Transcriptome-wide association study of breast cancer risk by estrogen-receptor status

Previous transcriptome-wide association studies (TWAS) have identified breast cancer risk genes by integrating data from expression quantitative loci and genome-wide association studies (GWAS), but analyses of breast cancer subtype-specific associations have been limited. In this study, we conducted a TWAS using gene expression data from GTEx and summary statistics from the hitherto largest GWAS meta-analysis conducted for breast cancer overall, and by estrogen receptor subtypes (ER+ and ER-). We further compared associations with ER+ and ER- subtypes, using a case-only TWAS approach. We also conducted multigene conditional analyses in regions with multiple TWAS associations. Two genes, STXBP4 and HIST2H2BA, were specifically associated with ER+ but not with ER- breast cancer. We further identified 30 TWAS-significant genes associated with overall breast cancer risk, including four that were not identified in previous studies. Conditional analyses identified single independent breast-cancer gene in three of six regions harboring multiple TWAS-significant genes. Our study provides new information on breast cancer genetics and biology, particularly about genomic differences between ER+ and ER- breast cancer.

Clinical findings in families with chordoma with and without T gene duplications and in patients with sporadic chordoma reported to the Surveillance, Epidemiology, and End Results program

OBJECTIVE

To gain insight into the role of germline genetics in the development of chordoma, the authors evaluated data from 2 sets of patients with familial chordoma, those with and without a germline duplication of the T gene (T-dup+ vs T-dup-), which was previously identified as a susceptibility mechanism in some families. The authors then compared the patients with familial tumors to patients with sporadic chordoma in the US general population reported to the National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) program through 2015.

METHODS

Evaluation of family members included review of personal and family medical history, physical and neurological examination, and pre- and postcontrast MRI of the skull base and spine. Sixteen patients from 6 white families with chordoma had a chordoma diagnosis at family referral. Screening MR images of 35 relatives revealed clival lesions in 6, 4 of which were excised and confirmed to be chordoma. Thus, data were available for 20 patients with histologically confirmed familial chordoma. There were 1759 patients with histologically confirmed chordoma in SEER whose race was known.

RESULTS

The median age at chordoma diagnosis differed across the groups: it was lowest in T-dup+ familial patients (26.8 years, range 5.3-68.4 years); intermediate in T-dup- patients (46.2 years, range 11.8-60.1 years); and highest in SEER patients (57 years, range 0-98 years). There was a marked preponderance of skull base tumors in patients with familial chordoma (93% in T-dup+ and 83% in T-dup-) versus 38% in the SEER program (37% in white, 53% in black, and 48.5% in Asian/Pacific Islander/American Indian/Alaska Native patients). Furthermore, 29% of white and 16%-17% of nonwhite SEER patients had mobile-spine chordoma, versus no patients in the familial group. Several T-dup+ familial chordoma patients had putative second/multiple primary chordomas.

CONCLUSIONS

The occurrence of young age at diagnosis, skull base presentation, or multiple primary chordomas should encourage careful review of family history for patients diagnosed with chordoma as well as screening of at-risk family members by MRI for early detection of chordoma. Furthermore, given genetic predisposition in some patients with familial chordoma, identification of a specific mutation in a family will permit surveillance to be limited to mutation carriers-and consideration should be given for imaging the entire neuraxis in any chordoma patient presenting at an early age or with a blood relative with chordoma. Finally, future studies should explore racial differences in age at diagnosis and presenting site in chordoma.

Heterogeneous Associations Between Obesity and Reproductive-Related Factors and Specific Breast Cancer Subtypes Among Hong Kong Chinese Women

Previous studies reported heterogeneous associations between obesity and reproductive-related breast cancer risk factors and breast cancer intrinsic subtypes; however, few studies have been conducted in Asian populations. Here, we aimed to examine whether risks associated with established breast cancer risk factors varied by breast cancer subtypes in Chinese women. We conducted a hospital-based case-control study in Hong Kong, including a total of 2169 Chinese women. Unconditional polytomous logistic regression models were used to calculate adjusted odds ratios (AORs) and 95% confidence intervals(95%CIs) to estimate relative risks associated with examined risk factors in case-control analyses and to test for heterogeneity across breast cancer subtypes in case-case analyses. In case-case analyses, compared with luminal A patients, luminal B (AOR = 1.76, 95% CI = 1.07-2.88), HER2 overexpressing (AOR = 3.40, 95% CI = 1.56-7.39), and triple negative (TNBC, AOR = 2.39, 95% CI = 1.18-4.82) patients were more likely to be postmenopausal. In case-control analyses, reduced risks associated with parity and younger age at first birth were only seen for luminal A and B cases especially among postmenopausal women, whereas having ≥ 3 children was associated with increased risk for HER2 overexpressing and TNBC among premenopausal women. Obesity was associated with increased risk for all subtypes. We found heterogeneous associations between parity-related risk factors by menopausal status and breast cancer subtypes among Chinese patients, which is similar to those observed in Western populations. Interestingly, obesity was associated with increased breast cancer risk regardless of menopausal status or subtypes, except for premenopausal luminal patients, which appears to be unique in Asian populations.

[microRNA-16-5p targeted tetraspanin 15 gene to inhibit the proliferation, migration and invasion of osteosarcoma cell through phospoinositide 3-kinase/protein kinase B signaling pathway]

Objective: To study the effects of miR-16-5p on proliferation, migration and invasion of osteosarcoma cells and its mechanism. Methods: Quantitative polymerase chain reaction (qPCR) and Western blotting were used to detect the mRNA and protein expression of miR-16-5p and TSPAN15 in human normal osteoblasts hFOB 1.19 and osteosarcoma cells MG63, Saos2 and HOS. The miR-16-5p or si-TSPAN15 was transfected into MG63 cells to observe its role in cell proliferation, migration and invasion. Cell proliferation was measured with MTT assay, cell migration and invasion were examined by Transwell, and the protein expression of CyclinD1, matrix metalloproteinase 2 (MMP-2), MMP-9, tetraspanin 15 (TSPAN15), phospha-tidylinositol3-kinase(p-PI3K) and phospha-protein kinase B(p-AKT) were determined by using Western blotting. The starbase website prediction combined with dual luciferase gene reporter assay was performed to analyze the targeting relationship between miR-16-5p and TSPAN15. miR-16-5p and pcDNA-TSPAN1 were co-transfected to assess the effect of high expression of TSPAN15 on overexpression of miR-16-5p-induced proliferation, migration and invasion of MG63 cells. Data comparison between the two groups was performed by using t test. Results: Compared with hFOB 1.19 cells (1.00±0.12), the expression of miR-16-5p was significantly decreased in MG63, Saos2 and HOS cells (0.32±0.05, 0.40±0.04, 0.45±0.06, respectively)(F=156.204, P<0.05), and TSPAN15 mRNA and protein levels were greatly increased (F=71.718, 110.350, both P<0.05). Overexpression of miR-16-5p obviously reduced the expression of CyclinD1, MMP-2, MMP-9 protein, cell viability, cell migration and invasion (F=150.136,117.228, 154.971, 89.479, 98.373, 130.880, all P<0.05) in MG63 cells. Knockdown of TSPAN15 greatly reduced CyclinD1, MMP-2, MMP-9 protein levels, cell survival rate, cell migration, and invasion number (F=93.206, 107.030, 109.326, 115.625, 146.113, 139.300, all P<0.05). Overexpression of miR-16-5p markedly decreased the expression of p-PI3K and p-AKT protein in MG63 cells (F=156.755, 181.419, both P<0.05). miR-16-5p targeted to regulate the expression of TSPAN15. High expression of TSPAN15 partially reversed the inhibitory effect of miR-16-5p on TSPAN15, CyclinD1, MMP-2, MMP-9, p-PI3K, p-AKT protein expression, cell viability, cell migration number and invasion number in MG63 cells. Conclusion: miR-16-5p inhibits the proliferation, migration and invasion of osteosarcoma cells by targeting the TSPAN15 gene and regulating the PI3K/AKT signaling pathway.

Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses

Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype1-3. To identify novel loci, we performed a genome-wide association study including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1 mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. We identified 32 novel susceptibility loci (P < 5.0 × 10-8), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate < 0.05). Five loci showed associations (P < 0.05) in opposite directions between luminal and non-luminal subtypes. In silico analyses showed that these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 54.2% for luminal A-like disease and 37.6% for triple-negative disease. The odds ratios of polygenic risk scores, which included 330 variants, for the highest 1% of quantiles compared with middle quantiles were 5.63 and 3.02 for luminal A-like and triple-negative disease, respectively. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.

Histologic features of melanoma associated with germline mutations of CDKN2A, CDK4, and POT1 in melanoma-prone families from the United States, Italy, and Spain

BACKGROUND

CDKN2A, CDK4, and POT1 are well-established melanoma-susceptibility genes.

OBJECTIVE

We evaluated melanoma histopathology for individuals with germline mutations of CDKN2A, CDK4, and POT1.

METHODS

We assessed histopathology for melanomas diagnosed in melanoma-prone families (≥2 individuals with melanoma) from the United States, Italy, and Spain. Comparisons between mutation carriers and noncarriers (no mutation) were adjusted for age, sex, Breslow depth, and correlations among individuals within the same family.

RESULTS

Histologic slides were evaluated for 290 melanomas (139 from 132 noncarriers, 122 from 68 CDKN2A carriers, 10 from 6 CDK4 carriers, and 19 from 16 POT1 carriers). Superficial spreading was the predominant subtype for all groups. Spitzoid morphology (>25% of tumor) was observed in 10 of 15 invasive melanomas (67%) from POT1 carriers (P < .0001 vs noncarriers). This finding was independently confirmed by 3 expert melanoma dermatopathologists in 9 of 15 invasive melanomas (60%). In situ and invasive melanomas from CDKN2A and CDK4 carriers were histologically similar to melanomas from noncarriers.

LIMITATIONS

Limited sample sizes for rare melanoma-susceptibility syndromes (CDK4, POT1).

CONCLUSION

Spitzoid morphology was associated with POT1 mutations suggesting that telomere dysfunction (POT1 mutations) may contribute to spitzoid differentiation in melanocytic tumors.

[Molecular epidemiology of Listeria monocytogenes isolated from ready-to-eat food in 2017 in China]

Objective: To analyze the molecular characteristics of Listeria monocytogenes strains from ready-to eat food in China. Methods: A total of 239 Listeria monocytogenes strains isolated from ready-to-eat food in 2017, all strains underwent whole-genome sequencing (WGS) , and comparisons uncovered population structure derived from lineages, clonal complex, serogroups, antimicrobial susceptibility and virulence, which were inferred in silico from the WGS data. Core genome multilocus sequence typing was used to subtype isolates. Results: All strains were categorized into three different lineages, lineage Ⅱ was the predominant types in food, and IIa was the main serogroups. CC8, CC101 and CC87 were the first three prevalent CCs among 23 detected CCs, accounting for 49.4%. Only 4.6% (11 isolates) of tested strains harbored antibiotic resistance genes, which were mostly trimethoprim genes (7 isolates, 2.9%). All strains were positive for LIPI-1, and only a part of strains harbored LIPI-3 and LIPI-4, accounting for 13.8% (33 isolates) and 14.2% (34 isolates), respectively. ST619 carried both LIPI-3 and LIPI-4. 51.5% (123 isolates) of strains carried SSI-1, and all CC121 strains harbored SSI-2. Different lineages, serogroups and CCs can be separated obviously through cgMLST analysis, and 24 sublineages were highly concordant with CCs. Conclusion: Ⅱa was the main serogroups in ready-to-eat food isolates in China; CC8, CC101 and CC87 were the prevalent CCs, and CC87 isolates was hypervirulent isolates, cgMLST method can be adopted for prospective foodborne disease surveillance and outbreaks detection.

A network analysis to identify mediators of germline-driven differences in breast cancer prognosis

Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.

Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Background

Heterogeneity of immune gene expression patterns of luminal breast cancer (BC), which is clinically heterogeneous and overall considered as low immunogenic, has not been well studied especially in non-European populations. Here, we aimed at characterizing the immune gene expression profile of luminal BC in an Asian population and associating it with patient characteristics and tumor genomic features.

Methods

We performed immune gene expression profiling of tumor and adjacent normal tissue in 92 luminal BC patients from Hong Kong using RNA-sequencing data and used unsupervised consensus clustering to stratify tumors. We then used luminal patients from The Cancer Genome Atlas (TCGA, N = 564) and a Korean breast cancer study (KBC, N = 112) as replication datasets.

Results

Based on the expression of 130 immune-related genes, luminal tumors were stratified into three distinct immune subtypes. Tumors in one subtype showed higher level of tumor-infiltrating lymphocytes (TILs), characterized by T cell gene activation, higher expression of immune checkpoint genes, higher nonsynonymous mutation burden, and higher APOBEC-signature mutations, compared with other luminal tumors. The high-TIL subtype was also associated with lower ESR1/ESR2 expression ratio and increasing body mass index. The comparison of the immune profile in tumor and matched normal tissue suggested a tumor-derived activation of specific immune responses, which was only seen in high-TIL patients. Tumors in a second subtype were characterized by increased expression of interferon-stimulated genes and enrichment for TP53 somatic mutations. The presence of three immune subtypes within luminal BC was replicated in TCGA and KBC, although the pattern was more similar in Asian populations. The germline APOBEC3B deletion polymorphism, which is prevalent in East Asian populations and was previously linked to immune activation, was not associated with immune subtypes in our study. This result does not support the hypothesis that the germline APOBEC3B deletion polymorphism is the driving force for immune activation in breast tumors in Asian populations.

Conclusion

Our findings suggest that immune gene expression and associated genomic features could be useful to further stratify luminal BC beyond the current luminal A/B classification and a subset of luminal BC patients may benefit from checkpoint immunotherapy, at least in Asian populations.

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM -/- patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors.

A selection method of chickens with blue-eggshell and dwarf traits by molecular marker-assisted selection

The blue-eggshell and dwarf traits have an important economic value in poultry production. Using a genetic aggregation-based strategy, the molecular marker-assisted selection technology was jointly used to provide a rapid breeding method for pure strain chickens simultaneously with hens exhibiting the blue-eggshell and dwarf traits. Overall, 80 male dwarf chickens and 1,000 hybrid blue-eggshell hens (F0) were used for the hybridization experiment. Subsequently, the crossing of F1 or F2 chicks was performed in succession. The F1 and F2 chicks were respectively detected by the joint molecular markers of the solute carrier organic anion transporter family, namely, 1B3 (SLCO1B3) and the growth hormone receptor (GHR) genes, which relate to blue-eggshell and dwarf traits. Meanwhile, the selection of blue-eggshell and dwarf phenotypes was used to validate the data obtained by the molecular markers. The results showed that F1 chicks included the heterozygous and wild-type of SLCO1B3, as well as the homozygous (hens) and heterozygous (roosters) of GHR. However, F2 chicks included 3 different genotypes of both SLCO1B3 and GHR. Ultimately, 196 F1 roosters (concurrently with heterozygous genotype of SLCO1B3 and GHR) and 1,073 F1 hens (concurrently with heterozygous genotype of SLCO1B3 and homozygous genotype of GHR) were obtained from the initial 10,040 F1 chicks. Further, 27 F2 roosters and 345 F2 hens, which simultaneously carried the homozygous genotype of SLCO1B3 and GHR, were screened from the initial 6,000 F2 chicks. Data obtained on the blue-eggshell and dwarf phenotypes were consistent with the results by molecular markers. Similarly, the purity verification of the strain obtained through 2 crossing experiments (F0♂ × F2♀ and F2♂ × F2♀) revealed that all chickens had the blue-eggshell and dwarf traits, supporting that the obtained F2 strain was pure. In summary, for the first time, we successfully bred a pure strain chicken with blue-eggshell and dwarf traits by jointly using the molecular markers of the SLCO1B3 and GHR genes. Our study provides a new method for the rapid cultivation of new chicken strains.

Estimating CDKN2A mutation carrier probability among global familial melanoma cases using GenoMELPREDICT

BACKGROUND

Although rare in the general population, highly penetrant germline mutations in CDKN2A are responsible for 5%-40% of melanoma cases reported in melanoma-prone families. We sought to determine whether MELPREDICT was generalizable to a global series of families with melanoma and whether performance improvements can be achieved.

METHODS

In total, 2116 familial melanoma cases were ascertained by the international GenoMEL Consortium. We recapitulated the MELPREDICT model within our data (GenoMELPREDICT) to assess performance improvements by adding phenotypic risk factors and history of pancreatic cancer. We report areas under the curve (AUC) with 95% confidence intervals (CIs) along with net reclassification indices (NRIs) as performance metrics.

RESULTS

MELPREDICT performed well (AUC 0.752, 95% CI 0.730-0.775), and GenoMELPREDICT performance was similar (AUC 0.748, 95% CI 0.726-0.771). Adding a reported history of pancreatic cancer yielded discriminatory improvement (P < .0001) in GenoMELPREDICT (AUC 0.772, 95% CI 0.750-0.793, NRI 0.40). Including phenotypic risk factors did not improve performance.

CONCLUSION

The MELPREDICT model functioned well in a global data set of familial melanoma cases. Adding pancreatic cancer history improved model prediction. GenoMELPREDICT is a simple tool for predicting CDKN2A mutational status among melanoma patients from melanoma-prone families and can aid in directing these patients to receive genetic testing or cancer risk counseling.

Clinicopathological and epidemiological significance of breast cancer subtype reclassification based on p53 immunohistochemical expression

TP53 mutations are common in breast cancer and are typically associated with more aggressive tumor characteristics, but little is known about the clinicopathological and epidemiological relevance of p53 protein expression, a TP53 mutation surrogate, in breast cancer subtypes. In this study of 7226 Chinese women with invasive breast cancer, we defined breast cancer subtypes using immunohistochemical (IHC) measures of hormone receptors and HER2 in conjunction with histologic grade. p53 expression status was then used to further stratify subtypes into p53-positive and p53-negative. Odds ratios (ORs) and 95% confidence intervals (CIs) in case-only logistic regression analyses were used to examine heterogeneity across different subtypes. The frequency of p53 protein expression varied by breast cancer subtype, being lowest in the luminal A-like and highest in the triple-negative and HER2-enriched subtypes (P-value < 0.01). In luminal A-like and B-like/HER2-negative subtypes, p53 positivity was associated with early-onset tumors, high grade, high proliferative index, and basal marker (CK5/6 and EGFR) expression. Further, compared with luminal A-like/p53-negative patients, A-like/p53-positive patients were more likely to be parous [adjusted OR parous vs. nulliparous = 2.67 (1.60, 4.51); P-value < 0.01] and to have breastfed [adjusted OR ever vs. never = 1.38 (1.03, 1.85); P-value = 0.03]. p53 positivity was not associated with examined clinical and risk factors in other tumor subtypes. Overall, these findings suggest that p53 expression, which is readily available in many settings, can be used to identify phenotypes of luminal A-like breast cancer with distinct clinical and epidemiological implications.

Variation in Cutaneous Patterns of Melanomagenesis According to Germline CDKN2A/CDK4 Status in Melanoma-Prone Families

CDKN2A and CDK4 are well-established melanoma susceptibility genes, but their effect on tumor location and distribution is unknown. We used a case-case study design to assess for differences in tumor location between mutation carriers (CDKN2A = 141 patients, 348 melanomas; CDK4 = 15 patients, 54 melanomas) and noncarriers (104 patients, 157 melanomas) in US melanoma-prone families. Associations between groups were assessed with chi-square tests. Odds ratios (ORs) for tumor location were adjusted for diagnosis age, gender, and superficial spreading subtype. Models included random effects to account for within individual and family correlations. Compared with having a truncal melanoma, CDK4 (vs. noncarriers: lower extremities OR = 14.5, 95% confidence interval [CI] = 5.02-42.0, P < 0.001; upper extremities OR = 6.88, 95% CI = 2.37-19.9, P < 0.001; head and neck OR = 18.6, 95% CI = 4.04-85.2, P < 0.001) and CDKN2A (vs. noncarriers: lower extremities OR = 3.01, 95% CI = 1.56-5.82, P < 0.05; upper extremities OR = 1.91, 95% CI = 1.03-3.52, P < 0.05; head and neck OR = 5.40, 95% CI = 2.10-13.9, P < 0.001) carriers had higher odds of developing melanoma at all other sites. Similar findings were observed for analyses stratified by gender, age, and first versus subsequent melanoma diagnoses. Further studies are needed to understand the biology underlying these genotype-associated patterns of tumor development, which could provide new insights into melanoma treatment and prevention.

Abstract 617: Aggressive phenotypes of luminal breast cancer demonstrate associations with body mass index analogous to triple-negative breast cancer

Background

Results from epidemiological studies are in support of heterogeneous relationships between body mass index (BMI) and breast cancer (BC) subtypes. Compared with luminal BC (LBC), pre-menopausal obesity is more frequently associated with triple-negative (TN) BC, while the converse has been reported for post-menopausal obesity. Given the dynamic range of hormone receptor expression in LBC, categorical combinations of immunohistochemical (IHC) markers for subtype definition may mask etiological heterogeneity within this subtype. Herein, we leveraged quantitative measures of tumor clinicopathological and IHC characteristics to define phenotypes of luminal BC and to assess relationships with BMI.

Methods

Participants were 6,412 women with invasive breast cancer who were diagnosed and treated in a tertiary hospital in Beijing, China between 2008-2016. We computed the Nottingham prognostic index (NPI)-score (based on tumor size, grade and lymph nodes) and IHC4-score (based on ER, PR, HER2 and KI67) and stratified LBC patients into four subgroups using quartiles of these scores: Lum-Q1 (least aggressive), Lum-Q2, Lum-Q3, and Lum-Q4 (most aggressive). Multinomial logistic regression models, adjusted for age, parity, menarcheal age, and family history, were used to test the associations between BMI [Kg/m2: underweight (&lt;18.5); normal (18.5-25); overweight (25-30); obesity (&gt;30)] and luminal subgroups, overall and by age categories (as proxy for menopausal status). We also included TNBC as a comparison group.

Results

The most aggressive LBC patients (Lum-Q4), defined by the NPI-score, were significantly more likely to be overweight [OR (95% CI) vs normal = 1.44 (1.12-1.86)] and obese [OR (95% CI) vs normal = 1.55 (0.98-2.46)] than the least aggressive LBC (Lum-Q1) patients, regardless of menopausal status. On the other hand, Lum-Q4 patients, defined by the IHC4-score, were significantly more likely to be underweight [OR (95% CI) vs normal = 2.21 (1.07-4.56)] in all women but less likely to be overweight [OR (95% CI) vs normal = 0.65 (0.50-0.85)] and obese [OR (95% CI) vs normal = 0.53 (0.35-0.82)] among post-menopausal women compared to Lum-Q1 patients (P-interaction (BMI & age) = 0.004). These associations were very similar to those when comparing TNBC to Lum-Q1 patients (defined by either NPI or IHC4 scores).

Conclusion

Aggressive phenotypes of LBC demonstrate associations with BMI that are analogous to TNBC. Discordant BMI associations with NPI and IHC4, and by menopausal status for the IHC4-score only, may be indicative of a positive association between excess adiposity and tumor clinicopathological parameters in the NPI-score, regardless of menopausal status. Conversely, its association with the IHC4-score may be driven by complex hormonal mechanisms that vary by menopausal status. Future analysis will focus on disentangling these relationships.

Citation Format: Mustapha Abubakar, Changyuan Guo, Hela Koka, Bin Zhou, Eric Tang, Joseph Deng, Nan Hu, Ning Lu, Xiaohong R. Yang. Aggressive phenotypes of luminal breast cancer demonstrate associations with body mass index analogous to triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 617.

Abstract 1638: Whole-exome sequencing and protein interaction networks to prioritize candidate genes for cutaneous melanoma susceptibility

Background: Known cutaneous malignant melanoma (CMM) genes account for melanoma risk in less than 40% of melanoma-prone families, suggesting the existence of additional risk genes or other modifiers. Whole exome sequencing (WES) of high-risk families usually results in the identification of a large number of potential disease-causing genes. However, prioritizing these genes and finding the true disease-causing ones have been challenging. We hypothesize that physically interacting proteins might have a similar effect on cell function and therefore, might produce a shared phenotype or increase the risk when mutated. To test this hypothesis, we applied a network approach integrating WES and protein-protein interaction (PPI) data to detect and prioritize rare variants in melanoma-prone families.

Methods: We conducted WES analysis on germline DNA of 212 patients from 45 CMM families (2-5 affected people in a family) without known mutations. Variants that were rare (&lt;1% in public and our in-house control datasets), loss-of-function or missense predicted to be deleterious, and showed complete disease co-segregation (present in all affected members within a family) were included in the network analysis. For this analysis, we only focused on genes that interact with known CMM genes (gene list in Goldstein AM, et al. Hum Mol Genet, 2017) which we used as seed proteins. We then applied a degree-aware algorithm (DADA) to rank the set of candidate genes from WES with respect to the set of known CMM genes using human PPI networks. The goal of DADA is to prioritize a candidate set of genes based on their association level with genes known to be related to the disease. Network proximity calculations of the candidates with respect to the seed set were based on Random Walk with Restarts method. We used high quality and scored human proteins interactions collected from InWeb_IM. In the primary analysis, the network contains 625,641 interactions, aggregated from 8 source databases and spanning 87% of reviewed human proteins. We also conducted additional analyses with CMM PPI subnetworks generated using high confidence interaction data from different sources to compare results.

Results: The WES analysis described above identified 546 genes that harbored rare variants, likely affect protein function and co-segregated in affected members in CMM families. After applying DADA across all networks, the rankings of these genes were fairly consistent. Top genes included both known CMM genes (such as MC1R, CDKN2B, KITLG, and TINF2) and genes that have not yet been associated with CMM susceptibility (such as FOXK1, AR, LEF1, RGL4, PABPC1, CHEK2, CTBP2, and BLM). These results highlight the importance of known CMM genes and their networks in CMM susceptibility, and demonstrate the potential value of network approaches in gene prioritization. Further evaluation of novel genes is in progress.

Citation Format: Sally Yepes, Margaret Tucker, Hela Koka, Kristine Jones, Aurelie Vogt, Laurie Burdette, Wen Luo, Bin Zhu, Meredith Yeager, Belynda Hicks, Neal D. Freedman, Stephen J. Chanock, Alisa M. Goldstein, Xiaohong R. Yang. Whole-exome sequencing and protein interaction networks to prioritize candidate genes for cutaneous melanoma susceptibility [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1638.

Abstract 2905: Clinical features in relation to age at diagnosis in luminal breast cancer patients: A hospital-based case series study in Beijing, China

Background

Breast cancer (BC) is a heterogenous disease that can be classified into various molecular subtypes. Patients with younger age at diagnosis are less likely to develop luminal A cancers. However, a large proportion of early-onset luminal BCs are seen among Asian BC patients. While this may be explained by the increasing exposure to Westernized lifestyle, germline genetics, breast density, or immune factors may also give rise to a distinct age-related biology in Asian BC. We investigated several tumor characteristics in luminal BC patients with respect to age, among women in Beijing, China.

Methods

Subjects in this study were diagnosed with invasive breast cancer and treated at the Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, between 2008-2016. 7,543 luminal cases (ER+ and/or PR+), were further defined as Luminal A: ER+, PR+, HER2-, low grade (1/2); Luminal B/high grade: ER+ and/or PR+, HER2-, high grade (3); Luminal B/HER2+: ER+ and/or PR+, HER2+. Patients were divided into four age groups: &lt;40 (12.1%), 40-50 (34.2%), 50-60 (32.2%), and 60+ (21.5%) years old. We investigated the associations between age and tumor markers (ER, PR, HER2, KI67, P53, CK5/6, and EGFR) and features (tumor size, lymph node involvement, and histologic grade) using unconditional logistic regression.

Results

The mean age at diagnosis among these cases was 51.5 years (SD=10.8). Compared to older women (60+), patients diagnosed &lt;40 years old were more likely to have lower ER percentage/intensity, to be positive for HER2, P53, and EGFR, to have higher KI67, and luminal B/HER2+ tumors (p-values=&lt;.0001). PR showed a different and interesting pattern among patients in age group 40-50, who had higher values of PR percentage/intensity compared to women 60+ years old. After mutually adjusting for the significant tumor features, the associations for ER [OR&lt;40 vs 60+=0.34 (0.21, 0.55), OR40-50 vs 60+=0.22 (0.15, 0.32), strong vs. weak staining] and PR [OR&lt;40 vs 60+=2.95 (2.00, 4.35), OR40-50 vs 60+=4.22 (3.13, 5.68), strong vs. weak staining], HER2 positivity [OR&lt;40 vs 60+=1.60 (1.15, 2.23)], KI67 [OR&lt;40 vs 60+=1.52 (1.04, 2.21), quartile 4 vs. 1], and lymph nodal involvement [OR&lt;40 vs 60+=1.87 (1.38, 2.51)] remained significant. While younger patients in general were more likely to have luminal B/HER2+ tumors, women in age group 40-50 were less likely to develop luminal B/high grade BC [OR40-50 vs 60+=0.78 (0.63, 0.97)] compared to women 60+ years old.

Conclusion

We observed the known associations between younger age at diagnosis and more aggressive tumor features. We also found that patients in the age 40-50 group showed interesting associations with PR and the luminal B/high grade subtype. We intend to replicate these results in other Asian datasets and to explore the age associations with etiologic factors.

Citation Format: Hela Koka, Changyuan Guo, Mustapha Abubakar, Hyuna Sung, Hyuna Sung, Bin Zhuo, Eric Tang, Joseph Deng, Nan Hu, Ning Lu, Xiaohong R. Yang. Clinical features in relation to age at diagnosis in luminal breast cancer patients: A hospital-based case series study in Beijing, China [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2905.

Associations between mammographic density and tumor characteristics in Chinese women with breast cancer

PURPOSE

Mammographic density (MD) is a strong risk factor for breast cancer, yet its relationship with tumor characteristics is not well established, particularly in Asian populations.

METHODS

MD was assessed from a total of 2001 Chinese breast cancer patients using Breast Imaging Reporting and Data System (BI-RADS) categories. Molecular subtypes were defined using immunohistochemical status on ER, PR, HER2, and Ki-67, as well as tumor grade. Multinomial logistic regression was used to test associations between MD and molecular subtype (luminal A = reference) adjusting for age, body mass index (BMI), menopausal status, parity, and nodal status.

RESULTS

The mean age at diagnosis was 51.7 years (SD = 10.7) and the average BMI was 24.7 kg/m² (SD = 3.8). The distribution of BI-RADS categories was 7.4% A = almost entirely fat, 24.2% B = scattered fibroglandular dense, 49.4% C = heterogeneously dense, and 19.0% D = extremely dense. Compared to women with BI-RADS = A/B, women with BI-RADS = D were more likely to have HER2-enriched tumors (OR = 1.81, 95% CI 1.08-3.06, p = 0.03), regardless of menopausal status. The association was only observed in women with normal (< 25 kg/m²) BMI (OR = 2.43, 95% CI 1.24-4.76, p < 0.01), but not among overweight/obese women (OR: 0.98, 95% CI 0.38-2.52, p = 0.96).

CONCLUSIONS

Among Chinese women with normal BMI, higher breast density was associated with HER2-enriched tumors. The results may partially explain the higher proportion of HER2+ tumors previously reported in Asian women.

Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer

Genome-wide association studies (GWAS) have identified more than 170 breast cancer susceptibility loci. Here we hypothesize that some risk-associated variants might act in non-breast tissues, specifically adipose tissue and immune cells from blood and spleen. Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. We determine the directional effect of gene expression on disease risk measured based on single and multiple eQTL. In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer.

[The effect of extending proximal landing zone in thoracic endovascular aortic repair on the prognosis of Stanford type B aortic dissection]

With the continuous development of endovascular surgery, thoracic endovascular aortic repair (TEVAR) has gradually replaced traditional open surgery and has become the preferred treatment strategy for Stanford type B aortic dissection. However, the disadvantage of the short proximal landing zone greatly limited the indication of TEVAR surgery and affected the prognosis. In recent years, many strategies such as hybrid surgery, in vitro fenestrated and branched aortic endo-graft, chimney technique, in-situ fenestration technique, etc., have been developed, which greatly broadens the TEVAR indication and improved the prognosis.

Germline mutations in Protection of Telomeres 1 in two families with Hodgkin lymphoma

In a previous whole exome sequencing of patients from 41 families with Hodgkin lymphoma, we identified two families with distinct heterozygous rare coding variants in POT1 (D224N and Y36H), both in a highly conserved region of the gene. POT1 D224N mutant did not bind to a single-stranded telomere oligonucleotide in vitro suggesting the mutation perturbs POT1's ability to bind to the telomeric G-rich overhang. Human HT1080 cells expressing POT1 D224N and lymphoblastoid cells carrying Y36H both showed increased telomere length and fragility in comparison to wild type cells. This strongly suggests that mutant POT1 causes chromosome instability and may play a role in lymphomagenesis in these families.

[Advances in research on cell fate determinant Numb regulating liver cancer]

Liver cancer is one of the most common malignant tumors in China, ranking fifth in malignant tumors and the third in tumor-related deaths. As a membrane-related protein, the asymmetric distribution of cell fate determinant Numb plays a key role in cell differentiation. Research reports that Numb may be closely associated to the occurrence and development of tumors. Recently, scholars have gradually valued its important role in liver cancer. This article briefly reviews the structure of Numb molecule, relationship between Numb and tumorigenesis, the molecular mechanism of Numb-regulated tumors, and the role of Numb in the development of liver cancer.

Genome-wide association study of germline variants and breast cancer-specific mortality

BACKGROUND

We examined the associations between germline variants and breast cancer mortality using a large meta-analysis of women of European ancestry.

METHODS

Meta-analyses included summary estimates based on Cox models of twelve datasets using ~10.4 million variants for 96,661 women with breast cancer and 7697 events (breast cancer-specific deaths). Oestrogen receptor (ER)-specific analyses were based on 64,171 ER-positive (4116) and 16,172 ER-negative (2125) patients. We evaluated the probability of a signal to be a true positive using the Bayesian false discovery probability (BFDP).

RESULTS

We did not find any variant associated with breast cancer-specific mortality at P < 5 × 10-8. For ER-positive disease, the most significantly associated variant was chr7:rs4717568 (BFDP = 7%, P = 1.28 × 10-7, hazard ratio [HR] = 0.88, 95% confidence interval [CI] = 0.84-0.92); the closest gene is AUTS2. For ER-negative disease, the most significant variant was chr7:rs67918676 (BFDP = 11%, P = 1.38 × 10-7, HR = 1.27, 95% CI = 1.16-1.39); located within a long intergenic non-coding RNA gene (AC004009.3), close to the HOXA gene cluster.

CONCLUSIONS

We uncovered germline variants on chromosome 7 at BFDP < 15% close to genes for which there is biological evidence related to breast cancer outcome. However, the paucity of variants associated with mortality at genome-wide significance underpins the challenge in providing genetic-based individualised prognostic information for breast cancer patients.