Novel breast cancer susceptibility loci under linkage peaks identified in African ancestry consortia

BACKGROUND

Expansion of genome-wide association studies across population groups is needed to improve our understanding of shared and unique genetic contributions to breast cancer. We performed association and replication studies guided by a priori linkage findings from African ancestry (AA) relative pairs.

METHODS

We performed fixed-effect inverse-variance weighted meta-analysis under three significant AA breast cancer linkage peaks (3q26-27, 12q22-23, and 16q21-22) in 9241 AA cases and 10 193 AA controls. We examined associations with overall breast cancer as well as estrogen receptor (ER)-positive and negative subtypes (193,132 SNPs). We replicated associations in the African-ancestry Breast Cancer Genetic Consortium (AABCG).

RESULTS

In AA women, we identified two associations on chr12q for overall breast cancer (rs1420647, OR = 1.15, p = 2.50×10-6; rs12322371, OR = 1.14, p = 3.15×10-6), and one for ER-negative breast cancer (rs77006600, OR = 1.67, p = 3.51×10-6). On chr3, we identified two associations with ER-negative disease (rs184090918, OR = 3.70, p = 1.23×10-5; rs76959804, OR = 3.57, p = 1.77×10-5) and on chr16q we identified an association with ER-negative disease (rs34147411, OR = 1.62, p = 8.82×10-6). In the replication study, the chr3 associations were significant and effect sizes were larger (rs184090918, OR: 6.66, 95% CI: 1.43, 31.01; rs76959804, OR: 5.24, 95% CI: 1.70, 16.16).

CONCLUSION

The two chr3 SNPs are upstream to open chromatin ENSR00000710716, a regulatory feature that is actively regulated in mammary tissues, providing evidence that variants in this chr3 region may have a regulatory role in our target organ. Our study provides support for breast cancer variant discovery using prioritization based on linkage evidence.

Gene-based association tests in family samples using GWAS summary statistics

Genome-wide association studies (GWAS) have led to rapid growth in detecting genetic variants associated with various phenotypes. Owing to a great number of publicly accessible GWAS summary statistics, and the difficulty in obtaining individual-level genotype data, many existing gene-based association tests have been adapted to require only GWAS summary statistics rather than individual-level data. However, these association tests are restricted to unrelated individuals and thus do not apply to family samples directly. Moreover, due to its flexibility and effectiveness, the linear mixed model has been increasingly utilized in GWAS to handle correlated data, such as family samples. However, it remains unknown how to perform gene-based association tests in family samples using the GWAS summary statistics estimated from the linear mixed model. In this study, we show that, when family size is negligible compared to the total sample size, the diagonal block structure of the kinship matrix makes it possible to approximate the correlation matrix of marginal Z scores by linkage disequilibrium matrix. Based on this result, current methods utilizing summary statistics for unrelated individuals can be directly applied to family data without any modifications. Our simulation results demonstrate that this proposed strategy controls the type 1 error rate well in various situations. Finally, we exemplify the usefulness of the proposed approach with a dental caries GWAS data set.

Expression- and splicing-based multi-tissue transcriptome-wide association studies identified multiple genes for breast cancer by estrogen-receptor status

BACKGROUND

Although several transcriptome-wide association studies (TWASs) have been performed to identify genes associated with overall breast cancer (BC) risk, only a few TWAS have explored the differences in estrogen receptor-positive (ER+) and estrogen receptor-negative (ER-) breast cancer. Additionally, these studies were based on gene expression prediction models trained primarily in breast tissue, and they did not account for alternative splicing of genes.

METHODS

In this study, we utilized two approaches to perform multi-tissue TWASs of breast cancer by ER subtype: (1) an expression-based TWAS that combined TWAS signals for each gene across multiple tissues and (2) a splicing-based TWAS that combined TWAS signals of all excised introns for each gene across tissues. To perform this TWAS, we utilized summary statistics for ER + BC from the Breast Cancer Association Consortium (BCAC) and for ER- BC from a meta-analysis of BCAC and the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA).

RESULTS

In total, we identified 230 genes in 86 loci that were associated with ER + BC and 66 genes in 29 loci that were associated with ER- BC at a Bonferroni threshold of significance. Of these genes, 2 genes associated with ER + BC at the 1q21.1 locus were located at least 1 Mb from published GWAS hits. For several well-studied tumor suppressor genes such as TP53 and CHEK2 which have historically been thought to impact BC risk through rare, penetrant mutations, we discovered that common variants, which modulate gene expression, may additionally contribute to ER + or ER- etiology.

CONCLUSIONS

Our study comprehensively examined how differences in common variation contribute to molecular differences between ER + and ER- BC and introduces a novel, splicing-based framework that can be used in future TWAS studies.

Multi-tissue transcriptome-wide association studies identified 235 genes for intrinsic subtypes of breast cancer

BACKGROUND

Although genome-wide association studies (GWAS) of breast cancer (BC) identified common variants which differ between intrinsic subtypes, genes through which these variants act to impact BC risk have not been fully established. Transcriptome-wide association studies (TWAS) have identified genes associated with overall BC risk, but subtype-specific differences are largely unknown.

METHODS

We performed two multi-tissue TWASs for each BC intrinsic subtype including an expression-based approach that collated TWAS signals from expression quantitative trait loci (eQTLs) across multiple tissues and a novel splicing-based approach that collated signals from splicing QTLs (sQTLs) across intron clusters and subsequently across tissues. We utilized summary statistics for five intrinsic subtypes including Luminal A-like, Luminal B-like, Luminal B/HER2-negative-like, HER2-enriched-like, and Triple-negative BC, generated from 106,278 BC cases and 91,477 controls in the Breast Cancer Association Consortium.

RESULTS

Overall, we identified 235 genes in 88 loci across were associated with at least one of the five intrinsic subtypes. Most genes were subtype-specific, and many have not been reported in previous TWAS. We discovered common variants that modulate expression of CHEK2 confer increased risk to Luminal-A-like BC, in contrast to the viewpoint that CHEK2 primarily harbors rare, penetrant mutations. Additionally, our splicing-based TWAS provided population-level support for MDM4 splice variants that increased triple-negative BC risk.

CONCLUSION

Our comprehensive, multi-tissue TWAS corroborated previous GWAS loci for overall BC risk and intrinsic subtypes, while underscoring how common variation which impacts expression and splicing of genes in multiple tissue types can be used to further elucidate the etiology of BC.

Interdigitation of Radiation Earlier in the Multimodal Treatment of Patients with Lymphoma: The Effect on Opiate Analgesic Requirements

PURPOSE/OBJECTIVE(S)

Delay in radiation therapy (RT) as part of multimodality therapy in Hodgkin (HL) and non-Hodgkin lymphoma (NHL) is associated with worse pain scores. In a heterogeneous cohort of lymphoma patients, we hypothesize that interdigitating RT before fewer (versus more) lines of chemotherapy (C) will be associated with lower opiate analgesic requirement.

MATERIALS/METHODS

From 2009-2019, patients with HL or NHL received palliative (36.5%) or definitive (63.3%) RT at a single institution. An IRB approved database with baseline treatment/disease characteristics, including oral morphine equivalent (OME) requirement, was reviewed. OME was recorded for a) 3-month period prior to RT, b) the month during RT, and c) 3 months after RT. Post-RT change in OME was calculated as the difference in "b" and "c" such that greater or less OME use post-RT was defined as positive or negative value respectively. We performed one-tailed t-test analyses to determine differences in OME during RT between different cohorts. Correlations between baseline characteristics and OME were performed using Spearman correlations, controlling for lymphoma subtype, stage, tumor volume, relapsed/refractory disease, duration of radiation and bulky disease.

RESULTS

Of 180 patients, 57.8% had NHL, 40.6% were stage IV and 29.4% had bulky disease. At median of 19 days [6-80] from diagnosis, 74% of patients received C with a median of 2 lines [1-4] before RT. The median interval from diagnosis to RT was 11 months [4-36]. Pearson correlation showed a negative association between time from diagnosis to RT and postRT OME in the definitive cohort (R2 = 0.42, F = 4.54, p = 0.002) such that the longer the time to RT, the larger the decrease in OME postRT as compared to during RT. T-test showed higher mean OME during RT for those receiving > 2 lines of C preRT (148.3mg) as compared to those receiving ≤ 2 lines before RT (51.5mg, p = 0.02). In patients receiving definitive RT, the difference remained significant: those receiving >2 lines of C had higher OME during RT as compared to those receiving ≤ 2 lines (207.5mg versus 48.3mg, p = 0.02). The difference in mean OME for patients receiving >2 C lines versus ≤ 2 lines was not significantly different in the palliative cohort (75.6 vs 60.6, p = 0.33). OME use during RT was also found to be higher in patients with bulky disease as compared to non-bulky disease (175.7 versus 52.0, p = 0.04).

CONCLUSION

In our single-center experience, patients who received >2 lines of C prior to RT were found to have a significantly higher mean OME requirement during RT. In patients receiving definitive RT, longer time to receipt of RT was found to be associated with a larger decrease in OME post-RT, likely related to starting with a higher OME. Interdigitation of RT early on, prior to the 3rd line of chemotherapy, may help reduce pain and improve quality of life.

Characterizing the distribution of alterations in mesothelioma and their correlation to morphology

OBJECTIVES

Mesothelioma is a lethal disease that arises from the serosal lining of organ cavities. Several recurrent alterations have been observed in pleural and peritoneal -mesotheliomas, including in BAP1, NF2, and CDKN2A. Although specific histopathologic parameters have been correlated with prognosis, it is not as well known whether genetic alterations correlate with histologic findings.

METHODS

We reviewed 131 mesotheliomas that had undergone next-generation sequencing (NGS) at our institutions after pathologic diagnosis. There were 109 epithelioid mesotheliomas, 18 biphasic mesotheliomas, and 4 sarcomatoid mesotheliomas. All our biphasic and sarcomatoid cases arose in the pleura. Of the epithelioid mesotheliomas, 73 were from the pleura and 36 were from the peritoneum. On average, patients were 66 years of age (range, 26-90 years) and predominantly male (92 men, 39 women).

RESULTS

The most common alterations identified were in BAP1, CDKN2A, NF2, and TP53. Twelve mesotheliomas did not show a pathogenic alteration on NGS. For epithelioid mesotheliomas in the pleura, the presence of an alteration in BAP1 correlated with low nuclear grade (P = .04), but no correlation was found in the peritoneum (P = .62). Similarly, there was no correlation between the amount of solid architecture in epithelioid mesotheliomas and any alterations in the pleura (P = .55) or peritoneum (P = .13). For biphasic mesotheliomas, cases with either no alteration detected or with an alteration in BAP1 were more likely to be epithelioid predominant (>50% of the tumor, P = .0001), and biphasic mesotheliomas with other alterations detected and no alteration in BAP1 were more likely to be sarcomatoid predominant (>50% of the tumor, P = .0001).

CONCLUSIONS

This study demonstrates a significant association between morphologic features associated with a better prognosis and an alteration in BAP1.

A joint transcriptome-wide association study across multiple tissues identifies candidate breast cancer susceptibility genes

Genome-wide association studies (GWASs) have identified more than 200 genomic loci for breast cancer risk, but specific causal genes in most of these loci have not been identified. In fact, transcriptome-wide association studies (TWASs) of breast cancer performed using gene expression prediction models trained in breast tissue have yet to clearly identify most target genes. To identify candidate genes, we performed a GWAS analysis in a breast cancer dataset from UK Biobank (UKB) and combined the results with the GWAS results of the Breast Cancer Association Consortium (BCAC) by a meta-analysis. Using the summary statistics from the meta-analysis, we performed a joint TWAS analysis that combined TWAS signals from multiple tissues. We used expression prediction models trained in 11 tissues that are potentially relevant to breast cancer from the Genotype-Tissue Expression (GTEx) data. In the GWAS analysis, we identified eight loci distinct from those reported previously. In the TWAS analysis, we identified 309 genes at 108 genomic loci to be significantly associated with breast cancer at the Bonferroni threshold. Of these, 17 genes were located in eight regions that were at least 1 Mb away from published GWAS hits. The remaining TWAS-significant genes were located in 100 known genomic loci from previous GWASs of breast cancer. We found that 21 genes located in known GWAS loci remained statistically significant after conditioning on previous GWAS index variants. Our study provides insights into breast cancer genetics through mapping candidate target genes in a large proportion of known GWAS loci and discovering multiple new loci.

Allogeneic hematopoietic stem cell transplant outcomes in adults with inherited myeloid malignancies

There is increasing recognition that pathogenic germ line variants drive the development of hematopoietic cancers in many individuals. Currently, patients with hereditary hematologic malignancies (HHMs) receive similar standard therapies and hematopoietic stem cell transplant (HSCT) approaches as those with sporadic disease. We hypothesize that patients with myeloid malignancies and deleterious germ line predisposition variants have different posttransplant outcomes than those without such alleles. We studied 472 patients with myeloid neoplasms, of whom 26% had deleterious germ line variants and 34% underwent HSCT. Deleterious germ line variants in CHEK2 and DDX41 were most commonly seen in American and Australian cohorts, respectively. Patients with deleterious germ line DDX41 variants had a higher incidence of severe (stage 3-4) acute graft-versus-host disease (GVHD) (38%) than recipients with deleterious CHEK2 variants (0%), other HHM variants (12%), or patients without such germ line variants (9%) (P = .002). Importantly, the use of posttransplant cyclophosphamide reduced the risk of severe acute GVHD in patients receiving HSCT for deleterious germ line DDX41-associated myeloid neoplasms (0% vs 53%, P = .03). Based on these results, we advocate the use of posttransplant cyclophosphamide when individuals with deleterious germ line DDX41 variants undergo allogeneic HSCT for myeloid malignancies, even when transplantation has been performed using wild-type donors.

MOVER-R and Penalized MOVER-R Confidence Intervals for the Ratio of Two Quantities

Developing a confidence interval for the ratio of two quantities is an important task in statistics because of its omnipresence in real world applications. For such a problem, the MOVER-R (method of variance recovery for the ratio) technique, which is based on the recovery of variance estimates from confidence limits of the numerator and the denominator separately, was proposed as a useful and efficient approach. However, this method implicitly assumes that the confidence interval for the denominator never includes zero, which might be violated in practice. In this article, we first use a new framework to derive the MOVER-R confidence interval, which does not require the above assumption and covers the whole parameter space. We find that MOVER-R can produce an unbounded confidence interval, just like the well-known Fieller method. To overcome this issue, we further propose the penalized MOVER-R. We prove that the new method differs from MOVER-R only at the second order. It, however, always gives a bounded and analytic confidence interval. Through simulation studies and a real data application, we show that the penalized MOVER-R generally provides a better confidence interval than MOVER-R in terms of controlling the coverage probability and the median width.

Could immune-related hepatitis rapidly progress to immune-related cirrhosis?

BACKGROUND

Immune-related hepatitis is one of the prevalent adverse events associated with immunotherapy, especially immune checkpoint inhibitors (ICIs). For patients without a history of liver disease, autoimmune disease, or alcohol consumption, it is not clear whether immune-related hepatitis could rapid progress to immune-related cirrhosis.

CASE REPORT

We report the case of a 54-year-old female with stage IIIB primary pulmonary lymphoepithelioma-like carcinoma (PLELC) diagnosed with immune-related hepatitis. After 15 months, a liver biopsy demonstrated the rapid progression of liver cirrhosis although systematic corticosteroid administration.

CONCLUSIONS

Long-term immune activation caused by ICIs may exacerbate the process of cirrhosis. Great attention should be paid to the rapid progression to liver cirrhosis of immune-related hepatitis in the clinic.

Outcomes of Universal Point-of-Care Genetic Testing in Diverse Patients With Pancreatic Ductal Adenocarcinoma

PURPOSE

Guidelines recommend all patients with pancreatic ductal adenocarcinoma (PDAC) undergo germline genetic testing (GT). Rates of recommendation and completion of GT among diverse patients with PDAC are not known. The aim was to determine rates of recommendation and completion of point-of-care GT in diverse patients with PDAC.

METHODS

A retrospective review of patients with PDAC seen at an academic center between April 2019 and December 2020 was performed. Recommendation, completion and results of point-of-care GT, and demographic and clinical factors were recorded. Univariate and multivariate analyses of GT were performed using the chi-square test and logistic regression.

RESULTS

In total, 579 patients with PDAC were included. The median age at diagnosis was 67 years; 52% were male; 63% were non-Hispanic White (NHW) patients, and 20% were African American (AA) patients. GT was performed in 216 (37%) patients. Of those tested, 47 (22%) had a pathogenic/likely pathogenic variant identified of which 25 (12%) were in PDAC-associated genes. On multivariate analysis, age, NHW race, personal and family cancer history, medical oncology visit, and number of visits were independent predictors of GT completion. AA patients had significantly lower rates of recommendation and completion of GT compared with NHW patients.

CONCLUSION

Point-of-care GT in patients with PDAC is unacceptably low, especially among AA patients. Testing disparity might be due to lack of provider recommendation more than patient uptake. Lack of testing leads to missed opportunities for potential targeted therapies, improved outcomes, and identification of at-risk family members who could potentially benefit from surveillance.

Genome-wide association study for reproduction-related traits in Chinese domestic goose

1. This study measured six reproduction traits in a Sichuan white goose population (209 individuals), including fertility, qualified egg rate, plasma concentrations of progesterone (P), follicle-stimulating hormone (FSH), prolactin (PRL) and oestrogen (E2).2. Whole-genome resequencing data from the same goose population (209 individuals) were used in a genome-wide association study (GWAS) utilising a mixed linear model to investigate the genes and genetic markers associated with reproduction traits. The frequency of the selected SNPs and haplotypes were determined using the Matrix-Assisted Laser Desorption Ionisation Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) method.3. In total, 42 SNPs significantly associated with these traits were identified. A haplotype block was constructed based on five SNPs that were significantly associated with qualified egg rate, with individuals having the haplotype CCTTAAGGAA having the lowest qualified egg rate.4. In conclusion, these results provided potential markers for marker-assisted selection to improve goose reproductive performance and a basis for elucidating the genetics of goose reproduction.

Polygenic risk scores for prediction of breast cancer risk in women of African ancestry: a cross-ancestry approach

Polygenic risk scores (PRSs) are useful for predicting breast cancer risk, but the prediction accuracy of existing PRSs in women of African ancestry (AA) remains relatively low. We aim to develop optimal PRSs for the prediction of overall and estrogen receptor (ER) subtype-specific breast cancer risk in AA women. The AA dataset comprised 9235 cases and 10 184 controls from four genome-wide association study (GWAS) consortia and a GWAS study in Ghana. We randomly divided samples into training and validation sets. We built PRSs using individual-level AA data by a forward stepwise logistic regression and then developed joint PRSs that combined (1) the PRSs built in the AA training dataset and (2) a 313-variant PRS previously developed in women of European ancestry. PRSs were evaluated in the AA validation set. For overall breast cancer, the odds ratio per standard deviation of the joint PRS in the validation set was 1.34 [95% confidence interval (CI): 1.27-1.42] with the area under receiver operating characteristic curve (AUC) of 0.581. Compared with women with average risk (40th-60th PRS percentile), women in the top decile of the PRS had a 1.98-fold increased risk (95% CI: 1.63-2.39). For PRSs of ER-positive and ER-negative breast cancer, the AUCs were 0.608 and 0.576, respectively. Compared with existing methods, the proposed joint PRSs can improve prediction of breast cancer risk in AA women.

Penalized Fieller's confidence interval for the ratio of bivariate normal means

Constructing a confidence interval for the ratio of bivariate normal means is a classical problem in statistics. Several methods have been proposed in the literature. The Fieller method is known as an exact method, but can produce an unbounded confidence interval if the denominator of the ratio is not significantly deviated from 0; while the delta and some numeric methods are all bounded, they are only first-order correct. Motivated by a real-world problem, we propose the penalized Fieller method, which employs the same principle as the Fieller method, but adopts a penalized likelihood approach to estimate the denominator. The proposed method has a simple closed form, and can always produce a bounded confidence interval by selecting a suitable penalty parameter. Moreover, the new method is shown to be second-order correct under the bivariate normality assumption, that is, its coverage probability will converge to the nominal level faster than other bounded methods. Simulation results show that our proposed method generally outperforms the existing methods in terms of controlling the coverage probability and the confidence width and is particularly useful when the denominator does not have adequate power to reject being 0. Finally, we apply the proposed approach to the interval estimation of the median response dose in pharmacology studies to show its practical usefulness.

Novel strategy for disease risk prediction incorporating predicted gene expression and DNA methylation data: a multi-phased study of prostate cancer

Background

DNA methylation and gene expression are known to play important roles in the etiology of human diseases such as prostate cancer (PCa). However, it has not yet been possible to incorporate information of DNA methylation and gene expression into polygenic risk scores (PRSs). Here, we aimed to develop and validate an improved PRS for PCa risk by incorporating genetically predicted gene expression and DNA methylation, and other genomic information using an integrative method.

Methods

Using data from the PRACTICAL consortium, we derived multiple sets of genetic scores, including those based on available single‐nucleotide polymorphisms through widely used methods of pruning and thresholding, LDpred, LDpred‐funt, AnnoPred, and EBPRS, as well as PRS constructed using the genetically predicted gene expression and DNA methylation through a revised pruning and thresholding strategy. In the tuning step, using the UK Biobank data (1458 prevalent cases and 1467 controls), we selected PRSs with the best performance. Using an independent set of data from the UK Biobank, we developed an integrative PRS combining information from individual scores. Furthermore, in the testing step, we tested the performance of the integrative PRS in another independent set of UK Biobank data of incident cases and controls.

Results

Our constructed PRS had improved performance (C statistics: 76.1%) over PRSs constructed by individual benchmark methods (from 69.6% to 74.7%). Furthermore, our new PRS had much higher risk assessment power than family history. The overall net reclassification improvement was 69.0% by adding PRS to the baseline model compared with 12.5% by adding family history.

Conclusions

We developed and validated a new PRS which may improve the utility in predicting the risk of developing PCa. Our innovative method can also be applied to other human diseases to improve risk prediction across multiple outcomes.

Evaluating Polygenic Risk Scores for Breast Cancer in Women of African Ancestry

BACKGROUND

Polygenic risk scores (PRSs) have been demonstrated to identify women of European, Asian, and Latino ancestry at elevated risk of developing breast cancer (BC). We evaluated the performance of existing PRSs trained in European ancestry populations among women of African ancestry.

METHODS

We assembled genotype data for women of African ancestry, including 9241 case subjects and 10 193 control subjects. We evaluated associations of 179- and 313-variant PRSs with overall and subtype-specific BC risk. PRS discriminatory accuracy was assessed using area under the receiver operating characteristic curve. We also evaluated a recalibrated PRS, replacing the index variant with variants in each region that better captured risk in women of African ancestry and estimated lifetime absolute risk of BC in African Americans by PRS category.

RESULTS

For overall BC, the odds ratio per SD of the 313-variant PRS (PRS313) was 1.27 (95% confidence interval [CI] = 1.23 to 1.31), with an area under the receiver operating characteristic curve of 0.571 (95% CI = 0.562 to 0.579). Compared with women with average risk (40th-60th PRS percentile), women in the top decile of PRS313 had a 1.54-fold increased risk (95% CI = 1.38-fold to 1.72-fold). By age 85 years, the absolute risk of overall BC was 19.6% for African American women in the top 1% of PRS313 and 6.7% for those in the lowest 1%. The recalibrated PRS did not improve BC risk prediction.

CONCLUSION

The PRSs stratify BC risk in women of African ancestry, with attenuated performance compared with that reported in European, Asian, and Latina populations. Future work is needed to improve BC risk stratification for women of African ancestry.

Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women

Our study describes breast cancer risk loci using a cross-ancestry GWAS approach. We first identify variants that are associated with breast cancer at P < 0.05 from African ancestry GWAS meta-analysis (9241 cases and 10193 controls), then meta-analyze with European ancestry GWAS data (122977 cases and 105974 controls) from the Breast Cancer Association Consortium. The approach identifies four loci for overall breast cancer risk [1p13.3, 5q31.1, 15q24 (two independent signals), and 15q26.3] and two loci for estrogen receptor-negative disease (1q41 and 7q11.23) at genome-wide significance. Four of the index single nucleotide polymorphisms (SNPs) lie within introns of genes (KCNK2, C5orf56, SCAMP2, and SIN3A) and the other index SNPs are located close to GSTM4, AMPD2, CASTOR2, and RP11-168G16.2. Here we present risk loci with consistent direction of associations in African and European descendants. The study suggests that replication across multiple ancestry populations can help improve the understanding of breast cancer genetics and identify causal variants.

Abstract 215: Developing an integrated prognostic score using germline risk variants and RNA expression from primary breast cancers for prognostication of survival across subtypes

Introduction: RNA expression offers prognostication in early-stage, hormone-receptor positive breast cancer. We hypothesized that germline risk variants may influence patients after breast cancer onset, and that integration of common germline risk variants with RNA expression may broaden prognostication across subtypes.

Methods: We designed two prognostic scores for women of European ancestry using genome-wide association study (GWAS) summary statistics on cancer risk from the Breast Cancer Association Consortium (133,384 cases and 113,789 controls) and individual-level genotype/clinical information from 694 women in The Cancer Genome Atlas (TCGA). PrediXcan, a transcriptome-wide association tool family, was used to generate gene-level weights of association to breast cancer risk that were then multiplied by gene expression levels. A predicted transcriptomic score (PTRS) used predicted expression levels based on germline genotypes, and an observed transcriptomic score (OTRS) used normalized RNA expression. Cox proportional hazards tested score performance on overall survival (OS) and progression-free survival (PFS).

Results: Estimation performance is shown in Table 1. A 1388-gene PTRS with range from -0.5 to 4 offered initial prognostic ability in OS across subtypes (HR: 0.69 per 1-point increase, 95% CI: 0.48-1.00, p-value 0.05). This trend persisted with clinical covariates in a multivariate regression (HR: 0.61, 95% CI: 0.36-1.00, p=0.06). No associations were seen between PTRS/PFS or OTRS/OS. OTRS/PFS trended toward statistical significance with clinical factors included (age, AJCC staging). PTRS for OS did not show subtype-specific performance.

Conclusion: Patients with breast cancer do not have broad access to prognostic data across subtypes. Integration of germline and somatic data types offers potential to improve current limitations in prognostic testing for patients.

Table 1.Performance of predicted transcriptomic score (PTRS) and observed transcriptomic score (OTRS)Cox regression hazard ratio95% CIp-valuePolygenic score - OS0.960.64-1.400.84PTRS-OS0.690.48-1.000.05OTRS-OS0.990.97-1.000.66Polygenic score - PFS1.100.77-1.600.55PTRS - PFS1.100.80-1.600.49OTRS - PFS0.980.96-1.000.10

Citation Format: Padma Sheila Rajagopal, Yanyu Liang, Alvaro Barbeira, Owen Melia, Jiamao Zheng, Yonglan Zheng, Toshio Yoshimatsu, Dezheng Huo, Guimin Gao, Olufunmilayo F. Olopade, Hae K. Im. Developing an integrated prognostic score using germline risk variants and RNA expression from primary breast cancers for prognostication of survival across subtypes [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 215.

Racial Distribution and Characterization of Pelvic Organ Prolapse in a Hospital-Based Subspecialty Clinic

OBJECTIVES

Prior literature has suggested a decreased prevalence of pelvic organ prolapse (POP) in Black women. We sought to describe POP rates by race, investigate whether specific types of prolapse differ based on race, and investigate the role of uterine weight and fibroids on POP.

METHODS

We conducted a retrospective cohort study of new patients seen between April 2017 and April 2019 at a tertiary urogynecology clinic. Variables collected included POP quantification, race, age, smoking history, medical history, gravity, parity, vaginal delivery, hysterectomy, fibroids, and uterine weight. χ2 tests were used to compare the proportions of types of POP between Black and non-Black women. Binary and ordinal logistic regression tested the association between types of prolapse and race, adjusting for covariates.

RESULTS

Nine hundred thirty-six patients were identified by ICD codes, 768 met inclusion criteria. There were 85.3% of the women identified as non-Black and 14.7% identified as Black. There were 39.8% of the Black women that had a fibroid diagnosis compared with 20.8% of non-Black women (P < 0.001). Black women had a higher median uterine weight, 112.2 g versus 56 g (P = 0.002), and median fibroid size, 3.4 cm versus 1.92 cm (P = 0.0001). 56.9% of women presented with anterior prolapse. No difference was found in POP type between Black and non-Black women after adjusting for age, body mass index, parity, and delivery route (P = 0.45).

CONCLUSIONS

Black women had increased body mass index, rates of comorbidities (diabetes and hypertension), higher uterine weight and fibroid size than non-Black women in our study. However, there was no significant difference in POP type based on race.

Abstract PS18-12: Comparative analysis of differential gene expression by ancestry using primary breast cancers from Nigeria and the cancer genome atlas (TCGA)

Introduction: Breast cancers differ between genomic and transcriptomic features by ancestry within the TCGA, but current understanding of how gene expression differs across global ancestral populations is extremely limited. We hypothesized that differential expression performed by ancestry and geography may provide insight into population-specific, clinically relevant expression patterns.

Objective: To compare differentially expressed protein-coding genes and pathways among primary breast tumors of Nigerian origin versus African- and European-American ancestry in TCGA

Methods: We analyzed an integrated dataset of RNA-seq from 93 women in Nigeria, 31 African-ancestry women (TCGA AA), and 39 European-ancestry women from TCGA (TCGA EA) with whole-genome data. Ancestry within TCGA was classified by principal component analysis, with African ancestry as &gt;50% contribution and European ancestry as &gt;90% contribution. RNA was obtained from tumors in Nigeria using Qiagen PAXgene kits. A STAR/HTSeq pipeline generated read counts. To optimize assay-associated batch effects, we performed differential expression within each PAM50 subtype using limma-voom with quantile normalization. Significance was defined as a &gt; 1.5-fold change in gene expression (log2 scale) with a false-discovery-rate-adjusted p-value of 0.05. Pathway analysis was performed via Gene Ontology and the Web-Based Gene Set Analysis Toolkit. We also compared gene expression, claudin-low (30 genes) and VEGF (13 genes) signatures to an additional set of 189 primary breast cancers from Nigeria assayed on the NanoString nCounter System using a custom Nano110 probe set (PAM50 + claudin-low & VEGF genes). RNA for these cancers was isolated from paraffin-embedded tumor using the Roche High Pure paraffin kit.

Results: Differential expression was performed pairwise across ancestry groups within PAM50 subtypes (see Table). Fewer genes were differentially expressed, and fold change smaller across shared genes, when comparing Nigerian vs. TCGA AA versus Nigerian vs. TCGA EA comparisons, supporting quantile normalization. The strongest gene ontology pathway associations, seen for all subtypes, were intracellular protein targeting and viral gene expression. The epigenetic regulation pathway was significantly associated with comparisons in Basal-like tumors (padj=1.54e-7 for TCGA EA, padj=0.001 for TCGA AA). The PI3K-Akt pathway was significantly associated with Nigerian vs. TCGA-EA within Luminal A (padj=0.006). The Nanostring cohort shared a similar distribution of PAM50 subtypes (see Table, X2 p=0.21). We found concordance in both Nigerian cohorts of relative claudin-low and VEGF expression signature patterns across subtypes. Of 17 genes with significant differential expression by ancestry in the Nanostring dataset, 9 (ADM, ACTB, BIRC5, CDC6, CENPF, MKI67, MPP1, RAD17, and VEGFA) showed significant differential expression by ancestry in the PAXgene dataset.

Discussion: This is one of the first analyses of differential gene expression across tumors from a global population. We identified differential pathways in breast tumors between African and European ancestry populations to target for future work. We also validated several ancestry-specific genes across platforms with potential clinical relevance. Understanding how molecular features differ across global populations will improve precision oncology for all patients.

PAM50ClassificationNigerian: PAXgene (n=93)TCGA AA (n=31)TCGA EA (n=39)Nigerian: Nanostring (n=189)Nigerian (PAXgene) vs. TCGA EA ComparisonNigerian (PAXgene) vs. TCGA AAComparisonBasal-like41 (42.8%)23 (74.1%)17 (43.6%)78 (41.3%)4893 genes4687 genesHer2-enriched27 (28.1%)05 (12.8%)31 (16.4%)961 genesN/ALuminal A14 (14.5%)4 (12.9%)8 (20.5%)39 (20.6%)2596 genes480 genesLuminal B11 (11.4%)4 (12.9%)9 (23.1%)25 (13.2%)2112 genes222 genes

Citation Format: Padma Sheila Rajagopal, Yi-Hsuan S Tsai, Ashley Hardeman, Ian Hurley, Aminah Sallam, Yonglan Zheng, Toshio Yoshimatsu, Anna Woodard, Dezheng Huo, Guimin Gao, Charles M Perou, Joel S Parker, Mengjie Chen, Olufunmilayo I Olopade. Comparative analysis of differential gene expression by ancestry using primary breast cancers from Nigeria and the cancer genome atlas (TCGA) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-12.

Whole-genome sequencing reveals breed-differential CNVs between Tongcheng and Large White pigs

Large phenotypic differences have been observed between Tongcheng and Large White pigs. However, little is known about their genetic basis. This study performed a genome-wide comparison of CNVs between Tongcheng and Large White pigs using genome sequencing data. By combining the advantages of three different strategies (read depth, paired-end mapping and split read), we detected in total 18 687 CNVs that covered approximately 3.5% of the pig genome length for Tongcheng and Large White pigs. We identified 1864 breed-stratified CNVs (top 10%) by performing V_ST statistics. Functional enrichment analyses for genes located in breed-stratified CNVs were found to be involved in pigmentation, behavior, immune system and reproductive processes, which coincide with phenotypic differences between the two breeds. Using a systematic analysis of the genome and transcriptome data, we further identified four novel breed-differential CNVs on the functional genes (disease-resistant, DCUN1D2 and SPARCL1; lipid metabolism, PLEKHA2 and SLCO1A2). Subsequent PCR validation confirmed their accurate breakpoint positions in 33 Tongcheng pigs and 33 Large White pigs. This study provides essential information on differential CNVs for further research on the genetic basis of phenotypic differences between Tongcheng and Large White pigs.

Abstract 4613: Cross-ancestry genome-wide association study identifies six new loci for breast cancer in women of African and european ancestry

Background: Over 180 genetic variants have been identified as risk loci for breast cancer. However, most loci were discovered using European ancestry populations. As some common susceptibility loci are shared across populations, we aim to discover new risk loci for breast cancer using a cross-ancestry genome-wide association study (GWAS) approach.

Methods: Data from five GWAS studies in women of African ancestry with a combined sample size of 9241 cases and 10192 controls were used to generate pooled breast cancer risk estimates in a fixed effect meta-analysis, and this served as the discovery dataset. Summary statistics from the GWAS conducted in European ancestry populations (Breast Cancer Association Consortium, 122977 cases and 105974 controls) served as the validation dataset. The variants that were associated with breast cancer risk at P &lt; 0.01 in the GWAS of African ancestry were meta-analyzed with the GWAS in European ancestry. A locus was considered novel if the lead index variant was genome-wide significant (5 × 10−8) in the cross-ancestry meta-analysis and &gt;500kb away from known breast cancer risk loci. Conditional on the lead index variants, we searched for additional signals in each locus using multivariable logistic regression. Analyses were done separately for ER-positive, ER-negative and overall breast cancer risk.

Results: We discovered four novel loci for overall breast cancer risk (1p13.3, 5q31.1, 15q24, and 15q26.3) and two novel loci for ER-negative breast cancer (1q41 and 7q11.23) at the genome-wide significance level of P &lt; 5 × 10−8. Three index single nucleotide polymorphism (SNPs) lie within introns of genes (KCNK2, C5orf56, and SIN3A) and the other index SNPs are located in intergenic regions (close to GSTM4 and AMPD2, CASTOR2, and the antisense DNA RP11-168G16.2). The direction of the associations was consistent between the GWASs of African and European descendants. At the 15q24 locus, we found an additional SNP (in the intron of the SCAMP2 gene) to be independently associated with overall breast cancer risk.

Conclusions: We have identified six new risk loci that may contribute to better prediction of breast cancer risk in African ancestry populations and provide new insights into mechanisms of breast cancer carcinogenesis. Replication of these loci in multiple populations and functional studies can help to identify causal variants.

Citation Format: Babatunde Adedokun, Zhaohui Du, Guimin Gao, Thomas Ahearn, Kathryn L. Lunetta, Gary Zirpoli, Jonine Figueroa, Esther M. John, Leslie Bernstein, Wei Zheng, Jennifer J. Hu, Regina G. Ziegler, Sarah Nyante, Elisa V. Bandera, Sue A. Ingles, Michael F. Press, Sandra L. Deming, Jorge L. Rodriguez-Gil, Song Yao, Temidayo O. Ogundiran, Oladosu Ojengbede, William Blot, Melissa Troester, Katherine L. Nathanson, Anselm Hennis, Barbara Nemesure, Stefan Ambs, Lara E. Sucheston-Campbell, Jeannette T. Bensen, Stephen J. Chanock, Andrew F. Olshan, Christine B. Ambrosone, David V. Conti, Olufunmilayo I. Olopade, Montserrat Garcia-Closas, Julie R. Palmer, Christopher A. Haiman, Dezheng Huo. Cross-ancestry genome-wide association study identifies six new loci for breast cancer in women of African and european ancestry [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4613.

Abstract 2320: Evaluating a polygenic risk score for breast cancer in women of African ancestry

Background: A polygenic risk score (PRS) for breast cancer including 313 common variants developed by the Breast Cancer Association Consortium (BCAC) has been demonstrated to identify women who are at high risk of developing breast cancer [odds ratio (OR 95%CI) = 1.61 (1.57-1.65) per SD] in women of European ancestry. In the present study, we examined the performance of the 313-variant PRS and a PRS including 179 variants reaching genome-wide significance in previous genome-wide association studies (GWAS), in women of African ancestry.

Methods: We assembled genotype data for women of African ancestry from 28 breast cancer studies, including a total of 9,241 cases and 10,193 controls. We constructed the 179-variant and 313-variant PRSs with relative risk weights for each variant estimated in women of European ancestry in BCAC. The associations between the two PRSs and overall, ER+ and ER- breast cancer risk were estimated using logistic regression adjusting for age, study site and principal components. Discriminatory accuracy of the PRSs was evaluated using the receiver operating characteristic curve (AUROC). We then recalibrated the 179-variant PRS by replacing index variants with variants in each region that better captured risk in women of African ancestry and used relative risk weights estimated in women of African ancestry. We also assessed PRS performance by age (&lt;55 versus ≥ 55 years).

Results: Both the 179 and 313- variant PRSs were significantly associated with overall, ER+ and ER- breast cancer risk, with odds ratios (OR) per standard deviation of 1.21~1.37 and AUROCs ranging from 0.57 to 0.59. The 179-variant PRS outperformed in ER- cancer [1.31(1.24,1.37) per SD] while the 313-SNP PRS was better for overall [1.27(1.23,1.31) per SD] and ER+ cancer [1.37(1.32,1.43) per SD]. For overall breast cancer, compared to women with average risk (40th-60th PRS percentiles), women in the top decile of PRS had a 1.54 (95% CI: 1.38, 1.72)-fold increased risk. The performance of the recalibrated 179-variant PRS was not improved (average AUROC=0.56). The PRS ORs did not differ significantly across age strata (P-value for age interaction = 0.63).

Conclusion: Our study shows that both 179 and 313 variant PRS stratify breast cancer risk in women of African ancestry, with attenuated performance compared to that reported in European and in Latina populations. Future work is needed to improve breast cancer risk stratification for women of African ancestry.

Citation Format: Zhaohui Du, Guimin Gao, Babatunde Adedokun, Thomas Ahearn, Kathryn L. Lunetta, Gary Zirpoli, Melissa Troester, Edward A. Ruiz-Narváez, Stephen Haddad, Jonine Figueroa, Esther M. John, Leslie Bernstein, Wei Zheng, Jennifer J. Hu, Regina G. Ziegler, Sarah Nyante, Elisa V. Bandera, Sue A. Ingles, Michael F. Press, Sandra L. Deming, Jorge L. Rodriguez-Gil, Song Yao, Temidayo O. Ogundiran, Oladosu A. Ojengbede, William Blot, Katherine L. Nathanson, Anselm Hennis, Barbara Nemesure, Stefan Ambs, Lara E. Sucheston-Campbell, Jeannette T. Bensen, Stephen J. Chanock, Andrew F. Olshan, Christine B. Ambrosone, David V. Conti, Olufunmilayo I. Olopade, Julie R. Palmer, Montserrat Garcia-Closas, Dezheng Huo, Christopher A. Haiman. Evaluating a polygenic risk score for breast cancer in women of African ancestry [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2320.

miR-152 promotes spinal cord injury recovery via c-jun amino terminal kinase pathway

OBJECTIVE

The aim of this research is to explore the possible role of miR-152 in spinal cord injury and its underlying mechanism.

MATERIALS AND METHODS

After a mouse model of spinal cord injury (SCI) was developed, Real Time-quantitative Polymerase Chain Reaction (RT-qPCR) was used to detect the expression of miR-152 and c-jun in the mouse. In addition, the expression levels of interleukin-1b (IL-1b), interleukin-18 (IL-18) and tumor necrosis factor-α (TNF-α) were detected by enzyme-linked immunosorbent assay (ELISA). Subsequently, miR-152 was overexpressed and the levels of inflammation and c-jun after spinal cord injury were detected by Western blot. Furthermore, the grip strength of double forelimb, left forelimb or right forelimb of the mice was detected using a grip force test after miR-152 was overexpressed in the injured area of each group.

RESULTS

By constructing a mouse model of spinal cord injury, we found that the expression of miR-152 in the injured area decreased with time; meanwhile, the inflammatory relative genes including IL-1b, IL18, TNF-α, and c-jun were significantly increased. However, miR-152 overexpression significantly reduced the levels of inflammation genes as well as the expression of c-jun. Besides, the strength of the forelimbs in the spinal cord injury mice was restored.

CONCLUSIONS

MiR-152 could inhibit inflammatory responses and promote the recovery of the spinal cord injury through the c-jun N-terminal kinase pathway and it can be a target molecular for treating spinal cord injury.

Discrimination of benign from malignant breast lesions in dense breasts with model-based analysis of regions-of-interest using directional diffusion-weighted images

Background

There is an increasing interest in non-contrast-enhanced magnetic resonance imaging (MRI) for detecting and evaluating breast lesions. We present a methodology utilizing lesion core and periphery region of interest (ROI) features derived from directional diffusion-weighted imaging (DWI) data to evaluate performance in discriminating benign from malignant lesions in dense breasts.

Methods

We accrued 55 dense-breast cases with 69 lesions (31 benign; 38 cancer) at a single institution in a prospective study; cases with ROIs exceeding 7.50 cm² were excluded, resulting in analysis of 50 cases with 63 lesions (29 benign, 34 cancers). Spin-echo echo-planar imaging DWI was acquired at 1.5 T and 3 T. Data from three diffusion encoding gradient directions were exported and processed independently. Lesion ROIs were hand-drawn on DWI images by two radiologists. A region growing algorithm generated 3D lesion models on augmented apparent-diffusion coefficient (ADC) maps and defined lesion core and lesion periphery sub-ROIs. A lesion-core and a lesion-periphery feature were defined and combined into an overall classifier whose performance was compared to that of mean ADC using receiver operating characteristic (ROC) analysis. Inter-observer variability in ROI definition was measured using Dice Similarity Coefficient (DSC).

Results

The region-growing algorithm for 3D lesion model generation improved inter-observer variability over hand drawn ROIs (DSC: 0.66 vs 0.56 (p < 0.001) with substantial agreement (DSC > 0.8) in 46% vs 13% of cases, respectively (p < 0.001)). The overall classifier improved discrimination over mean ADC, (ROC- area under the curve (AUC): 0.85 vs 0.75 and 0.83 vs 0.74 respectively for the two readers).

Conclusions

A classifier generated from directional DWI information using lesion core and lesion periphery information separately can improve lesion discrimination in dense breasts over mean ADC and should be considered for inclusion in computer-aided diagnosis algorithms. Our model-based ROIs could facilitate standardization of breast MRI computer-aided diagnostics (CADx).

[Clinicopathological and molecular features of pulmonary enteric adenocarcinoma]

Objective: To investigate the clinicopathological and molecular characteristics of pulmonary enteric adenocarcinoma (PEAC). Methods: The clinical and pathological data of 19 cases of PEAC in the Affiliated Cancer Hospital of Zhengzhou University were retrospectively collected from 2015 to 2019. Immunohistochemistry (IHC) was used to detect the relevant immunophenotypes, amplification refractory mutation system (ARMS) and fluorescence in situ hybridization (FISH) were used to detect the expression of EGFR, KRAS and ALK genes. The patients were followed up, and the relevant literature was reviewed and analyzed. Results: There were 19 cases, including 10 males and 9 females, with a mean age of 58 years (range 33-71 years). Microscopically, the tumors showed moderately to highly differentiated adenoid and/or papillary growth patterns. The tumor cells were highly columnar and sometimes showed pseudostratification. Inflammatory necrosis and scattered nuclear fragmentation were seen in some glandular lumens. IHC showed variable expression of CK7 (19/19), TTF1 (8/19), Napsin A (6/19), villin (17/19), CK20 (16/19) and CDX2 (10/19). Molecular testing showed KRAS mutation in nine cases (9/19), EGFR mutation in one case (1/19), and positive ALK split signal in one case (1/19). In the literature, the reported mutation rate of KRAS in PEAC was much higher than that of EGFR and ALK. All 19 cases underwent surgical resection and 11 cases were subjected to chemotherapy or radiotherapy. Conclusions: PEAC is a rare variant of invasive pulmonary adenocarcinoma, and has similar histological and cytological features to that of colorectal adenocarcinoma. However, detailed medical history, histologic heterogeneity, an IHC combination of CK7(+)/villin(+) and high KRAS mutation rate are the key points of diagnosis. The prognosis needs long-term follow-up and big data statistics.

Outcome in patients with refractory high-risk neuroblastoma

10537

Background: Outcome for high-risk neuroblastoma (HRNBL) patients (pts) with refractory disease at end of induction (EOI) is poor. The impact of therapies such as I-131-MIBG or irinotecan/temozolomide/dinutuximab (I/T/DIN) prior to autologous stem cell transplant (ASCT) on outcome is unknown. Methods: A multi-center, retrospective study of HRNBL pts diagnosed between 2008-2018 with refractory disease at EOI was conducted. Demographics, tumor biology, treatment response, and outcomes were abstracted. 3-year (yr) EFS and OS from time of diagnosis were estimated by the Kaplan-Meier method. Results: 3-yr EFS and OS were 54% and 79% for the 136 pts analyzed. 91 pts received no additional therapy prior to ASCT (Cohort 1); 32 pts received post-induction therapy prior to ASCT (Cohort 2); and 13 pts did not undergo ASCT (Cohort 3). The prevalence of metastatic disease in Cohort 1, 2, and 3 was 65%, 97%, and 85%. 3-yr EFS and OS were not statistically different between Cohort 1 (3-yr EFS and OS; 62% and 81%) and Cohort 2 [3-yr EFS and OS; 49% (p = 0.48) and 82% (p = 0.19)]. Outcome for Cohort 3 pts was significantly worse than Cohort 1 [3-yr EFS: 15% vs. 62% (p < .001); and 3-yr OS: 48% vs. 81% (p = 0.003)] and Cohort 2 [3-yr EFS: 15% vs. 49% (p < .001); and 3-yr OS 48% vs. 82% (p = 0.035)]. For Cohort 2 pts with metastatic disease, post-induction therapy included I/T/DIN (n = 12), MIBG (n = 16), MIBG plus I/T/DIN (n = 1), and other (n = 2). Metastatic disease response was observed in 10/12 (83%) pts who received I/T/DIN and 9/16 (56%) who received MIBG. MIBG plus I/T/DIN (n = 1) or MIBG with chemotherapy (n = 1) also induced response. Among the 21 pts with metastatic disease response, 3-yr EFS and OS were 69% and 94%; significantly better than Cohort 2 patients who did not respond to post-induction therapy [3-yr EFS and OS: 11% (p = 0.016) and 66% (p = 0.2)]. 6 Cohort 2 pts achieved a complete response (CR) in metastatic sites following I/T/DIN (n = 5) or MIBG (n = 1), and all are alive without relapse with median follow-up of 3.4 years (range 2.7-8.1). The single Cohort 3 patient who achieved a metastatic CR with I/T/DIN and did not undergo ASCT remains disease-free 2.4 years from diagnosis. Conclusions: Patient characteristics differed in the 3 Cohorts, reflecting the influence of refractory disease on treatment decisions. For Cohort 2 pts, outcome was better for those with metastatic disease at EOI who responded to post-induction therapy compared to those who did not. Pts who achieved a metastatic CR of refractory disease had excellent survival. Prospective studies testing the efficacy of I/T/DIN in pts with refractory metastatic disease at EOI are warranted.

Molecular cloning of the goose GnRH gene and identification of GnRH polymorphisms associated with laying traits

1. Egg-laying traits are important economic characteristics in goose production (Anser cygnoides). The gene GnRH, which encodes gonadotropin-releasing hormone, is a strong candidate gene for egg-laying traits in avian species. 2. In this study, a 3520 bp genomic sequence and a 279 bp mRNA sequence for GnRH, which encoded 92 amino acids, were determined. The GnRH DNA sequence contains four exons and three introns, and the DNA and deduced amino acid sequences were highly conserved across mammals (human, macaque, cow, and sheep) and avians (chicken, fulmar and quail). 3. Using a direct sequencing method, 46 single nucleotide polymorphisms (SNPs) were identified in the GnRH genomic sequence that were shared between two Sichuan White goose populations (217 and 208 individuals). Furthermore, 44 haplotypes were constructed using a sliding window approach. Association analysis between the SNPs and haplotypes and egg-laying traits showed that 10 SNPs affected the first egg weight, average egg weight, egg number at 48 weeks and egg number at 64 weeks. 4. These results lay the foundation for further studies of the function of GnRH in geese and provide a theoretical basis for marker-assisted selection of egg-laying traits in the Sichuan white goose population.

Daily Aspirin Use Does Not Impact Clinical Outcomes in Patients With Inflammatory Bowel Disease

BACKGROUND

Although several studies have associated the use of nonsteroidal anti-inflammatory drugs with disease flares in patients with inflammatory bowel disease (IBD), little is known about the impact of daily aspirin use on clinical outcomes in patients with IBD.

METHODS

We conducted a retrospective analysis of a prospectively collected registry of patients with IBD from May 2008 to June 2015. Patients with any disease activity with daily aspirin use were matched 1:4 to controls by age, sex, disease, disease location, and presence of cardiac comorbidity. Patients with at least 18 months of follow-up were included in the final analysis. The primary outcomes of interest were having an IBD-related hospitalization, IBD-related surgery, and requiring corticosteroids during the follow-up period.

RESULTS

A total of 764 patients with IBD were included in the analysis, of which 174 patients were taking aspirin. There was no statistical difference in age, gender, diagnosis (Crohn's disease vs ulcerative colitis), disease duration, Charlson Comorbidity Index, smoking status, medication usage, or baseline C-reactive protein between groups. After controlling for covariables and length of follow-up in the entire population, aspirin use was not associated with a risk of being hospitalized for an IBD-related complication (odds ratio [OR], 1.46; P = 0.10), corticosteroid use (OR, 0.99; P = 0.70), or having an IBD-related surgery (OR, 0.99; P = 0.96).

CONCLUSION

In this single-center analysis, aspirin use did not impact major clinical outcomes in patients with IBD. Although the effect of aspirin use on mucosal inflammation was not directly assessed in this study, these findings support the safety of daily aspirin use in this population.

HER2 exon 20 insertions in non-small-cell lung cancer are sensitive to the irreversible pan-HER receptor tyrosine kinase inhibitor pyrotinib

BACKGROUND

Effective targeted therapy for non-small-cell lung cancer (NSCLC) patients with human epidermal growth factor receptor 2 (HER2) mutations remains an unmet need. This study investigated the antitumor effect of an irreversible pan-HER receptor tyrosine kinase inhibitor, pyrotinib.

PATIENTS AND METHODS

Using patient-derived organoids and xenografts established from an HER2-A775_G776YVMA-inserted advanced lung adenocarcinoma patient sample, we investigated the antitumor activity of pyrotinib. Preliminary safety and efficacy of pyrotinib in 15 HER2-mutant NSCLC patients in a phase II clinical trial are also presented.

RESULTS

Pyrotinib showed significant growth inhibition of organoids relative to afatinib in vitro (P = 0.0038). In the PDX model, pyrotinib showed a superior antitumor effect than afatinib (P = 0.0471) and T-DM1 (P = 0.0138). Mice treated with pyrotinib displayed significant tumor burden reduction (mean tumor volume, -52.2%). In contrast, afatinib (25.4%) and T-DM1 (10.9%) showed no obvious reduction. Moreover, pyrotinib showed a robust ability to inhibit pHER2, pERK and pAkt. In the phase II cohort of 15 patients with HER2-mutant NSCLC, pyrotinib 400 mg resulted in a objective response rate of 53.3% and a median progression-free survival of 6.4 months.

CONCLUSION

Pyrotinib showed activity against NSCLC with HER2 exon 20 mutations in both patient-derived organoids and a PDX model. In the clinical trial, pyrotinib showed promising efficacy.

CLINICAL TRIAL REGISTRATION

NCT02535507.

The direct effects of gonadotropin-releasing hormone on proliferation of granulosa cells and development of follicles in goose

1. The study objectives were to determine the direct effects of gonadotropin-releasing hormone (GnRH) on the proliferation of ovarian granulosa cells (GCs) and the development of follicles in geese (Anser cygnoides) by colorimetry and ethynyl-2'-deoxyuridine (EdU) cell proliferation assays, in which primary GCs were treated with different concentrations of GnRH agonist (alarelin acetate) and an antagonist (cetrorelix acetate). Differently expressed genes (DEGs) were identified by RNA-sequencing and validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blotting. 2. The EdU assays showed that the proliferation of GCs was affected by the GnRH agonist and antagonist in a dose-dependent manner. The effect of treatment on cell proliferation was statistically significant at the concentrations of 10^-5 mol/l alarelin and 1 mg/l cetrorelix acetate. A total of 134 DEGs (76 downregulated and 58 upregulated for alarelin treatment) and 226 DEGs (90 downregulated and 136 upregulated for cetrorelix) were identified by RNA-sequencing analysis, respectively. Enrichment analysis indicated that DEGs were enriched in the GO terms of cell-cell signalling and cell junctions. The pathways that regulate the development of follicles were identified, including the biological progress of cAMP accumulation, ovulation cycle and vasculature that are essential to follicular selection. 3. The results suggested that GnRH might directly regulate GC proliferation via autocrine or paracrine pathways related to cell junctions. In particular, it was confirmed that the mRNA and protein expression levels of the oestrogen receptor 2 (ESR2) gene, a negative transcription factor involved in follicular maturation and ovulation, were affected by GnRH agonist or antagonist in GCs. 4. In conclusion, GnRH might play an important role in follicular development by changing the expression of genes that participate in cAMP accumulation, ovulation cycle and cell junctions in ovarian GCs.

Improved Sleep Quality Improves Blood Pressure Control among Patients with Chronic Kidney Disease: A Pilot Study

BACKGROUND

Despite the abundance of data documenting the consequences of poor sleep quality on blood pressure (BP), no previous study to our knowledge has addressed the impact of sleep improvement on resistant hypertension among patients with chronic kidney disease (CKD).

METHODS

The aim of this pilot study was to determine whether improved sleep quality and duration will improve BP control in patients with resistant hypertension and CKD. It was a prospective single-center cohort study that involved 30 hypertensive subjects with CKD presenting with primary resistant hypertension and poor sleep quality or duration <6 h/night. Sleep quality and duration were modified using either sleep hygiene education alone or adding sleep medication. The cohort's BP was followed every 3 months for 6-month duration. The average home and clinic BPs were collected at each follow-up visit. The primary outcome baseline change in systolic BP (SBP) and diastolic BP (DBP; home and clinic) at 3 and 6 months after documented sleep improvement. Secondary outcomes included change from baseline in mean arterial pressure, and delta SBP after sleep improvement.

RESULTS

African American patients represented 50% of the cohort. All patients had evidence of CKD with GFR ≤60 mL/min and were obese with 40% having type 2 diabetes mellitus. The primary endpoint of change in clinic SBP and DBP was significantly reduced at 3 months, baseline 156 ± 15/88 ± 8 vs. 3 months 125 ± 14/73 ± 7 (p < 0.0001). This difference persisted at 6 months. However, there was no further reduction in-home or clinic BPs between the 3- and 6-month periods. Home and clinic average delta SBP change at 3 months from baseline was -34.4 ± 15 and -30.8 ± 19 mm Hg respectively. Delta SBP change was associated with sleep improvement of >6 h/night, that is, gaining an extra 3-4 h' sleep duration, home; R2 = 0.66, p < 0.0001 and clinic; R2 = 0.49, p < 0.0001.

CONCLUSION

Optimizing sleep quality and duration to >6 h/night improved BP control and was associated with a significant delta change in SBP within 3 months of follow-up. Physicians should obtain a sleep history in patients with CKD who present with resistant hypertension.

STEPS: an efficient prospective likelihood approach to genetic association analyses of secondary traits in extreme phenotype sequencing

It has been well acknowledged that methods for secondary trait (ST) association analyses under a case-control design (ST$_{\text{CC}}$) should carefully consider the sampling process to avoid biased risk estimates. A similar situation also exists in the extreme phenotype sequencing (EPS) designs, which is to select subjects with extreme values of continuous primary phenotype for sequencing. EPS designs are commonly used in modern epidemiological and clinical studies such as the well-known National Heart, Lung, and Blood Institute Exome Sequencing Project. Although naïve generalized regression or ST$_{\text{CC}}$ method could be applied, their validity is questionable due to difference in statistical designs. Herein, we propose a general prospective likelihood framework to perform association testing for binary and continuous STs under EPS designs (STEPS), which can also incorporate covariates and interaction terms. We provide a computationally efficient and robust algorithm to obtain the maximum likelihood estimates. We also present two empirical mathematical formulas for power/sample size calculations to facilitate planning of binary/continuous STs association analyses under EPS designs. Extensive simulations and application to a genome-wide association study of benign ethnic neutropenia under an EPS design demonstrate the superiority of STEPS over all its alternatives above.