Common and rare variant analyses combined with single-cell multiomics reveal cell-type-specific molecular mechanisms of COVID-19 severity

The determinants of severe COVID-19 in non-elderly adults are poorly understood, which limits opportunities for early intervention and treatment. Here we present novel machine learning frameworks for identifying common and rare disease-associated genetic variation, which outperform conventional approaches. By integrating single-cell multiomics profiling of human lungs to link genetic signals to cell-type-specific functions, we have discovered and validated over 1,000 risk genes underlying severe COVID-19 across 19 cell types. Identified risk genes are overexpressed in healthy lungs but relatively downregulated in severely diseased lungs. Genetic risk for severe COVID-19, within both common and rare variants, is particularly enriched in natural killer (NK) cells, which places these immune cells upstream in the pathogenesis of severe disease. Mendelian randomization indicates that failed NKG2D-mediated activation of NK cells leads to critical illness. Network analysis further links multiple pathways associated with NK cell activation, including type-I-interferon-mediated signalling, to severe COVID-19. Our rare variant model, PULSE, enables sensitive prediction of severe disease in non-elderly patients based on whole-exome sequencing; individualized predictions are accurate independent of age and sex, and are consistent across multiple populations and cohorts. Risk stratification based on exome sequencing has the potential to facilitate post-exposure prophylaxis in at-risk individuals, potentially based around augmentation of NK cell function. Overall, our study characterizes a comprehensive genetic landscape of COVID-19 severity and provides novel insights into the molecular mechanisms of severe disease, leading to new therapeutic targets and sensitive detection of at-risk individuals.

Clinical value of monitoring of plasma docetaxel concentration in patients with breast cancer in AC -T sequential chemotherapy / 中国基层医药

Objective To investigate the relationship between plasma docetaxel concentration and the efficacy as well as toxic and side effects in patients with breast cancer after chemotherapy.Methods Seventy -one patients with breast cancer who accepted AC sequential T chemotherapy regimen as first line treatment were selected from April 2015 to September 2015 in Hubei Provicial Tumor Hospital.The plasma concentration of docetaxel was detected by latex immunoturdidimetry after the docetaxel continuous infusion in each cycle.The three groups were assigned according to the concentration distribution of docetaxel:group A (plasma concentration docetaxel ≤ 2.0mg·h -1 · L -1 ),group B (2.1 -2.5mg·h -1 ·L -1 )and group C (≥2.6 mg·h -1 ·L -1 ).The relationship between the drug plasma concentration,therapeutic efficacy and adverse reactions in different docetaxel plasma concentration was analyzed retrospectively by Chi -square tests.Results The average plasma concentrations of docetaxel of the three groups were (1.55 ±0.36)mg·h -1 ·L -1 ,(2.28 ±0.13)mg·h -1 ·L -1 ,(2.87 ±0.38)mg· h -1 · L -1 respectively.The adverse reactions were enhanced with the increasing of docetaxel plasma concentration (χ2 =5.169, 4.463,3.630,P =0.023,0.035,0.047).The therapeutic efficacy of group C and group B was same(95.8%),which was higher than 87.0% of group A,but there was no statistically significant difference (χ2 =1.559,P =0.24). Conclusion Breast cancer patients whose plasma concentration of docetaxel is between 2.1 ~2.5mg·h -1 ·L -1 has a better prognosis,and its adverse reactions are controlled in a certain extent.

Isolation and in vitro propagation of aldehyde dehydrogenases positive breast cancer stem cells and investigation on biological property of these cells / 肿瘤研究与临床

Objective To identify a aldehyde dehydrogenases positive (ALDH+) cancer stem cell subpopulation in MCF-7 cells and to investigate the proliferation and differentiation characteristics of these cells in vitro.Methods ALDH+ breast cancer stem cells were isolated from MCF-7 cells by flow cytometry and the biological property of ALDH+ breast cancer stem cells were examined by scarification test,MTT,growth curvature and Transwell migration assay.Results The ratio of CD-/low24 CD+44 cells was about 1.4 ％ in MCF-7 cells.The ratio of ALDH+ CD-/low24CD+44 cells was about 1.2 ％.The growth curvature of ALDH+ breast cancer stem cells was almost the same with that of CD-/low24 CD+44 cells.The distance between cells was obviously shorter in both CD-/low24 CD+44 cells scarification zone and ALDH+ CD-/low24 CD+44 cells scarification zone.The migration ability of CD-/low24CD+44 cells and ALDH+ CD-/low24CD+44 cells was stronger than control group cells.There were migration ability differences between CD-/low24CD+44 cells and ALDH+ CD-/low24CD+44 cells.The results of Transwell experiments were in coincidence with above results.Lots of CD-/low24CD+44 cells and ALDH+ CD-/low24CD+44 cells were through the membrane.In MTT assay,absorbance values were 1.05±0.098,1.56±0.075 and 1.67±0.032.Conclusion CD--/low24CD+44 and ALDH+ CD-/low24CD+44 breast cancer stem cell subpopulation exist in MCF-7 cells.ALDH could potentially be used as a molecular marker to identify breast cancer stem cell subpopulation.

Clinical study of the axillary conservative surgery by sentinel lymph node biopsy using preoperative lymphoscintigraph technique with 99mTc-SC and methylene blue in breast cancer surgical therapy / 中国医师进修杂志

Objective To evaluate the clinical significance of the axillary conservative surgery by sentinel lymph node biopsy (SLNB) using preoperative lymphoscintigraph technique with 99mTc-SC and methylene blue in early-stage breast cancer patients. Methods The sentinel lymph node (SLN) of 187 patients were located with preoperative lymphoscintigraph technique with 99mTc-SC and labeled with methylene blue during the operations. The metastasis of SLN was detected using frozen section technique. There were 51 patients whose SLN were positive having been carried with modified radical mastectomy of breast cancer and axillary lymph node dissection (ALND), 136 patients' SLN were negative,58 patients of those were carried with mammectomy or partial mastcctomy and ALND (group A),while 78 patients were carried out with mammectomy or partial mastectomy only (group B). The sentinel lymph nodes were detected with HE stain after surgery. All the patients were treated with chemotherapy,and the patients with partial mastcctomy must be treated with radiotherapy. There were 2 patients with micrometastasis in group B being treated with mammectomy or partial mastcctomy only,and carried out with ALND again. Results The number of cases with upper limb numbness, edema, dysfunction in group A were 36,8 and 45 cases, in group B were 2,0,0 case respectively. Group A compared with group B was increased significantly (P 0.05). Conclusion It is simple and accurate to carry out SLNB using preoperative lymphoscintigraph technique with 99mTc-SC combined with methylene blue,and the effect is reliable.