Innate immune system activation in zebrafish and cellular models of Diamond Blackfan Anemia.

Deficiency of ribosomal proteins (RPs) leads to Diamond Blackfan Anemia (DBA) associated with anemia, congenital defects, and cancer. While p53 activation is responsible for many features of DBA, the role of immune system is less defined. The Innate immune system can be activated by endogenous nucleic acids from non-processed pre-rRNAs, DNA damage, and apoptosis that occurs in DBA. Recognition by toll like receptors (TLRs) and Mda5-like sensors induces interferons (IFNs) and inflammation. Dying cells can also activate complement system. Therefore we analyzed the status of these pathways in RP-deficient zebrafish and found upregulation of interferon, inflammatory cytokines and mediators, and complement. We also found upregulation of receptors signaling to IFNs including Mda5, Tlr3, and Tlr9. TGFb family member activin was also upregulated in RP-deficient zebrafish and in RPS19-deficient human cells, which include a lymphoid cell line from a DBA patient, and fetal liver cells and K562 cells transduced with RPS19 shRNA. Treatment of RP-deficient zebrafish with a TLR3 inhibitor decreased IFNs activation, acute phase response, and apoptosis and improved their hematopoiesis and morphology. Inhibitors of complement and activin also had beneficial effects. Our studies suggest that innate immune system contributes to the phenotype of RPS19-deficient zebrafish and human cells

Acalabrutinib monotherapy in patients with chronic lymphocytic leukemia who are intolerant to ibrutinib.

The Bruton tyrosine kinase (BTK) inhibitor ibrutinib improves patient outcomes in chronic lymphocytic leukemia (CLL); however, some patients experience adverse events (AEs) leading to discontinuation. Acalabrutinib is a potent, covalent BTK inhibitor with greater selectivity than ibrutinib. We evaluated the safety and efficacy of 100 mg of acalabrutinib twice daily or 200 mg once daily in patients with CLL who discontinued ibrutinib because of intolerance as determined by the investigators. Among 33 treated patients (61% men; median age, 64 years; range, 50-82 years), median duration of prior ibrutinib treatment was 11.6 months (range, 1-62 months); median time from ibrutinib discontinuation to acalabrutinib start was 47 days (range, 3-331 days). After a median of 19.0 months (range, 0.2-30.6 months), 23 patients remained on acalabrutinib; 10 had discontinued (progressive disease, n = 4; AEs, n = 3). No acalabrutinib dose reductions occurred. During acalabrutinib treatment, the most frequent AEs included diarrhea (58%), headache (39%), and cough (33%). Grade 3/4 AEs occurred in 58%, most commonly neutropenia (12%) and thrombocytopenia (9%). Of 61 ibrutinib-related AEs associated with intolerance, 72% did not recur and 13% recurred at a lower grade with acalabrutinib. Overall response rate was 76%, including 1 complete and 19 partial responses and 5 partial responses with lymphocytosis. Among 25 responders, median duration of response was not reached. Median progression-free survival (PFS) was not reached; 1-year PFS was 83.4% (95% confidence interval, 64.5%-92.7%). Acalabrutinib was well tolerated with a high response rate in patients who were previously intolerant to ibrutinib. This trial was registered at www.clinicaltrials.gov as #NCT02029443

Synergy effect of combined near and mid-infrared fibre spectroscopy for diagnostics of abdominal cancer

Cancers of the abdominal cavity comprise one of the most prevalent forms of cancers, with the highest contribution fromcolon and rectal cancers (12% of the human population), followed by stomach cancers (4%). Surgery, as the preferred choice of treatment, includes the selection of adequate resection margins to avoid local recurrences due to minimal residual disease. The presence of functionally vital structures can complicate the choice of resection margins. Spectral analysis of tissue samples in combination with chemometric models constitutes a promising approach for more e cient and precise tumour margin identification. Additionally, this technique provides a real-time tumour identification approach not only for intraoperative application but also during endoscopic diagnosis of tumours in hollow organs. The combination of near-infrared and mid-infrared spectroscopy has advantages compared to individual methods for the clinical implementation of this technique as a diagnostic tool

IgG glycosylation and DNA methylation are interconnected with smoking

Background: Glycosylation is one of the most common post-translation modifications with large influences on protein structure and function. The effector function of immunoglobulin G (IgG) alters between pro- and anti-inflammatory, based on its glycosylation. IgG glycan synthesis is highly complex and dynamic. Methods: With the use of two different analytical methods for assessing IgG glycosylation, we aim to elucidate the link between DNA methylation and glycosylation of IgG by means of epigenome-wide association studies. In total, 3000 individuals from 4 cohorts were analyzed. Results: The overlap of the results from the two glycan measurement panels yielded DNA methylation of 7 CpG-sites on 5 genomic locations to be associated with IgG glycosylation: cg25189904 (chr.1, GNG12); cg05951221, cg21566642 and cg01940273 (chr.2, ALPPL2); cg05575921 (chr.5, AHRR); cg06126421 (6p21.33); and cg03636183 (chr.19, F2RL3). Mediation analyses with respect to smoking revealed that the effect of smoking on IgG glycosylation may be at least partially mediated via DNA methylation levels at these 7 CpG-sites. Conclusion: Our results suggest the presence of an indirect link between DNA methylation and IgG glycosylation that may in part capture environmental exposures. General significance: An epigenome-wide analysis conducted in four population-based cohorts revealed an association between DNA methylation and IgG glycosylation patterns. Presumably, DNA methylation mediates the effect of smoking on IgG glycosylation

DNA methylation age of blood predicts all-cause mortality in later life

Background: DNA methylation levels change with age. Recent studies have identified biomarkers of chronological age based on DNA methylation levels. It is not yet known whether DNA methylation age captures aspects of biological age. Results: Here we test whether differences between people's chronological ages and estimated ages, DNA methylation age, predict all-cause mortality in later life. The difference between DNA methylation age and chronological age ({increment}age) was calculated in four longitudinal cohorts of older people. Meta-analysis of proportional hazards models from the four cohorts was used to determine the association between {increment}age and mortality. A 5-year higher {increment}age is associated with a 21% higher mortality risk, adjusting for age and sex. After further adjustments for childhood IQ, education, social class, hypertension, diabetes, cardiovascular disease, and APOE e4 status, there is a 16% increased mortality risk for those with a 5-year higher {increment}age. A pedigree-based heritability analysis of {increment}age was conducted in a separate cohort. The heritability of {increment}age was 0.43. Conclusions: DNA methylation-derived measures of accelerated aging are heritable traits that predict mortality independently of health status, lifestyle factors, and known genetic factors

Identification of Novel Pathways in the Pathogenesis of Diamond-Blackfan Anemia

Diamond-Blackfan Anemia (DBA) is a genetic bone marrow failure syndrome, typically diagnosed in infants within the first year of life. It is characterized by macrocytic anemia, congenital abnormalities affecting the head, limbs, heart, and genitourinary system, and higher incidence of cancer, including leukemia and solid tumors. DBA is associated with mutations in ribosomal proteins, most commonly RPS19, and several groups have shown p53 pathway upregulation to play a significant role in DBA pathogenesis, though the overall mechanism of disease development remains unclear. Current treatments for DBA include corticosteroids, which have multiple side-effects in children, including short stature and delayed growth; blood transfusions, which carry a risk of organ failure from iron overload; and bone marrow transplants, which require immunosuppression and can result in mortality. Given the undesirable side effects of current DBA treatments, and the tumor suppressor function of p53, which makes it a poor target for therapy, more research is needed to uncover pathways involved in DBA pathogenesis and to identify new drug targets that may be useful for treating DBA.In this dissertation, we used primary human hematopoietic progenitor cells from fetal liver and cord blood that were transduced with lentivirus carrying shRNA against RPS19 as a model to identify novel pathways that play a role in DBA. In Chapter 2, we show that RPS19 deficient cells have reduced expression of the erythroid transcription factor GATA1, and that this reduction is p53-dependent and mediated by the inflammatory cytokine TNF-α. In Chapter 3, we describe the use of next-generation RNA sequencing to identify pathways dysregulated in RPS19 deficient cells, including inflammation mediated by chemokine and cytokine signaling, WNT signaling pathway, TGF-β signaling pathway, and the transcription factor c-MYC. Finally, in Chapter 4, we explore the role of microRNAs in DBA pathogenesis identified by next-generation microRNA-sequencing, and describe the role of the microRNA miR-34a in RPS19 deficient cells and in erythropoiesis. Taken together, our results suggest a novel role for inflammatory pathways in the pathogenesis of DBA, which can potentially be targeted to develop new treatments for this disease

Identification of Novel Pathways in the Pathogenesis of Diamond-Blackfan Anemia

Diamond-Blackfan Anemia (DBA) is a genetic bone marrow failure syndrome, typically diagnosed in infants within the first year of life. It is characterized by macrocytic anemia, congenital abnormalities affecting the head, limbs, heart, and genitourinary system, and higher incidence of cancer, including leukemia and solid tumors. DBA is associated with mutations in ribosomal proteins, most commonly RPS19, and several groups have shown p53 pathway upregulation to play a significant role in DBA pathogenesis, though the overall mechanism of disease development remains unclear. Current treatments for DBA include corticosteroids, which have multiple side-effects in children, including short stature and delayed growth; blood transfusions, which carry a risk of organ failure from iron overload; and bone marrow transplants, which require immunosuppression and can result in mortality. Given the undesirable side effects of current DBA treatments, and the tumor suppressor function of p53, which makes it a poor target for therapy, more research is needed to uncover pathways involved in DBA pathogenesis and to identify new drug targets that may be useful for treating DBA.In this dissertation, we used primary human hematopoietic progenitor cells from fetal liver and cord blood that were transduced with lentivirus carrying shRNA against RPS19 as a model to identify novel pathways that play a role in DBA. In Chapter 2, we show that RPS19 deficient cells have reduced expression of the erythroid transcription factor GATA1, and that this reduction is p53-dependent and mediated by the inflammatory cytokine TNF-α. In Chapter 3, we describe the use of next-generation RNA sequencing to identify pathways dysregulated in RPS19 deficient cells, including inflammation mediated by chemokine and cytokine signaling, WNT signaling pathway, TGF-β signaling pathway, and the transcription factor c-MYC. Finally, in Chapter 4, we explore the role of microRNAs in DBA pathogenesis identified by next-generation microRNA-sequencing, and describe the role of the microRNA miR-34a in RPS19 deficient cells and in erythropoiesis. Taken together, our results suggest a novel role for inflammatory pathways in the pathogenesis of DBA, which can potentially be targeted to develop new treatments for this disease

The oldest crust in the Ukrainian Shield - Eoarchaean U-Pb ages and Hf-Nd constraints from enderbites and metasediments

The oldest crust in the Ukrainian Shield occurs in the Podolian and Azov domains which both include Eoarchaeanarchaean components. U-Pb age data for Dniestr-Bug enderbites, Podolian Domain, indicate these are ca. 3.75 Ga old, and Lu-Hf isotope date indicate extraction from chondritic to mildly isotopically depleted sources with εHf up to ca. +2. Nd model ages support their Eoarchaeanarchaean age, while model ages for Dniestr-Bug metasedimentary gneisses indicate that these also include younger crustal material. Most of the Hf-age data for metasedimentary zircon from the Soroki greenstone belt, Azov Domain, reflects Eoarchaeanarchaean primary crustal sources with chondritic to mildly depleted Hf isotope signatures at 3.75 Ga. A minor portion is derived from Mesoarchaeanarchaean crust with a depleted εHf signature of ca. +4 at 3.1 Ga. U-Pb zircon ages from Fedorivka greenstone belt metasediments are consistent with the Soroki age data, but also include a 2.7‒2.9 Ga component. Nd whole rock model ages provide support for a younger crustal component in the latter. Both domains have been subject to Neoarchaeanarchaean, ca. 2.8 Ga, and Palaeoproterozoic, ca. 2.0 Ga metamorphism. The spatial distribution indicates that the Podolian and Azov domains have evolved independently of each other before the amalgamation of the Ukrainian Shield