Metagenomic sequencing reveals swine lung microbial communities and metagenome-assembled genomes associated with lung lesions-a pilot study

Low microbial biomass in the lungs, high host-DNA contamination and sampling difficulty limit the study on lung microbiome. Therefore, little is still known about lung microbial communities and their functions. Here, we perform a preliminary exploratory study to investigate the composition of swine lung microbial community using shotgun metagenomic sequencing and compare the microbial communities between healthy and severe-lesion lungs. We collected ten lavage-fluid samples from swine lungs (five from healthy lungs and five from severe-lesion lungs), and obtained their metagenomes by shotgun metagenomic sequencing. After filtering host genomic DNA contamination (93.5% ± 1.2%) in the lung metagenomic data, we annotated swine lung microbial communities ranging from four domains to 645 species. Compared with previous taxonomic annotation of the same samples by the 16S rRNA gene amplicon sequencing, it annotated the same number of family taxa but more genera and species. We next performed an association analysis between lung microbiome and host lung-lesion phenotype. We found three species (Mycoplasma hyopneumoniae, Ureaplasma diversum, and Mycoplasma hyorhinis) were associated with lung lesions, suggesting they might be the key species causing swine lung lesions. Furthermore, we successfully reconstructed the metagenome-assembled genomes (MAGs) of these three species using metagenomic binning. This pilot study showed us the feasibility and relevant limitations of shotgun metagenomic sequencing for the characterization of swine lung microbiome using lung lavage-fluid samples. The findings provided an enhanced understanding of the swine lung microbiome and its role in maintaining lung health and/or causing lung lesions.

Low-Dose Fractionated Radiotherapy Combined with Neoadjuvant Chemotherapy for T3-4 Nasopharyngeal Carcinoma Patients: The Preliminary Results of a Phase II Randomized Controlled Trial

PURPOSE/OBJECTIVE(S)

Over 70% of NPC patients were local advanced NPC (LANPC). The 5-year local recurrence-free survival rate is only 70% in T3-4 patients. Neoadjuvant chemotherapy (NACT) followed with concurrent chemoradiotherapy (CCRT) was recommended for LANPC patients. Low-dose fractionated radiotherapy (LDFRT), which is <100cGy, induces enhanced cell killing by the hyper-radiation sensitivity phenomenon and potentiates effects of chemotherapy. The synergy of LDFRT and NACT has not been used in the clinical practice and few studies focused on it. A single arm study found the ORR of primary site was improved to 90% for head and neck squamous carcinoma patients treated with LDFRT and NACT. Our previous study found the ORR of lymph nodes was higher in LDFRT group for high-risk LANPC patients. However, another study showed there was no significant difference between LDFRT and control group for LANPC patients. So, we aimed to investigate the potential efficacy of this novel neoadjuvant therapy for T3-4 NPC patients.

MATERIALS/METHODS

A total of 60 pathological confirmed T3-4 (UICC/AJCC8th) NPC patients were prospectively enrolled in our study. They were randomly assigned to two groups. For the LDFRT group, the patients received 3 cycles of NACT (docetaxel 75mg/m2 D1, cisplatin 80mg/m2 D1) with LDFRT, and followed with CCRT. LDFRT was delivered as 50cGy per fraction twice a day to primary site on D1,2 for each cycle of NACT. The patients in the control group only received NACT and followed with CCRT. All the patients underwent IGRT. RECIST criteria and CTCAE 5.0 was used to evaluate the ORR and toxicity at post-NACT and the completion of CCRT.

RESULTS

From February 2022 to December 2022, 60 T3-4 NPC patients were included, and 30 patients for each group. For the primary site, the median volume reduction rate and the ORR after NACT was significantly improved in LDFRT group (69.27% vs 40.10%, p<0.001;93.33% vs 73.33%, p = 0.038). For the median volume reduction rate of primary site and lymph node, it was also obviously improved in LDFRT group (86.59% vs 55.43%, p<0.001). Though there was a tendency of ORR improvement in LDFRT group, but no significant difference (96.67% vs 83.33%, p = 0.195). After the completion of CCRT, the median volume reduction rate of primary site had an increased tendency in LDFRT group (96.16% vs 88.3%, p = 0.065), but the ORR had no statistical significance (LDFRT group: CR 45.8%, PR 54.2%; control group: CR 37.5%, PR 62.5%). For the toxicity, the incidence of grade 3-4 adverse events had no difference between two groups (p = 0.786). No grade 5 adverse events occurred.

CONCLUSION

LDFRT combined with NACT could obviously improve the median volume reduction rate and ORR of primary tumor for T3-4 NPC patients, and the toxicity was similar and tolerable. This novel treatment could be a promising strategy to improve treatment response and needed to be confirmed further.

Long-Term Survival Outcome for Metastatic Nasopharyngeal Carcinoma Patients Receiving Radiation to Primary and Metastatic Sites with Palliative Chemotherapy

PURPOSE/OBJECTIVE(S)

A total of 6% - 8% of NPC patients were initial diagnosed as distant metastatic disease. The median overall survival (OS) is only 10-15 months with palliative chemotherapy for these patients. A phase III study showed that palliative chemotherapy combined with radical radiotherapy to primary site could be a newly effective treatment method for metastatic NPC. Another phase 2, RCT found that the patients who had the solid tumors with 1-5 metastases received standard palliative care plus stereotactic body radiation therapy (SABR), and the 5-year OS were improved to 42.3%. Nevertheless, there was few studies focus on the radiation to both primary site and metastatic lesions. Therefore, we aimed to investigate the potential clinical benefits for initial diagnosed metastatic NPC patients with radiation to both primary site and distant metastatic lesions plus palliative chemotherapy.

MATERIALS/METHODS

Metastatic NPC patients treated with radiation to both primary site and distant metastatic lesions plus palliative chemotherapy were retrospectively collected in our hospital from May 2008 to May 2022. For treatment group, all patients underwent IGRT according to ICRU reports 50 and 62. The prescribed dose for primary site: GTVT: ≥66Gy, GTVn: ≥66Gy, CTV1: 60-66Gy, CTV2 54-60Gy, CTVln 50-54Gy. And the prescribed dose for distant metastatic lesions was more than 30Gy. For the control group, the patients treated with palliative chemotherapy were selected by propensity score matching from our hospital. The regimen for palliative chemotherapy was cisplatin-based chemotherapy every three weeks (100mg/m2 D1) for both groups. Kaplan-Meier method was used to analyze the OS. Cox regression model was used for multivariate analysis.

RESULTS

A total of 54 metastatic NPC patients with radiation to both primary site and distant metastatic lesions were retrospectively included in the treatment group, and another 54 patients were selected as the control group. The median follow-up time was 52 months. In the treatment group, the median age was 52 years (37-82), male (68%), female (32%), the main metastatic sites were bone (36 cases, 66%), lung (18 cases, 33%) and liver (10 cases, 18%). There were 23 oligometastasis cases and 31 cases. 3-year and 5-year OS in the treatment group were both dramatically improved than control group (63.2% vs 50.6%, p<0.05; 49.6% vs 38.9%, p<0.05). Multivariate analysis showed that T stage, liver metastatic lesion and oligometastases were the independent prognostic factors for them.

CONCLUSION

Palliative chemotherapy combined with radiation to primary sites and distant metastatic lesions might improve the OS for initial diagnosed distant metastatic NPC patients. More prospective clinical trials were needed to confirm it further.

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences

High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retrieve 207 resequencing datasets, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures, amounting to 1096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genomic selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.

Characterization of the pig lower respiratory tract antibiotic resistome

Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.

Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array

Introduction: Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic mechanism of glycolytic metabolism in skeletal muscle of pigs remains poorly understood. With a history of more than 400 years and some unique characteristics, the Erhualian pig is called the “giant panda” (very precious) in the world’s pig species by Chinese animal husbandry.

Methods: Here, we performed a genome-wide association study (GWAS) using 1.4M single nucleotide polymorphisms (SNPs) chips for longissimus RG, G6P, LAT, and GP levels in 301 purebred Erhualian pigs.

Results: We found that the average GP value of Erhualian was unusually low (68.09 μmol/g), but the variation was large (10.4–112.7 μmol/g). The SNP-based heritability estimates for the four traits ranged from 0.16–0.32. In total, our GWAS revealed 31 quantitative trait loci (QTLs), including eight for RG, nine for G6P, nine for LAT, five for GP. Of these loci, eight were genome-wide significant (p &lt; 3.8 × 10−7), and six loci were common to two or three traits. Multiple promising candidate genes such as FTO, MINPP1, RIPOR2, SCL8A3, LIFR and SRGAP1 were identified. The genotype combinations of the five GP-associated SNPs also showed significant effect on other meat quality traits.

Discussion: These results not only provide insights into the genetic architecture of GP related traits in Erhualian, but also are useful for pig breeding programs involving this breed.

[The value of CMR high-risk attributes in predicting ventricular remodeling in ST-segment-elevation myocardial infarction patients with mildly reduced or preserved ejection fraction]

Objective: To evaluate the predictive value of a multiparametric cardiac magnetic resonance (CMR) approach for ventricular remodeling in ST-segment-elevation myocardial infarction (STEMI) patients with mildly reduced or preserved left ventricular ejection fraction (LVEF). Methods: This study is a prospective cohort study. STEMI patients with acute LVEF>40% after primary percutaneous coronary intervention (PCI) in Beijing Anzhen Hospital from October 2019 to September 2021 were enrolled. All patients received acute (3-7 days) and follow-up (3 months) CMR post-PCI. According to absence or presence of ventricular remodeling, patients were divided into ventricular remodeling group and non-ventricular remodeling group. Basic clinical characteristics and CMR indicators were analyzed and compared between the two groups. Logistic regression and receiver operating characteristic (ROC) curves were used to explore the predictive performance of CMR high-risk attributes for ventricular remodeling in STEMI patients with mildly reduced or preserved LVEF. The predictive value of combining multiple high-risk characteristics of CMR for ventricular remodeling was analyzed and compared with the traditional clinical risk factor model. Results: A total of 123 STEMI patients were enrolled (aged (57.1±11.1) years, 102 (82.9%) males). There were 97 cases (78.9%) patients in the non-ventricular remodeling group and 26 cases (21.1%) in the ventricular remodeling group. After adjustment for clinical risk factors, stroke volume<51.6 ml, global circumferential strain>-13.7%, infarct size>39.2%, microvascular obstruction>0.5%, and myocardial salvage index<43.9 were independently associated with ventricular remodeling in STEMI patients with mildly reduced or preserved LVEF. The incidence of ventricular remodeling increased with the increasing number of CMR high-risk attributes (P<0.01). The number of CMR high-risk attributes ≥3 was an independent predictor of adverse remodeling (adjusted OR=5.95, 95 CI%: 2.25-15.72, P<0.01) in STEMI patients with mildly reduced or preserved LVEF. Furthermore, the number of CMR high-risk attributes had incremental predictive value over baseline clinical risk factors (area under curve: 0.843 vs. 0.696, P<0.01). Conclusions: In STEMI patients with mild reduced or preserved LVEF, 5 CMR characteristics are associated with ventricular remodeling. The combination of ≥3 CMR high-risk characteristics is an independent predictor of ventricular remodeling, which has incremental predictive value beyond traditional risk factors in this patient cohort.

[Efficacy analysis of Venetoclax combined with TKI and dexamethasone-containing low-dose chemotherapy for relapsed/refractory Ph+acute B-lymphoblastic leukemia]

The clinical data of five cases of relapsed/refractory (R/R) Philadelphia chromosome-positive acute B-lymphocytic leukaemia (Ph⁺B-ALL) treated with Bcl-2 inhibitor venetoclax combined with tyrosine kinase inhibitor (TKI) and dexamethasone-containing low-dose chemotherapy regimen at Zhengzhou University Cancer Hospital were analyzed, and the efficacy and safety were evaluated. Ponatinib was used in two of the five patients with T315I mutation, and flumatinib was used in other three patients. The results showed that, of the four minimal residual disease (MRD) positive patients, three achieved complete molecular remission (CMR) in the short term and one was ineffective. Another patient with morphological recurrence reached CR in one month. The overall response rate was 80%. Treatment related adverse reactions included mild skin pigmentation, gastrointestinal reactions, fatigue, and grade Ⅰ-Ⅱ bone marrow suppression.

Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree

The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history. Herein, we estimated the de novo mutation rate of pigs as 3.6 × 10^-9 per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation. Using this mutation rate, we re-investigated the evolutionary history of pigs. The estimated divergence time of ∼ 10 kiloyears ago (KYA) between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological evidence. However, other divergence events inferred here were not as ancient as previously described. Our estimates suggested that Sus speciation occurred ∼ 1.36 million years ago (MYA); European wild pigs split from Asian wild pigs only ∼ 219 KYA; and south and north Chinese wild pigs split ∼ 25 KYA. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao plain, North China, approximately 20 KYA, supporting the possibly independent domestication in North China along the middle Yellow River. We also found that the maximum effective population size of pigs was ∼ 6 times larger than the previous estimate. An archaic migration from other Sus species originating ∼ 2 MYA to European pigs was detected during western colonization of pigs; this interfered with the previous demographic inference. Our de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We resequenced 80 Eurasian pigs from nine different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex-biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y chromosomes.

A further look at quantitative trait loci for growth and fatness traits in a White Duroc × Erhualian F3 intercross population

Genetic analysis of porcine growth and fatness traits is beneficial to the swine industry and provides a reference to understand human obesity. Here, we obtained 29 growth and fatness traits for 473 individuals from a White Duroc × Erhualian F₃ intercross population. Basic statistical analyses showed that: (1) Positive correlations between different-stage body weights were detected, the shorter the time interval the stronger the correlation. (2) Strong correlations existed in the paired fatness traits. (3) With the growth of age, the correlation between fatness and body weight was increasing. All pigs were genotyped by Illumina 50 K SNP chips and their whole-genome genotypes were imputed referred to 109 re-sequencing data. We performed common and imputation-based GWASs for these traits. Two genome-wide significant loci on swine chromosome (SSC) 4 and 7 were repeatedly detected. The strongest association (P = 3.24 × 10^-19) was detected at 31.96 Mb on SSC7 for leaf fat weight. On this locus, seven major haplotypes were identified, of which two were novel and had an increasing-fatness effect. In the imputation-based GWAS, three new loci were identified. Our findings provide further insights into and enhance our understanding of genetic mechanism of porcine growth and fat deposition.

A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations

Background

Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs.

Results

This study screened 394 deep-sequenced genomes from 22 domesticated pig breeds/populations worldwide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identified a set of 878,967 polymorphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date. We found multiple lines of evidence that pSTRs in coding regions were affected by purifying selection. The enrichment of trinucleotide pSTRs in coding sequences (CDS), 5′UTR and H3K4me3 regions suggests that trinucleotide STRs serve as important components in the exons and promoters of the corresponding genes. We demonstrated that, compared to SNPs, pSTRs provide comparable or even greater accuracy in determining the breed identity of individuals. We identified pSTRs that showed significant population differentiation between domestic pigs and wild boars in Asia and Europe. We also observed that some pSTRs were significantly associated with environmental variables, such as average annual temperature or altitude of the originating sites of Chinese indigenous breeds, among which we identified loss-of-function and/or expanded STRs overlapping with genes such as AHR, LAS1L and PDK1. Finally, our results revealed that several pSTRs show stronger signals in domestic pig—wild boar differentiation or association with the analysed environmental variables than the flanking SNPs within a 100-kb window.

Conclusions

This study provides a genome-wide high-density map of pSTRs in diverse pig populations based on genome sequencing data, enabling a more comprehensive characterization of their roles in evolutionary and environmental adaptation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00631-4.

Impacts of Mycoplasma loads and lung lesions on immune and hematological statuses of pigs in an eight-breed cross heterogeneous population

Developments of pulmonary diseases, often accompanied by infections of bacteria, severely affect the meat production and welfare of pigs. This study investigated 307 pigs at age of 240 d from an eight-breed cross reared under standardized housing conditions for associations among the extent of lung lesions, bacteria load inferred from 16S rRNA sequencing of bronchoalveolar lavage fluid, as well as 57 immune cells and 25 hematological traits. We showed that the pigs under study suffered substantial and varied lung lesions, and the Mycoplasma is the most associated bacteria genera. At a false discovery rate of 0.05 (FDR < 0.05), the severity of lung lesions were significantly associated with greater CD8+ to CD3+ cell ratio, neutrophil-to-lymphocyte ratio (NLR), and standard deviation of red blood cell volume distribution width (RDW-SD), and lower CD4-CD8-/CD3+, CD3+CD4-CD8-/PBMCs (peripheral blood mononuclear cells) and CD14-CD16-/PBMCs cell ratios, mean corpuscular hemoglobin concentration, lymphocyte count, and lymphocyte count percentage, reflecting an status of inflammation, immune suppression, and hypoxia of the pigs accompanying the progression of the lung lesions. The Mycoplasma abundance showed positive correlations with neutrophil count, neutrophil count percentage, NLR, monocyte count, coefficient of variation in red blood cell volume distribution width , and RDW-SD, and negative correlations with mean corpuscular hemoglobin concentration, lymphocyte count, and lymphocyte count percentage; these correlations are largely consistent with those of lung lesions, supporting the comorbidity of lung lesions and Mycoplasma infection. We also observed nonlinear associations that sharp increases in neutrophil count and neutrophil count percentage occurred only when Mycoplasma abundance raised above the population-average level. The results provide helpful insights into the changes of host immune status in response to Mycoplasma relevant lung diseases in pigs.

[Safety and efficacy of patients with refractory B-lymphoblastic leukemia treated with anti-CD19 CAR-T cell bridging to allogeneic hematopoietic stem cell transplantation]

目的

探讨抗CD19 CAR-T细胞治疗达深度缓解后序贯异基因造血干细胞移植（allo-HSCT）治疗难治B淋巴细胞白血病的疗效及不良反应。

方法

回顾性分析2017年11月至2019年3月河南省肿瘤医院收治的10例抗CD19 CAR-T细胞治疗达深度缓解后序贯allo-HSCT难治B淋巴细胞白血病患者的临床资料。

结果

①10例患者中，男5例，女5例，中位年龄23.5（10～31）岁，其中难治急性B淋巴细胞白血病（B-ALL）9例，慢性淋巴细胞白血病（CLL）1例。10例患者抗CD19 CAR-T细胞治疗后第30天及移植前评估微小残留病（MRD）均为阴性。②亲缘全相合移植2例，亲缘单倍型移植8例，抗CD19 CAR-T细胞治疗获得深度缓解至allo-HSCT中位时间为32.5（20～60）d。③10例患者获得造血重建，中性粒细胞植入中位时间为15（15～21）d，血小板植入中位时间为19（17～30）d。④预处理过程中，10例患者均未出现肝静脉闭塞病及出血性膀胱炎。1例患者出现渗漏综合征，予以限制入量、补充白蛋白及利尿等治疗后好转。移植过程中8例（80％）出现发热，均经抗感染治疗后好转。发生Ⅱ度急性移植物抗宿主病（aGVHD）2例，Ⅲ度aGVHD 1例；至随访截止9例存活患者中8例出现局限性慢性移植物抗宿主病。⑤中位随访262（150～540）d，预期1年总生存率为（90.0±1.0）％，无病生存率为（85.7±1.3）％。

结论

抗CD19 CAR-T细胞治疗达深度缓解后序贯allo-HSCT可作为难治B淋巴细胞白血病患者的可选治疗方案。

The fine-scale genetic structure and selection signals of Chinese indigenous pigs

Genome-wide SNP profiling has yielded insights into the genetic structure of China indigenous pigs, but has focused on a limited number of populations. Here, we present an analysis of population structure and signals of positive selection in 42 Chinese pig populations that represent the most extensive pig phenotypic diversity in China, using genotype data of 1.1 million SNPs on customized Beadchips. This unravels the fine-scale genetic diversity, phylogenic relationships, and population structure of these populations, which shows remarkably concordance between genetic clusters and geography with few exceptions. We also reveal the genetic contribution to North Chinese pigs from European modern pigs. Furthermore, we identify possible targets of selection in the Tibetan pig, including the well-characterized hypoxia gene (EPAS1) and several previously unrecognized candidates. Intriguingly, the selected haplotype in the EPAS1 gene is associated with higher hemoglobin contents in Tibetan pigs, which is different from the protective role of EPAS1 in the high-altitude adaptation in Tibetan dogs and their owners. Additionally, we present evidence for the causality between EDNRB variants and the two-end-black (TEB) coat color phenotype in all Chinese pig populations except the Jinhua pig. We hypothesize that distinct targets have been independently selected for the formation of the TEB phenotype in Chinese pigs of different geographic origins. This highlights the importance of characterizing population-specific genetic determinants for heritable phenotype in diverse pig populations.

[Clinical observation of 12 patients with refractory/relapsed acute myeloid leukemia treated with allogeneic hematopoietic stem cell transplantation containing cladribine regimen]

Objective: To investigate the safety and efficacy of allogeneic hematopoietic stem cell transplantation (allo-HSCT) containing cladribine sequential busulfan regimen for refractory/relapsed acute myeloid leukemia (AML) . Methods: The clinical data of 12 refractory/relapsed AML patients received allo-HSCT with cladribine sequential busulfan regimen. Results: ① Of the 12 patients, 9 were males and 3 females, with a median age of 36 (27-50) years. The donors were identical sibling (3) , matched unrelated (1) and haploidentical family member (9) respectively. Nine patients reached partial remission and other remained no remission after chemotherapy before allo-HSCT. The median previous chemotherapy courses before allo-HSCT were 6 (2-13) . ② Conditioning regimen: Smostine 250 mg·m(-2)·d(-1), d-7; Cladribine 5 mg·m(-2)·d(-1), d-6 to d-2; Cytarabine Arabinoside 2 g·m(-2)·d(-1), d-6 to d-2; Busulfan 3.2 mg·m(-2)·d(-1), d-6 to d-3; Rabbit anti-human thymocyte immunoglobulin (ATG) 1.5 mg·m(-2)·d(-1) (unrelated donor transplantation) or 2.0-2.5 mg·m(-2)·d(-1) (haplo-HSCT) , d-4 to d-1. ③ Of the 12 patients, 11 patients attained complete haploidentical engraftment, one case occurred primary graft failure. The median durations for neutrophils and platelet implantations were 15 (15-21) and 19 (17-30) days respectively. ④After conditioning, no hepatic veno-occlusive diseases were observed, hemorrhagic cystitis occurred in 2 patients, 8 patients had fever, 3 cases experienced acute GVHD grade II, localized chronic GVHD occurred in 8 patients. ⑤The median follow-up was 8 (4-12) months. Leukemia relapse occurred in 2 patients at time of 6, 12 months after allo-HSCT. The estimated 1-year OS and DFS were (71.1±1.8) % and (62.2±1.8) %, respectively. Conclusions: allo-HSCT with cladribine sequential busulfan regimen was a feasible choice with favorable outcome for refractory/relapsed AML.

[Fecal microbiota transplantation for patients with refractory diarrhea after allogeneic hematopoietic stem cell transplantation]

Objective: To explore the availability and safety of fecal microbiota transplantation for patients with refractory diarrhea after allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Methods: Four acute leukemia patients suffered from refractory diarrhea after allo-HSCT. One of them was refractory intestinal infection, the others were intestinal graft versus host disease. One or two doses of fecal microbiota, 3.4-6.0 U for one dose, were infused via nasal-jejunal tube. The curative effect and side effects were reviewed. Results: Three cases achieved complete remission while 1 was stable disease. The side effects included fever, abdominal pain and diarrhea, which all were Ⅰ grade. Conclusion: Fecal microbiota transplantation was effective and safe for refractory diarrhea after allo-HSCT.

[The safety and efficacy of low dose subcutaneous decitabine combined with arsenic trioxide in patients with inermediate or higer-risk myelodysplastic syndrome]

To retrospectively analyze the safety and efficacy of low dose subcutaneous decitabine combined with arsenic trioxide in patients with intermediate or high-risk myelodysplastic syndrome (MDS). Three of the total 11 MDS patients achieved complete remission (CR) and 6 achieved hematological improvement (HI), 1 stable disease (SD), and 1 progressive disease (PD). One patient was treated with allogeneic hematopoietic stem cell transplantation (allo-HSCT). The median follow-up time was 413(90-1 275) d. Nine patients were still alive. Low dose subcutaneous decitabine combined with arsenic trioxide can be an alternative regimen for intermediate or high-risk MDS patients.

The down-regulation of long non-coding RNA LINC01088 is associated with the poor prognosis of epithelial ovarian cancer patients

OBJECTIVE

Long intergenic non-coding RNA 1088 (LINC01088) has been suggested to act as a tumor suppressor in epithelial ovarian cancer (EOC); however, the prognostic role of LINC01088 has not been evaluated in cancer patients. This study aimed to investigate the expression of LINC01088 in EOC, along with evaluating its clinical-pathological and prognostic importance.

PATIENTS AND METHODS

A bioinformatics tool (GEPIA) was used to screen the dysregulated lncRNAs. Quantitative Real-time PCR (qRT-PCR) was used to measure expression level of LINC01088 in EOC tumor samples and adjacent non-tumor tissues. Then, the association between LINC01088 expression and pathological parameters were further evaluated. Overall survival (OS) was estimated using the Kaplan-Meier method, and the differences in survival were compared using the log-rank test. Univariate and multivariate analysis were performed using the Cox proportional hazard analysis.

RESULTS

We found that LINC01088 expression was significantly down-regulated in EOC tissues via "GEPIA". Then, the results of RT-PCT confirmed that the expression levels of LINC01088 were significantly lower in EOC tissues compared to adjacent noncancerous tissues (p < 0.01). Interestingly, lower LINC01088 expression levels were associated with FIGO stage (p = 0.000), grade (p = 0.003) and distant metastasis (p = 0.006). Moreover, Kaplan-Meier analysis indicated that patients with low LINC01088 expression had a poor overall survival (p = 0.0013). Finally, univariate and multivariate analysis show that LINC01088 expression is an independent predictor for overall survival.

CONCLUSIONS

Low LINC01088 expression was associated with the progression of EOC and could serve as a potential independent prognostic biomarker for patients with EOC.

[The role of mesenchymal stem cells in allogeneic hematopoietic stem cell transplantation for patients with refractory severe aplastic anemia]

Objective: To evaluate the efficacy and safety of mesenchymal stem cells in allogeneic hematopoietic stem cell transplantation for patients with refractory severe aplastic anemia (R-SAA) . Method: The clinical data of 25 R-SAA patients receiving co-transplantation of mesenchymal stem cells combined with peripheral blood stem cells from sibling donors (10 cases) and unrelated donors (15 cases) from March 2010 to July 2018 in Zhengzhou University Affiliated Tumor Hospital were retrospectively analyzed. Antithymocyte globulin (ATG) treatment was ineffective/relapsed in 11 cases, and cyclosporine (CsA) treatment ineffective/relapsed in 14 cases. Results: There were 13 male and 12 female among these patients. One patient had a primary graft failure, one patient had a poorly engraftment of platelets, and the remaining 23 patients achieved hematopoietic engraftment. The median time of granulocyte engraftment was 12.5 (10-23) days and 15 (11-25) days for megakaryocyte. Incidences of grade Ⅰ/Ⅱ acute graft-versus-host disease (aGVHD) and chronic graft-versus-host disease (cGVHD) were 37.5% (9/24) and 21.7% (5/23) , respectively. There was no severe GVHD and no severe complications that related to transplantation. 21 of 25 (84%) patients were alive with a median follow-up of 22.9 (1.6-107.8) months. The 5-year overall survival rate after transplantation was (83.6±7.5) %. Conclusion: The combination of mesenchymal stem cells is reliable and safe in the treatment of R-SAA in peripheral blood stem cell transplantation of unrelated donors and sibling donors, which could significantly reduce the incidence of GVHD and severe transplantation-related complications.

[Ibrutinib combined with CAR-T cells in the treatment of del (17p) chronic lymphocytic leukemia with BCL-2 inhibitor resistance: a case report and literature review]

目的

总结伊布替尼联合嵌合抗原受体T细胞（CAR-T）治疗TP53基因异常超高危慢性淋巴细胞白血病（CLL）/小细胞淋巴瘤（SLL）的经验，提高对此类疾病的认识。

方法

报告1例伴del（17p）CLL/SLL患者BCL-2抑制剂耐药后，采用伊布替尼联合CAR-T成功治疗并顺利桥接异基因造血干细胞移植（allo-HSCT）的治疗经过，并进行文献复习。

结果

患者为年轻女性，发病初表现为全身浅表淋巴结肿大，淋巴结活检病理确诊为SLL，无del（17p）；2年后疾病快速进展为CLL/SLL，伴del（17p），骨髓造血衰竭。采用BCL-2抑制剂维奈托克治疗2个月余肿大淋巴结明显缩小，3个月后疾病快速进展，脾脏增大至肋缘下16 cm，颈部淋巴结增大融合，并出现上腔静脉压迫综合征，考虑维奈托克耐药；遂更换为BTK抑制剂伊布替尼治疗，2个月余疾病达部分缓解（PR），联合靶向CD19的CAR-T治疗，细胞因子释放综合征（CRS）1级，1个月后达骨髓及外周血完全缓解（CR），且微小残留病（MRD）阴性，2个月后桥接allo-HSCT。

结论

TP53基因异常CLL/SLL临床进展快、易耐药、预后差，伊布替尼联合CAR-T治疗可快速达CR。

[The efficacy and safety of co-transplantation of unrelated donor peripheral blood stem cells combined with umbilical mesenchymal stem cells in patients with refractory severe aplastic anemia-Ⅱ]

The efficacy and safety of co-transplantation of unrelated donor peripheral blood stem cells (UD-PBSCs) combined with umbilical cord mesenchymal stem cells (UC-MSCs) in refractory severe aplastic anemia-Ⅱ(RSAA-Ⅱ) were analyzed retrospectively. Fifteen patients with RSAA-Ⅱ underwent UD-PBSCs and UC-MSCs co-transplantation, among whom 14 cases had hematopoietic reconstitution without severe graft versus-host disease (GVHD). The 5-year overall survival rate was 78.57%. Combination of UD-PBSCs and UC-MSCs transplantation could be a safe and effective option for RSAA-Ⅱ.

Landscape of Loci and Candidate Genes for Muscle Fatty Acid Composition in Pigs Revealed by Multiple Population Association Analysis

Genome wide association analyses in diverse populations can identify complex trait loci that are specifically present in one population or shared across multiple populations, which help to better understand the genetic architecture of complex traits in a broader genetic context. In this study, we conducted genome-wide association studies and meta-analysis for 38 fatty acid composition traits with 12–19 million imputed genome sequence SNPs in 2446 pigs from six populations, encompassing White Duroc × Erhualian F₂, Sutai, Duroc-Landrace-Yorkshire (DLY) three-way cross, Laiwu, Erhualian, and Bamaxiang pigs that were originally genotyped with 60 K or 1.4 million single nucleotide polymorphism (SNP) chips. The analyses uncovered 285 lead SNPs (P < 5 × 10^-8), among which 78 locate more than 1 Mb to the lead chip SNPs were considered as novel, largely augmented the landscape of loci for porcine muscle fatty acid composition. Meta-analysis enhanced the association significance at loci near FADS2, ABCD2, ELOVL5, ELOVL6, ELOVL7, SCD, and THRSP genes, suggesting possible existence of population shared mutations underlying these loci. Further haplotype analysis at SCD loci identified a shared 3.7 kb haplotype in F₂, Sutai and DLY pigs showing consistent effects of decreasing C18:0 contents in the three populations. In contrast, at FASN loci, we found an Erhualian specific haplotype explaining the population specific association signals in Erhualian pigs. This study refines our understanding on landscape of loci and candidate genes for fatty acid composition traits of pigs.

Genome-wide association and evolutionary analyses reveal the formation of swine facial wrinkles in Chinese Erhualian pigs

Wrinkles are uneven concave-convex folds, ridges or creases in skin. Facial wrinkles appear in head, typically increasing along with aging. However in several Chinese indigenous pigs, such as Erhualian pigs, rich facial wrinkles have been generated during the growth stages as one of their breed characteristics. To investigate the genetic basis underlying the development of swine facial wrinkles, we estimated the folding extent of facial wrinkles in a herd of Erhualian pigs (n=332), and then conducted genome-wide association studies and multi-trait meta-analysis for facial wrinkles using 60K porcine chips. We found that facial wrinkles had high heritability estimates of ~0.7 in Erhualian pigs. Notably, only one genome-wide significant QTL was detected at 34.8 Mb on porcine chromosome 7. The most significant SNP rs80983858 located at the 3255-bp downstream of candidate gene GRM4, and the G allele was of benefit to increase facial wrinkles. Evolutionary and selection analyses suggested that the haplotypes containing G allele were under artificial selection, which was consistent with local animal sacrificial custom praying for longevity. Our findings made important clues for further deciphering the molecular mechanism of swine facial wrinkles formation, and shed light on the research of skin wrinkle development in human or other mammals.

[Risk factors and prognoses analysis of new-onset atrial fibrillation in patients with acute myocardial infarction]

Objective: To explore the risk factors and prognoses of new-onset atrial fibrillation (NOAF) in patients with acute myocardial infarction (AMI). Methods: A total of 468 patients with AMI were admitted into Beijing Anzhen Hospital for emergency pereutaneous coronary intervention (PCI). According to the NOAF occurred during hospitalization, the patients were divided into two groups: the NOAF (n=37) group and the non-NOAF (n=431) group. Parameters including general clinical conditions, coronary lesions, echocardiography, biochemical markers, C-reactive protein (CRP) , N-terminal pro-brain natriuretic peptide (NT-pro-BNP), and myocardial markers were collected. In-hospital mortality and incidence of in-hospital main adverse cardiovascular and cerebrovascular events (MACCE) were compared between the two groups. Logistic multivariate regression analyses were performed for the association between the risk factors and NOAF. Results: The incidence of NOAF was 7.9% in AMI patients undergoing emergency PCI. There were no significant differences in door-to-balloon time, weight, platelet counts, baseline serum creatinine (SCr), postoperative SCr, triglyceride, total cholesterol, low density lipoprotein cholesterol, high density lipoprotein cholesterol, uric acid, glycosylated hemoglobin A1c, preoperative medication, number of lesions, thrombus aspiration, location of myocardial infarction, and history of hypertension, diabetes, peripheral vascular disease and old myocardial infarction between the two groups. The percentage of women was in the NOAF group (32.4% vs. 16.7%, P<0.05) and subjects in this group were significantly elder than those in the non-NOAF groups [(66±10) years vs. (571±11) years, P<0.001]. Moreover, the levels of no-reflow rate (40.5% vs. 12.6%, P<0.001) , CRP [25.2 (15.43, 29.97) mg/L vs.5.21 (2.33, 16.98) mg/L, P<0.001], white blood cell counts [(11.19±3.44)×10(9) vs. (9.91±3.23)×10(9), P=0.022], NT-pro-BNP [(652.6±108.8) ng/L vs. (258.3±105.9) ng/L, P<0.001], and troponin I (TnI) [20.41(1.78, 87.89) μg/L vs.7.72(1.29, 36.39) μg/L, P=0.006] were significantly higher in the NOAF group than in the non-NOAF group, while left ventricular ejection fraction [(47.70±7.34)% vs. (53.35±8.05)%, P<0.001], and hemoglobin [137.0(125.5, 146.0) g/L vs.144.0(133.0,156.0) g/L, P=0.042] were significantly lower in the NOAF group than the non-NOAF group. Patients in the NOAF group had significantly longer hospital stay than those in the non-NOAF group [(8.7±5.6) d vs. (6.0±2.3) d, P=0.007]. The in-hospital mortality (8.1% vs 1.4% P=0.004) and the incidence of in-hospital MACCE (37.8% vs. 7.7%, P<0.001) in the NOAF group were significantly higher than those in the non-NOAF group. Logistic multivariate regression analyses showed that age (HR 1.083, 95%CI 1.028-1.141, P=0.003), CRP (HR 1.116, 95%CI 1.049-1.187, P=0.001), NT-pro-BNP (HR 1.463, 95%CI 1.001-4.064, P=0.001) and no-reflow (HR 4.388, 95%CI 1.006-19.144, P=0.049) were independent predictors of NOAF after AMI. Conclusions: Age, elevated levels of CRP, NT-pro-BNP, and the absence of no-reflow are risk factors for incident NOAF in patients with AMI in hospital.

[Changes of intestinal mucosal barrier function and effects of early enteral nutrition in patients with severe organophosphorus poisoning]

Objective: To observe the changes of intestinal barrier function in patients with acute severe organophosphorus pesticide poisoning (ASOPP) and the effect of early enteral nutrition on them. Methods: A single-center, single-sample, prospective, randomized controlled clinical trial was conducted. A total of 50 patients with ASOPP were divided into 24 h enteral nutrition group (group A) and 48 h (48-72 h) enteral nutrition group (B group) according to the order of hospitalization. The two groups received equal calorie nutritional support, and Serum D-lactic acid (D-LA) and serum human diamine oxidase (DAO) were detected immediately after admission and at 48 h, 72 h and 144 h. At the same time, the worst value of APACHE-Ⅱ score was recorded, and the correlation between DAO, D-LA and APACHE-Ⅱ score was analyzed. The serum concentration of D-LA and DAO in 15 healthy adults were detected as healthy control group. Results: There was no statistical difference in gender, age, poisoning time and organophosphorus pesticide components between group A and B (P>0.05). The distribution of D-LA concentration in group A poisoned patients at admission, 48 h, 72 h and 144 h was (66±19) μg/L, (68±21) μg/L, (66±19) μg/L, (63±17) μg/L, while in group B they were (62±15) μg/L, (58±17) μg/L, (58±16) μg/L, (67±9) μg/L. There was no statistical difference between the two groups in D-LA concentration and that of healthy people [(67±17) μg/L, P>0.05]. The distribution of DAO concentration in group A poisoned patients at admission, 48 h, 72 h and 144 h was (2.1±0.6) μg/ml, (2.1±0.5) μg/ml, (2.2±0.4) μg/ml, (2.2±0.5) μg/ml, while in group B they were (2.1±0.5) μg/ml, (2.1±0.5) μg/ml, (2.2±0.5) μg/ml, (2.1±0.4) μg/ml. DAO concentration in the early stage of the intoxication of the two groups were higher than that of healthy people (0.1±0.0 μg/ml) (P<0.05). There is no statistical difference in DAO concentration between group A and B at different time points (P>0.05). The APACHEE-Ⅱ score of 48 hours and 72 hours in group A (12.2+1.7, 5.5+2.1) was significantly lower than that in group B (14.1+2.4, 8.2+2.6) (P<0.05). D-LA, DAO concentration at different time points was not correlated with APACHE-Ⅱ score (P>0.05). D-LA (r, P) was immediate admission (-0.17, 0.24), 48 h (0.04, 0.79), 72 h (0.32, 0.06), 144 h (0.29, 0.07), and DAO (r, P) was immediate admission (-0.12, 0.43), 48 h (0.02, 0.92), 72 h (0.03, 0.85), 144 h (0.03, 0.82). Conclusions: Patients with ASOPP may have obvious injury at intestinal mucosa at early stage (144 h), but the intestinal permeability is normal. Early enteral nutrition therapy can promote the recovery of patients, but has low correlation with intestinal barrier function improvement.

[The expression of CRLF2 in adult Ph negative acute B lymphocytic leukemia and its prognostic significance]

目的

检测CRLF2蛋白在初诊成人非Ph阳性急性B淋巴细胞白血病（B-ALL）中的表达情况，探讨CRLF2蛋白的表达与患者临床特征、疗效及预后的关系。

方法

收集郑州大学附属肿瘤医院血液科2016年4月1日至2017年12月31日收治的103例初治成人B-ALL患者骨髓标本，应用流式细胞术CD45/SSC设门检测原始细胞CRLF2表达率，将CRLF2表达率≥20%定义为高表达组，<20%定义为低表达组，比较两组患者的临床特征及预后差异。

结果

CRLF2高表达组中位总生存（OS）、无病生存（DFS）时间分别为9.0和4.25个月，CRLF2低表达组分别为15.5和10.25个月，差异有统计学意义（P值分别为0.007、0.000）。CRLF2高表达组18个月OS率、DFS率分别为38.6%和25.1%，CRLF2低表达组分别为57.8%和42.3%，差异有统计学意义（P值分别为0.047、0.016）。多因素分析显示CRLF2高表达是影响患者OS（HR=2.991，95%CI 1.429~6.261，P=0.004）和DFS（HR=2.374，95%CI 1.146~4.960，P=0.041）的独立危险因素。

结论

合并CRLF2高表达的成人初治B-ALL患者预后不良。

New insights into host adaptation to swine respiratory disease revealed by genetic differentiation and RNA sequencing analyses

Swine respiratory disease (SRD) causes massive economic losses in the swine industry and is difficult to control and eradicate on pig farms. Here, we employed population genetics and transcriptomics approaches to decipher the molecular mechanism of host adaptation to swine respiratory disease. We recorded two SRD-related traits, the enzootic pneumonia-like (EPL) score and lung lesion (LL) levels, and performed four body weight measurements, at ages of 150, 180, 240, and 300 days, in a Chinese Bamaxiang pig herd (n = 314) raised under consistent indoor rearing conditions. We divided these animals into disease-resistant and disease-susceptible groups based on the most likely effects of both SRD-related traits on their weight gain, and performed genetic differentiation analyses in these two groups. Significant loci showing the top 1% of genetic differentiation values, exceeding the threshold of p = 0.005 set based on 1,000-times permutation tests, were defined as candidate regions related to host resistance or susceptibility to SRD. We identified 107 candidate genes within these regions, which are mainly involved in the biological processes of immune response, fatty acid metabolism, lipid metabolism, and growth factor signaling pathways. Among these candidate genes, TRAF6, CD44, CD22, TGFB1, CYP2B6, and SNRPA were highlighted due to their central regulatory roles in host immune response or fat metabolism and their differential expression between healthy lung tissues and lung lesions. These findings advance our understanding of the molecular mechanisms of host resistance or susceptibility to respiratory disease in pigs and are of significance for the breeding pigs resistant to respiratory disease in the swine industry.

[Long-term clinical outcome of children and adolescents with Burkitt's lymphoma treated with rituximab combined with modified NHL-BFM-90 regimen]

Objective: To evaluate the efficacy and safety of rituximab combined with the modified NHL-BFM-90 protocol in childhood and adolescence with Burkitt's lymphoma (BL). Methods: A retrospective analysis of 67 untreated childhood and adolescence patients with BL was made. All patients were treated with the modified NHL-BFM-90 protocol with or without rituximab. Results: The 64 patients (95.52%) achieved complete remission (CR), 3 patients (4.48%) partial remission (PR), and the overall response rate (CR+PR) was 100%. 67 patients were followed up for a median of 44 (3-89) months. The 3 and 5-year overall survival (OS) were 92.54% and 88.98%, respectively. The 3 and 5-year progression-free survival (PFS) were all 90.34%. The 5-year OS were 100%,91.7% and 80.0% in low risk, moderate risk and high risk group, respectively, and the difference was statistically significant (P=0.048). Of the 67 patients, 55 patients (82.09%) were treated with rituximab plus chemotherapy. Compared with the 5-year OS and PFS of 74.3% and 78.6% in the chemotherapy group, the 5-year OS and PFS in the rituximab plus chemotherapy group were 95.2% and 95.5%, respectively, and the difference was statistically significant (P value was 0.021, and 0.036, respectively). Major toxicity was myelosuppression and mucositis. No treatment related death was found. Conclusions: Rituximab combined with the modified NHL-BFM-90 protocol was highly effective for children and adolescents with BL, and significantly improved long-term survival.

Microbial communities in swine lungs and their association with lung lesions

Under natural farming, environmental pathogenic microorganisms may invade and affect swine lungs, further resulting in lung lesions. However, few studies on swine lung microbiota and their potential relationship with lung lesions were reported. Here, we sampled 20 pigs from a hybrid herd raised under natural conditions; we recorded a lung‐lesion phenotype and investigated lung microbial communities by sequencing the V3‐V4 region of 16S rRNA gene for each individual. We found reduced microbial diversity but more biomass in the severe‐lesion lungs. Methylotenera, Prevotella, Sphingobium and Lactobacillus were the prominent bacteria in the healthy lungs, while Mycoplasma, Ureaplasma, Sphingobium, Haemophilus and Phyllobacterium were the most abundant microbes in the severe‐lesion lungs. Notably, we identified 64 lung‐lesion‐associated OTUs, of which two classified to Mycoplasma were positively associated with lung lesions and 62 showed negative association including thirteen classified to Prevotella and six to Ruminococcus. Cross‐validation analysis showed that lung microbiota explained 23.7% phenotypic variance of lung lesions, suggesting that lung microbiota had large effects on promoting lung healthy. Furthermore, 22 KEGG pathways correlated with lung lesions were predicted. Altogether, our findings improve the knowledge about swine lung microbial communities and give insights into the relationship between lung microbiota and lung lesions.

Ocnus is essential for male germ cell development in Drosophila melanogaster

The ocnus (ocn) gene encodes a protein abundant in the testes, implying its role in testis development. When Drosophila melanogaster is infected with the endosymbiont wMel Wolbachia, which affects the spermatogenesis of its hosts, ocn is downregulated in the third-instar larval testes, suggesting a role of ocn in spermatogenesis. In this study, we knocked down ocn in the testes and found that the hatch rates of embryos derived from ocn-knockdown males were significantly decreased, and 84.38% of the testes were much smaller in comparison to controls. Analysis of the smaller testes showed no germ cells but they had an extended hub. Using RNA-sequencing (RNA-Seq), we identified 69 genes with at least a twofold change (q-value < 5%) in their expression after ocn knockdown; of these, eight testes-specific and three reproduction-related genes were verified to be significantly downregulated using quantitative reverse transcription-PCR. Three genes (orientation disruptor, p24-2 and CG13541) were also significantly downregulated in the presence of Wolbachia. Furthermore, 98 genes were not expressed when ocn was knocked down in testes. These results suggest that ocn plays a crucial role in male germ cell development in Drosophila, possibly by regulating the expression of multiple spermatogenesis-related genes. Our data provide important information to help understand the molecular regulatory mechanisms underlying spermatogenesis.

Signatures of Selection and Interspecies Introgression in the Genome of Chinese Domestic Pigs

Chinese domestic pigs have experienced strong artificial selection for thousands of years. However, the molecular mechanisms underlying the selection-causing phenotypic changes in Chinese domestic pigs are still largely unknown. Here we used whole-genome resequencing data of 54 pigs from 9 Chinese diverse breeds and 16 wild boars from 7 localities across China to identify genes that show evidence of positive selection in the process of domestication. A total of 14 candidate domestication regions were detected by selective sweep analyses of genetic differentiation and variability, and a set of genes in these candidate domestication regions were found to be related to metabolic process, development, reproduction, olfactory, behavior, and nervous system. The most promising candidate gene under selection - TBX19 - probably underlies the metabolic alteration and developmental traits, and may also associate with timidity of Chinese domestic pigs. Intriguingly, we found that the haplotype at TBX19 locus shared by nearly all Chinese domestic pigs was possibly introgressed from another Sus species. We also revealed the AHR gene associated with female reproduction is under strong positive selection. These results advance our understanding of the evolutionary history of Chinese domestic pigs and shed insights into identifying functionally important genes/mutations contributing to the phenotypic diversity in pigs.

Genetic mapping using 1.4M SNP array refined loci for fatty acid composition traits in Chinese Erhualian and Bamaxiang pigs

Chinese indigenous pigs display marked genetic and phenotypic differences compared with western commercial pigs. In this study, we tested the association between 660K SNPs and longissimus muscle fatty acid composition traits in Chinese Erhualian (n = 331) and Bamaxiang (n = 315) pigs based on a customized 1.4 million SNP array. We identified a total of 64 significant associations for 20 fatty acid composition traits at the p-value threshold of 1 × 10^-6 among which 42 associations in low linkage disequilibrium (r²  < .2) with previously reported loci were considered novel. We substantially improved the strength and precision of the associations at four previously detected loci near FADS2, ELOVL7, ELOVL6 and FASN genes, facilitating follow-up candidate gene studies. Moreover, we also identified loci near ABCD2, ACSBG1, ELOVL5, HPGDS, DAGT2, ACAD10 and ACSL1 genes with function relevant to metabolism of fatty acids. In this study, valuable genetic variants and candidate genes associated with fatty acid composition traits were identified in Erhualian and Bamaxiang pigs. Some identified loci could be used to improve pork nutrition in pig breeding practice. Using the SNP array with higher marker density and less ascertainment bias improved QTL detection power and precision in Chinese indigenous pigs.

[Thalidomide combined with interferon and interleukin-2 in treatment of relapsed or refractory acute myelogenous leukemia]

In 12 patients with relapsed or refractory acute myelogenous leukemia (AML), the efficacy and safety of a novel regimen, namely thalidomide combined with interferon and interleukin 2 (IL-2), were initially explored.All the patients have received the triple-drug regimen for at least one cycle.Three patients achieved incomplete remission (CRi), 3 patients with partial remission.The overall response rate (ORR) was 50%.

Spodoptera litura autophagy-related protein 1 interacts with autophagy-related protein 5 and enhances its degradation

It is known that the autophagy-related protein 1 (ATG1) plays critical roles in the regulation of autophagy in mammals and yeast, whereas the function of ATG1 in lepidopteran insects is not well elucidated. Here Spodoptera litura ATG1 (SlATG1) and its interactions with other ATG proteins were characterized. Alternative splicing of SlAtg1 produced at least four transcript variants. Over-expression and RNA interference knockdown of SlAtg1 demonstrated that SlATG1 enhanced autophagy. SlATG1A-Green fluorescent protein (GFP) tagged localized in the cytoplasm and formed some punctuate dots, which were colocalized with red fluorescent protein mCherry tagged Spodoptera exigua ATG5 (SeATG5). SlATG1A-GFP over-expression reduced the nuclear abundance of mCherry-SeATG5 but increased its cytoplasmic abundance. Pull-down, co-immunoprecipitation and bimolecular fluorescence complementation assays showed that SlATG1A bound to SeATG5 through the N-terminus of SlATG1A. The over-expression of FLAG epitope tagged SlATG1A significantly increased the accumulation of the cleaved GFP from GFP-SeATG5, suggesting the enhanced degradation of GFP-SeATG5. In addition, we confirmed that the interactions of SlATG1 with other autophagy-related proteins were conserved. These results provide the first evidence that ATG1 interacts with ATG5 and enhances its degradation in lepidopteran insect cells, which may have important physiological functions.

Genome-wide detection of genetic markers associated with growth and fatness in four pig populations using four approaches

BACKGROUND

Genome-wide association studies (GWAS) have been extensively used to identify genomic regions associated with a variety of phenotypic traits in pigs. Until now, most GWAS have explored single-trait association models. Here, we conducted both single- and multi-trait GWAS and a meta-analysis for nine fatness and growth traits on 2004 pigs from four diverse populations, including a White Duroc × Erhualian F₂ intercross population and Chinese Sutai, Laiwu and Erhualian populations.

RESULTS

We identified 44 chromosomal regions that were associated with the nine traits, including four genome-wide significant single nucleotide polymorphisms (SNPs) on SSC2 (SSC for Sus scrofa chromosome), 4, 7 and X. Compared to the single-population GWAS, the meta-analysis was less powerful for the identification of SNPs with population-specific effects but more powerful for the detection of SNPs with population-shared effects. Multiple-trait analysis reduced the power to detect trait-specific SNPs but significantly enhanced the power to identify common SNPs across traits. The SNP on SSC7 had pleiotropic effects on the nine traits in the F₂ and Erhualian populations. Another pleiotropic SNP was observed on SSCX for these traits in the F₂ and Sutai populations. Both population-specific and shared SNPs were identified in this study, thus reflecting the complex genetic architecture of pig growth and fatness traits.

CONCLUSIONS

We demonstrate that the multi-trait method and the meta-analysis on multiple populations can be used to increase the power of GWAS. The two significant SNPs on SSC7 and X had pleiotropic effects in the F₂, Erhualian and Sutai populations.

[A clinical study of fungal esophagitis in 13 patients with hematologic malignancies]

目的

提高对血液系统恶性疾病并发真菌性食管炎的认识。

方法

回顾性分析2012年1月至2015年11月河南省肿瘤医院血液科收治的279例行胃镜检查的恶性血液病患者临床资料，观察恶性血液病并发真菌性食管炎的临床特征及转归。

结果

279例患者中真菌性食管炎13例（4.66%），刷片镜检5例可见真菌孢子，3例可见真菌孢子及菌丝，5例仅见真菌菌丝。12例致病菌为白色念珠菌，1例为隐球菌。13例患者中弥漫大B细胞淋巴瘤8例，外周T细胞淋巴瘤1例，急性淋巴细胞白血病2例，多发性骨髓瘤1例；6例患者伴消化道症状（咽部异物感、恶心、纳差3例，胸骨后疼痛或烧灼感2例，吞咽困难伴疼痛1例），7例患者无明显症状体征。6例患者予氟康唑注射液400 mg/d治疗14 d，均有效；7例患者予制霉菌素片（100万U，每天3次）治疗14 d, 6例有效，1例持续不缓解，调整为氟康唑注射液400 mg/d治疗7 d后症状消失。治疗相关不良反应为一过性转氨酶升高及轻度消化道不良反应。

结论

恶性血液病并发真菌性食管炎并非少见，以淋巴系统疾病患者居多，致病菌主要为白色念珠菌；其临床症状不典型，约半数以上患者无明显临床表现；氟康唑及制霉菌素单药治疗安全有效。

The application value of the detection of the level of tissue polypeptide antigen, ovarian cancer antigen X1, cathepsin L and CA125 on the diagnosis of epithelial ovarian cancer

OBJECTIVE

We investigated the value of the joint detection of tissue polypeptide antigen (TPA), ovarian cancer antigen X1 (OVX1), cathepsin L (CTSL) and CA125 on the early diagnosis of epithelial ovarian carcinoma (EOC).

PATIENTS AND METHODS

From October 2011 to February 2015, 84 cases of patients under surgical treatment of epithelial ovarian cancer, 98 cases of patients with benign epithelial ovarian tumor and 51 subjects in healthy control group were selected to detect the level of TPA, OVX1 and CTSL in serum from the Obstetrics and Gynecology Department of the First Affiliated Hospital of Liaoning Medical University. The clinical data of patients with ovarian tumor were collected and analyzed, and the levels of CA12 were measured.

RESULTS

3 indicators in the malignant group were significantly higher than those in the benign group and healthy control group (p < 0.05). The total positive rate and the positive rate of early detection of TPA on EOC were the highest, and the total positive rate of OVX1 was lower than that of CA125. The total positive rate and the positive rate of early detection of CA125+TPA on EOC were the highest. The positive rate of early detection and the total positive rate of the pairwise combined detection of the other index and CA125 on EOC were significantly higher than those of the single detection of CA125 (p < 0.05). The joint detection of CA125+ OVX1 and the single detection of CA125 were not statistically significant. However, the remaining differences were statistically significant (p < 0.05).

CONCLUSIONS

The level of TPA, OVX1 and CTSL in serum was potential detection index, the joint detection of TPA and CA125 was the ideal combination, which took into account the total positive rate, the positive rate of early detection on EOC and the improved diagnostic rate of EOC.