Recent Research Publications- January 2023
Gonzalez-Bosquet J, Gabrilovich S, McDonald ME, Smith BJ, Leslie KK, Bender DD, Goodheart MJ, Devor E.
Int J Mol Sci. 2022 Dec 16;23(24):16014. doi: 10.3390/ijms232416014. PMID: 36555654; PMCID: PMC9785370.
Endometrial cancer (EC) incidence and mortality continues to rise. Molecular profiling of EC promises improvement of risk assessment and treatment selection. However, we still lack robust and accurate models to predict those at risk of failing treatment. The objective of this pilot study is to create models with clinical and genomic data that will discriminate patients with EC at risk of disease recurrence. We performed a pilot, retrospective, case-control study evaluating patients with EC, endometrioid type: 7 with recurrence of disease (cases), and 55 without (controls). RNA was extracted from frozen specimens and sequenced (RNAseq). Genomic features from RNAseq included transcriptome expression, genomic, and structural variation. Feature selection for variable reduction was performed with univariate ANOVA with cross-validation. Selected variables, informative for EC recurrence, were introduced in multivariate lasso regression models. Validation of models was performed in machine-learning platforms (ML) and independent datasets (TCGA). The best performing prediction models (out of >170) contained the same lncRNA features (AUC of 0.9, and 95% CI: 0.75, 1.0). Models were validated with excellent performance in ML platforms and good performance in an independent dataset. Prediction models of EC recurrence containing lncRNA features have better performance than models with clinical data alone.
Gonzalez-Bosquet J, Cardillo ND, Reyes HD, Smith BJ, Leslie KK, Bender DP, Goodheart MJ, Devor EJ.
Int J Mol Sci. 2022 Nov 26;23(23):14814. doi: 10.3390/ijms232314814. PMID: 36499142; PMCID: PMC973893
The preoperative diagnosis of pelvic masses has been elusive to date. Methods for characterization such as CA-125 have had limited specificity. We hypothesize that genomic variation can be used to create prediction models which accurately distinguish high grade serous ovarian cancer (HGSC) from benign tissue.
Methods: In this retrospective, pilot study, we extracted DNA and RNA from HGSC specimens and from benign fallopian tubes. Then, we performed whole exome sequencing and RNA sequencing, and identified single nucleotide variants (SNV), copy number variants (CNV) and structural variants (SV). We used these variants to create prediction models to distinguish cancer from benign tissue. The models were then validated in independent datasets and with a machine learning platform.
Results: The prediction model with SNV had an AUC of 1.00 (95% CI 1.00-1.00). The models with CNV and SV had AUC of 0.87 and 0.73, respectively. Validated models also had excellent performances.
Conclusions: Genomic variation of HGSC can be used to create prediction models which accurately discriminate cancer from benign tissue. Further refining of these models (early-stage samples, other tumor types) has the potential to lead to detection of ovarian cancer in blood with cell free DNA, even in early stage.
Enhancing progestin therapy via HDAC inhibitors in endometrial cancer.
Li Y, Zhou W, Li L, Li JW, Li T, Huang C, Lazaro-Camp VJ, Kavlashvili T, Zhang Y, Reyes H, Li Y, Dai D, Zhu W, Meng X, Leslie KK, Yang S.
Am J Cancer Res. 2022 Nov 15;12(11):5029-5048. PMID: 36504895; PMCID: PMC9729913.
Uterine endometrial cancer (EC) incidence and deaths are on the rise. Hormone therapy, a traditional treatment regimen for this disease, uses progesterone and its synthetic analogue, progestin, to induce cell differentiation, apoptosis, and inhibition of invasion. This therapy is highly effective for progesterone receptor (PR) positive tumors in the short term. However, responsiveness decreases over time due to loss of PR expression; acquired resistance leads to treatment failure and poor prognosis. Primary resistance occurs in advanced, PR-negative tumors. Regardless, progestin therapy can be effective if the PR downregulation mechanism is reversed and if functional PR expression is restored. Using histone deacetylase inhibitors (HDACi), we inhibited cell proliferation in three EC cell lines and restored functional PR expression at the mRNA and protein levels. Two HDACi were tested using an endometrial xenograft tumor model: entinostat, an oral drug, and romidepsin, an IV drug. In vitro and in vivo studies support that entinostat decreased EC tumor growth, induced differentiation, and increased expression of the PR-targeted gene, PAEP. These findings supported the approval of a new NIH NCTN clinical trial, NRG-GY011, which concluded that dual treatment of MPA and entinostat, decreased expression of the proliferation marker, Ki67, but did not increase PR expression relative to single treatment with MPA in this short-term study. Therefore, a more potent HDACi, romidepsin, was investigated. Romidepsin treatment inhibited tumor growth and enhanced progestin treatment efficacy. More importantly, PR, PAEP, and KIAA1324 expressions were upregulated. Using a chromatin immunoprecipitation assay, we verified that HDACi can reverse PR downregulation mechanisms in mice models. Other potential drug efficacy markers, such as CD52, DLK1, GALNT9, and GNG2, were identified by transcriptome analysis and verified by q-PCR. Many of the upregulated drug efficacy markers predict favorable patient outcomes, while downregulated genes predict worse survival. Here, our current data suggests that romidepsin is a more potent HDACi that has the potential to achieve more robust upregulation of PR expression and may be a more promising candidate for future clinical trials.
Gonzalez-Bosquet J, Weroha SJ, Bakkum-Gamez JN, Weaver AL, McGree ME, Dowdy SC, Famuyide AO, Kipp BR, Halling KC, Yadav S, Couch FJ, Podratz KC.
PLoS One. 2022 Dec 1;17(12):e0278408. doi: 10.1371/journal.pone.0278408. PMID: 36454788; PMCID: PMC9714733.
In endometrial cancer, occult high-risk subtypes (rooted in histomorphologically low-risk disease) with insensitivity to adjuvant therapies impede improvements in therapeutic efficacy. Therefore, we aimed to assess the ability of molecular high-risk (MHR) and low-risk (MLR) ECPPF (E2F1, CCNA2, POLE, PPP2R1A, FBXW7) stratification to profile recurrence in early, low-risk endometrioid endometrial cancer (EEC) and insensitivity to platinum-based chemotherapy or radiotherapy (or both) in high-risk EEC. Using The Cancer Genome Atlas endometrial cancer database, we identified 192 EEC cases with available DNA sequencing and RNA expression data. Molecular parameters were integrated with clinicopathologic risk factors and adverse surveillance events. MHR was defined as high (-H) CCNA2 or E2F1 log2 expression (≥2.75), PPP2R1A mutations (-mu), or FBXW7mu; MLR was defined as low (-L) CCNA2 and E2F1 log2 expression (<2.75). We assessed 164 cases, plus another 28 with POLEmu for favorable-outcomes comparisons. MHR and MLR had significantly different progression-free survival (PFS) rates (P < .001), independent of traditional risk factors (eg, TP53mu), except for stage IV disease. PFS of CCNA2-L/E2F1-L paralleled that of POLEmu. ECPPF status stratified responses to adjuvant therapy in stage III-IV EEC (P < .01) and profiled stage I, grade 1-2 cases with risk of recurrence (P < .001). MHR was associated with CTNNB1mu-linked treatment failures (P < .001). Expression of homologous recombination repair (HR) and cell cycle genes was significantly elevated in CCNA2-H/E2F1-H compared with CCNA2-L/E2F1-L (P<1.0E-10), suggesting that HR deficiencies may underlie the favorable PFS in MLR. HRmu were detected in 20.7%. No treatment failures were observed in high-grade or advanced EEC with HRmu (P = .02). Favorable PFS in clinically high-risk EEC was associated with HRmu and MLR ECPPF (P < .001). In summary, MLR ECPPF and HRmu were associated with therapeutic efficacy in EEC. MHR ECPPF was associated with low-risk, early-stage recurrences and insensitivity to adjuvant therapies.
Chatmethakul T, Schmelzel ML, Johnson KJ, Walker JR, Santillan DA, Colaizy TT, Roghair RD.
Nutrients. 2022 Dec 8;14(24):5224. doi: 10.3390/nu14245224. PMID: 36558383; PMCID: PMC9782260.
Perinatal leptin deficiency and reduced intake of mother's milk may contribute to the development of childhood obesity. Preterm infants have reduced leptin production, and they are at heightened risk of neonatal leptin deficiency. Because fresh human milk contains significantly more leptin than donor milk, we used a cross-over design to determine if blood leptin levels in maternal milk-fed preterm infants fall during conversion to donor human milk. Infants born between 22 0/7 and 31 6/7 weeks gestation on exclusive maternal milk feedings were enrolled into a 21-day cross-over trial. On days 1-7 and 15-21, infants were fed maternal milk, and on days 8-14, infants were fed donor milk. On day 1, study infants had a mean postmenstrual age of 33 weeks. Plasma leptin correlated with milk leptin, and leptin levels in maternal milk far exceed the leptin levels of donor milk. Plasma leptin did not increase during donor milk administration, but it did following resumption of maternal milk (p < 0.05). In this crossover trial, preterm infant blood leptin levels correlated with milk leptin content. This suggests that preterm infants can enterally absorb leptin from human milk, and leptin-rich breast milk may be a targeted therapy for the prevention of obesity.