RNAs in triple-negative breast cancer

Cancer is the second leading cause of death in the United States and is a major public health concern worldwide. Basic, clinical and epidemiological research is leading to improved cancer detection, prevention, and outcomes. Recent technological advances have allowed unbiased and comprehensive screening of genome-wide gene expression. Small non-coding RNAs (sncRNAs) have been shown to play an important role in biological processes and could serve as a diagnostic, prognostic and therapeutic biomarker for specific diseases. Recent findings have begun to reveal and enhance our understanding of the complex architecture of sncRNA expression including miRNAs, piRNAs, sn/snoRNAs and their relationships with biological systems. We used publicly available small RNA sequencing data that was derived from 24 triple negative breast cancers (TNBC) and 14 adjacent normal tissue samples to remap various types of sncRNAs. We found a total of 55 miRNAs were aberrantly expressed (p&lt;0.005) in TNBC samples (8 miRNAs upregulated; 47 downregulated) compared to adjacent normal tissues whereas the original study reported only 25 novel miRs. In this study, we used pathway analysis of differentially expressed miRNAs which revealed TGF-beta signaling pathways to be profoundly affected in the TNBC samples. Furthermore, our comprehensive re-mapping strategy allowed us to discover a number of other differentially expressed sncRNAs including piRNAs, sn/snoRNAs, rRNAs, miscRNAs and nonsense-mediated decay RNAs. We believe that our sncRNA analysis workflow is extremely comprehensive and suitable for discovery of novel sncRNAs changes, which may lead to the development of innovative diagnostic and therapeutic tools for TNBC.

Citation Format: Srinivas V. Koduru, Amit K. Tiwari, Ashley Leberfinger, Sprague W. Hazard, Yuka Imamura Kawasawa, Milind Mahajan, Dino J. Ravnic. Differentially expressed small noncoding RNAs in triple-negative breast cancer [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 3499. doi:10.1158/1538-7445.AM2017-3499

Exploration of small RNA-seq data for small non-coding RNAs in Human Colorectal Cancer

Background: Improved healthcare and recent breakthroughs in technology have substantially reduced cancer mortality rates worldwide. Recent advancements in next-generation sequencing (NGS) have allowed genomic analysis of the human transcriptome. Now, using NGS we can further look into small non-coding regions of RNAs (sncRNAs) such as microRNAs (miRNAs), Piwi-interacting-RNAs (piRNAs), long non-coding RNAs (lncRNAs), and small nuclear/nucleolar RNAs (sn/snoRNAs) among others. Recent studies looking at sncRNAs indicate their role in important biological processes such as cancer progression and predict their role as biomarkers for disease diagnosis, prognosis, and therapy. Results: In the present study, we data mined publically available small RNA sequencing data from colorectal tissue samples of eight matched patients (benign, tumor, and metastasis) and remapped the data for various small RNA annotations. We identified aberrant expression of 13 miRNAs in tumor and metastasis specimens [tumor vs benign group (19 miRNAs) and metastasis vs benign group (38 miRNAs)] of which five were upregulated, and eight were downregulated, during disease progression. Pathway analysis of aberrantly expressed miRNAs showed that the majority of miRNAs involved in colon cancer were also involved in other cancers. Analysis of piRNAs revealed six to be over-expressed in the tumor vs benign cohort and 24 in the metastasis vs benign group. Only two piRNAs were shared between the two cohorts. Examining other types of small RNAs [sn/snoRNAs, mt_rRNA, miscRNA, nonsense mediated decay (NMD), and rRNAs] identified 15 sncRNAs in the tumor vs benign group and 104 in the metastasis vs benign group, with only four others being commonly expressed. Conclusion: In summary, our comprehensive analysis on publicly available small RNA-seq data identified multiple differentially expressed sncRNAs during colorectal cancer progression at different stages compared to normal colon tissue. We speculate that deciphering and validating the roles of sncRNAs may prove useful in colorectal cancer prognosis, diagnosis, and therapy.

A Comprehensive NGS Data Analysis of Differentially Regulated miRNAs, piRNAs, lncRNAs and sn/snoRNAs in Triple Negative Breast Cancer

Cancer is the second leading cause of death in the United States and is a major public health concern worldwide. Basic, clinical and epidemiological research is leading to improved cancer detection, prevention, and outcomes. Recent technological advances have allowed unbiased and comprehensive screening of genome-wide gene expression. Small non-coding RNAs (sncRNAs) have been shown to play an important role in biological processes and could serve as a diagnostic, prognostic and therapeutic biomarker for specific diseases. Recent findings have begun to reveal and enhance our understanding of the complex architecture of sncRNA expression including miRNAs, piRNAs, lncRNAs, sn/snoRNAs and their relationships with biological systems. We used publicly available small RNA sequencing data that was derived from 24 triple negative breast cancers (TNBC) and 14 adjacent normal tissue samples to remap various types of sncRNAs. We found a total of 55 miRNAs were aberrantly expressed (p<0.005) in TNBC samples (8 miRNAs upregulated; 47 downregulated) compared to adjacent normal tissues whereas the original study reported only 25 novel miRs. In this study, we used pathway analysis of differentially expressed miRNAs which revealed TGF-beta signaling pathways to be profoundly affected in the TNBC samples. Furthermore, our comprehensive re-mapping strategy allowed us to discover a number of other differentially expressed sncRNAs including piRNAs, lncRNAs, sn/snoRNAs, rRNAs, miscRNAs and nonsense-mediated decay RNAs. We believe that our sncRNA analysis workflow is extremely comprehensive and suitable for discovery of novel sncRNAs changes, which may lead to the development of innovative diagnostic and therapeutic tools for TNBC.

Topical vanadate enhances the repair of median laparotomy incisions

BACKGROUND

There are over two million laparotomies performed in the United States each year with an incisional hernia rate between 2% and 11%. A total of 100,000 ventral hernia repairs are undertaken each year with recurrences as high as 50%.

MATERIALS AND METHODS

Full thickness midline fascia incisions from the xiphoid to the pubic symphysis were made in rats. The fascia and/or muscular layer was sutured closed and a gel with 300 μM of sodium orthovanadate or saline was placed over the suture line with the skin closed over it. On day 10, 1-cm strips from the superior, middle, and inferior regions of the abdominal wall were tested for breaking strength and processed for histology.

RESULTS

The mean wound breaking strength of vanadate-treated wounds was 18.6 ± 2.7 N compared with 9.4 ± 3.6 N for controls (P < 0.0001). Similar quantities of granulation tissue were deposited in treated and control wounds. Fine green birefringence patterns, characteristic of immature connective tissue, were seen in control samples viewed with polarized light. In contrast, vanadate-treated wounds showed thick yellow-orange birefringence patterns characteristics of more mature connective tissue. Using α-smooth muscle actin immunostaining, myofibroblasts were prominent in control incisions, but few were identified in vanadate-treated incisions.

CONCLUSIONS

In rat laparotomy wounds, a single application of vanadate increases wound breaking strength, through enhanced connective tissue organization. These combined data suggest topical application of vanadate immediately after fascial closure will increase wound strength, possibly reducing hernia recurrences in the repaired abdominal wall.

Abstract 1758: Deconstructing protein and gene expression pathways to define the anticancer effects of XPO1 inhibition in ovarian cancer

Emerging evidence across multiple cancers, including ovarian cancer (OvCA), has identified disruption in nuclear-cytoplasmic shuttling with overexpression of exportin-1 (XPO1), a key regulator of nuclear transport, being linked to cancer aggressiveness, chemoresistance, and decreased patient survival. These findings and that XPO1 is the sole transporter of a number of tumor suppressors and cell cycle regulators including TP53, BRCA1, CDKN1A, CDKN1B and FOXO, establishes the rationale for targeted therapeutic inhibition of XPO1. KPT-185 and KPT-330 (generic name: selinexor) are two Selective Inhibitors of Nuclear Export (SINE) that inhibit XPO1 and selinexor is currently in phase I trials. We now demonstrate that despite similar XPO1 expression levels, patient-derived ovarian cancer cell lines (PD-OvCA) exhibit a broad differential IC50 response to SINE. To define the mechanism(s) of action underlying sensitivity and resistance and better understand the role of defective nuclear:cytoplasmic shuttling in OvCa, we examined the global differences between pathway activation/inhibition following XPO1 inhibition using nuclear:cytoplasmic fractionated protein lysates (reverse phase protein arrays, RPPA) and genome-wide RNA expression analysis.

Treatment of differentially KPT-185 sensitive OvCa cell lines resulted in nuclear accumulation of XPO1 and multiple known XPO1 cargo proteins including TP53 and CDKN1A, with a subsequent decrease in cytoplasmic XPO1 levels. RPPA analysis (MD Anderson RPPA Core) was then used to examine the expression and subcellular localization of &gt;200 proteins involved in a variety of biological and cancer-relevant processes. Numerous proteins accumulated in the nucleus including several known XPO1 cargoes (TP53 and YWHAZ), whereas a number of oncoproteins had decreased nuclear levels including MYC and RELA. These findings were shared across multiple cell lines. However, many of the proteins had differential accumulation patterns between cell lines. The effects of these changes on the transcriptome were defined by microarray analysis (Illumina, HumanHT12, v4 Expression BeadChip). Ingenuity Pathway Analysis (IPA) revealed multiple shared pathways activated by XPO1 inhibition between OvCa cell lines (TP53, FOXO3, EPAS1, MITF, and MYOD1) and these were consistent with the RPPA data. However, multiple pathways, both activated and inhibited, did not overlap between OvCa cell lines.

These data begin to reveal not only the multiple pathways by which SINE effect their anticancer activity but also that depending on cell context, these pathways can differ and may not overlap completely. The pathways and their more complete investigation defining their effect on differential sensitivity to XPO1 inhibition and their role in OvCa will be discussed.

Citation Format: Brad R. Evans, Thomas R. Silvers, Ying A. Chen, Jason Garcia, Catalina Camacho, Andrew J. Sharp, Paras Garag, Srinivas V. Koduru, Jean-Noel Billaud, Richard L. Halpert, Peter R. Dottino, Yosef Landesman, Sharon Shacham, John A. Martignetti. Deconstructing protein and gene expression pathways to define the anticancer effects of XPO1 inhibition in ovarian cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1758. doi:10.1158/1538-7445.AM2015-1758