Recent studies have characterized the genomic structures of many eukaryotic cells,often focusing on their relation to gene expression.However,these studies have largely investigated cells grown in 2D cultures,although the transcriptomes of 3D-cultured cells are generally closer to their in vivo phenotypes.To examine the effects of spatial constraints on chromosome conformation,we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C.Our results reveal significant differences in higher-order genomic interactions,notably in compartment identity and strength as well as in topologically associating domain(TAD)-TAD interactions,but only minor differences are found at the TAD level.Our RNA-seq analysis reveals up-regulated expression of genes involved in physiological hepatocyte functions in the 3D-cultured cells.These genes are associated with a subset of structural changes,suggesting that differences in genomic structure are critically important for transcriptional regulation.However,there are also many structural differences that are not directly associated with changes in gene expression,whose cause remains to be determined.Overall,our results indicate that growth in 3D significantly alters higher-order genomic interactions,which may be consequential for a subset of genes that are impor-tant for the physiological functioning of the cell.

Objective:To explore the clinical features and survival of newly diagnosed follicular lymphoma (FL) patients with diffuse large B-cell lymphoma (DLBCL) component.Methods:1845 newly diagnosed FL patients aged ≥ 18 years with grades 1-3a in 11 medical centers in China from 2000 to 2020 were included, and patients with DLBCL component were screened. The clinical data and survival data of the patients were retrospectively analyzed, and the prognostic factors were screened by univariate and multivariate analysis.Results:146 patients (7.9% ) with newly diagnosed FL had DLBCL component. The median age was 56 (25-83) years, 79 males (54.1% ) . The pathology of 127 patients showed the proportion of DLBCL component. Patients were divided into two groups according to whether the proportion of DLBCL component was ≥ 50% . The study found that patients with DLBCL component ≥ 50% had higher grade 3 ratio (94.3% vs 91.9% , P=0.010) , Ki-67 index ≥ 70% ratio (58.5% vs 32.9% , P=0.013) and PET-CT SUVmax ≥ 13 ratio (72.4% vs 46.3% , P=0.030) than patients with DLBCL component<50% . All patients received CHOP or CHOP like ± rituximab chemotherapy. The overall response rate (ORR) was 88.2% , and the complete response (CR) rate was 76.4% . In the groups with different proportions of DLBCL component, there was no significant difference in the remission rate after induction treatment and the incidence of disease progression within 2 years after initiation of treatment (POD24) ( P<0.05) . The overall estimated 5-year progression free survival (PFS) rate was 58.9% , and the 5-year overall survival (OS) rate was 90.4% . The 5-year OS rate of POD24 patients was lower than that of non POD24 patients (70.3% vs 98.5% , P<0.001) . Compared with non maintenance treatment of rituximab, maintenance treatment of rituximab could not benefit the 5-year PFS rate (57.7% vs 58.8% , P=0.543) , and the 5-year OS rate had a benefit trend, but the difference was not statistically significant (100% vs 87.8% , P=0.082) . Multivariate analysis showed that failure to reach CR after induction treatment was an independent risk factor for PFS ( P=0.006) , while LDH higher than normal was an independent risk factor for OS ( P=0.031) . Conclusion:FL patients with DLBCL component ≥50% have more invasive clinical and pathological features. CHOP/CHOP like ± rituximab regimen can improve the clinical efficacy of patients. Rituximab maintenance therapy can not benefit the PFS and OS of patients. Failure to reach CR after induction therapy was the independent unfavorable factor for PFS.

Objective:To investigate the occurrence of carotid artery abnormalities in human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) patients and the related risk factors affecting the occurrence of carotid artery abnormalities.Methods:A total of 169 regular follow-up outpatients with HIV/AIDS from April 2003 to December 2019 in Peking Union Medical College Hospital, whose carotid artery ultrasound examination were performed from July 2015 to December 2019 were included. The patients were divided into young (≤44 years old), middle-aged and elderly (≥45 years old) according to their ages, and the physical examination data of the included patients were collected.The statistical methods were logistic regression analysis and single sample t test. Results:Among the 169 HIV/AIDS patients, 40(23.7%) had abnormal carotid artery and 129(76.3%) had no abnormal carotid artery. Middle-aged and elderly people (odds ratio ( OR)=3.85, 95%confidence interval (95% CI) 1.54-9.65, P<0.01), hypertension ( OR=6.24, 95% CI 1.95-20.00, P<0.01), hyperlipidemia ( OR=2.44, 95% CI 1.00-5.93, P<0.05), and elevated human leucocyte antigen (HLA)-DR + CD8 + /CD8 + ( OR=1.03, 95% CI 1.01-1.06, P<0.05) were the risk factors for carotid artery abnormality. The common carotid artery inner medium film thickness (IMT) of patients in HIV/AIDS group Ⅰ (20 to 30 years old), group Ⅱ (31 to 40 years old), group Ⅲ (41 to 50 years old) were (0.061 0±0.001 2), (0.062 9±0.001 4) and (0.065 6±0.002 6) cm, respectively, which were thicker than the control groups ((0.051±0.003), (0.056±0.004) and (0.063±0.002) cm, respectively). The differences were all statistically significant ( t=5.119, 4.775 and 1.739, respectively, all P<0.05). The common carotid artery IMT of patients in HIV/AIDS group A (30 to 44 years old) and group B (45 to 59 years old) were (0.062 6±0.001 1) and (0.072 3±0.003 4) cm, respectively, which were thicker than the control groups ((0.052±0.011) and (0.064±0.015) cm, respectively), the differences were both statistically significant ( t=9.520 and 3.012, respectively, both P<0.01). Conclusion:Younger HIV-positive people have a higher probability of abnormal carotid arteries and may be at greater risk of cardiovascular disease than HIV-negative people of the same age, suggesting that HIV-positive people, especially young people, should be examined early with ultrasound of the neck arteries to detect abnormalities and intervene as soon as possible.

Objective: To investigate the characteristics and prognostic value of peripheral blood T lymphocyte subsets in patients with severe influenza. Methods: This was a single-center cross-sectional study in influenza patients admitted to Peking Union Medical College Hospital from August 2017 to April 2018. Peripheral blood lymphocyte subsets were detected by flow cytometry in both patients and 108 healthy controls. Influenza patients were divided into mild group and severe group. Severe patients were further classified into alive and fatal subgroups. Results: A total of 42 influenza patients were recruited in this study, including 24 severe cases (6 deaths). The remaining 18 cases were mild. The peripheral blood lymphocyte counts and lymphocyte subset counts (B, NK, CD4⁺T, CD8⁺T) in either mild patients[795 (571,1 007), 43 (23,144), 70 (47,135), 330 (256,457), 226 (148,366) cells/μl respectively] or severe patients[661 (474,1 151),92 (52,139), 54 (34,134), 373 (235,555), 180 (105,310) cells/μl respectively] were both significantly lower than those of healthy controls [1 963 (1 603,2 394),179 (119,239), 356 (231,496), 663 (531,824), 481 (341,693) cells/μl respectively]. Meanwhile, the T cells and CD8⁺T counts in fatal patients [370 (260,537) cells/μl and 87 (74,105) cells/μl] were significantly lower than those in severe and alive patients [722 (390,990) cells/μl and 222 (154,404) cells/μl]. CD8⁺HLA-DR/CD8⁺and CD8⁺CD38⁺/CD8⁺T cell activating subgroups in mild cases[(53.7±19.2)% and 74.8% (64.1%,83.7%) respectively] were significantly higher than those in severe cases[(38.5±21.7)% and 53.3% (45.3%,67.2%) respectively].Moreover,CD8⁺HLA-DR/CD8⁺count in severe and alive group was higher than that in fatal group [(46.1±19.1)% vs. (18.2±14.6)%, P<0.01]. Logistic regression analysis showed that CD8⁺T cell count (OR=0.952, 95%CI 0.910-0.997, P=0.035) and CD8⁺HLA-DR/CD8⁺T (OR=0.916, 95%CI 0.850-0.987, P=0.022) were both negatively correlated with mortality.Peripheral blood lymphocyte counts in mild cases rapidly decreased within 1 day after diagnosis, and returned to the basic level one week later. Conclusions All peripheral blood lymphocyte subsets (T,B,NK) in patients with influenza are significantly reduced. These findings are consistent with the immunological characteristics of respiratory viral infections, in which peripheral lymphocytes (especially T cells) migrate to respiratory tract in the early stage and circulate to the peripheral blood after recovery. The activated CD8⁺T cell counts in peripheral blood are negatively correlated with the severity of disease, which could be considered as a prognostic indicator of severe influenza.

The distribution of peripheral blood lymphocyte subsets were compared between patients with colorectal cancer and healthy controls.The number of natural killer(NK) cells and CD8+T cells and the percentage of naive CD4+T cells were all decreased significantly in patients.On the contrary,the percentages of memory CD4+T cells,HLA-DR+ CD8+ T cells and CD38+ CD8+ T cells were significantly increased.It suggests that the tumor killing effect of cytotoxic lymphocytes in peripheral blood is impaired in patients with colorectal cancer,whereas the immune response is over stimulated.

Objective To investigate the clinical features and T lymphocytes subsets in patients with acquired immune deficiency syndrome (AIDS) and cytomegalovirus (CMV) infection.Methods A total of 48 hospitalized patients with human immunodeficiency virus (HIV)-1/AIDS and CMV infections were recruited at Peking Union Medical College Hospital from Jan 2010 to Aug 2017.Their clinical features and immune function were retrospectively analyzed.Patients with only HIV/AIDS in previous study were recruited as controls,Results All 48 patients were at C3 stage,including 36 men and 12 women.Five of them were younger than 30 years old,33 cases within 31-50 years old,and 10 cases older than 50 years old.Thirty-five patients had CD4+T lymphocytes ≤ 50 cells/μl,7 cases with CD4+T cells 51-100/μl,3 cases with 101-200 cells/μl,and 3 cases over 200 cells/μl.As to CMV infections,there were 31 cases of CMV viremia,1 case of CMV encephalitis,1 case of CMV enteritis,5 cases of CMV pneumonia,and 9 cases of CMV retinitis.Other opportunistic infections were also common including 16 cases of pneumocystis pneumonia,9 cases of tuberculosis,5 cases of syphilis,18 cases of digestive tract fungal infections,8 cases of pulmonary fungal infections,2 cases of EB virus infections,2 cases of HIV encephalopathy/progressive multifocal leukoencephalopathy (PML),3 cases of cryptococcal meningitis,1 case of toxoplasma infection.In group of both CMV and HIV/AIDS infections,100％ patients had inverted CD4+/CD8+ ratio.The immune activation marker CD8+CD38+/CD8+ was higher (61.6％-98.8％) with a median value of 91.2％ in 40 patients.HLA-DR+ CD8+/CD8+,another marker for T cell activation,was 25.5％-98.0％ in 44 patients with a median value of 60.3％.Thirty-six patients had both immune activation markers positive.There was no significant difference in counts of B cells,natural killer cells,CD4+ T cells,CD8+ T cells and immune activation subsets stratified by gender and age (P＞0.05).Meanwhile,neither serum HIV viral load nor serum CMV viral load was correlated with HLA-DR+CD8+/CD8+,CD8+CD38+/CD8+,CD4+T cell counts,and CD4+/CD8+ ratio in the CMV and HIV/AIDS co-infection group(all P＞0.05),while HIV viral load in HIV/AIDS only group was significantly correlated with HLA-DR+CD8+T/CD8+,CD38+CD8+/CD8+,CD4+ T cell counts,CD4+/CD8+ ratio (r=0.473,0.575,-0.767 and-0.678,respectively,all P＜0.05).Conclusions CMV infections develop in HIV patients with advanced stage.CMV infection can cause life-threatening multiple organ lesions,especially in those with CD4+ T cells less than 100 cells/μl.It is of great importance to screen CMV-IgM,pp65 antigen,CMV DNA to make early diagnosis and treatment.

Objective To investigate the common opportunistic infections and the characteristics of peripheral lymphocyte subsets in patients with systemic lupus erythematosus (SLE). Methods From December 2013 to December 2016, peripheral lymphocyte subsets were consecutively detected by flow cytometry in treated SLE patients with or without opportunistic infections(OIs).The lymphocyte subsets in healthy donors were used as normal control group. Results A total of 145 treated SLE patients were enrolled including 108 with OIs and 37 without OIs.The common OIs were cytomegalovirus(CMV)diseases (66/108), Pneumocystis jirovecii pneumonia (PJP, 16/108), other fungal infections (16/108), Epstein-Barr virus (EBV, 15/108) and tuberculosis (14/108). Compared with treated SLE without OIs, total lymphocyte, CD4+T,and CD8+T lymphocyte counts were significantly reduced in SLE with OIs[1 260(780,1 810)cells/μl vs. 565(399,1 043)cells/μl,P<0.001; 485(280,811)cells/μl vs. 173(95,327)cells/μl,P<0.001; 464 (339,764)cells/μl vs.265(158,424)cells/μl,P=0.003,respectively].Conclusions The common OIs in treated SLE patients were CMV diseases,PJP,other fungi,EBV and tuberculosis.OIs are prone to develop in SLE patients with severe lymphocytopenia,especially CD4+T cell depletion.

Objective The effect of different doses of ethylnitrosourea(ENU)and cyclophosphamide(CP)on the loss rate of CD59 on peripheral blood erythrocytes was explored to optimize the detection method of Pig-a gene mutation. Methods According to the weight and loss rate of CD59 on peripheral blood erythrocytes,rats were divided into 4 groups:the control group,CP 40 mg/kg group,ENU 10 mg/kg group and ENU 40 mg/kg group(n=6). The control group was injected i.p. with PBS,other groups were injected i.p. with corresponding solutions. The body weight of rats on days 0,7,14,21, 28, 42 and 56 were recorded. At the same time, blood samples were collected and incubated with antibodies,and the loss rate of RBCCD59-was detected by flow cytometry. Results Compared with the control group, at different time points, the body weight and weight gain of ENU 10 mg/kg group and ENU 40 mg/kg group had no statistically significant difference(P > 0.05),while those in the CP 40 mg/kg group were significantly decreased(P <0.05). The loss rate of RBCCD59-was significantly increased in the CP 40 mg/kg group at 28,42 and 56 days, ENU 10 mg/kg group at 42 and 56 days,and ENU 40 mg/kg group at 7,14,21,28,42 and 56 days,(P < 0.05). The results showed a dose-response relationship. Conclusions Under the conditions of this Pig-a mutation detection method,ENU is superior to CP on raising loss rate of RBCCD59-,ENU 40 mg/kg is better than 10 mg/kg,and 28 days is suitable as the test period.

Objective To better understand the infection status of HIV in the patients seeking medical care in Peking Union Medical College Hospital.Methods The HIV detection data of the patients in the hospital from 2003-2014 were collected for a statistical analysis with software SPSS 19.0.Results A total of 715 421 patients were screened,and 1 012 (0.14％) patients were HIV positive,and HIV infection were confirmed in 776 (0.11％) patients by Western Blot testing.The detection rate of HIV infection increased from 0.05％ in 2003 to 0.17％ in 2014 (trend x2=66.83,P=0.000),and the increase during 2012-2014 was obvious.Of the 776 newly diagnosed HIV-infected individuals,631 (81.31％) were men and 145 (18.69％) were women.The percentage of the males infected with HIV increased from 50.00％ to 90.26％ (trend x2=58.41,P=0.000).The median age was 36 years (interquartile range:27-43),and the age group 18-50 years were mostly affected.In the 776 patients infected with HIV,634 (81.70％) were infected through sexual contacts,and the proportion of sexual transmissions increased with year (trend x2=126.38,P=0.000).The proportion of infected men who have sex with men (MSM) increased from 0％ in 2003 to 53.90％ in 2014 (trend X2=11.96,P=0.001),similar to the trend in western countries.The proportion of infected patients who were not married increased from 18.75％ to 42.21％ (trend x2=43.74,P=0.000).The top three source departments of HIV/AIDS cases were internal medicine (51.03％),emergency room (18.30％) and dermatology (13.53％).The proportion of the HIV/AIDS patients from department of gynecology and obstetrics declined from 18.75％ in 2003 to 2.60％ in 2014.No HIV/AIDS patients were detected in department of surgery,department of otorhinolaryngology,department of ophthalmology,department of stomatology and health examination center in 2003,but 14 cases (9.10％),11 cases (7.14％) and 4 cases (2.60％) were detected in these departments respectively in 2014.Conclusion The HIV detection rate increased with year in Peking Union Medical College Hospital,suggesting the necessity of strengthened HIV test in general hospitals.MSM are the population at high risk,to whom more attention should be paid.

Objective To understand the changes of cardiac systolic and diastolic function in human immunodeficiency virus (HIV)-infected patients without evidence of cardiac disease in China.Methods Forty-two HIV-infected patients who were followed up in the Department of Infectious Diseases at Peking Union Medical College Hospital without cardiac involvement were recruited.All the HIV-infected patients had received highly active antiroviral therapy (HAART) for more than 12 months with viral suppression.And 30 age and sex matched healthy subjects without cardiac disease manifestations were enrolled as controls.Every group members underwent transthoracic echocardiography evaluation.The indexes of cardiac systolic and diastolic function between HIV-infected patients and healthy controls were compared.Results Diastolic abnormality occurred in 20 cases in HIV-infected group and 6 cases in control group, with statistically significant difference (χ2=5.79, P=0.007).The E wave deceleration time (EDT) in HIV-infected patients were significantly decreased than healthy controls ([161.87±21.64] ms vs.[190.34±37.22], t=-3.20, P=0.002).There were no significant differences of E/A ratio ([1.16±0.35] vs.[1.19±0.26]), E/Ea ratio ([5.43±1.99] vs.[5.78±0.91]), isovolumic relaxation time (IVRT), ([93.18±20.34] ms vs.[93.57±18.55]ms), Ea ([10.18±2.80] cm/s vs.[11.45±2.75] cm/s) between HIV-infected patients and controls (t=1.13,1.53,0.67 and 0.29, respectively, all P>0.05).Among cardiac systolic function markers, left ventricular ejection fractions in HIV-infected patients and control group were (66.7±6.4)% and (68.7±4.2)%, respectively.And left ventricular shortening rates were (37.08±4.79)% and (38.17±3.96)%, respectively.Both showed no significant difference between the two groups (t=-1.51 and-1.00, respectively, both P>0.05).Conclusions Compared with control group, subclinical cardiac diastolic dysfunction is more frequently observed in HIV-infected patients.However, there are no significant differences of cardiac systolic function markers between HIV-infected patients and controls.