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  • 1
    In: Nature Genetics, Springer Science and Business Media LLC, Vol. 55, No. 7 ( 2023-07), p. 1126-1137
    Type of Medium: Online Resource
    ISSN: 1061-4036 , 1546-1718
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 1494946-5
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    American Society of Clinical Oncology (ASCO) ; 2021
    In:  Journal of Clinical Oncology Vol. 39, No. 15_suppl ( 2021-05-20), p. e20510-e20510
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 39, No. 15_suppl ( 2021-05-20), p. e20510-e20510
    Abstract: e20510 Background: As the incidence of lung cancer soars, the number of patients diagnosed with multiple primary lung cancers (MPLC) was also rising. It was already known that genetic and immune microenvironment were involved in oncogenesis and treatment of tumors. The aim of this study was to investigate genetic and T Cell Receptor (TCR) Repertoire characteristic in patients with multiple primary lung cancers. Methods: We queried 84 lesions analyzed by 1021 gene panel and TCRβ repertoire for 32 patients with MPLC profiled by NGS. Shannon index was calculated on the clonal abundance of all productive TCR sequences. T cell clonality was defined as 1 − (Shannon index)/ln(# of productive unique sequences). MOI was a measure of the similarity in the T cell repertoire between tissue and blood taking into account the specific rearrangements and their respective frequencies. Results: 98.7% (77/78) of lesions from 30 patients were detected somatic mutations and EGFR mutations were detected in 44.2% (34/77) lesions; BRAF were detected in 22.1% (17/77) lesions; and KRAS were detected in 14.3% (11/77) lesions. We found different combinations of three driving genes in 13 patients. Almost all lesions (97.4%) had mutations in the RAS-RTK pathway. Shared mutations were detected between different lesions from 8 patients, and two patients were intrapulmonary metastases; The others were more meet to convergent evolution. The overall immune characteristics of 76 lesions from 30 patients were further studied. The shannon index showed heterogeneity in difference lesions of each patients and the comparing the most and least shannon index lesions variations ranged between 0.066 to 3.344. The lesions with shared mutations showed higher Shannon index than the non-share lesions (7.31 vs 6.96; p = 0.011). The heterogeneity also identified in MOI and 55% MOI of lesions was less than 0.5. The lesions with MOI higher than 0.5 had some pathologically identical and some have shared mutations. Furthermore, the shared TCR between lesions in same patient were analyzed. The more than 78% of T cell clones were restricted to individual lesions, which indicated the presence of heterogeneity between lesions due to T cell clones distribution heterogeneity. Meanwhile, the shared TCR was significantly higher in identical pathology group than difference pathology group (17.18% vs 6.60%; p = 0.0006); Besides, we found that shared TCR was comparable in both shared mutations and non-shared mutations groups (13.1% vs 15.33%, p = 0.537). These results suggested that the pathology between lesions in patients was affected to 100% shared TCR. Conclusions: In conclusion, the multiple lesions of MPLC showed heterogeneity and this heterogeneity is due to the distribution of T cell clones between lesions. Besides, the MOI and shared TCR was higher in MPLC with same pathology, which may increase the understanding of MPLC and influence the treatment choice of MPLC patients.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2021
    detail.hit.zdb_id: 2005181-5
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  • 3
    In: Blood, American Society of Hematology, Vol. 109, No. 9 ( 2007-05-01), p. 3839-3848
    Abstract: Bone homeostasis is regulated by a delicate balance between osteoblastic bone formation and osteoclastic bone resorption. Osteoclastogenesis is controlled by the ratio of receptor activator of NF-κB ligand (RANKL) relative to its decoy receptor, osteoprotegerin (OPG). The source of OPG has historically been attributed to osteoblasts (OBs). While activated lymphocytes play established roles in pathological bone destruction, no role for lymphocytes in basal bone homeostasis in vivo has been described. Using immunomagnetic isolation of bone marrow (BM) B cells and B-cell precursor populations and quantitation of their OPG production by enzyme-linked immunosorbent assay (ELISA) and real-time reverse transcriptase–polymerase chain reaction (RT-PCR), cells of the B lineage were found to be responsible for 64% of total BM OPG production, with 45% derived from mature B cells. Consistently B-cell knockout (KO) mice were found to be osteoporotic and deficient in BM OPG, phenomena rescued by B-cell reconstitution. Furthermore, T cells, through CD40 ligand (CD40L) to CD40 costimulation, promote OPG production by B cells in vivo. Consequently, T-cell–deficient nude mice, CD40 KO mice, and CD40L KO mice display osteoporosis and diminished BM OPG production. Our data suggest that lymphocytes are essential stabilizers of basal bone turnover and critical regulators of peak bone mass in vivo.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2007
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 4
    Online Resource
    Online Resource
    American Society of Clinical Oncology (ASCO) ; 2021
    In:  Journal of Clinical Oncology Vol. 39, No. 15_suppl ( 2021-05-20), p. e21076-e21076
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 39, No. 15_suppl ( 2021-05-20), p. e21076-e21076
    Abstract: e21076 Background: Cancer is most commonly diagnosed disease worldwide and also a leading cause of death. Cancer is more common in older people, but it can also be found in younger people. As the importance of T cell receptor (TCR) repertoire gains appreciation, particularly given their potential utility for cancer immunotherapeutic prognostication, the characteristics of TCR repertoire are needed. We detected the complementarity determining region 3 (CDR3) by TCR sequence to describe the correlation between diversity and clonality in human’s immune system and age. Methods: The TCRβ repertoire of 47 stage Ia lung cancer patients were analyzed. Genomic DNA was extracted from peripheral blood or tissue, and used to amplified and sequenced the CDR3 region of rearranged TCRβ genes. Finally, we got the relative frequencies of patients T cell clones. Shannon index was calculated on the clonal abundance of all productive TCR sequences. Simpson index also was calculated to measure the clonality of TCR repertoire. MOI was a measure of the similarity in the T cell repertoire between tissue and blood taking into account the specific rearrangements and their respective frequencies. Results: In tissue, the Simpson index ranged from 0.00075 to 0.11466 (mean = 0.01343); Shannon index ranged from 2.91 to 8.95 (mean = 6.26). The age ranged from 27 to 78 (median = 63). Patients were divided into two groups based on median age. The older showed higher Shannon index (p = 0.005) but lower Simpson index (p = 0.0072) than younger patients in tissue. Further, the higher Shannon index was found in younger group in blood(p = 0.0411). Interestingly, the MOI of the older group was significantly higher than that of the younger group (p = 0.0181), suggesting that the older group had a relatively better TME immune response. Then, the usage of V and J gene segments were analyzed. Through statistical analysis and the frequencies of V and J gene usage, we identified that more V and J gene usage were different in older and younger patients. The TRBJ1-1 and TRBJ1-2 were more common in younger patients and TRBJ2-1 and TRBJ2-2 were more common in older patients. There was also more V gene usage different in both groups. Conclusions: Given that the use of certain TRBV regions is predominant in tumor tissues, our results suggested that there may be differences in immune responses of TME to tumors in younger and older patients.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
    RVK:
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2021
    detail.hit.zdb_id: 2005181-5
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. 5887-5887
    Abstract: Background: Recent advances in CT screening of lung cancer has led to an increased incidence of detecting multifocal lung cancers (MFLCs). It has been suggested that the development of lung adenocarcinoma progresses from preinvasive atypical adenomatous hyperplasia (AAH) and adenocarcinoma in situ (AIS), to minimally invasive adenocarcinoma (MIA), and finally invasive lung adenocarcinoma (ADC). In patients with MFLCs, pulmonary nodules at different size and stage can be observed. Discrimination of synchronous multiple primary lung cancers (SMPLCs) from intrapulmonary metastases is challenging, which may influence the optimal approach for patient management. Method:Whole-exome sequencing (WES) was performed on 100 resected lung nodule samples (18 AAH, 15 AIS, 12 MIA, 55 ADC) from 33 patients with clinical diagnosed SMPLCs (3 samples per patient in average, ranging from 1 to 8 samples per patient). Result:In this cohort, 76% of patients (25/33) had at least one invasive ADC nodules while four patients had preinvasive (AAH/AIS) nodules only. Progressive evolution of lung tumors was marked by elevated chromosome instability (CIN) and tumor mutational burden (TMB). CIN was significantly higher in ADC lesions compared to other stage lesions. High frequencies of somatic copy number alterations (SCNAs) were identified in both arms of chr19 and the short arm of chr17 (17p) with a trend of progressively increase from AAH to ADC. Mutational signatures associated with age, APOBEC, BRAC and DNA mismatch repair (MMR) deficiency had the tendency to be enriched in later-stage nodules. 54.5% of the patients carried EGFR driver mutations, mainly L858R (89%), but the ratio of EGFR alterations displayed progressively increase from AAH (11%) to ADC (42%). Within the 29 patients with multiple nodules sampled, 10 cases displayed focal-specific EGFR-L858R, three of which had concurrent focal-specific EGFR-e19del. Five patients had EGFR-L858R detected in all the nodules. Pathway analysis revealed that dominant alterations along development of lung adenocarcinoma were centered around MAPK/ERK pathway, evolving from altered downstream genes, such as MAP2K1 and BRAF, in early stage to mutated upstream activator, such as EGFR, in later stage. Majority of MFLCs showed difference in clonal evolution and developmental stage, suggesting independent clonal origins. Multiple overlapping alterations were observed between intra-focal tumor lesions from the same or different lobes in 27.5% of patients (8/29), indicating intrapulmonary metastases. Conclusion: Evolution of lung tumors was associated with increased CIN, TMB, SCNV and altered MAPK/ERK pathway. Independent tumors with obviously molecular heterogeneity were revealed in majority of MFLCs while metastasis might exist. Patients with SMPLCs had the tendency to harbour shared EGFR driver L858R. Citation Format: Naixin Liang, Zhongxing Bing, Yang Song, Yadong Wang, Yanyu Wang, Pancheng Wu, Ziqi Jia, Xiaoying Yang, Lei Cao, Zhili Cao, Ruoying Yu, Rui Liu, Qiuxiang Ou, Hua Bao, Xue Wu, Peng Liu, Shuyang Zhang, Shanqing Li. Clonal heterogeneity and evolution of multifocal lung cancers revealed by whole exome sequencing to facilitate molecular diagnosis of multiple primary lung cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5887.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 6
    Online Resource
    Online Resource
    American Society of Clinical Oncology (ASCO) ; 2020
    In:  Journal of Clinical Oncology Vol. 38, No. 15_suppl ( 2020-05-20), p. e21031-e21031
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 38, No. 15_suppl ( 2020-05-20), p. e21031-e21031
    Abstract: e21031 Background: The incidence and detection rates of multiple primary lung cancer are increasing, as a result of the advances in lung cancer screening techniques. However, the molecular and immune mechanisms of their carcinogenesis were little known, which may have important diagnostic, prognostic and therapeutic implications. Methods: We retrospective analyzed 10 patients (pts) with clinically designated synchronous multiple primary lung cancers (sMPLC). 28 different tumor lesions were included and mutation profiles were analyzed using 1021 genes panel based next-generation sequencing (NGS). Meanwhile, the T-cell receptor (TCR) β repertoire of 28 tumor lesions and peripheral blood were analyzed by amplifying and sequencing the CDR3 region. T-cell clonality was defined as 1-normalized Shannon entropy, which was normalized by dividing Shannon entropy by the natural logarithm of the number of unique productive TCR sequences. Results: 8 of 10 pts were female and only one pts was smoker. The genetic profiles of 28 tissues were analyzed and almost no common mutations were detected between different tumors of one patient. The most common mutation was EGFR and it was detected in 11 tissues belonging to 7 pts. KRAS mutations were detected in 6 tissues belonging to 4 pts and only one patient detected both EGFR and KRAS mutation in different lesions. TP53 mutations were found in 6 tissues, which 5 co-existed with EGFR. Unlike the mutually exclusive between KRAS and EGFR, 4 pts were detected BRAF mutation whose other tissue aslo carried EGFR mutation. Next, we studied T-cell clonality, which ranges from 0 to 1 and describes the shape of T-cell frequency distribution. Analysis of TCR clonality revealed that this metric ranged from 0.092 in Pts T8 to 0.192 in Pts T5. Furthermore, heterogeneity of different lesions of pts was observed, with differences as large as 78% in T-cell clonality across different tumor lesions in Pts T2, which is bigger than difference of between patients. Beside, EGFR mutation lesions showed lower clonality but no significant differences (0.105 vs 0.130,p = 0.245). There no difference of number of non-synonymous mutation (NNSM) between EGFR-mutant and EGFR-wt group (3 vs 2, p = 0.748), and same in KRAS (3.5 vs 2, p = 0.410). However, frequency of share TCR of tissue and blood was positive correlated with NNSM (spearman r = 0.384,p = 0.048), which might means local immune microenvironment was related with regions mutation. Conclusions: Our results reveals independent molecular and immune feature of sMPLC pts, which may have contradictory therapeutic implications.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2020
    detail.hit.zdb_id: 2005181-5
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  • 7
    In: Antimicrobial Agents and Chemotherapy, American Society for Microbiology, Vol. 66, No. 6 ( 2022-06-21)
    Abstract: Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis (NmY) is rare in China; recently, an invasive NmY isolate, Nm512, was discovered in Shanghai with decreased susceptibility to penicillin (Pen NS ). Here, we investigated the epidemiology of NmY isolates in Shanghai and explored the potential commensal Neisseria lactamica donor of the Pen NS NmY isolate. A total of 491 N. meningitidis and 724 commensal Neisseria spp. isolates were collected. Eleven NmY isolates were discovered from IMD ( n  = 1) and carriers ( n  = 10), including two Pen NS isolates with five-key-mutation-harboring (F504L-A510V-I515V-H541N-I566V) penA genes. Five of the eight ST-175 complex (CC175) isolates had a genotype [Y:P1.5-1,2-2:F5-8:ST-175(CC175)] identical to that of the predominant invasive clone found in South Africa. Only one invasive NmY CC23 isolate (Nm512) was discovered; this isolate carried a novel Pen NS penA832 allele, which was identified in commensal N. lactamica isolates locally. Recombination analysis and transformation of the penA allele highlighted that N. meningitidis Nm512 may acquire resistance from its commensal donor; this was supported by the similar distribution of transformation-required DNA uptake sequence variants and the highly cognate receptor ComP between N. meningitidis and N. lactamica . In 2,309 NmY CC23 genomes from the PubMLST database, isolates with key-mutation-harboring penA genes comprised 12% and have been increasing since the 1990s, accompanied by recruitment of the bla ROB-1 and/or quinolone resistance allele. Moreover, penA22 was predominant among genomes without key mutations in penA . These results strongly suggest that Nm512 is a descendant of the penA22 -harboring CC23 isolate from Europe and acquired its penicillin resistance locally from commensal N. lactamica species by natural transformation.
    Type of Medium: Online Resource
    ISSN: 0066-4804 , 1098-6596
    RVK:
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 1496156-8
    SSG: 12
    SSG: 15,3
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  • 8
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 38, No. 15_suppl ( 2020-05-20), p. e21074-e21074
    Abstract: e21074 Background: Patients with small tumor size but lymph node metastases (T1N1-N3, T1N1+) and patients with large tumor size but without lymph node metastases (T3-4N0, T3+N0) mainly belong to stage IIB to IIIA according to the 8 th version TNM staging. However, whether the contradictory between tumor size and lymph node may influence the survival and the underlying genomic differences have not been fully studied. Methods: Whole-exome sequencing and RNA sequencing data for 1001 patients with NSCLC including 514 lung adenocarcinoma (LUAD) and 487 lung squamous cell carcinoma (LUSC) were downloaded from TCGA. The prognosis between patients with T1N1+ and T3+N0 has been investigated. The DNA sequencing data and RNA sequencing data from TCGA were used to study the underlying mechanism. Results: Patients with T3N0+ consisted of 80.2% Stage IIB and 17.4% Stage IIIA and patients with T1N1+ consist of 66.7% Stage IIB and 25.9% Stage IIIA. There were no differences in race, age, staging or neoadjuvant history between T1N1+ and T3+N0 cases. T1N1+ patients were more frequent among females (P = 0.02) and were more likely to be adenocarcinomas (P = 0.01) compared to T3+N0. Patients with T1N1+ was associated with a prolonged disease-free survival (DFS) (HR, 0.47; 95% CI, 0.28-0.79; P 〈 0.05) and progression-free survival (PFS) (HR, 0.31; 95% CI, 0.17-0.56; P 〈 0.001) than patients with T3+N0. In the multivariable cox proportional hazards regression model including stage, patients with T1N1+ still had increased PFS (HR, 0.45; 95% CI, 0.26-0.82; P = 0.009) and DFS (HR, 0.38; 95% CI, 0.16-0.95; P = 0.04) compared to T3+N0 cases. Moreover, patients with T1N2, belong to Stage IIIA according to AJCC 8 th edition TNM staging, had a superior DFS (P = 0.01) and PFS (P = 0.04) compared with the patients with T3N0, who are in Stage IIB. Further investigation revealed that the tumor mutation burden was no significant difference between two groups (P 〉 0.05). There was no difference in genomic alterations between groups in LUSC and LUAD. GSEA analysis revealed that gene expression involved in DNA repair signaling was enriched in T1N1+ patients in LUSC and LUAD. Conclusions: Patients with T1N1+ shows a longer DFS and PFS compared with patients with T3+N0, especially T1N2 cases who belong to Stage IIIA show a better prognosis compared with T3N0 patients who are in Stage IIB, indicating the AJCC 8 th edition TNM staging need to be refined. Moreover, the better prognosis in T1N1+ patients may be related with DNA repair signaling genes enrichment.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2020
    detail.hit.zdb_id: 2005181-5
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  • 9
    In: Antimicrobial Agents and Chemotherapy, American Society for Microbiology, Vol. 64, No. 7 ( 2020-06-23)
    Abstract: For patients hospitalized with severe influenza A virus infection, morbidity and mortality remain high. MHAA4549A, a human monoclonal antibody targeting the influenza A virus hemagglutinin stalk, has demonstrated pharmacological activity in animal studies and in a human influenza A challenge study. We evaluated the safety and efficacy of MHAA4549A plus oseltamivir against influenza A virus infection in hospitalized patients. The CRANE trial was a phase 2b randomized, double-blind, placebo-controlled study of single intravenous (i.v.) doses of placebo, 3,600 mg MHAA4549A, or 8,400 mg MHAA4549A each combined with oral oseltamivir (+OTV) in patients hospitalized with severe influenza A virus infection. Patients, enrolled across 68 clinical sites in 18 countries, were randomized 1:1:1. The primary outcome was the median time to normalization of respiratory function, defined as the time to removal of supplemental oxygen support to maintain a stable oxygen saturation (SpO 2 ) of ≥95%. Safety, pharmacokinetics, and effects on influenza viral load were also assessed. One hundred sixty-six patients were randomized and analyzed during a preplanned interim analysis. Compared to placebo+OTV, MHAA4549A+OTV did not significantly reduce the time to normalization of respiratory function (placebo+OTV, 4.28 days; 3,600 mg MHAA4549A+OTV, 2.78 days; 8,400 mg MHAA4549A+OTV, 2.65 days), nor did it improve other secondary clinical outcomes. Adverse event frequency was balanced across cohorts. MHAA4549A+OTV did not further reduce viral load versus placebo+OTV. In hospitalized patients with influenza A virus infection, MHAA4549A did not improve clinical outcomes over OTV alone. Variability in patient removal from oxygen supplementation limited the utility of the primary endpoint. Validated endpoints are needed to assess novel treatments for severe influenza A virus infection. (This study has been registered at ClinicalTrials.gov under registration no. NCT02293863.)
    Type of Medium: Online Resource
    ISSN: 0066-4804 , 1098-6596
    RVK:
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 1496156-8
    SSG: 12
    SSG: 15,3
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