Evolution of plant cell-type-specific cis -regulatory elements

Cis -regulatory elements (CREs) are critical in regulating gene expression, and yet our understanding of CRE evolution remains a challenge. Here, we constructed a comprehensive single-cell atlas of chromatin accessibility in Oryza sativa , integrating data from 104,029 nuclei representing 128 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved chromatin accessibility between O. sativa and 57,552 nuclei from four additional grass species ( Zea mays, Sorghum bicolor, Panicum miliaceum , and Urochloa fusca ). Accessible chromatin regions (ACRs) had different levels of conservation depending on the degree of cell-type specificity. We found a complex relationship between ACRs with conserved noncoding sequences, cell-type specificity, conservation, and tissue-specific switching. Additionally, we found that epidermal ACRs were less conserved compared to other cell types, potentially indicating that more rapid regulatory evolution has occurred in the L1 epidermal layer of these species. Finally, we identified and characterized a conserved subset of ACRs that overlapped the repressive histone modification H3K27me3, implicating them as potentially critical silencer CREs maintained by evolution. Collectively, this comparative genomics approach highlights the dynamics of cell-type-specific CRE evolution in plants.

Investigating the cis-Regulatory Basis of C3 and C4 Photosynthesis in Grasses at Single-Cell Resolution

While considerable knowledge exists about the enzymes pivotal for C4 photosynthesis, much less is known about the cis-regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C4 enzymes for five different grass species. This study spans four C4 species, covering three distinct photosynthetic subtypes: Zea mays and Sorghum bicolor (NADP-ME), Panicum miliaceum (NAD-ME), Urochloa fusca (PEPCK), along with the C3 outgroup Oryza sativa. We studied the cis-regulatory landscape of enzymes essential across all C4 species and those unique to C4 subtypes, measuring cell-type-specific biases for C4 enzymes using chromatin accessibility data. Integrating these data with phylogenetics revealed diverse co-option of gene family members between species, showcasing the various paths of C4 evolution. Besides promoter proximal ACRs, we found that, on average, C4 genes have two to three distal cell-type-specific ACRs, highlighting the complexity and divergent nature of C4 evolution. Examining the evolutionary history of these cell-type-specific ACRs revealed a spectrum of conserved and novel ACRs, even among closely related species, indicating ongoing evolution of cis-regulation at these C4 loci. This study illuminates the dynamic and complex nature of CRE evolution in C4 photosynthesis, particularly highlighting the intricate cis-regulatory evolution of key loci. Our findings offer a valuable resource for future investigations, potentially aiding in the optimization of C3 crop performance under changing climatic conditions.

Peritumoural MRI radiomics signature of brain metastases can predict epidermal growth factor receptor mutation status in lung adenocarcinoma

AIM

To investigate whether magnetic resonance imaging (MRI) radiomics features of brain metastases (BMs) can predict epidermal growth factor receptor (EGFR) mutation status in lung adenocarcinoma.

MATERIALS AND METHODS

Between June 2014 and December 2022, 58 histopathologically confirmed lung adenocarcinoma patients (27 with EGFR wild-type, 31 with EGFR mutation) who underwent gadobenate dimeglumine-enhanced brain MRI were recruited retrospectively. A total of 123 metastatic brain lesions were allocated randomly into the training cohort (n=86) and test cohort (n=37) at a ratio of 7:3. Radiomics models based on multi-sequence MRI images in different regions such as volume of interest (VOI)enhancing tumour, VOIwholetumour, VOIperitumour 1mm, VOIperitumour 3mm, and VOIperitumour 5mm were built. The optimal radiomics model was integrated into the clinical or radiological indicators to construct a fusion model through multivariable logistic regression analysis.

RESULTS

The optimal radiomics model based on the VOIperitumour 1mm, a combination of nine features selected from the fluid-attenuated inversion recovery (FLAIR) sequence, yielded areas under the curves (AUCs) of >0.75 in the training and test cohorts. The prediction of the fusion model with integration of clinical factors (age) and radiomics score (the optimal radiomics model) was not better than that of the optimal radiomics model alone in the test cohort (AUC: 0.808 and 0.785, respectively, p=0.525).

CONCLUSION

The FLAIR radiomics model based on VOIperitumour 1mm as an effective biomarker helps predict EGFR mutation status in lung adenocarcinoma patients with BMs and then assists clinicians in selecting optimal treatment strategies.

Uterine Tumor Resembling Ovarian Sex Cord Tumors: 23 Cases Indicating Molecular Heterogeneity With Variable Biological Behavior

Uterine tumor resembling ovarian sex cord tumor (UTROSCT) is a rare mesenchymal neoplasm that mainly harbors NCOA1-3 rearrangements with partner genes ESR1 or GREB1 . Here, we explored 23 UTROSCTs by targeted RNA sequencing. The association between molecular diversity and clinicopathologic features was investigated. The mean age of our cohort was 43 years (23-65 y). Only 15 patients (65%) were originally diagnosed with UTROSCTs. Mitotic figures ranged from 1 to 7/10 high power fields, of primary tumors and increased from 1 to 9/10 high power fields in recurrent tumors. Five types of gene fusions were identified in these patients, including GREB1::NCOA2 (n=7), GREB1::NCOA1 (n=5), ESR1::NCOA2 (n=3), ESR1::NCOA3 (n=7), and GTF2A1::NCOA2 (n=1). To our knowledge, our group included the largest cohort of tumors with GREB1::NCOA2 fusions. Recurrences were most common in patients with GREB1::NCOA2 fusion (57%), followed by 40% ( GREB1::NCOA1 ), 33% ( ESR1::NCOA2 ), and 14% ( ESR1::NCOA3 ). The recurrent patient who harbored an ESR1::NCOA2 fusion was characterized by extensive rhabdoid features. Both of the recurrent patients who harbored GREB1::NCOA1 and ESR1::NCOA3 had the largest tumor sizes in their own gene alteration groups, and another recurrent GREB1::NCOA1 patient had extrauterine involvement. The GREB1 -rearranged patients were of older age, larger tumor size, and higher stage than non- GREB1 -rearranged patients ( P =0.004, 0.028, and 0.016, respectively). In addition, the GREB1 -rearranged tumors presented more commonly as intramural masses rather than non- GREB1 -rearranged tumors presenting as polypoid/submucosal masses ( P =0.021). Microscopically, nested and whorled patterns were frequently seen in GREB1- rearranged patients ( P =0.006). Of note, estrogen receptor expression was weaker than progesterone receptor in all 12 GREB1- rearranged tumors, whereas the similar staining intensity of estrogen receptor and progesterone receptor was observed in all 11 non- GREB1- rearranged tumors ( P <0.0001). This study demonstrated that UTROSCTs were present at a younger age in the Chinese population. The genetic heterogeneity of UTROSCTs was correlated with variable recurrence rate. Tumors with GREB1::NCOA2 fusions are more likely to recur compared with those with other genetic alterations.

[Anti-inflammatory mechanism of Balanophora involucrata: a network pharmacology and molecular docking-based analysis and verification in lipopolysaccharide-induced RAW264.7 cells]

OBJECTIVE

To investigate the main chemical constituents of Balanophora involucrata and the mechanism of its antiinflammatory effect based on network pharmacology and molecular docking technology.

METHODS

Literature reports, Materia Medica, GeneCards and other databases were searched for anti-inflammatory compounds and their targets. String database and Cytoscape 3.7.2 software were used to obtain the protein-protein interaction (PPI) network and the drug-active ingredienttargets network and for GO and KEGG enrichment analyses. Molecular docking was performed using Auto Dock Tools 1.5.6. In an inflammatory RAW264.7 cell model induced by lipopolysaccharide (LPS), the effect of 25, 50, 100, 200 μg/mL Balanophora involucrata extract was tested on the production of inflammatory cytokines and phosphorylation level of PI3K and Akt using ELISA and Western blotting.

RESULTS

A total of 318 common targets of drugs and diseases were identified, and the core targets were Src, HSP90AA1 and PIK3CA, involving cancer, PI3K/Akt, MAPK and other signaling pathways as shown by KEGG analysis. Molecular docking showed that both the main active constituents of Balanophora involucrata could spontaneously bind to the core targets. In the inflammatory cell model, treatment with Balanophora involucrata extract significantly inhibited the production of IL-1β at the concentrations of 100 and 200 μg/mL, reduced IL-6 and TNF-α expressions at the concentrations of 50, 100, and 200 μg/mL, and lowered phosphorylation levels of PI3K and Akt proteins at the concentrations of 25, 50, 100, and 200 μg/mL (all P < 0.05).

CONCLUSIONS

The anti-inflammatory mechanism of Balanophora involucrata involves multiple targets and multiple pathways, and its effect is mediated possibly by reducing IL-1β, IL-6 and TNF-α production and inhibiting phosphorylation levels of PI3K and Akt proteins to suppress the activation of the PI3K/Akt signaling pathway.

Histone H2A monoubiquitination marks are targeted to specific sites by cohesin subunits in Arabidopsis

Histone H2A monoubiquitination (H2Aub1) functions as a conserved posttranslational modification in eukaryotes to maintain gene expression and guarantee cellular identity. Arabidopsis H2Aub1 is catalyzed by the core components AtRING1s and AtBMI1s of polycomb repressive complex 1 (PRC1). Because PRC1 components lack known DNA binding domains, it is unclear how H2Aub1 is established at specific genomic locations. Here, we show that the Arabidopsis cohesin subunits AtSYN4 and AtSCC3 interact with each other, and AtSCC3 binds to AtBMI1s. H2Aub1 levels are reduced in atsyn4 mutant or AtSCC3 artificial microRNA knockdown plants. ChIP-seq assays indicate that most binding events of AtSYN4 and AtSCC3 are associated with H2Aub1 along the genome where transcription is activated independently of H3K27me3. Finally, we show that AtSYN4 binds directly to the G-box motif and directs H2Aub1 to these sites. Our study thus reveals a mechanism for cohesin-mediated recruitment of AtBMI1s to specific genomic loci to mediate H2Aub1.

Conversion of ER and HER2 status after neoadjuvant therapy in Chinese breast cancer patients

BACKGROUND

Few studies have focused on converting ER-low-positive and HER2-low status following neoadjuvant therapy (NAT). We aimed to assess the evolution in ER and HER2 status after NAT in breast cancer patients.

PATIENTS AND METHODS

Our study included 481 patients with residual invasive breast cancer after NAT. ER and HER2 status were assessed in the primary tumor and residual disease, and associations between ER and HER2 conversion and clinicopathological factors were explored.

RESULTS

In primary tumors, 305 (63.4%) cases were ER-positive (including 36 cases of ER-low-positive), 176 (36.6%) were ER-negative. In residual disease, ER status changed in 76 (15.8%) cases, of which 69 cases switched from positive to negative. ER-low-positive tumors (31/36) were the most likely to change. In primary tumors, 140 (29.1%) tumors were HER2-positive, and 341 (70.9%) were HER2-negative (including 209 cases of HER2-low and 132 cases of HER2-zero). In residual disease, 25 (5.2%) cases had HER2 conversion between positive and negative. Considering HER2-low status, 113 (23.5%) cases had HER2 conversion, mostly driven by cases switching either to or from HER2-low. ER conversion had a positive correlation with pretreatment ER status (r = 0.25; P = .00). There was a positive correlation between HER2 conversion and HER2-targeted therapy (r = 0.18; P = .00).

CONCLUSION

Conversion of ER and HER2 status was observed in some breast cancer patients after NAT. Both ER-low-positive and HER2-low tumors showed high instability from the primary tumor to residual disease. ER and HER2 status should be retested in residual disease for further treatment decisions, especially in ER-low-positive and HER2-low breast cancer.

Intramolecular Ring Expansion of 3-Silaazetidine with Alkynes Enabled by Pd-Catalyzed Si-C Bond Activation

An intramolecular ring expansion of in situ formed 3-silaazetidine with internal alkynes has been developed via Pd-catalyzed Si-C bond activation. The reaction gives rise to 6,5- and 6,6-fused bicyclic 1,3-azasilines, in which the silicon atom locates at the ring junction position.

Feedback regulation of auxin signaling through the transcription of H2A.Z and deposition of H2A.Z to SMALL AUXIN UP RNAs in Arabidopsis

Auxin is a critical phytohormone that is involved in the regulation of most plant growth and developmental responses. In particular, epigenetic mechanisms, like histone modifications and DNA methylation, were reported to affect auxin biosynthesis and transport. However, the involvement of other epigenetic factors, such as histone variant H2A.Z, in the auxin-related developmental regulation remains unclear. We report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col-0 ecotype, h2a.z-kd, has more lateral roots and weak gravitational responses related to auxin-regulated growth performances. Further study revealed that auxin promotes the eviction of H2A.Z from the auxin-responsive genes SMALL AUXIN-UP RNAs (SAURs) to activate their transcriptions. We found that IAA promotes the transcription of H2A.Z genes through HOMEOBOX PROTEIN 22/25 (AtHB22/25) transcription factors which work as downstream targets of ARF7/19 in auxin signaling. Double mutant of hb22 hb25 showed similar lateral root and gravitropism phenotypes to h2a.z-kd. Our results shed light on a reciprocal regulation hub through INOSITOL AUXOTROPHY 80-mediated H2A.Z eviction and ARF7/19-HB22/25-mediated H2A.Z transcription to modulate the activation of SAURs and plant growth in Arabidopsis.

The compliance of digital exercise with smart tools in subjects with cardiac arrythmias

Background

The exercise has well-documented health benefits on cardiovascular disease, and the use of mobile health (mHealth) may promote physical activity to reduce the risk.

Objective

The present study aimed to investigate the compliance of exercise dose and pattern through wearables and mHealth in subjects with cardiac arrhythmia in a real-world setting.

Method

The photoplethysmography (PPG)-algorithms with wearables to detect the ectopic and AF have been developed in the HUAWE HEART STUDY. Using the PPG-based smart devices, the adult subjects with identified arrhythmia received the personalized App-based lifestyle and exercise package was proposed. The V̇O2 peak (mL kg–1 min–1)was estimated from a non-exercise prediction model. The metabolic equivalent (MET)/week and Borg scale were utilized for the assessment of intensity of exercise. All subjects followed up for 3 months for the compliance to the exercise package.

Results

There were 7419 subjects (mean age ± standard deviation, SD, 35±12 years old, 92.1% male) who identified with the arrhythmia between April 1, 2021 and Dec 31, 2021. Among them, there were 165 subjects with identified AF, and 5277 subjects with the ectopic. The obstructive sleep apnea was the most reported risk profile (2643, 35.6%), while 1326 (17.9%) subjects were overweight.

Upon the baseline assessment, the personalized exercise package for cardiovascular disease prevention were proposed for 2864 subjects, exercise package to control the weight for 2510 subjects, and exercise package to reduce the weight for 1886 subjects.

Among 6366 subjects who took the exercise packages, 1867 (29.3%) subjects achieved target exercise, 395 (6.2%) subjects over target exercise, and 4104 (64.5%) under target exercise. The V̇O2 peak (mL kg–1 min–1, SD)in subjects who achieved the target exercise package, under target exercise, and over target exercise were (47.36±5.12, 32.14±22.47, and 65.99±10.38, p&lt;0.001).

For subjects who achieved target exercise, the intensity of exercise was as follows: 0.4% with low-intensity exercise, 95.8% with moderate-intensity exercise, and 3.7% with high-intensity exercise. Nonetheless, there were 37.7% of low-intensity, 60.6% of moderate-intensity exercise, and 1.7% with high-intensity exercise in subjects who didn't achieve exercise target.

77.9% subjects under target exercise had less than 1/week of physical activity, while there was only 12.9% in subjects with target exercise (p&lt;0.001).

Compared to randomly selected 8000 subjects (mean age ± SD, 39±13 years, 80.8% male) without exercise package, the proportion of steps/day over 10000 of 20% was significantly increased in subjects (37±13 years, 91.3% male) receiving the personalized App-based exercise package (31.2%, vs. 12.2%, p&lt;0.001).

Conclusion

The wearables facilitated the improvement of physical activity habit in subjects with cardiac arrhythmia, but subjects-centered self-management would be enhanced to the target exercise.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Natural Science Foundation of China

Characterization of regulatory modules controlling leaf angle in maize

Leaf angle is an important agronomic trait determining maize (Zea mays) planting density and light penetration into the canopy and contributes to the yield gain in modern maize hybrids. However, little is known about the molecular mechanisms underlying leaf angle beyond the ZmLG1 (liguleless1) and ZmLG2 (Liguleless2) genes. In this study, we found that the transcription factor (TF) ZmBEH1 (BZR1/BES1 homolog gene 1) is targeted by ZmLG2 and regulates leaf angle formation by influencing sclerenchyma cell layers on the adaxial side. ZmBEH1 interacted with the TF ZmBZR1 (Brassinazole Resistant 1), whose gene expression was also directly activated by ZmLG2. Both ZmBEH1 and ZmBZR1 are bound to the promoter of ZmSCL28 (SCARECROW-LIKE 28), a third TF that influences leaf angle. Our study demonstrates regulatory modules controlling leaf angle and provides gene editing targets for creating optimal maize architecture suitable for dense planting.

A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells

Understanding how cis-regulatory elements facilitate gene expression is a key question in biology. Recent advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs in animal models. However, the high equipment and reagent costs of commercial systems limit their applications for many laboratories. In this study, we developed a combinatorial index and dual PCR barcode strategy to profile the Arabidopsis thaliana root single-cell epigenome without any specialized equipment. We generated chromatin accessibility profiles for 13 576 root nuclei with an average of 12 784 unique Tn5 integrations per cell. Integration of the single-cell assay for transposase-accessible chromatin sequencing and RNA sequencing data sets enabled the identification of 24 cell clusters with unique transcription, chromatin, and cis-regulatory signatures. Comparison with single-cell data generated using the commercial microfluidic platform from 10X Genomics revealed that this low-cost combinatorial index method is capable of unbiased identification of cell-type-specific chromatin accessibility. We anticipate that, by removing cost, instrumentation, and other technical obstacles, this method will be a valuable tool for routine investigation of single-cell epigenomes and provide new insights into plant growth and development and plant interactions with the environment.

Clinicopathological and molecular characteristics of fumarate-hydratase-deficient uterine smooth muscle tumors: A single-center study of 52 cases

AIMS

The fumarate hydratase (FH) gene germline mutations cause hereditary leiomyomatosis and renal cell carcinoma syndrome (HLRCC), predisposing carriers to uterine and cutaneous leiomyomas and renal cell carcinoma (RCC). In this study, we aim to investigate morphology and the correlation between FH mutation in FH-deficient (FH-d) uterine smooth muscle tumors (uSMTs).

METHODS AND RESULTS

We conducted immunohistochemical staining in 161 cases of uSMTs to detect FH deficiency. We identified 52 (52/161, 32%) cases of FH-d, including 34 leiomyomas with bizarre nuclei, 10 uSMTs of uncertain malignant potential (STUMPs), 4 cellular leiomyomas, 3 usual type leiomyomas, and 1 leiomyosarcoma. Patients with FH-d were aged 24-67 years (median, 40 years). The most common FH-d morphological features included staghorn-shaped blood vessels (87%), bizarre nuclei (81%), alveolar pattern edema (65%), macronucleoli surrounded by a halo (65%), cytoplasmic eosinophilic globules (56%), and chain-like distribution of smooth muscle cells (52%). A targeted next generation sequence was performed in 11 of 52 FH-d tumors. Five (5/11, 45%) cases were found with FH germline mutations, including four leiomyomas with bizarre nuclei and one STUMP. The median age of patients with germline FH mutation was 30 years. The germline mutations including three pathogenic, one likely pathogenic, and one rare uncertain clinical significance variants.

CONCLUSIONS

Our results revealed that FH-d uSMTs usually exhibit the distinct morphology features and high frequency of FH germline mutations. The combination of predictive morphology evaluation, FH immunotype and molecular testing is helpful for the screening of HLRCC in uSMTs.

Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize

C₄ plants partition photosynthesis enzymes between the bundle sheath (BS) and the mesophyll (M) cells for the better delivery of CO₂ to RuBisCO and to reduce photorespiration. To better understand how C₄ photosynthesis is regulated at the transcriptional level, we performed RNA-seq, ATAC-seq, ChIP-seq and Bisulfite-seq (BS-seq) on BS and M cells isolated from maize leaves. By integrating differentially expressed genes with chromatin features, we found that chromatin accessibility coordinates with epigenetic features, especially H3K27me3 modification and CHH methylation, to regulate cell type-preferentially enriched gene expression. Not only the chromatin-accessible regions (ACRs) proximal to the genes (pACRs) but also the distal ACRs (dACRs) are determinants of cell type-preferentially enriched expression. We further identified cell type-preferentially enriched motifs, e.g. AAAG for BS cells and TGACC/T for M cells, and determined their corresponding transcription factors: DOFs and WRKYs. The complex interaction between cis and trans factors in the preferential expression of C₄ genes was also observed. Interestingly, cell type-preferentially enriched gene expression can be fine-tuned by the coordination of multiple chromatin features. Such coordination may be critical in ensuring the cell type-specific function of key C₄ genes. Based on the observed cell type-preferentially enriched expression pattern and coordinated chromatin features, we predicted a set of functionally unknown genes, e.g. Zm00001d042050 and Zm00001d040659, to be potential key C₄ genes. Our findings provide deep insight into the architectures associated with C₄ gene expression and could serve as a valuable resource to further identify the regulatory mechanisms present in C₄ species.

Age and Sex Differences in the Association of Sleep Duration and Overweight/Obesity among Chinese Participants Age above 45 Years: A Cohort Study

OBJECTIVES

We aimed to evaluate the association between sleep duration and obesity and estimate the attributable risk of sleep in the China Health and Retirement Longitudinal Study surveys (CHARLS).

METHODS

A total of 9061 adults aged 45 years above from CHARLS (2011-2015) were included. The main outcome of this study was incident overweight/obesity specific to general and abdominal obesity. Overweight/obesity was defined as BMI ≥ 23.0 (kg/m2) and BMI≥27.5 (kg/m2), respectively. Abdominal obesity was defined as waist circumference ≥90 cm for men and ≥80 cm for women. Self-reported sleep durations were obtained using a structured questionnaire. We assessed hazard ratios (HRs) and 95% confidence intervals (CIs) as well as the population attributable fraction (PAF) for associations between sleep duration and obesity.

RESULTS

986 and 606 participants were identified as overweight and general obesity respectively, 1253 experienced abdominal obesity events. In multivariable-adjusted models, participants with daytime sleep of 0-30 minutes and more than 30 minutes associated with 30% (HR: 0.70, 95% CI: 0.56-0.87) and 35% (HR: 0.65, 95% CI: 0.55-0.78) decreased incident overweight risk respectively compared to those having no daytime sleep, this association also found among females and middle-aged, not males or elderly. Similarly, 0-30 minutes (HR: 0.68, 95% CI: 0.48-0.96) and more than 30 minutes of daytime sleep (HR: 0.73, 95% CI: 0.59-0.91) were associated with a reduced risk of abdominal obesity, similar results also found among females and middle-aged. Compared with 7-9 hours of nocturnal sleep, people who slept 5-7 hours had a reduced risk of overweight (HR: 0.59, 95% CI=0.47-0.74),but not found in subgroups. The hazard role of long nocturnal sleep for abdominal obesity was only found among elderly (HR: 2.33, 95% CI=1.35-4.04) and males (HR: 2.24, 95% CI=1.17-4.29). Compared with moderate total sleepers (7-9hours/day), participants with short total sleep duration exhibited an elevated risk of overweight (HR: 1.13, 95% CI=1.00-1.28), this also found among middle-aged. The PAF for inadequate total sleep duration (<7 hours/day) was 10.77% for overweight individuals.

CONCLUSIONS

Insufficient sleep duration was associated with an elevated risk of overweight only detected among middle-aged not elderly and other subgroups specific by age. The risks for abdominal obesity were increased for males and middle-aged with long nocturnal sleep. Daytime sleep may significantly reduce the risk of overweight and abdominal obesity in female and middle-aged individuals. The link between sleep duration and obesity requires further study.

Clinicopathological significance of WT1 expression in invasive breast carcinoma with >90% mucinous component

AIMS

This study was aimed to investigate the clinicopathological significance of immunohistochemical (IHC) Wilm's tumour 1 (WT1) expression in invasive breast carcinoma with >90% mucinous components.

METHODS

One hundred specimens of invasive breast carcinoma with >90% mucinous component were collected. All H&E-stained slides were reviewed, and the clinicopathological data, including sex, age, tumour size, nuclear grade, histological grade, growth pattern and lymph node (LN) status, were collected. IHC staining of WT1, oestrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and Ki-67 was performed. Fluorescence in situ hybridisation was used to verify the amplification of the HER2 gene. The relationship between WT1 expression and clinicopathological features was analysed statistically.

RESULTS

WT1 expression was detected in 67% (67/100) of invasive breast carcinoma with >90% mucinous components. WT1 expression was significantly associated with low-to-intermediate nuclear grade/histological grade, ER and PR positivity, HER2 negativity, Ki-67 proliferation index <30% and noLN metastasis (all p<0.001). Micropapillary architecture was observed in 80% of cases. WT1 expression was not significantly correlated with different percentage of micropapillary components (p=0.422). None of the histological grade 3 tumours, tumours with HER2 overexpression/amplification and triple-negative specimens showed WT1 expression.

CONCLUSIONS

WT1 expression was significantly related with low-intermediate nuclear/histological grade, ER positivity, HER2 negativity, a lower Ki-67 proliferation index and no LN metastasis in invasive breast carcinoma with >90% mucinous component. The micropapillary growth pattern in this type of tumour did not show a specific relationship with WT1 expression.

Clinicopathologic and Molecular Cytogenetic Analysis of 8 Cases With Uterine Cervical Ewing Sarcoma: Case Series With Literature Review

Ewing sarcoma (ES) is a highly malignant tumor that rarely occurs in the uterine cervix. Herein, we report 8 cases with ES arising primarily in the uterine cervix by focusing on clinicopathologic and molecular cytogenetic features and differential diagnoses. Eight cases of cervical ES were diagnosed between February, 2012, and September, 2018. The age of patients ranged from 13 to 47 years. Abnormal vaginal bleeding and lower abdominal pain were the most common symptoms. Histologically, the tumor was composed of uniform, round, and oval cells with a narrow rim of eosinophilic cytoplasm. Fibrous septa were observed between tumor cell nests. The tumors showed brisk mitotic activity and areas of coagulative necrosis. According to immunohistochemical studies, 50% (4/8) of the cases were positive for cytokeratin (AE1/AE3), and 87.5% (7/8) were positive for synaptophysin, which resulted in a diagnostic confusion with small cell carcinoma, primarily when dealing with small cervical biopsies. Molecular testing demonstrated the rearrangement of the EWSR1 gene in all of the 8 cases, which confirmed the diagnosis of ES. Although rare, ES should be considered as indicators of cervical small round cell neoplasms. Molecular analysis may greatly contribute to the final diagnosis of ES occurring in this unusual location.

Germline and tumor BRCA1/2 mutations in Chinese high grade serous ovarian cancer patients

Background

Studies on the prevalence of BRCA1/2 mutations in ovarian cancer mainly focused on germline single-nucleotide variant (SNV)/insertion/deletion (indel). The status of large genomic rearrangement (LRG) and somatic mutation were poorly investigated.

Methods

Paired blood and tumor DNA from an unselected cohort of 115 Chinese high grade serous ovarian cancer (HGSOC) patients were collected and analyzed for BRCA1/2 SNV and indel by NGS. BRCA1/2 LRG was detected by MLPA. Clinicopathological characteristics including age at diagnosis, FIGO stage, family history and follow-up data were collected for further analysis.

Results

A total of 115 HGSOC patients were screened. Among them, 30 (26.1%) had germline BRCA1/2 mutations, including 19 (16.5%) SNV/indels, 5 (4.3%) LGRs in BRCA1, and 6 (5.2%) SNV/indels in BRCA2. Ten (8.7%) had somatic BRCA1/2 mutations, including 5 (4.3%) in BRCA1 and 5 (4.3%) in BRCA2. The entire tumor BRCA1/2 mutation frequency was 34.8%. No patients were found with two or more deleterious BRCA1/2 mutations. The proportion of germline (66.7%) and tumor (75%) mutation carriers was significantly increased for patients with family history when compared with those without (P<0.05). Patients with germline BRCA1/2 mutation appeared to be younger than non-carriers (mean age, 50.9 vs. 54.4 years, P=0.004) and somatic mutation carriers (mean age, 50.9 vs. 58.7 years, P=0.009). No significant association was found between BRCA1/2 status and clinicopathological characteristics including stage and family history of other cancer than breast and ovarian cancer. In univariate and Cox regression analysis, patients with tumor BRCA1/2 mutations had significant improvements than non-carriers in overall survival in the first two years after surgery (P<0.05). No significant impacts were found between various mutation status in PFS.

Conclusions

There is a high germline and tumor BRCA1/2 mutation incidences in Chinese HGSOC patients. Germline mutations were associated with family history and age at diagnosis, whereas somatic mutations were not. In our study, tumor BRCA1/2 mutations showed a time-depended improved survival outcome. A larger cohort should be examined to clarify the relation between BRCA1/2 mutation and survival outcomes.

Mismatch repair deficiency is associated with specific morphologic features and frequent loss of ARID1A expression in ovarian clear cell carcinoma

BACKGROUND

Ovarian clear cell carcinoma (OCCC) is the second subtype of ovarian epithelial carcinoma reported to be closely related to Lynch syndrome (LS). ARID1A mutation is an important pathogenetic mechanism in OCCC that leads to loss of ARID1A expression in approximately half of OCCCs. However, the correlation of MMR status and ARID1A deficiency is unclear. The current study aimed to identify the clinical and histopathological characteristics of OCCC associated with dMMR and to further explore the association between dMMR and ARID1A deficiency.

METHODS

A cohort of 176 primary OCCC patients was enrolled and review included histological characteristics (nuclear atypia, necrosis, mitosis, stromal hyalinization, and background precursors) and host inflammatory response (tumor-infiltrating lymphocytes, peritumoral lymphocytes, intratumoral stromal inflammation and plasma cell infiltration). Immunohistochemical staining of MLH1, PMS2, MSH2, MSH6 and ARID1A was performed using tissue microarrays.

RESULTS

dMMR was detected in 10/176 tumors (6 %), followed by MSH2/MSH6 (6/176), MLH1/PMS2 (3/176), and MSH6 (1/176). The average age of patients with dMMR was younger than that of patients with intact MMR (46 y vs. 53 y). Tumors with diffuse intratumoral stromal inflammation remained significantly associated after multivariate analysis. ARID1A expression was absent in 8 patients with dMMR (8/10), which is a significantly higher frequency than that observed in patients with intact MMR (80 % vs. 43.2 %).

CONCLUSIONS

Our study indicates that diffuse intratumoral stromal inflammation of OCCCs is associated with dMMR, with loss of MSH2/MSH6 expression being most frequent. dMMR is strongly associated with the loss of ARID1A expression in OCCC.

Progestin-Primed Ovarian Stimulation Versus Mild Stimulation Protocol in Advanced Age Women With Diminished Ovarian Reserve Undergoing Their First In Vitro Fertilization Cycle: A Retrospective Cohort Study

OBJECTIVE

To assess and compare the feasibility of progestin-primed ovarian stimulation (PPOS) protocol with mild stimulation protocol for advanced age women with diminished ovarian reserve (DOR) undergoing their first in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) cycle.

METHODS

Patients aged ≥35 years and DOR undergoing their first IVF/ICSI cycle were enrolled in this retrospective cohort study: 139 and 600 patients underwent the PPOS and mild stimulation protocols, respectively. The primary outcomes were cumulative clinical pregnancy rate (CCPR) and cumulative live birth rate (CLBR). The secondary outcomes were the number of oocytes retrieved and top-quality embryos.

RESULTS

There was nearly no significant difference of baseline characteristics between the two groups. Although a greater amount of total gonadotropin (1906.61 ± 631.04 IU vs. 997.72 ± 705.73 IU, P<0.001) and longer duration of stimulation (9 (10-7) vs. 6 (8-4), P<0.001) were observed in the PPOS group, the number of retrieved oocytes (3 (6-2) vs. 2 (4-1), P<0.001) and top-quality embryos (1 (2-0) vs. 1 (2-0), P=0.038) was greater in the PPOS group than the mild stimulation group. Meanwhile, the incidence of premature luteinizing hormone (LH) surge rate was significantly lower in the PPOS group (0.7% vs.8.3%, P=0.001) than the mild stimulation group. However, there was no significant difference in conservative CCPR, conservative CLBR, optimistic CCPR, and optimistic CLBR between the two groups (all P>0.05). A multivariate logistic regression model showed significant positive effects of the number of retrieved oocytes and number of top-quality embryos on conservative CCPR (OR=1.236, 95%CI: 1.048-1.456, P=0.012, OR=2.313, 95%CI: 1.676-3.194, P<0.001) and conservative CLBR (OR=1.250, 95%CI: 1.036-1.508, P=0.020, OR=2.634, 95%CI: 1.799-3.857, P<0.001) respectively, while significant negative effects of age were identified for conservative CCPR (OR=0.805, 95%CI: 0.739-0.877, P<0.001) and conservative CLBR (OR=0.797, 95%CI: 0.723-0.879, P<0.001).

CONCLUSION

The PPOS protocol is an effective alternative to the mild stimulation protocol for advanced age patients with DOR, as it provides comparable reproductive outcomes and better control of premature LH surge. Further, more oocytes and top-quality embryos were obtained in the PPOS group, which had a positive association with conservative CCPR and CLBR.

The Value of Anti-Müllerian Hormone in the Prediction of Spontaneous Pregnancy: A Systematic Review and Meta-Analysis

OBJECTIVE

To determine whether serum anti-Müllerian hormone (AMH) level is a predictor of clinical pregnancy in women trying to achieve a natural conception.

METHODS

The PubMed, Embase, and Cochrane Library databases were searched for articles published until August 2020. Studies that met the inclusion and exclusion criteria were included in the meta-analysis; no language limitations were imposed. Quality was appraised using the Quality Assessment of Diagnostic Accuracy Studies-2 checklist. Heterogeneity due to the threshold effect was identified; thus, we plotted a summary receiver operating characteristic curve and calculated its area under the summary receiver operating characteristic curve (AUC) and Cochran's Q index to assess whether AMH level is a predictor of spontaneous pregnancy. Publication bias and sensitivity were also assessed.

RESULTS

Eleven studies (4,388 women) were ultimately included in this meta-analysis. The AUC and Cochran's Q indices were 0.5932 and 0.5702, respectively. For women younger than 35 years, the AUC was 0.6355 and the Q index was 0.6025. For those older than 35 years, the AUC was 0.5536 and the Q index was 0.5403. Subgroup analyses by study type and population characteristics showed results similar to the overall outcome. No publication bias was identified, and the sensitivity analysis confirmed the robustness of the final result.

CONCLUSIONS

Serum AMH levels have poor predictive value for natural pregnancy. The predictive value of AMH was poor in the younger and older subgroups. Our findings suggest that low serum AMH levels are not associated with reduced fertility.

INTRODUCTION

This study investigated the predictive value of anti-Müllerian hormone (AMH) level for natural pregnancy. Other than age, few factors can predict the chances of natural fertility. AMH is an established biomarker of ovarian reserve that is widely used to predict oocyte yield in cases of in vitro fertilization (IVF) and menopause. In clinical practice, the applications of AMH are increasing. However, its predictive value for natural conception remains controversial. In this study, since AMH is closely related with ovarian reserve, we evaluated whether it has predictive value for natural pregnancy. Our findings will fine-tune the clinical application of AMH in pre-pregnancy counseling. The topic should be of wide interest to investigators in the reproductive endocrinology and gynecology fields.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO 2020 CRD42020216265, Available from: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020216265.

Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors

The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex network. In this study, we use large-scale ChIP-seq to reconstruct it in the maize leaf, and train machine-learning models to predict TF binding and co-localization. The resulting network covers 77% of the expressed genes, and shows a scale-free topology and functional modularity like a real-world network. TF binding sequence preferences are conserved within family, while co-binding could be key for their binding specificity. Cross-species comparison shows that core network nodes at the top of the transmission of information being more conserved than those at the bottom. This study reveals the complex and redundant nature of the plant transcription regulatory network, and sheds light on its architecture, organizing principle and evolutionary trajectory.

Plant and animal chromatin three-dimensional organization: similar structures but different functions

Chromatin is the main carrier of genetic information and is non-randomly distributed within the nucleus. Next-generation sequence-based chromatin conformation capture technologies have enabled us to directly examine its three-dimensional organization at an unprecedented scale and resolution. In the best-studied mammalian models, chromatin folding can be broken down into three hierarchical levels, compartment, domains, and loops, which play important roles in transcriptional regulation. Although similar structures have now been identified in plants, they might not possess exactly the same functions as the mammalian ones. Here, we review recent Hi-C studies in plants, compare plant chromatin structures with their mammalian counterparts, and discuss the differences between plants with different genome sizes.

Intense basolateral membrane staining indicates HER2 positivity in invasive micropapillary breast carcinoma

Invasive micropapillary carcinoma is characterized by the inside-out growth of tumor clusters and displays incomplete membrane immunostaining of HER2. According to the 2018 American Society of Clinical Oncology and the College of American Pathologists (ASCO/CAP) HER2-testing recommendation, moderate to intense but incomplete staining could be scored as immunohistochemical 2+. Furthermore, the criteria of immunohistochemical 3+ for this staining pattern are not mentioned. One hundred and forty-seven cases of invasive micropapillary carcinoma with moderate-to-intense HER2 immunostaining were enrolled. Invasive micropapillary carcinoma components of all cases were scored as immunohistochemical 2+ based on the 2018 ASCO/CAP recommendation. The invasive micropapillary carcinoma component varied from 10% to 100% (mean, 80%). Invasive micropapillary carcinoma components of all 147 tumors exhibited reversed polarity and incomplete basolateral HER2 membrane staining. One hundred and seventeen of the tumors (80%, 117/147) had moderate staining, and 38 (32%, 38/117) showed HER2 gene amplification by fluorescence in-situ hybridization. HER2 gene was amplified in all the remaining 30 tumors (20%, 30/147) that exhibited intense basolateral membrane staining. Besides, average HER2 signals per cell and ratio of HER2/CEP17 were significantly higher in the intense-staining tumors compared with the moderate-staining tumors (p < 0.0001). Follow-up data were available for 140 patients. None of the patients were died. The follow-up time ranged from 1 month to 99 months (median, 57 months). Thirteen (9%, 13/140) patients exhibited disease progression (recurrence or metastasis). HER2 gene amplification was correlated inversely with estrogen receptor (p = 0.000) and progesterone receptor (p = 0.000) expression, and positively with histological grade (p = 0.003) and disease progression (p = 0.000). Invasive micropapillary carcinoma with intense clear linear basolateral membrane immunostaining indicates HER2 positivity, even if the staining is incomplete. They should be classified as immunohistochemical 3+ rather than immunohistochemical 2+, which would avoid further fluorescence in-situ hybridization-testing procedure and greatly save the related time, labor, and financial costs. Ultimately, ensure all patients with HER2 gene amplification obtain effective targeted therapy in time.

Non-homology-based prediction of gene functions in maize (Zea mays ssp. mays)

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions. As a result, homology is widely used for gene function prediction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random-forest-based prediction consistently provided the most accurate gene function prediction. Non-homology-based functional annotation provides complementary strengths to homology-based annotation, with higher average performance in Biological Process GO terms, the domain where homology-based functional annotation performs the worst, and weaker performance in Molecular Function GO terms, the domain where the accuracy of homology-based functional annotation is highest. GO prediction models trained with homology-based annotations were able to successfully predict annotations from a manually curated "gold standard" GO annotation set. Non-homology-based functional annotation based on machine learning may ultimately prove useful both as a method to assign predicted functions to orphan genes which lack functionally characterized homologs, and to identify and correct functional annotation errors which were propagated through homology-based functional annotations.

Factors Predicting Severe Myelosuppression and Its Influence on Fertility in Patients with Low-Risk Gestational Trophoblastic Neoplasia Receiving Single-Agent Methotrexate Chemotherapy

Purpose

To investigate the potential factors to predict severe myelosuppression among low-risk gestational trophoblastic neoplasia (GTN) patients with single-agent methotrexate (MTX) chemotherapy. To analyze reproductive outcomes of patients with or without severe myelosuppression after achieving complete remission (CR).

Patients and Methods

The retrospective study included 319 low-risk GTN patients registered from January 2008 to December 2018 in our hospital. Patients were divided into two groups according to myelosuppression grading. Their clinical data and reproductive outcomes were compared and analyzed.

Results

A higher proportion of patients in group A received second-line chemotherapy than group B (P<0.001). The number of total chemotherapy courses was more in group A than group B (P=0.001), while the number of MTX chemotherapy courses was more in group B than group A (P=0.001). When the joint predictor of pretreatment albumin (ALB) was not more than 44.5 g/L, pretreatment serum creatinine (Scr) was not less than 75.6 μmol/L, and the number of MTX chemotherapy courses was not less than four, there was a moderate predictive value. There was no significant difference of reproductive outcomes between the two groups after achieving CR.

Conclusion

Although some patients developed severe myelosuppression, MTX was still the effective first-line treatment for low-risk GTN patients. Patient’s pretreatment ALB was not more than 44.5 g/L, pretreatment Scr was not less than 75.6 μmol/L, and the number of MTX chemotherapy courses not less than four could be used as combined predictors to recognize the risk of severe myelosuppression. Severe myelosuppression had no significant adverse influence on fertility after achieving CR.

Cost-effectiveness analysis of GnRH-agonist long-protocol and GnRH-antagonist protocol for in vitro fertilization

The gonadotropin releasing hormone agonist (GnRH-a) long-protocols and the GnRH-antagonist protocols are two commonly used protocols for in vitro fertilization (IVF), but their cost-effectiveness has not been studied, especially in China. A retrospective study involving 1638 individuals in GnRH-a long-protocol and 621 in GnRH-antagonist protocol were conducted and a decision tree model analysis was used to analyze the cost-effectiveness. Both direct and indirect costs were calculated. As a result, during the fresh embryo transplantation cycles, there was no significant difference in the rate of ongoing pregnancy between the two protocols, the average cost of per ongoing pregnancy in the GnRH-antagonist protocol was $ 16970.85, and that in the GnRH-agonist long-protocol was $19902.24. The probability of cumulative ongoing pregnancy per start cycle was estimated at 60.65% for the GnRH-antagonist protocol and 71.6% for the GnRH-agonist long-protocol (P < 0.01). Considering the cumulative ongoing pregnancy rate, the mean costs per ongoing pregnancy were estimated at $8176.76 and at $7595.28 with GnRH-antagonist protocol and GnRH-agonist long protocol, respectively. In conclusion, in fresh embryo transplantation cycle, the GnRH-antagonist protocol has economic advantage. However, the GnRH-agonist long protocol is more cost effective considering the cumulative ongoing pregnancy rate in the fresh embryo and frozen embryo transplantation cycles.

Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains

Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation, which is best studied in the mammalian models. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We found that their global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic associated with differential gene expression. Plant domains are largely stable across tissues, while new domain border formations are often associated with transcriptional activation in the region. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian TADs. Although we only observed chromatin loops between gene islands in the large genomes, the maize loop gene pairs' syntenic orthologs have shorter physical distances in small genome monocots, suggesting that loops instead of domains might have conserved biological function. Our study showed that plants' chromatin features might not have conserved biological functions as the mammalian ones.

The ovarian estrogen synthesis function was impaired in Y123F mouse and partly restored by exogenous FSH supplement

BACKGROUND

LepR tyrosine site mutation mice (Y123F) exhibit decreased serum E2 levels, immature reproductive organs, infertility as well as metabolic abnormalities. Although the actions of leptin and lepR in the control of reproductive function are thought to be exerted mainly via the hypothalamic-pituitary-gonadal axis, relatively less is known regarding their local effects on the peripheral ovary, especially on steroid hormone synthesis. Meanwhile, whether the decreased fertility of Y123F mouse could be restored by gonadotropin has not been clear yet.

METHODS

The serum levels of E2, P4, FSH, LH, T and leptin of Y123F and WT mice at the age of 12 weeks were measured by enzyme-linked immunosorbent assay. Immunohistochemistry was used to compare the distribution of hormone synthases (STAR, CYP11A1, CYP19A1, HSD17B7) and FSHR in adult mouse ovaries of two genotypes. Western blot and real-time PCR were used to detect the expression levels of four ovarian hormone synthases and JAK2-STAT3 / STAT5 signaling pathway in 4 and 12 weeks old mice, as well as the effects of exogenous hFSH stimulation on hormone synthases and FSHR.

RESULTS

Compared with WT mice, the serum levels of FSH, LH and E2 in 12-week-old Y123F mice were significantly decreased; T and leptin levels were significantly increased; but there was no significant difference of serum P4 levels. STAR, CYP11A1, HSD17B7 expression levels and the phosphorylation levels of JAK2 and STAT3 were significantly decreased in adult Y123F mice, while the expression of CYP19A1 and phospho-STAT5 were significantly increased. No significant differences were found between 4-week-old Y123F and WT mice. After exogenous hFSH stimulation, E2 levels and expression of CYP19A1 and HSD17B7 were significantly higher than that in the non-stimulated state, but significant differences still existed between Y123F and WT genotype mice under the same condition.

CONCLUSIONS

Abnormal sex hormone levels of Y123F mice were due to not only decreased gonadotropin levels in the central nervous system, but also ovarian hormone synthase abnormalities in the peripheral gonads. Both FSH signaling pathway and JAK2-STAT3/STAT5 signaling pathway were involved in regulation of ovarian hormone synthases expression. Exogenous FSH just partly improved the blood E2 levels and ovarian hormone synthase expression.

Low frequency of BRAF and KRAS mutations in Chinese patients with low-grade serous carcinoma of the ovary

BACKGROUND

Mounting evidence has shown that KRAS and BRAF are somatic mutations associated with low grade serous carcinoma (LGSC) of the ovary. However, the frequency of KRAS or BRAF mutation was variable in literatures, with a frequency of 16-54% for KRAS mutation and 2-33% for BRAF mutation. Meanwhile, the prognostic significance of KRAS or BRAF mutation remains controversial.

METHODS

Codons 12 and 13 of exon 2 of KRAS gene and exon 15 of BRAF gene were analyzed using direct Sanger sequencing in 32 cases of LGSC of the ovary. The associations between KRAS or BRAF mutation and clinicopathological characteristics, overall survival (OS) and disease-free survival (DFS) were statistically analyzed.

RESULTS

KRAS mutation was observed in nine cases (9/32, 28%) and BRAF mutation in two cases (2/32, 6%). KRAS and BRAF mutations were mutually exclusive. Neither KRAS nor BRAF mutation was statistically associated with OS or DFS in our cohort, although there was a favorable prognostic trend in patients with KRAS G12D mutation than those with KRAS G12 V mutation or wild-type KRAS for OS.

CONCLUSIONS

The present study indicated a low frequency of BRAF or KRAS mutation in Chinese patients with LGSC of the ovary, and neither KRAS nor BRAF mutation is a prognostic factor.

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments

The spatial organization of the genome plays an important role in the regulation of gene expression. However, the core structural features of animal genomes, such as topologically associated domains (TADs) and chromatin loops, are not prominent in the extremely compact Arabidopsis genome. In this study, we examine the chromatin architecture, as well as their DNA methylation, histone modifications, accessible chromatin, and gene expression, of maize, tomato, sorghum, foxtail millet, and rice with genome sizes ranging from 0.4 to 2.4 Gb. We found that these plant genomes can be divided into mammalian-like A/B compartments. At higher resolution, the chromosomes of these plants can be further partitioned to local A/B compartments that reflect their euchromatin, heterochromatin, and polycomb status. Chromatins in all these plants are organized into domains that are not conserved across species. They show similarity to the Drosophila compartment domains, and are clustered into active, polycomb, repressive, and intermediate types based on their transcriptional activities and epigenetic signatures, with domain border overlaps with the local A/B compartment junctions. In the large maize and tomato genomes, we observed extensive chromatin loops. However, unlike the mammalian chromatin loops that are enriched at the TAD border, plant chromatin loops are often formed between gene islands outside the repressive domains and are closely associated with active compartments. Our study indicates that plants have complex and unique 3D chromatin architectures, which require further study to elucidate their biological functions.

LEPR gene polymorphism and plasma soluble leptin receptor levels are associated with polycystic ovary syndrome in Han Chinese women

Aim: To investigate the association of LEPR polymorphisms and plasma leptin and soluble leptin receptor (sOB-R) levels with polycystic ovary syndrome (PCOS) in Chinese women. Patients & methods: LEPR Lys109Arg (rs1137100) and Gln223Arg (rs1137101) polymorphisms of PCOS patients and the controls were genotyped. Plasma leptin and sOB-R levels of two groups were measured. Results: The genotypic distributions of Lys109Arg (rs1137100) differed between the PCOS and control groups. Plasma sOB-R levels increased significantly in PCOS patients and were associated with PCOS independent of BMI. Furthermore, luteinizing hormone, triglyceride and fasting blood glucose correlated significantly to PCOS patients’ sOB-R levels. Conclusion: LEPR Lys109Arg (rs1137100) was associated with PCOS susceptibility and genotype AA was deduced to be a protective factor for PCOS; sOB-R levels might be recognized as a new indicator for the severity of PCOS.

Characterization of ovarian clear cell carcinoma using target drug-based molecular biomarkers: implications for personalized cancer therapy

BACKGROUND

It has long been appreciated that different subtypes (serous, clear cell, endometrioid and mucinous) of epithelial ovarian carcinoma (EOC) have distinct pathogenetic pathways. However, clinical management, especially chemotherapeutic regimens, for EOC patients is not subtype specific. Ovarian clear cell carcinoma (CCC) is a rare histological subtype of EOC, which exhibits high rates of recurrence and low chemosensitivity. We assessed potential therapeutic targets for ovarian CCC patients through analyzing the variation of drug-based molecular biomarkers expression between ovarian CCC and high-grade serous carcinoma (HGSC).

METHODS

Seven candidate drug-based molecular biomarkers, human epidermal growth factor receptor (EGFR), human epidermal growth factor receptor-2 (HER2), phosphatase and tensin homolog deleted on chromosome ten (PTEN), aurora kinase A (AURKA), breast cancer susceptibility gene 1 (BRCA1), breast cancer susceptibility gene 2 (BRCA2) and programmed death-ligand 1 (PD-L1) were measured in 96 ovarian CCC and 113 HGSC by immunohistochemistry in paraffin embedded tissues. The relationship between these biomarkers and clinicopathological factors were explored.

RESULTS

The expression level of four of the seven drug-based molecular biomarkers was markedly different between HGSC and CCC. High expression levels of HER2 and PD-L1 were more commonly observed in CCC patients (12.6% vs 2.7%, 21.1% vs 11.6%, P = 0.006, 0.064, respectively), while loss of BRCA1 and BRCA2 expression were more frequently occurred in HGSC patients (72.6% vs 54.3%, 89.4% vs 79.8%, P = 0.007, 0.054, respectively). Survival analysis showed that five of seven biomarkers had prognostic values but varied between subtypes. Furthermore, EGFR expressed frequently in CCC patients with endometriosis than in HGSC patients (44.4% vs 8.3%, P = 0.049). AURKA and PD-L1 correlated with the resistance to platinum-based chemotherapy in CCC patients (P = 0.043, 0.028, respectively) while no similar results were observed in HGSC patients.

CONCLUSION

Ovarian CCC showed a markedly different expression map of drug-based molecular biomarkers from HGSC, which suggested a new personalized target therapy in this rare subtype.

Mutations in WT1 in boys with sporadic isolated steroid-resistant nephrotic syndrome

Mutations in the Wilms' tumor gene, WT1, can lead to syndromic steroid-resistant nephrotic syndrome and isolated steroid-resistant nephrotic syndrome. WT1 mutations have been identified in the majority of children with Denys-Drash or Frasier syndrome. WT1 mutations have not previously been identified in boys with sporadic isolated steroid-resistant nephrotic syndrome, but, recently, four boys with isolated nephrotic syndrome were identified to have WT1 mutations. However, whether boys with sporadic isolated steroid-resistant nephrotic syndrome should be routinely subjected to mutation analysis of WT1 has not been established. We examined 35 boys with sporadic isolated steroid-resistant nephrotic syndrome for mutations in WT1. Mutation analysis of all 10 exons of WT1 was performed by polymerase chain reaction and direct sequencing. Karyotype analysis or Y chromosome identification was performed for all patients. A Y chromosome or a 46, XY karyotype was demonstrated for all 35 patients. No causative WT1 mutation was identified in any of the patients. The WT1 mutation, IVS4+14T>C, which is not predicted to affect splicing, was identified in one patient who achieved complete remission after 8 weeks of oral prednisone treatment, indicating that IVS4+14T>C is not a causative mutation. Five WT1 polymorphisms were also identified in some patients and controls. Our results suggest that mutation analysis of WT1 should not be routinely performed for genetically defined boys with sporadic isolated steroid-resistant nephrotic syndrome.

[Small cell carcinoma of ovary, hypercalcemic type: analysis of clinicopathologic characteristics and the diagnostic utility of loss expression of SMARCA4 protein]

OBJECTIVE

To study the clinicopathologic features of small cell carcinoma of ovary, hypercalcemic type (SCCOHT) and to evaluate the diagnostic significance of loss of SMARCA4 expression.

METHODS

The clinicopathologic characteristics of 5 cases of SCCOHT were reviewed. The expression of SMARCA4 protein was detected by immunohistochemistry in the cases of SCCOHT and 240 cases of other primary malignant tumors of ovary and peritoneum.

RESULTS

The mean and medium age of these patients was 30 years and 28 years, respectively. The presenting symptoms included abdominal pain, distention and a pelvic mass. Hypercalcemia was found in 3 patients. The maximum diameter of tumors ranged from 13.5 to 22.0 cm. Extraovarian spread was demonstrated in all of the patients on presentation. Histologically, the tumors were composed of closely packed small round cells with scanty cytoplasm, hyperchromatic nuclei and irregular chromatin clumps. The tumor cells grew in sheets, nests, cords or trabecular pattern. Follicle-like spaces were observed in 4 cases. Three of the tumors contained large cells with abundant eosinophilic cytoplasm. Spindle cell morphology was found in 1 case. There were 2 cases with myxoid or hyaline stroma. Four out of five of SCCOHT cases showed loss of SMARCA4 protein while only 6.3% (15/240) of the other primary malignant tumors of ovary and peritoneum , including undifferentiated carcinoma (1/5), high-grade serous carcinoma (4.6%, 5/109), endometrioid carcinoma (7.7%, 2/26), clear cell carcinoma (1/9), mucinous carcinoma (1/5), mixed carcinoma (4.9%, 3/61), carcinosarcoma (1/9) and high-grade serous carcinoma of peritoneum (1/9), were negative.

CONCLUSIONS

SCCOHT is a rare malignant tumor and often misdiagnosed as other types of ovarian small cell tumor. Loss expression of SMARCA4 protein is characteristic and facilitates the diagnosis and differential diagnosis of SCCOHT.

The Influence of LepR Tyrosine Site Mutations on Mouse Ovary Development and Related Gene Expression Changes

Leptin exerts many biological functions, such as in metabolism and reproduction, through binding to and activating the leptin receptor, LepRb, which is expressed in many regions of the brain. To better understand the roles of LepR downstream signaling pathways, Y123F mice, which expressed mutant leptin receptors with phenylalanine (F) substituted for three tyrosines (Y) (Tyr985, Tyr1077 and Tyr1138), were generated. The body weight and abdominal fat deposits of Y123F homozygous mice (HOM) were higher than those of wild-type mice (WT). HOM ovaries were atrophic and the follicles developed abnormally; however, the HOM ovaries did not exhibit polycystic phenotypes. Moreover, Y123F HOM adults had no estrous cycle and the blood estrogen concentration remained stable at a low level below detection limit of 5 pg/ml. LepR expression in HOM ovaries was higher than in WT ovaries. Using cDNA Microarrays, the mRNA expressions of 41 genes were increased, and 100 were decreased in HOM vs. WT ovaries, and many signaling pathways were evaluated to be involved significantly. The expressions of 19 genes were validated by real-time quantitative PCR, most of which were consistent with the microarray results. Thus, Y123F HOM mice were suggested as a new animal model of PCOS for research that mainly emphasizes metabolic disorders and anovulation, but not the polycystic phenotype. Meanwhile, using the model, we found that JAK-STAT and hormone biosynthesis pathways were involved in the follicular development and ovulation disorders caused by LepR deficiency in ovaries, although we could not exclude indirect actions from the brain.