Towards a Better Characterisation of Leukemic Cells in Chronic Lymphocytic Leukaemia: Cell-Size Heterogeneity Reflects Their Activation Status and Migratory Abilities.

Chronic lymphocytic leukaemia (CLL) is a genetically, morphologically and phenotypically heterogeneous chronic disease with clinical variability between patients. Whether the significant heterogeneity of cell size within the CLL population contributes to the heterogeneous features of this disease has not been investigated. The present study aimed to characterise the phenotypic and functional properties of two subpopulations of typical CLL cells that differ in cell size: small (s-CLL) and large (l-CLL) CLL cells delineated by forward scatter cytometry. The s-CLL cells were characterised by the CD5lowCXCR4hi phenotype, while the l-CLL cells were characterised by the CD5hiCXCR4dim phenotype and indicated a higher expression of CXCR3, CD20, CD38 and HLA-DR. The l-CLL cells displayed higher migration activity towards CXCL12, a tendency towards a higher proliferation rate and an increased capacity to produce IgM in the presence of CpG compared with s-CLL cells. When stimulated with CpG and CXCL12, l-CLL cells were characterised by a higher polarisation phenotype and motility than s-CLL cells. Our study revealed that the differences in CLL cell size reflected their activation status, polarisation and migratory abilities. Our data provide evidence of the importance of cell-size heterogeneity within a CLL pool and the dynamics of cell-size changes for disease pathogenesis, thus deserving further investigation.

Dysregulated KRAS gene-signaling axis and abnormal chromatin remodeling drive therapeutic resistance in heterogeneous-sized circulating tumor cells in gastric cancer patients.

The mechanism by which heterogeneous-sized circulating tumor cells (CTCs) in gastric cancer (GC) patients are resistant to the targeted therapy and/or chemotherapy remains unclear. This study investigated prognostic value and genomic variations of size-heterogenous CTCs, in an attempt to unravel the molecular mechanisms underlying the therapeutic resistance, which is relevant to poor prognosis in GC. Aneuploid CTCs, detected in 111 advanced GC patients, were categorized into small (≤white blood cell [WBC], 25.54%) and large (>WBC, 74.46%) cells. Pre-treatment patients possessing ≥3 baseline small CTCs with trisomy 8 (SCTCstri) or ≥6 large multiploid CTCs (LCTCsmulti) showed an inferior median progression-free survival. Moreover, the cut-off value of ≥6 LCTCsmulti was also an effective prognosticator for poor median overall survival. Single cell-based DNA sequencing of 50 targeted CTCs indicated that SCTCstri and LCTCsmulti harbored distinct gene variations respectively. Mutations in the KRAS and Rap1 pathway were remarkably abundant in SCTCstri, whereas several unique mutations in the MET/PI3K/AKT pathway and SMARCB1 gene were identified in LCTCsmulti. Obtained results suggested that SCTCstri and LCTCsmulti exhibited different mechanisms to therapy resistance and correlated with patients' poor outcome.

Trans-ethnic meta-analysis of rare variants in sequencing association studies.

Trans-ethnic meta-analysis is a powerful tool for detecting novel loci in genetic association studies. However, in the presence of heterogeneity among different populations, existing gene-/region-based rare variants meta-analysis methods may be unsatisfactory because they do not consider genetic similarity or dissimilarity among different populations. In response, we propose a score test under the modified random effects model for gene-/region-based rare variants associations. We adapt the kernel regression framework to construct the model and incorporate genetic similarities across populations into modeling the heterogeneity structure of the genetic effect coefficients. We use a resampling-based copula method to approximate asymptotic distribution of the test statistic, enabling efficient estimation of p-values. Simulation studies show that our proposed method controls type I error rates and increases power over existing approaches in the presence of heterogeneity. We illustrate our method by analyzing T2D-GENES consortium exome sequence data to explore rare variant associations with several traits.

Effects of genetics and early-life mild hypoxia on size variation in farmed gilthead sea bream (Sparus aurata).

The present study evaluated, in an 18-month gilthead sea bream trial, the time course effects of genetics on individual size variation and growth compensation processes in families selected by heritable growth in the PROGENSA® breeding program. Families categorized as fast, intermediate, and slow growing had different growth trajectories with a more continuous growth in fast growth families. This feature was coincident with a reduced size variation at the beginning of the trial that clustered together the half-sib families sharing the same father. Regression analysis evidenced that the magnitude of compensatory growth was proportional to the initial size variation with no rescaling of families at this stage. By contrast, the finishing growth depensation process can mask, at least partially, the previous size convergence. This reflects the different contribution across the production cycle of genetics in growth. How early-life experiences affect growth compensation at juvenile stages was also evaluated in a separate cohort, and intriguingly, a first mild-hypoxia pulse at 60-81 days post-hatching (dph) increased survival rates by 10%, preventing growth impairment when fish were exposed to a second hypoxia episode (112-127 dph). The early hypoxia experience did not have a negative impact on growth compensatory processes at juvenile stages. By contrast, a diminished capacity for growth compensation was found with repeated or late hypoxia experiences. All this reinforces the use of size variation as a main criterion for improving intensive fish farming and selective breeding.

Specific and high-resolution identification of monoclonal antibody fragments detected by capillary electrophoresis-sodium dodecyl sulfate using reversed-phase HPLC with top-down mass spectrometry analysis.

In recent years, capillary electrophoresis-sodium dodecyl sulfate (cSDS) has been widely used for high resolution separation and quantification of the fragments and aggregates of monoclonal antibodies (mAbs) to ensure the quality of mAb therapeutics. However, identification of the low-molecular-weight (LMW) and high-molecular-weight (HMW) species detected in cSDS electropherograms has been based primarily on the approximate MWs calculated from standard curves using known MW standards and correlations with fragments and aggregates identified by other methods. It is not easy to collect sufficient amounts of H/LMW species from cSDS for analysis by orthogonal methods and the direct coupling of cSDS with mass spectrometry (MS) is very difficult due to interference from SDS. In this study, we describe the precise identification of H/LMW species detected by cSDS using reversed-phase high performance liquid chromatography (RP-HPLC) coupled with top-down tandem MS analysis. The H/LMW species were first identified by on-line RP-HPLC MS analysis and the RP-HPLC fractions were then analyzed by cSDS to connect the identified H/LMW species with the peaks in the cSDS electropherogram. With this method, 58 unique H/LMW species were identified from an immunoglobulin G1 (IgG1) mAb. The identified fragments ranged from 10 kDa single chain fragments to 130 kDa triple chain fragments, including some with post-translational modifications. This is the first study to clearly identify the antibody fragments, including the exact clipping sites, observed in cSDS electropherograms. The methodology and results presented here should be applicable to most other IgG1 mAbs.

A novel random effect model for GWAS meta-analysis and its application to trans-ethnic meta-analysis.

Meta-analysis of trans-ethnic genome-wide association studies (GWAS) has proven to be a practical and profitable approach for identifying loci that contribute to the risk of complex diseases. However, the expected genetic effect heterogeneity cannot easily be accommodated through existing fixed-effects and random-effects methods. In response, we propose a novel random effect model for trans-ethnic meta-analysis with flexible modeling of the expected genetic effect heterogeneity across diverse populations. Specifically, we adopt a modified random effect model from the kernel regression framework, in which genetic effect coefficients are random variables whose correlation structure reflects the genetic distances across ancestry groups. In addition, we use the adaptive variance component test to achieve robust power regardless of the degree of genetic effect heterogeneity. Simulation studies show that our proposed method has well-calibrated type I error rates at very stringent significance levels and can improve power over the traditional meta-analysis methods. We reanalyzed the published type 2 diabetes GWAS meta-analysis (Consortium et al., 2014) and successfully identified one additional SNP that clearly exhibits genetic effect heterogeneity across different ancestry groups. Furthermore, our proposed method provides scalable computing time for genome-wide datasets, in which an analysis of one million SNPs would require less than 3 hours.

Continuously Cumulating Meta-Analysis and Replicability.

The current crisis in scientific psychology about whether our findings are irreproducible was presaged years ago by Tversky and Kahneman (1971), who noted that even sophisticated researchers believe in the fallacious Law of Small Numbers-erroneous intuitions about how imprecisely sample data reflect population phenomena. Combined with the low power of most current work, this often leads to the use of misleading criteria about whether an effect has replicated. Rosenthal (1990) suggested more appropriate criteria, here labeled the continuously cumulating meta-analytic (CCMA) approach. For example, a CCMA analysis on a replication attempt that does not reach significance might nonetheless provide more, not less, evidence that the effect is real. Alternatively, measures of heterogeneity might show that two studies that differ in whether they are significant might have only trivially different effect sizes. We present a nontechnical introduction to the CCMA framework (referencing relevant software), and then explain how it can be used to address aspects of replicability or more generally to assess quantitative evidence from numerous studies. We then present some examples and simulation results using the CCMA approach that show how the combination of evidence can yield improved results over the consideration of single studies.

Size heterogeneity analysis of monoclonal antibody products / 中华微生物学和免疫学杂志

Objective To compare the capability of capillary electrophoresis-sodium dodecyl sul-fate ( CE-SDS) and size exclusion-high performance liquid chromatography ( SE-HPLC) for analysis of size heterogeneity of monoclonal antibody products .Methods The size heterogeneity of one humanized anti-VEGF monoclonal antibody was analyzed by using non-reduced and reduced CE-SDS, and conventional , de-natured and denatured reduced SE-HPLC.Results The percentage of aggregates detected by non-reduced CE-SDS (0.82%±0.01%) was equal to that by using denatured SE-HPLC (1.05%±0.02%), but it was significantly lower than that by using conventional SE-HPLC analysis (5.08%±0.10%).With regard to fragments analyzed with non-reduced antibodies, its percentage was (7.12±0.04)% measured by non-re-duced CE-SDS analysis that was significantly higher than that by conventional SE -HPLC analysis (0.02%± 0.01%) and denatured SE-HPLC analysis (0.62%±0.01%).Using reduced antibodies , the percentage of fragments was (3.19±0.50)%tested by reduced CE-SDS analysis that was significantly higher than that by using denatured reduced SE-HPLC analysis (0.07%±0.01%).Conclusion Conventional SE-HPLC was more objective than CE-SDS for content analysis of aggregates , as both the covalent and non-covalent forms of aggregates could be detected .Non-reduced CE-SDS could demonstrate the content of clips , while reduced CE-SDS showed the degraded fragments .Therefore, CE-SDS had an advantage over conventional SE-HPLC for content analysis of fragments .The use of the two analytical methods in combination provided solid techni-cal supports for the quality control of size heterogeneity of monoclonal antibodies .

Comparative study of size and charge heterogeneities of anti-TNF-αantibodies by high performance liquid chromatography / 中华微生物学和免疫学杂志

Objective To analyze the differences of size and charge heterogeneities between origi-nal humanized anti-TNF-αantibody and four similar biotherapeutic products ( SBP ) .Methods The size exclusion chromatography ( SEC-HPLC ) and weak cation exchange chromatography ( WCX-HPLC ) were used to analyze the size and charge heterogeneities , respectively.Carboxypeptidase B (CpB) treatment was employed to analyze the source of charge heterogeneity of the antibody products .Results Four SBPs showed the same pattern with the originator in SEC-HPLC, and no significant difference with the percentage of mono-mer was observed .The percentages of the aggregates of SBP-3 and SBP-4 were a little higher than those of the originator .The charge distribution of SBPs was significantly different from the originator ′s, especially in the basic region .The results from the samples treated with CpB indicated that the difference of charge distri -bution in the basic region might be caused by the C-terminal lysine variants .Conclusion Four SBPs showed similar size heterogeneity with the originator , but significant differences with charge heterogeneity were observed among them .The study suggested that more attention should be paid to the charge heterogene -ity analysis of the biosimilar products .