Spatial-temporal trends in leprosy burden and its associations with socioeconomic and physical geographic factors: results from the Global Burden of Disease Study 2019

OBJECTIVES

The purpose of our study was to assess the multiscalar changes in leprosy burden and its associated risk factors over the last three decades.

STUDY DESIGN

We conducted an in-depth examination of leprosy's spatial-temporal trends at multiple geographical scale (global, regional, and national), utilizing information from Global Burden of Disease, Injuries, and Risk Factors Study (GBD 2019).

METHODS

Incidence and the estimated annual percentage change (EAPC) in age-standardized incidence rate (ASIR) of leprosy were determined, with countries categorized based on leprosy incidence changes. We examined socioeconomic and physical geography influences on leprosy incidence via Spearman correlation analysis, using ternary phase diagrams to reveal the synergetic effects on leprosy occurrence.

RESULTS

Globally, incident cases of leprosy decreased by 27.86% from 1990 to 2019, with a reduction in ASIR (EAPC = -2.53), yet trends were not homogeneous across regions. ASIR and EAPC correlated positively with sociodemographic index (SDI), and an ASIR growth appeared in high SDI region (EAPC = 3.07). Leprosy burden was chiefly distributed in Tropical Latin America, Oceania, Central Sub-Saharan Africa, and South Asia. Negative correlations were detected between the incidence of leprosy and factors of SDI, GDP per capita, urban population to total population, and precipitation, whereas the number of refugee population, temperature, and elevation showed opposite positive results.

CONCLUSIONS

Despite a global decline in leprosy over the past three decades, the disparities of disease occurrence at regional and national scales still persisted. Socioeconomic and physical geographic factors posed an obvious influence on the transmission risk of leprosy. The persistence and regional fluctuations of leprosy incidence necessitate the ongoing dynamic and multilayered control strategies worldwide in combating this ancient disease.

Blood Calcium, Genetic Risk, and Risk of Incident Kidney Stone: A Population-Based Cohort Study

OBJECTIVE

To investigate the association between blood calcium concentration and incident kidney stone as well as to assess the role played by genetic susceptibility.

METHODS

We performed a population-based cohort study based on participants from the UK Biobank. A multivariable Cox proportional hazards regression model was used to estimate hazard ratios (HRs) and 95% CIs of incident kidney stone for blood calcium level and polygenic risk score (PRS). In addition, the potential interaction was explored. The study was conducted from January 28, 2023, through June 4, 2023.

RESULTS

During the follow-up of 423,301 participants with a total of 5,490,332 person-years (median follow-up of 13.4 years), 4502 cases of kidney stone were recorded. Compared with the low blood calcium concentration group (first tertile), individuals in the high (third tertile) and moderate (second tertile) concentration groups had higher risks of kidney stone with HRs of 1.24 (95% CI, 1.15 to 1.33) and 1.11 (1.04 to 1.20), respectively. The PRS for kidney stone contained 40 independent single-nucleotide polymorphisms and was used to assign individuals to 3 groups according to the quintile. Participants with high (Q5) and moderate (Q2 to Q4) genetic risks had increased risks of kidney stone compared with low (Q1) genetic risk with HRs of 1.70 (1.53 to 1.89) and 1.31 (1.20 to 1.44), respectively. There was a joint cumulative risk of incident kidney stone between blood calcium concentration and genetic susceptibility.

CONCLUSIONS

Blood calcium concentration and PRS are significantly associated with incident kidney stone risk. Excessive blood calcium concentration might bring additional stone risk in populations at high genetic risk. A nonlinear correlation between blood calcium concentration and kidney stone risk was indicated.

Associations of prior pulmonary tuberculosis with the incident COPD: a prospective cohort study

BACKGROUND

Prior pulmonary tuberculosis (PTB) might be associated with the development of chronic obstructive pulmonary disease (COPD). However, the impact of prior PTB on the risk of incident COPD has not been studied in a large prospective cohort study of the European population.

OBJECTIVES

This study aimed to investigate the association of prior PTB with the risk of COPD.

DESIGN

Prospective cohort study.

METHODS

A multivariable Cox proportional model was used to estimate the hazard ratio (HR) and 95% confidence interval (95% CI) for the association of prior PTB with COPD. Subgroup analyses were further conducted among individuals stratified by age, sex, body mass index, smoking status, drinking status, physical activity, and polygenic risk score (PRS).

RESULTS

The study involved a total of 216,130 participants, with a median follow-up period of 12.6 years and 2788 incident cases of COPD. Individuals with a prior history of PTB at baseline had an 87% higher risk of developing incident COPD compared to those without such history [adjusted hazard ratio (aHR) = 1.87; 95% confidence interval (CI): 1.26-2.77; p = 0.002]. Subgroup analysis revealed that individuals having prior PTB history presented a higher risk of incident COPD among individuals who were aged from 50 to 59 years with aHR of 2.47 (1.02-5.95, p = 0.044), older than 59 years with aHR of 1.81 (1.16-2.81, p = 0.008), male with aHR of 2.37 (1.47-3.83, p < 0.001), obesity with aHR of 3.35 (2.16-5.82, p < 0.001), previous smoking with aHR of 2.27 (1.39-3.72, p < 0.001), current drinking with aHR of 1.98 (1.47-3.83, p < 0.001), low physical activity with aHR of 2.62 (1.30-5.26, p = 0.007), and low PRS with aHR of 3.24 (1.61-6.53, p < 0.001), as well as high PRS with aHR of 2.43 (1.15-5.14, p = 0.019).

CONCLUSION

A history of PTB is an important independent risk factor for COPD. Clinical staff should be aware of this risk factor in patients with prior PTB, particularly in countries or regions with high burdens of PTB.

Integrative genome-wide analyses identify novel loci associated with kidney stones and provide insights into its genetic architecture

Kidney stone disease (KSD) is a complex disorder with high heritability and prevalence. We performed a large genome-wide association study (GWAS) meta-analysis for KSD to date, including 720,199 individuals with 17,969 cases in European population. We identified 44 susceptibility loci, including 28 novel loci. Cell type-specific analysis pinpointed the proximal tubule as the most relevant cells where susceptibility variants might act through a tissue-specific fashion. By integrating kidney-specific omics data, we prioritized 223 genes which strengthened the importance of ion homeostasis, including calcium and magnesium in stone formation, and suggested potential target drugs for the treatment. The genitourinary and digestive diseases showed stronger genetic correlations with KSD. In this study, we generate an atlas of candidate genes, tissue and cell types involved in the formation of KSD. In addition, we provide potential drug targets for KSD treatment and insights into shared regulation with other diseases.

Stereotactic Radiotherapy or Whole Brain Radiotherapy Combined with Pyrotinib and Capecitabine in HER2-Positive Advanced Breast Cancer Patients with Brain Metastases (BROPTIMA): A Prospective, Phase Ib/II Single-Arm Clinical Study

PURPOSE/OBJECTIVE(S)

Approximately half of patients with advanced HER2-positive breast cancer (BC) will develop brain metastases (BM) over time. Local therapy including stereotactic radiotherapy (SRT) and whole brain radiotherapy (WBRT) is the main initial treatment in malignant tumor patients with BM. However, more than 50% patients after radiotherapy in one year suffered intracranial recurrence. Pyrotinib, a small molecule, irreversible, pan-ErbB receptor tyrosine kinase inhibitor (TKI), has a high potency for controlling BM and reducing the occurrence of brain metastases in advanced HER2-positive BC patients. We hypothesized that SRT or WBRT combined with pyrotinib and capecitabine could decrease intracranial progression in HER2 positive BC with newly diagnosed BM.

MATERIALS/METHODS

In this prospective single-arm phase Ib/II trial (NCT04582968), eligible patients were assigned to either fractionated stereotactic radiotherapy (FSRT) or whole-brain radiation therapy (WBRT), combined with pyrotinib and capecitabine. The primary endpoint was one-year CNS progression-free survival (PFS) rate. Secondary endpoints included intracranial objective response rate (IC-ORR) according to RANO-BM criteria, progression-free survival (PFS), overall survival (OS) and evaluation of safety and neurocognitive function.

RESULTS

From January 2020 to August 2022, 40 patients were enrolled. Twenty-nine patients were treated with FSRT in 8 Gy per fraction with 3 to 5 fractions and 11 were treated with WBRT in 3 Gy per fraction with 10 fractions, and then received chemotherapy in a time frame starting from 0 to 7 days after radiotherapy. At a median follow-up of 17.3 months, 1-year CNS-PFS rate was 74.9% (95% CI 61.9-90.7%) and median CNS-PFS was 18 months (95% CI, 15.5 to NA months). One-year PFS rate was 66.9% (53.1-84.2%) and median PFS time was 17.6 months (95% CI 12.8-34.1 months). The best intracranial response rate (IC-ORR: complete response and partial response) was 92.5% (37/40). The most common grade 3 or worse toxicity was diarrhea (7.5%) and asymptomatic radiation necrosis was detected in 4 of 67(6.0%) lesions treated with FSRT. No differences of neurocognitive function evaluated by MMSE (Mini-Mental State Exam) were observed between different groups at any time point.

CONCLUSION

Radiotherapy combined with pyrotinib and capecitabine resulted in a promising efficacy that crossed the pre-specified boundary in patients with HER2-positive advanced breast cancer with brain metastases. This is the first prospective study showing the efficacy and safety of CNS radiotherapy concurrent with pyrotinib and capecitabine in patients with BM from HER2-positive breast cancer. Further investigation in a randomized controlled study is warranted.

How can childhood maltreatment affect post-traumatic stress disorder in adult: Results from a composite null hypothesis perspective of mediation analysis

Background

A greatly growing body of literature has revealed the mediating role of DNA methylation in the influence path from childhood maltreatment to psychiatric disorders such as post-traumatic stress disorder (PTSD) in adult. However, the statistical method is challenging and powerful mediation analyses regarding this issue are lacking.

Methods

To study how the maltreatment in childhood alters long-lasting DNA methylation changes which further affect PTSD in adult, we here carried out a gene-based mediation analysis from a perspective of composite null hypothesis in the Grady Trauma Project (352 participants and 16,565 genes) with childhood maltreatment as exposure, multiple DNA methylation sites as mediators, and PTSD or its relevant scores as outcome. We effectively addressed the challenging issue of gene-based mediation analysis by taking its composite null hypothesis testing nature into consideration and fitting a weighted test statistic.

Results

We discovered that childhood maltreatment could substantially affected PTSD or PTSD-related scores, and that childhood maltreatment was associated with DNA methylation which further had significant roles in PTSD and these scores. Furthermore, using the proposed mediation method, we identified multiple genes within which DNA methylation sites exhibited mediating roles in the influence path from childhood maltreatment to PTSD-relevant scores in adult, with 13 for Beck Depression Inventory and 6 for modified PTSD Symptom Scale, respectively.

Conclusion

Our results have the potential to confer meaningful insights into the biological mechanism for the impact of early adverse experience on adult diseases; and our proposed mediation methods can be applied to other similar analysis settings.

Overall survival in the OlympiA phase III trial of adjuvant olaparib in patients with germline pathogenic variants in BRCA1/2 and high risk, early breast cancer

BACKGROUND

The randomized, double-blind OlympiA trial compared 1 year of the oral poly(adenosine diphosphate-ribose) polymerase inhibitor, olaparib, to matching placebo as adjuvant therapy for patients with pathogenic or likely pathogenic variants in germline BRCA1 or BRCA2 (gBRCA1/2pv) and high-risk, human epidermal growth factor receptor 2-negative, early breast cancer (EBC). The first pre-specified interim analysis (IA) previously demonstrated statistically significant improvement in invasive disease-free survival (IDFS) and distant disease-free survival (DDFS). The olaparib group had fewer deaths than the placebo group, but the difference did not reach statistical significance for overall survival (OS). We now report the pre-specified second IA of OS with updates of IDFS, DDFS, and safety.

PATIENTS AND METHODS

One thousand eight hundred and thirty-six patients were randomly assigned to olaparib or placebo following (neo)adjuvant chemotherapy, surgery, and radiation therapy if indicated. Endocrine therapy was given concurrently with study medication for hormone receptor-positive cancers. Statistical significance for OS at this IA required P < 0.015.

RESULTS

With a median follow-up of 3.5 years, the second IA of OS demonstrated significant improvement in the olaparib group relative to the placebo group [hazard ratio 0.68; 98.5% confidence interval (CI) 0.47-0.97; P = 0.009]. Four-year OS was 89.8% in the olaparib group and 86.4% in the placebo group (Δ 3.4%, 95% CI -0.1% to 6.8%). Four-year IDFS for the olaparib group versus placebo group was 82.7% versus 75.4% (Δ 7.3%, 95% CI 3.0% to 11.5%) and 4-year DDFS was 86.5% versus 79.1% (Δ 7.4%, 95% CI 3.6% to 11.3%), respectively. Subset analyses for OS, IDFS, and DDFS demonstrated benefit across major subgroups. No new safety signals were identified including no new cases of acute myeloid leukemia or myelodysplastic syndrome.

CONCLUSION

With 3.5 years of median follow-up, OlympiA demonstrates statistically significant improvement in OS with adjuvant olaparib compared with placebo for gBRCA1/2pv-associated EBC and maintained improvements in the previously reported, statistically significant endpoints of IDFS and DDFS with no new safety signals.

Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing

Background

Detecting trans-ethnic common associated genetic loci can offer important insights into shared genetic components underlying complex diseases/traits across diverse continental populations. However, effective statistical methods for such a goal are currently lacking.

Methods

By leveraging summary statistics available from global-scale genome-wide association studies, we herein proposed a novel genetic overlap detection method called CONTO (COmposite Null hypothesis test for Trans-ethnic genetic Overlap) from the perspective of high-dimensional composite null hypothesis testing. Unlike previous studies which generally analyzed individual genetic variants, CONTO is a gene-centric method which focuses on a set of genetic variants located within a gene simultaneously and assesses their joint significance with the trait of interest. By borrowing the similar principle of joint significance test (JST), CONTO takes the maximum P value of multiple associations as the significance measurement.

Results

Compared to JST which is often overly conservative, CONTO is improved in two aspects, including the construction of three-component mixture null distribution and the adjustment of trans-ethnic genetic correlation. Consequently, CONTO corrects the conservativeness of JST with well-calibrated P values and is much more powerful validated by extensive simulation studies. We applied CONTO to discover common associated genes for 31 complex diseases/traits between the East Asian and European populations, and identified many shared trait-associated genes that had otherwise been missed by JST. We further revealed that population-common genes were generally more evolutionarily conserved than population-specific or null ones.

Conclusion

Overall, CONTO represents a powerful method for detecting common associated genes across diverse ancestral groups; our results provide important implications on the transferability of GWAS discoveries in one population to others.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03637-8.

Final results of the global and Asia cohorts of KAMILLA, a phase IIIB safety trial of trastuzumab emtansine in patients with HER2-positive advanced breast cancer

Background

KAMILLA is a single-arm safety study of trastuzumab emtansine (T-DM1) in patients with human epidermal growth factor receptor 2 (HER2)-positive advanced breast cancer (BC; NCT01702571). We report the final analysis of cohort 2 (Asia) within the context of published cohort 1 (Global) findings.

Methods

Patients had HER2-positive, locally advanced, or metastatic BC progressing after chemotherapy and anti-HER2 therapy or ≤6 months after adjuvant therapy. The primary objective was to further evaluate T-DM1 (3.6 mg/kg, administered intravenously every 3 weeks) safety/tolerability, including the following adverse events of primary interest (AEPIs): grade ≥3 AEPIs (hepatic events, allergic reactions, thrombocytopenia, hemorrhage events), all grade ≥3 treatment-related AEs, and all-grade pneumonitis.

Results

KAMILLA enrolled 2185 patients (cohort 1, n = 2003; cohort 2, n = 182) as of 31 July 2019. Of these, 2002 and 181 per cohort were treated and included in the safety population. Approximately 70% of patients had two or more previous treatment lines in the metastatic setting. Median T-DM1 exposure was 5.6 and 5.0 months per cohort; median follow-up was 20.6 and 15.1 months. The overall AEPI rate was higher in cohort 2 (93/181; 51.4%) versus cohort 1 (462/2002; 23.1%), mostly driven by a higher grade ≥3 thrombocytopenia rate in cohort 2. In cohort 2, grade ≥3 thrombocytopenia was not associated with grade ≥3 hemorrhagic events and most (128/138) fully resolved. Grade ≥3 treatment-related AEPI rates were 18.4% (cohort 1) and 48.6% (cohort 2), the latter mainly due to thrombocytopenia. Any-grade pneumonitis rates were 1.0% and 2.2%. No new safety signals were identified. Median (95% confidence interval) progression-free survival was 6.8 months (5.8-7.6 months) and 5.7 months (5.5-7.0 months) in cohorts 1 and 2, respectively; median overall survival was 27.2 months (25.5-28.7 months) and 29.5 months (21.1 months to non-estimable). In both cohorts, median progression-free survival and overall survival decreased with increasing prior therapy lines.

Conclusions

Cohort 2 results aligned with previous findings in Asian patients, supporting the manageable safety profile and use of T-DM1 in advanced BC.

•

KAMILLA safety results for cohorts 1 (global; n = 2002) and 2 (Asia; n = 181) aligned with results from prior T-DM1 mBC trials.

•

The overall rate of adverse events of primary interest (AEPIs) was higher in cohort 2 (51.4%) versus cohort 1 (23.1%).

•

The higher AEPI rate was mostly due to a higher grade ≥3 thrombocytopenia event rate in cohort 2, most of which resolved.

•

Median PFS and OS were similar for both cohorts, and decreased with increasing prior therapy lines.

•

The manageable safety profile and efficacy of T-DM1 further support its favorable benefit/risk balance.

A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies

Background

Multilocus analysis on a set of single nucleotide polymorphisms (SNPs) pre-assigned within a gene constitutes a valuable complement to single-marker analysis by aggregating data on complex traits in a biologically meaningful way. However, despite the existence of a wide variety of SNP-set methods, few comprehensive comparison studies have been previously performed to evaluate the effectiveness of these methods.

Results

We herein sought to fill this knowledge gap by conducting a comprehensive empirical comparison for 22 commonly-used summary-statistics based SNP-set methods. We showed that only seven methods could effectively control the type I error, and that these well-calibrated approaches had varying power performance under the simulation scenarios. Overall, we confirmed that the burden test was generally underpowered and score-based variance component tests (e.g., sequence kernel association test) were much powerful under the polygenic genetic architecture in both common and rare variant association analyses. We further revealed that two linkage-disequilibrium-free P value combination methods (e.g., harmonic mean P value method and aggregated Cauchy association test) behaved very well under the sparse genetic architecture in simulations and real-data applications to common and rare variant association analyses as well as in expression quantitative trait loci weighted integrative analysis. We also assessed the scalability of these approaches by recording computational time and found that all these methods can be scalable to biobank-scale data although some might be relatively slow.

Conclusion

In conclusion, we hope that our findings can offer an important guidance on how to choose appropriate multilocus association analysis methods in post-GWAS era. All the SNP-set methods are implemented in the R package called MCA, which is freely available at https://github.com/biostatpzeng/.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04897-3.

Abstract ES5-1: Genomic and transcriptomic landscape of TNBC

Triple-negative breast cancer (TNBC) is highly heterogeneous. Due to the limited number of TNBCs that have been analyzed, molecular events driving subtypes and prognosis are not firmly established, and little is known regarding TNBC in non-Caucasian patients. Our findings advance the understanding of TNBC subtypes, subdivide the established transcriptome-based subtypes in search of more targeted therapeutic strategies, and offer potential insights to guide subtype-specific therapy. We further conducted a phase Ib/II subtyping-based and genomic biomarker guided umbrella trial to evaluate the efficacy of these targets. Objective response rate (ORR) of these 69 refractory metastatic TNBC patients was 29.0%, while the ORR of arm C (immunotherapy) was 52.6%. Still, genomic and transcriptomic-based target mining do not solve all the problems in TNBC treatment, for example the poor treatment efficacy in luminal androgen receptor (LAR) and basal-like immune-suppressed (BLIS) subtypes. Increasing the dimensions of omics to look for potential therapeutic targets would hopefully solve this problem.

Citation Format: Z Shao. Genomic and transcriptomic landscape of TNBC [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr ES5-1.

Assessing Causal Relationship Between Human Blood Metabolites and Five Neurodegenerative Diseases With GWAS Summary Statistics

Background: Neurodegenerative diseases (NDDs) are the leading cause of disability worldwide while their metabolic pathogenesis is unclear. Genome-wide association studies (GWASs) offer an unprecedented opportunity to untangle the relationship between metabolites and NDDs.

Methods: By leveraging two-sample Mendelian randomization (MR) approaches and relying on GWASs summary statistics, we here explore the causal association between 486 metabolites and five NDDs including Alzheimer’s Disease (AD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Parkinson’s disease (PD), and multiple sclerosis (MS). We validated our MR results with extensive sensitive analyses including MR-PRESSO and MR-Egger regression. We also performed linkage disequilibrium score regression (LDSC) and colocalization analyses to distinguish causal metabolite-NDD associations from genetic correlation and LD confounding of shared causal genetic variants. Finally, a metabolic pathway analysis was further conducted to identify potential metabolite pathways.

Results: We detected 164 metabolites which were suggestively associated with the risk of NDDs. Particularly, 2-methoxyacetaminophen sulfate substantially affected ALS (OR = 0.971, 95%CIs: 0.961 ∼ 0.982, FDR = 1.04E-4) and FTD (OR = 0.924, 95%CIs: 0.885 ∼ 0.964, FDR = 0.048), and X-11529 (OR = 1.604, 95%CIs: 1.250 ∼ 2.059, FDR = 0.048) and X-13429 (OR = 2.284, 95%CIs: 1.457 ∼ 3.581, FDR = 0.048) significantly impacted FTD. These associations were further confirmed by the weighted median and maximum likelihood methods, with MR-PRESSO and the MR-Egger regression removing the possibility of pleiotropy. We also observed that ALS or FTD can alter the metabolite levels, including ALS and FTD on 2-methoxyacetaminophen sulfate. The LDSC and colocalization analyses showed that none of the identified associations could be driven by genetic correlation or confounding by LD with common causal loci. Multiple metabolic pathways were found to be involved in NDDs, such as “urea cycle” (P = 0.036), “arginine biosynthesis” (P = 0.004) on AD and “phenylalanine, tyrosine and tryptophan biosynthesis” (P = 0.046) on ALS.

Conclusion: our study reveals robust bidirectional causal associations between servaral metabolites and neurodegenerative diseases, and provides a novel insight into metabolic mechanism for pathogenesis and therapeutic strategies of these diseases.

A comprehensive gene-centric pleiotropic association analysis for 14 psychiatric disorders with GWAS summary statistics

BACKGROUND

Recent genome-wide association studies (GWASs) have revealed the polygenic nature of psychiatric disorders and discovered a few of single-nucleotide polymorphisms (SNPs) associated with multiple psychiatric disorders. However, the extent and pattern of pleiotropy among distinct psychiatric disorders remain not completely clear.

METHODS

We analyzed 14 psychiatric disorders using summary statistics available from the largest GWASs by far. We first applied the cross-trait linkage disequilibrium score regression (LDSC) to estimate genetic correlation between disorders. Then, we performed a gene-based pleiotropy analysis by first aggregating a set of SNP-level associations into a single gene-level association signal using MAGMA. From a methodological perspective, we viewed the identification of pleiotropic associations across the entire genome as a high-dimensional problem of composite null hypothesis testing and utilized a novel method called PLACO for pleiotropy mapping. We ultimately implemented functional analysis for identified pleiotropic genes and used Mendelian randomization for detecting causal association between these disorders.

RESULTS

We confirmed extensive genetic correlation among psychiatric disorders, based on which these disorders can be grouped into three diverse categories. We detected a large number of pleiotropic genes including 5884 associations and 2424 unique genes and found that differentially expressed pleiotropic genes were significantly enriched in pancreas, liver, heart, and brain, and that the biological process of these genes was remarkably enriched in regulating neurodevelopment, neurogenesis, and neuron differentiation, offering substantial evidence supporting the validity of identified pleiotropic loci. We further demonstrated that among all the identified pleiotropic genes there were 342 unique ones linked with 6353 drugs with drug-gene interaction which can be classified into distinct types including inhibitor, agonist, blocker, antagonist, and modulator. We also revealed causal associations among psychiatric disorders, indicating that genetic overlap and causality commonly drove the observed co-existence of these disorders.

CONCLUSIONS

Our study is among the first large-scale effort to characterize gene-level pleiotropy among a greatly expanded set of psychiatric disorders and provides important insight into shared genetic etiology underlying these disorders. The findings would inform psychiatric nosology, identify potential neurobiological mechanisms predisposing to specific clinical presentations, and pave the way to effective drug targets for clinical treatment.

Relationship between birth weight and chronic kidney disease: evidence from systematics review and two-sample Mendelian randomization analysis

Observational studies showed an inverse association between birth weight and chronic kidney disease (CKD) in adulthood existed. However, whether such an association is causal remains fully elusive. Moreover, none of prior studies distinguished the direct fetal effect from the indirect maternal effect. Herein, we aimed to investigate the causal relationship between birth weight and CKD and to understand the relative fetal and maternal contributions. Meta-analysis (n = ~22 million) showed that low birth weight led to ~83% (95% confidence interval [CI] 37-146%) higher risk of CKD in late life. With summary statistics from large scale GWASs (n = ~300 000 for birth weight and ~481 000 for CKD), linkage disequilibrium score regression demonstrated birth weight had a negative maternal, but not fetal, genetic correlation with CKD and several other kidney-function related phenotypes. Furthermore, with multiple instruments of birth weight, Mendelian randomization showed there existed a negative fetal casual association (OR = 1.10, 95% CI 1.01-1.16) between birth weight and CKD; a negative but non-significant maternal casual association (OR = 1.09, 95% CI 0.98-1.21) was also identified. Those associations were robust against various sensitivity analyses. However, no maternal/fetal casual effects of birth weight were significant for other kidney-function related phenotypes. Overall, our study confirmed the inverse association between birth weight and CKD observed in prior studies, and further revealed the shared maternal genetic foundation between low birth weight and CKD, and the direct fetal and indirect maternal causal effects of birth weight may commonly drive this negative relationship.

Increased risk of diabetes in cancer survivors: a pooled analysis of 13 population-based cohort studies

BACKGROUND

Diabetes is considered as an established risk factor for cancer development. However, the link between diabetes among cancer survivors remains inconclusive. The hypothesis of this study was to assess the hazard ratio (HR) of incidence of diabetes in cancer survivors compared with the HR in the general population.

PATIENTS AND METHODS

A comprehensive literature search was performed in PubMed, Embase, and the Cochrane Library from database inception to 15 December 2020 for population-based cohort studies. Summary effect estimates were combined using random-effects models. We also performed subgroup analyses to test sources of heterogeneity and the stability of the results stratified by various study and participant characteristics.

RESULTS

Thirteen population-based cohort studies involving 1 686 595 participants were analyzed. The HR for the development of diabetes in cancer survivors was 1.39 [95% confidence interval (CI) 1.29-1.50; I2 = 82.3%; P < 0.001] compared with that in noncancer controls, among which survivors of hematological, gynecologic, breast, colorectal and urinary tract cancer (all P < 0.05) showed consistent significant results, whereas no significant increased risk was observed for other cancer types. The effects were more prominent in populations of shorter cancer survival duration (<1 year) (HR 2.09, 95% CI 1.32-3.32; P = 0.009). Moreover, cancer survivors with a longer follow-up period (>10 years) had a relatively higher risk of diabetes (HR 1.54, 95% CI 1.34-1.77) than those with a shorter follow-up period.

CONCLUSIONS

In this large pooled analysis of population-based cohorts, evidence supports the hypothesis that the risk of developing diabetes is increased in cancer survivors compared with the general population. We should interpret the results with caution for considerable interstudy heterogeneity. However, health policy makers should take this as a challenge for the early prevention and effective intervention of diabetes.

IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA

Effective and powerful survival mediation models are currently lacking. To partly fill such knowledge gap, we particularly focus on the mediation analysis that includes multiple DNA methylations acting as exposures, one gene expression as the mediator and one survival time as the outcome. We proposed IUSMMT (intersection-union survival mixture-adjusted mediation test) to effectively examine the existence of mediation effect by fitting an empirical three-component mixture null distribution. With extensive simulation studies, we demonstrated the advantage of IUSMMT over existing methods. We applied IUSMMT to ten TCGA cancers and identified multiple genes that exhibited mediating effects. We further revealed that most of the identified regions, in which genes behaved as active mediators, were cancer type-specific and exhibited a full mediation from DNA methylation CpG sites to the survival risk of various types of cancers. Overall, IUSMMT represents an effective and powerful alternative for survival mediation analysis; our results also provide new insights into the functional role of DNA methylation and gene expression in cancer progression/prognosis and demonstrate potential therapeutic targets for future clinical practice.

Statistical methods for mediation analysis in the era of high-throughput genomics: Current successes and future challenges

Mediation analysis investigates the intermediate mechanism through which an exposure exerts its influence on the outcome of interest. Mediation analysis is becoming increasingly popular in high-throughput genomics studies where a common goal is to identify molecular-level traits, such as gene expression or methylation, which actively mediate the genetic or environmental effects on the outcome. Mediation analysis in genomics studies is particularly challenging, however, thanks to the large number of potential mediators measured in these studies as well as the composite null nature of the mediation effect hypothesis. Indeed, while the standard univariate and multivariate mediation methods have been well-established for analyzing one or multiple mediators, they are not well-suited for genomics studies with a large number of mediators and often yield conservative p-values and limited power. Consequently, over the past few years many new high-dimensional mediation methods have been developed for analyzing the large number of potential mediators collected in high-throughput genomics studies. In this work, we present a thorough review of these important recent methodological advances in high-dimensional mediation analysis. Specifically, we describe in detail more than ten high-dimensional mediation methods, focusing on their motivations, basic modeling ideas, specific modeling assumptions, practical successes, methodological limitations, as well as future directions. We hope our review will serve as a useful guidance for statisticians and computational biologists who develop methods of high-dimensional mediation analysis as well as for analysts who apply mediation methods to high-throughput genomics studies.

Senolytic agent Quercetin ameliorates intervertebral disc degeneration via the Nrf2/NF-κB axis

OBJECTIVE

Intervertebral disc degeneration (IDD) represents major cause of low back pain. Quercetin (QUE) is one of the approved senolytic agents. In this study, we evaluated the protective effects of QUE on IDD development and its underlying mechanism.

METHODS

Effects of senolytic agent QUE on the viability of nucleus pulposus cells (NPCs) were measured by CCK-8 assays and EdU staining. The senescence associated secreted phenotype (SASP) factors expressions were measured by qPCR, western blot, and ELISA; and NF-κB pathway was detected by immunofluorescence and western blot. Molecular docking was applied to predict the interacting protein of QUE; while Nrf2 was knocked down by siRNAs to confirm its role in QUE regulated senescence phenotype. X-ray, MRI, Hematoxylin-Eosin and Safranin O-Fast green staining were performed to evaluate the therapeutic effects of QUE on IDD in the puncture-induced rat model.

RESULTS

In in vitro experiments, QUE inhibited SASP factors expression and senescence phenotype in IL-1β-treated NPCs. Mechanistically, QUE suppressed IL-1β induced activation of the NF-κB pathway cascades; it was also demonstrated in molecular docking and knock down studies that QUE might bind to Keap1-Nrf2 complex to suppress NF-κB pathway. In vivo, QUE ameliorated the IDD process in the puncture-induced rat model.

CONCLUSIONS

Together the present work suggests that QUE inhibits SASP factors expression and senescence phenotype in NPCs and ameliorates the progression of IDD via the Nrf2/NF-κB axis, which supports senolytic agent QUE as a potential therapeutic agent for the treatment of IDD.

The role of structure and function changes of sensory nervous system in intervertebral disc-related low back pain

Low back pain (LBP) is a common musculoskeletal symptom, which can be developed in multiple clinical diseases. It is widely recognized that intervertebral disc (IVD) degeneration (IVDD) is one of the leading causes of LBP. However, the pathogenesis of IVD-related LBP is still controversial, and the treatment means are also insufficient to date. In recent decades, the role of structure and function changes of sensory nervous system in the induction and the maintenance of LBP is drawing more and more attention. With the progress of IVDD, IVD cell exhaustion and extracellular matrix degradation result in IVD structural damage, while neovascularization, innervation and inflammatory activation further deteriorate the microenvironment of IVD. New nerve ingrowth into degenerated IVD amplifies the impacts of IVD-derived nociceptive molecules on sensory endings. Moreover, IVDD is usually accompanied with disc herniation, which could injure and inflame affected nerves. Under mechanical and pro-inflammatory stimulation, the pain-transmitting pathway exhibits a sensitized function state and ultimately leads to LBP. Hence, relevant pathogenic factors, such as neurotrophins, ion channels, inflammatory factors, etc., are supposed to serve as promising therapeutic targets for LBP. The purpose of this review is to comprehensively summarize the current evidence on 1) the pathological changes of sensory nervous system during IVDD and their association with LBP, and 2) potential therapeutic strategies for LBP targeting relevant pathogenic factors.

On the molecular structure of Remdesivir for the treatment of Covid-19

(SARS-CoV-2), was first identified in December 2019 as the cause of a respiratory illness designated coronavirus disease 2019, or Covid-19. Several therapeutic agents have been evaluated for the treatment of Covid-19, but none have yet been shown to be efficacious. Remdesivir (GS-5734), an inhibitor of the viral RNA-dependent, RNA polymerase with inhibitory activity against SARS-CoV and the Middle East respiratory syndrome (MERS-CoV), was identified early as a promising therapeutic candidate for Covid-19 because of its ability to inhibit SARS-CoV-2 in vitro. Besides, in nonhuman primate studies, remdesivir initiated 12 hours after inoculation with MERS-CoV9,10 reduced lung virus levels and lung damage. In the field of Medical Science, concerning the definition of the topological index on the molecular structure and corresponding medical, biological, chemical, pharmaceutical properties of drugs can be studied by the topological index calculation. In this paper, we compute some of the general temperature topological properties of remdesivir that the results in this paper may be useful in finding new drug and vaccine for the treatment and prevention of COVID-19.

The effect of maize-alfalfa intercropping on the physiological characteristics, nitrogen uptake and yield of maize

In Northeastern China, the intensive cropping system and increased use of chemical fertilizer has caused severe problems in terms of sustainable agricultural development. Therefore, to improve agricultural sustainability and crop productivity the farming system needs to be modified in the region. A pot experiment was conducted to evaluate the effect of maize-alfalfa intercropping on the physiological characteristics, nitrogen (N) uptake and yield of the maize crops in northeast China in 2017-2018. The study findings showed that intercropping under N fertilization progressively improved the physio-agronomic indices of the maize crop as compared to mono-cropping. The grain yield, 100 seed weight and biomass dry matter of maize crop improved in intercropping when it was practiced with N fertilizer. Furthermore, intercropping with N fertilization increased the chlorophyll content of the maize crop at bell-mouthed, silking, filing and mature stages by 19%, 44%, 12%, and 9% in 2017 and by 23%, 43%, 15%, and 11% in 2018, respectively, as compared with the monocropping system. Unlike monocropping, intercropping with N fertilization increased the photosynthesis rate (14% and 15%), stomatal conductance (74% and 98%) and transpiration rate (74% and 75%) in 2017 and 2018, respectively. However, intercropping reduced intercellular CO₂ (C_i ). Moreover, intercropping with N fertilization increased the maize N content of grain and leaves as well as total N uptake by 49%, 31% and 93% in 2017 and 53%, 34% and 132%, respectively, in 2018 as compared to monocropping. In conclusion, our results suggest that maize-alfalfa intercropping with optimal N fertilization provides a practical method for improving growth, yield and N accumulation in the maize crop.

Are blood lipids risk factors for fracture? Integrative evidence from instrumental variable causal inference and mediation analysis using genetic data

BACKGROUND

The relationship between lipids and the risk of fracture is currently controversial and whether such association is causal remains elusive.

METHODS

We performed two-sample inverse variance weighted (IVW) Mendelian randomization (MR) analyses to evaluate causal effects of four lipids (i.e. high-density lipoprotein cholesterol [HDL], low-density lipoprotein cholesterol [LDL], total cholesterol [TC] and triglyceride [TG]) on fracture or bone mineral density (BMD) with summary statistics from large scale genome-wide association studies (up to ~190,000 for lipids, ~66,628 for BMD and ~53,000 for fracture). We validated our MR results with extensive sensitive analyses including MR-PRESSO and MR-Egger regression. Multivariable analyses were implemented to investigate whether other lipids (i.e. LDL and TG) may confound the causal effect of HDL on fracture and mediation analyses were conducted to assess indirect effects of lipids on fracture mediated by BMD.

RESULTS

The IVW MR showed there existed a statistically significant association between HDL and fracture, with the odd ratio (OR) per standard deviation change of HDL on fracture being 1.12 (95% CI: 1.02-1.22, p = 1.20E-02). HDL was also detected to be causally associated with BMD (beta = -0.116; 95% CI: -0.182 ~ -0.050, p = 5.47E-04). These associations were further confirmed by the weighted median and maximum likelihood methods, with the MR-Egger regression removing the possibility of pleiotropy and the multivariable analysis excluding the confounding effect of other lipids on HDL. Negative associations of HDL with BMD among the elderly and with BMD at the lumbar spine were also discovered. However, no causal associations were detected between other lipids (OR = 0.87, 95% CI: 0.74-1.03, p = .107 for LDL; OR = 1.03; 95% CI: 0.88-1.21, p = .696 for TC and OR = 1.04; 95% CI: 0.90-1.20, p = .610 for TG) and fracture; whereas TG was positively associated BMD (beta = 0.184; 95% CI: 0.048-0.319, p = 7.93E-03). Finally, the mediation effect of BMD was estimated to be -0.116 (95% CI: -0.182 to -0.05, p = 5.47E-04) for HDL or 0.184 (95% CI: 0.048-0.319, p = 7.93E-03) for TG, implying HDL and TG could be indirectly associated with fracture risk via the pathway of BMD.

CONCLUSION

Our study is supportive of the causal relationship between HDL and fracture but offers little direct evidence for causal associations between other lipids and fracture, and further reveals HDL and TG may have an indirect influence on fracture mediated by BMD.

TGF-β signaling in intervertebral disc health and disease

OBJECTIVE

This paper aims to provide a comprehensive review of the changing role of transforming growth factor-β (TGF-β) signaling in intervertebral disc (IVD) health and disease.

METHODS

A comprehensive literature search was performed using PubMed terms 'TGF-β' and 'IVD'.

RESULTS

TGF-β signaling is necessary for the development and growth of IVD, and can play a protective role in the restoration of IVD tissues by stimulating matrix synthesis, inhibiting matrix catabolism, inflammatory response and cell loss. However, excessive activation of TGF-β signaling is detrimental to the IVD, and inhibition of the aberrant TGF-β signaling can delay IVD degeneration.

CONCLUSIONS

Activation of TGF-β signaling has a promising treatment prospect for IVD degeneration, while excessive activation of TGF-β signaling may contribute to the progression of IVD degeneration. Studies aimed at elucidating the changing role of TGF-β signaling in IVD at different pathophysiological stages and its specific molecular mechanisms are needed, and these studies will contribute to safe and effective TGF-β signaling-based treatments for IVD degeneration.

Mandibular reconstruction using the deep circumflex iliac artery free flap: effect of the length of bone harvested on donor site morbidity

The aim of this study was to assess the amounts of pain and morbidity that are associated with the length of the harvested anterior iliac bone graft (cm), and their effect on the contour of the donor site and activities of daily life. A total of 62 patients who had mandibular reconstruction using an iliac bone graft were enrolled in this study at the Wuhan University Hospital. The same surgical standards were used throughout. We divided the patients into two groups depending to the length of the graft (<9cm or 9cm or more). The amount and duration of the pain, the time necessary to walk normally, abnormalities of sensation, contour of the donor site, length of the scar, and the patients' satisfaction with the donor site were evaluated, and outcomes in the two groups compared. The worst pain after operation (p=0.001) the length of the scar (p=0.001), and the time needed before the patients were able to walk (p=0.001) differed significantly between the two groups. There was no significant difference between the two groups regarding other complications. The anterior iliac crest might still be considered to be an ideal donor site for large mandibular defects.

[Analysis of prognostic factors for hyperamylasemia following pancreaticoduodenectomy]

Objective: To investigate the prognostic factors of hyperamylasemia following pancreaticoduodenectomy (PD) . Methods: Clinical data of 359 patients were collected prospectively who underwent PD by the same group at Changhai Hospital of Navy Medical University from January 2017 to June 2018.There were 212 males and 147 females.The median age was 63 years old (range: 23 to 82 years old) .According to whether the patient's serum amylase was greater than 120 U/L at 0 or 1 day after surgery,the patients were divided into hyperamylasemia group and non-hyperamylasemia group. Univariate analysis and multivariate analysis were used to find out the prognostic factors of hyperamylasemia after PD. Results: Of the 359 patients, 238 cases (66.3%) developed hyperamylasemia.The incidence rate of clinically related pancreatic fistula (15.1% vs.2.5%, P<0.01) , grade B/C post pancreatectomy hemorrhage (8.8% vs. 2.5%, P<0.01) , and surgical site infection (9.2% vs. 3.3%, P=0.04) was significantly higher in the hyperamylasemia group.The severity of complications (CD grade≥Ⅲ: 11.3% vs.4.1%, P=0.023) and postoperative hospital stay (11 days vs. 9 days, P=0.001) were higher in the hyperamylasemia group.In the multivariate analysis, the main pancreatic duct diameter (MPD) ≤3 mm (OR=4.469, 95% CI: 2.563-7.793, P<0.01) , pathological type of disease (pancreatic cancer or pancreatitis) (OR=0.230, 95% CI: 0.122-0.436, P<0.01) and soft texture of pancreas (OR=3.297, 95%CI: 1.930-5.635, P<0.01) were independent prognostic factors for hyperamylasemia. Conclusions: Post-PD hyperamylasemia increased the incidence and severity of postoperative complications after PD.MPD≤3 mm, soft texture of pancreas and pathological type of disease were independent prognostic factors of hyperamylasemia.

Resection of liver metastases from breast cancer: a multicentre analysis

BACKGROUND

Surgery is becoming more practical and effective than conservative treatment in improving the poor outcomes of patients with breast cancer liver metastasis (BCLM). However, there is no generally acknowledged set of standards for identifying BCLM candidates who will benefit from surgery.

METHODS

Between January 2011 and September 2018, 67 female BCLM patients who underwent partial hepatectomy were selected for analysis in the present study. Prognostic factors after hepatectomy were determined. Univariate and multivariate analyses were performed to identify predictors of overall survival (OS) and intrahepatic recurrence-free survival (IHRFS).

RESULTS

The 1-, 3- and 5-year OS of patients treated with surgery was 93.5%, 73.7% and 32.2%, respectively, with a median survival time of 57.59 months. The Pringle manoeuvre [hazard radio (HR) = 0.117, 95% CI0.015-0.942, p = 0.044] and an increased interval between breast surgery and BCLM diagnosis (HR0.178, 95% CI 0.037-0.869, p = 0.033) independently predicted improved overall survival for BCLM patients. The 1-, 2- and 3-year IHRFS of patients who underwent surgery was 62.8, 32.6% and 10.9%, respectively, with a median intrahepatic recurrence-free survival time of 13.47 months. Moderately differentiated tumours (HR  0.259, 95% CI 0.078-0.857, p = 0.027) and the development of liver metastasis more than 2 years after breast surgery (HR  0.270, 95% CI 0.108-0.675, p = 0.005) might be predictors of increased IHRFS.

CONCLUSIONS

An interval of more than 2 years between breast cancer surgery and liver metastasis seems to be an indication of liver surgery in BCLM patients. The Pringle manoeuvre and moderately differentiated tumours are potential predictors associated with OS and IHRFS, respectively, as benefits from liver resection. Studies with increased sample sizes are warranted to validate our results.

Abstract P6-17-17: Pertuzumab, trastuzumab, and docetaxel for HER2-positive early or locally advanced breast cancer in the neoadjuvant setting: Efficacy and safety analysis of a randomized phase III study in Asian patients (PEONY)

Background

Pertuzumab and trastuzumab (P and H; F. Hoffmann-La Roche Ltd, Basel, CH) bind to distinct HER2 subdomains and have complementary modes of anticancer activity in HER2-positive breast cancer (BC). A global Phase II study (NeoSphere) reported that neoadjuvant treatment with P+H+docetaxel (D) significantly increased breast pathologic complete response (bpCR) vs H+D in patients (pts) with early/locally advanced/inflammatory HER2-positive BC (Gianni et al. Lancet Oncol 2012). PEONY (NCT02586025), a randomized, multicenter, double-blind, placebo-controlled, Phase III trial conducted in an Asian population (mainland China, Taiwan, Korea, Thailand), primarily compared the efficacy, safety, and tolerability of P+H+D vs placebo (Pla)+H+D in the neoadjuvant setting. We present data from the primary analysis.

Methods

Pts with centrally confirmed HER2-positive early (T2–3, N0–1)/locally advanced (T2–3, N2 or N3; T4, any N) BC were randomized 2:1 to 4 cycles of P+H+D or Pla+H+D every 3 weeks, before surgery: P, 840 mg loading/420 mg maintenance doses (or Pla); H, 8 mg/kg loading/6 mg/kg maintenance; D, 75 mg/m2. Post-surgery, pts received 3 cycles of fluorouracil, epirubicin, and cyclophosphamide followed by 13 cycles of P+H or Pla+H for up to 1 year (total of 17 HER2-targeted therapy cycles). The primary endpoint was total pCR rate (tpCR; absence of any residual invasive cancer in the breast and lymph nodes [ypT0/is, ypN0]) assessed by independent review committee (IRC) when pts completed surgery with a tpCR assessment. Missing/invalid assessments were considered residual disease.

Results

A total of 329 pts were randomized: 219 to P, 110 to Pla. Baseline characteristics were well balanced. Most pts had early BC (69.6%) and were from mainland China (79.3%). In the intention-to-treat population, the tpCR rate by IRC was 39.3% in the P arm and 21.8% in the Pla arm; a clinically and statistically significant difference of 17.5% (95% CI 6.9–28.0; p=0.0014). The local pathologist-assessed tpCR rates were 39.3% and 20.9%, respectively. A consistent treatment benefit of P vs Pla was observed in subgroups. Incidences of grade ≥3 adverse events (Aes) were 48.6% in the P arm and 41.8% in the Pla arm. Of the most common grade 3 Aes (≥3% of pts), neutropenia was higher in the P arm (38.1% vs 32.7%). Of the most common any-grade Aes (≥5%), diarrhea was higher in the P arm (38.5% vs 16.4%). No heart failure (New York Heart Association Functional Classification III or IV) or significant left ventricular ejection fraction decline events (≥10 percentage points from baseline and to &lt;50%) were observed during neoadjuvant therapy.

Conclusions

PEONY met its primary endpoint: P+H+D resulted in a clinically meaningful and statistically significant improvement in the tpCR rate by IRC vs Pla+H+D for the neoadjuvant treatment of HER2-positive early/locally advanced BC in Asian pts. Safety data were in line with the known P safety profile and generally comparable between treatment arms. Results were similar to NeoSphere, and confirm that P+H+D provides superior anticancer activity to H+D alone.

Citation Format: Shao Z, Pang D, Yang H, Li W, Wang S, Cui S, Liao N, Wang Y, Wang C, Chang Y-C, Wang H, Kang SY, Jiang Z, Li J, Zhou J, Althaus B, Mao Y, Eng-Wong J. Pertuzumab, trastuzumab, and docetaxel for HER2-positive early or locally advanced breast cancer in the neoadjuvant setting: Efficacy and safety analysis of a randomized phase III study in Asian patients (PEONY) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-17-17.

Abstract P4-08-18: Not presented

This abstract was not presented at the conference.

Citation Format: Liu Y, Chen S, Jiang Y, Wu J, Shao Z. Not presented [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-18.

Abstract P1-06-10: Combined tandem affinity purification mass-spectrometry technique with genome-editing CRISPR-Cas9 knockout screening to identify potential subunits in the BRCA1 complex

Background: Genomic instability is one of tumor characteristics. Enhancing the DNA damage load or impairing the ability of DNA damage repair has been therapeutics of cancer. Breast cancer type 1 susceptibility gene (BRCA1) has been studied a lot about the DNA damage and repair in breast cancer and ovarian cancer. BRCA1 mutation increases the risk of developing breast cancer by an eighth to tenth. The C terminal domain of BRCA1 can associates with three proteins Abraxas, Bach1 and CtIP in a phosphorylation-dependent manner forming mutually exclusive complexes, namely BRCA1-A, B, and C complexes. The BRCA1-A complex is necessary in DNA damage repair, and study implicates the complex play roles in chemotherapy resistance.

Methods: We explored tandem affinity purification mass-spectrometry (TAP-MAS) technique to identify potential subunits associated with NBA1(one component of BRCA1-A complex). Then we made the genome-editing CRISPR-Cas9 sgRNA library into lentivirus to infect U2OS cells. And 5 Gy dose of Ionizing radiation (IR) was used to induce DNA damage on the cell. After 14 days cultivation, we extracted the DNA from the cells, performed polymerase chain reaction (PCR) and analyzed the correlation between potential genes and DNA damage-repair passage by bioinformatics methods. We generated 200 breast cancer patient tissue samples in our cancer center and performed immunostaining assay.

Results: By the TAP-MAS technique of NBA1 tagged with HA and Flag, we found 93 potential subunits except those known subunits in BRCA1-A complex. Combined with CRISPR-Cas9 sgRNA library screening, we scored the relativity of DNA damage and repair passageway of identified 93 potential subunits. We found that nucleoside-triphosphatase, cancer-related (NTPCR) as a new potential subunit of BRCA1-A complex (P value=0.0034) had the highest score. Endogenous and exogenous co-IP validated NTPCR physically associates with subunits within BRCA1-A complex. Besides, we found that NTPCR associated with the same domain of NBA1 as the other subunits in BRCA1-A complex. Immunohistochemistry of patient tissue samples indicated that high levels of NTPCR expression was correlated with poor prognosis in multivariate analysis (HR: 4.990; 95%CI: 1.433-17.378; p value: 0.012).

Conclusion: NTPCR is a new subunit in BRCA1-A complex. And high expression of NTPCR is a negative prognostic factor in breast cancer patients.

Citation Format: Zhao H, Jiang H, Sun W, Shao Z, Hu X. Combined tandem affinity purification mass-spectrometry technique with genome-editing CRISPR-Cas9 knockout screening to identify potential subunits in the BRCA1 complex [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-06-10.

Abstract P2-08-33: A novel seven-gene signature predicts prognosis in early-stage triple-negative breast cancer

Purpose:

Chemotherapy remains the only systemic treatment option for patients with triple-negative breast cancer (TNBC). However, due to the heterogeneity of TNBC, not all patients benefit from chemotherapy, especially those with early-stage disease. In order to improve prognostic assessment and reduce unnecessary adjuvant systemic therapy in these patients, we have developed a novel seven-gene signature.

Experimental Design:

With the ComBat method, we integrated the results from 150 transcriptome microarrays samples and 246 RNA-seq samples of early-stage TNBC patients, and identified mRNAs associated with recurrence-free survival (RFS) using Lasso-Cox model, We further analyzed these TNBC samples and compared them with 60 paired normal breast tissues (40 samples from RNA-seq and 20 samples from microarrays) to identify tumor-specific mRNAs. Twenty-one overlapped mRNAs of the RFS-associated mRNAs and the tumor-specific mRNAs are selected as candidate mRNAs. An additional 371 samples of frozen primary tumors were then collected from early-stage TNBC patients (mean follow-up of 45 months) and randomly divided into two sets: a training set (n = 186) and a validation (n = 185) set. Expression level of candidate mRNAs in these samples were measured using RT-qPCR assays, and a seven-gene signature was built through all subset regression in the training set. The prognostic and predictive accuracy of our signature was tested in the validation set and other public databases (GSE5327, GSE2034 and METABRIC).

Results:

Twenty-one candidate mRNAs were identified in early-stage TNBC patients, from which we developed a novel seven-gene signature (recurrence risk score [mRNA signature] = 1.108*TMEM101 - 0.213*KRT5 - 0.315*ACAN - 0.464*LCA5 + 0.446*RPP40 - 0.373*LAGE3 - 0.257*CDKL2). Patients in the training set were classified into high- or low-risk group based on our seven-gene signature and an optimum cut-off score derived from x-tile. The patients in high-risk group were more likely to suffer from recurrence (HR, 2.718; 95% confidence interval [CI], 1.928–3.726, P= 0.001), and a time-dependent receiver operating curve showed that the seven-gene mRNA signature had a better prognostic value than the clinicopathologic risk factors in both training set and validation set. The prognostic and predictive accuracy of the signature was also validated in the METABRIC and two other public GEO databases (GSE5327 and GSE2034). The time-dependent receiver operating curve showed that this signature had an area under the curve (AUC) of 0.742 (95% CI, 0.705-0.773) in METABRIC, 0.716 (95% CI, 0.682-0.739) and 0.723 (95% CI, 0.683-0.756) in GSE5327 and GSE2034 respectively.

Conclusion:

In this study, we developed a novel seven-gene signature which can provide additional prognostic information and may guidance in identifying early-stage TNBC patients eligible for adjuvant therapy or reduction of chemotherapy. To our knowledge, this is the first study investigating the prognostic potential of mRNA signature in early-stage triple-negative breast cancer. Our novel signature may provide an opportunity for de-escalating treatment in early-stage TNBC patients in the future.

Citation Format: Ren Y, Jiang Y, Zuo W, Xu X, Jin X, Ma D, Shao Z. A novel seven-gene signature predicts prognosis in early-stage triple-negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-08-33.

Mechanisms of endogenous repair failure during intervertebral disc degeneration

Intervertebral disc (IVD) degeneration is frequently associated with Low back pain (LBP), which can severely reduce the quality of human life and cause enormous economic loss. However, there is a lack of long-lasting and effective therapies for IVD degeneration at present. Recently, stem cell based tissue engineering techniques have provided novel and promising treatment for the repair of degenerative IVDs. Numerous studies showed that stem/progenitor cells exist naturally in IVDs and could migrate from their niche to the IVD to maintain the quantity of nucleus pulposus (NP) cells. Unfortunately, these endogenous repair processes cannot prevent IVD degeneration as effectively as expected. Therefore, theoretical basis for regeneration of the NP in situ can be obtained from studying the mechanisms of endogenous repair failure during IVD degeneration. Although there have been few researches to study the mechanism of cell death and migration of stem/progenitor cells in IVD so far, studies demonstrated that the major inducing factors (compression and hypoxia) of IVD degeneration could decrease the number of NP cells by regulating apoptosis, autophagy, and necroptosis, and the particular chemokines and their receptors played a vital role in the migration of mesenchymal stem cells (MSCs). These studies provide a clue for revealing the mechanisms of endogenous repair failure during IVD degeneration. This article reviewed the current research situation and progress of the mechanisms through which IVD stem/progenitor cells failed to repair IVD tissues during IVD degeneration. Such studies provide an innovative research direction for endogenous repair and a new potential treatment strategy for IVD degeneration.

Carboxypeptidase B2 and N play different roles in regulation of activated complements C3a and C5a in mice

Essentials Two basic carboxypeptidases are present in plasma, B2 (CPB2) and N (CPN). Cpb2-/- and Cpn-/- mice were challenged in a hemolytic uremic syndrome (HUS) model vs. wild type. Cpb2-/- exacerbates HUS while Cpn-/- exacerbates cobra venom factor challenge vs. wild type mice. CPB2 and CPN have overlapping but non-redundant roles.

SUMMARY

Background There are two basic carboxypeptidases in plasma. Carboxypeptidase B2 (CPB2) is activated from a circulating zymogen, proCPB2, and carboxypeptidase N (CPN) is constitutively active with both inactivating complement C3a and C5a. Aims To test the roles of CPB2 and CPN in complement-driven mouse models of cobra venom factor (CVF) challenge and hemolytic-uremic syndrome (HUS). Methods Cpb2-/- , Cpn-/- and wild-type (WT) mice were compared in an HUS model induced by Shiga toxin and lipopolysaccharide administration and following CVF administration. Results HUS was exacerbated in Cpb2-/- mice more than in Cpn-/- mice, compared with WT mice. Cpb2-/- mice developed the HUS clinical triad of microangiopathic hemolytic anemia, uremia and thrombocytopenia. Treatment with anti-C5 antibody improved survival of both Cpb2-/- and Cpn-/- mice. In contrast, when challenged acutely with CVF, the reverse phenotype was observed. Cpn-/- mice had markedly worse disease than Cpb2-/- mice, whereas the WT mice were resistant. Conclusions CPN and CPB2 play overlapping but non-redundant roles in regulating complement activation in vivo. The constitutively active CPN is key for inactivation of systemic C5a, whereas CPB2 functions as an on-demand supplementary anaphylatoxin inhibitor in inactivating excessive C5a formed locally.