Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes.

BACKGROUND: Rare oncogenic driver events, particularly affecting the expression or splicing of driver genes, are suspected to substantially contribute to the large heterogeneity of hematologic malignancies. However, their identification remains challenging. METHODS: To address this issue, we generated the largest dataset to date of matched whole genome sequencing and total RNA sequencing of hematologic malignancies from 3760 patients spanning 24 disease entities. Taking advantage of our dataset size, we focused on discovering rare regulatory aberrations. Therefore, we called expression and splicing outliers using an extension of the workflow DROP (Detection of RNA Outliers Pipeline) and AbSplice, a variant effect predictor that identifies genetic variants causing aberrant splicing. We next trained a machine learning model integrating these results to prioritize new candidate disease-specific driver genes. RESULTS: We found a median of seven expression outlier genes, two splicing outlier genes, and two rare splice-affecting variants per sample. Each category showed significant enrichment for already well-characterized driver genes, with odds ratios exceeding three among genes called in more than five samples. On held-out data, our integrative modeling significantly outperformed modeling based solely on genomic data and revealed promising novel candidate driver genes. Remarkably, we found a truncated form of the low density lipoprotein receptor LRP1B transcript to be aberrantly overexpressed in about half of hairy cell leukemia variant (HCL-V) samples and, to a lesser extent, in closely related B-cell neoplasms. This observation, which was confirmed in an independent cohort, suggests LRP1B as a novel marker for a HCL-V subclass and a yet unreported functional role of LRP1B within these rare entities. CONCLUSIONS: Altogether, our census of expression and splicing outliers for 24 hematologic malignancy entities and the companion computational workflow constitute unique resources to deepen our understanding of rare oncogenic events in hematologic cancers.

Impact of a family-centred clinical care programme on short-term outcomes of very low-birth weight infants.

AIM: We evaluated the effects of a family-centred clinical care pathway and case management programme on short-term clinical outcome in a cohort of very low-birth weight (VLBW) infants. METHODS: The programme, named NeoPAss, was developed at the Department of Neonatology Children's hospital Passau in 2013. Short-term outcomes of infants were compared to matched controls from the Bavarian neonatology surveillance database before (n = 111; 2008-2012) and after implementation (n = 170; 2014-2017). RESULTS: After implementation the rate of late-onset sepsis was significantly lower (2.5% vs. 10.7%, p = 0.005) and the length of stay was significantly shorter (VLBW 28 to 31 weeks' gestational age (GA) 47.5 vs. 53.1 days, p = 0.047; <28 weeks' GA 79.4 vs. 91.9 days, p = 0.007) in the intervention group compared to controls. Infants were discharged with significantly lower weight (mean 2351 vs. 2539 g, p = 0.013). There was no statistically significant difference in the rate of intraventricular haemorrhage (3.7% vs. 8.2%), necrotizing enterocolitis (0.6% vs. 1.9%) and bronchopulmonary dysplasia (0% vs. 6.9%). CONCLUSION: Our data confirm that of other studies demonstrating a beneficial effect of family-centred care programmes and provides evidence that structured parental involvement is not associated with increased risk of infection in a VLBW cohort.

AML classification in the year 2023: How to avoid a Babylonian confusion of languages.

In parallel to the 5th edition of the World Health Organization Classification of Haematolymphoid Tumours (WHO 2022), an alternative International Consensus Classification (ICC) has been proposed. To evaluate the impact of the new classifications on AML diagnoses and ELN-based risk classification, we analyzed 717 MDS and 734 AML non-therapy-related patients diagnosed according to the revised 4th WHO edition (WHO 2017) by whole genome and transcriptome sequencing. In both new classifications, the purely morphologically defined AML entities decreased from 13% to 5%. Myelodysplasia-related (MR) AML increased from 22% to 28% (WHO 2022) and 26% (ICC). Other genetically-defined AML remained the largest group, and the abandoned AML-RUNX1 was mainly reclassified as AML-MR (WHO 2022: 77%; ICC: 96%). Different inclusion criteria of AML-CEBPA and AML-MR (i.a. exclusion of TP53 mutated cases according to ICC) were associated with differences in overall survival. In conclusion, both classifications focus on more genetics-based definitions with similar basic concepts and a large degree of agreement. The remaining non-comparability (e.g., TP53 mutated AML) needs additional studies to definitely answer open questions on disease categorization in an unbiased way.

SF3B1 mutated MDS: Blast count, genetic co-abnormalities and their impact on classification and prognosis.

Recently, MDS with mutated SF3B1 and blast count <5% was proposed as distinct entity with favorable prognosis by the international working group for the prognosis of MDS (IWG-PM), the 5th edition of the WHO classification and the International Consensus Classification. To further characterize this entity with respect to the genomic landscape, AML transformation rate and clinical outcome, we analyzed 734 MDS patients by whole genome sequencing. SF3B1 mutations were identified in 31% (n = 231), most frequently accompanied by TET2 mutations (29%). 144/231 (62%) SF3B1mut samples fulfilled entity criteria proposed by IWG-PM (SF3B1ent). These cases were associated with longer survival, lower AML transformation rate, normal karyotypes and harbored less accompanying mutations compared to SF3B1mut samples not falling into the proposed SF3B1 entity (SF3B1nent). Of SF3B1mut cases 7% (15/231; SF3B1ent: 3/144 [2%]; SF3B1nent: 12/87 [14%]) progressed to AML compared to 15% SF3B1 wild-type patients (75/503). Of these 15 SF3B1mut cases, 10 (67%) showed RUNX1 mutations at MDS or AML stage. Multivariate analysis revealed that del(5q) and RUNX1 mutations were independent negative prognostic factors for overall survival, while blast count >5% was not. In conclusion, SF3B1mut MDS has a favorable prognosis independent of blast count if karyotype and RUNX1 mutations are considered.

Monitoring temporal trends of dioxins, organochlorine pesticides and chlorinated paraffins in pooled serum samples collected from Northern Norwegian women: The MISA cohort study.

The ubiquitous presence of legacy and emerging persistent organic pollutants (POPs) in the environmental matrices poses a potential hazard to the humans and creating public health concerns. The present study aimed to evaluate dioxins, dioxin-like polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and chlorinated paraffins (CPs) concentrations in serum of women (postpartum, pregnant and non-pregnant) from Northern Norway to better understand their exposure and contamination status as well as temporal trends across 2007-2009 (MISA 1) to 2019 (MISA 2). Sixty-two blood samples from the MISA 1 cohort and 38 samples from MISA 2 were randomly selected in this study (n = 100). Ninety samples from postpartum (MISA 1) and pregnant women (MISA 2) were randomly combined into 9 pools, with 9-11 individual samples contributing to each pool keeping the groups of pregnant and postpartum women. Remaining 10 samples from non-pregnant women (MISA 2) were allocated into separate group. Geometric mean, minimum and maximum were used to describe the serum concentrations of pooled POPs in MISA cohort. Mann-Whitney U test and independent sample t-test were applied for trend analysis of blood levels of POPs between MISA 1 and MISA 2. We found the serum concentrations of selected POPs in this study to be at lower range. Serum concentrations of dibenzo-p-dioxins (PCDDs) (p = 0.010), polychlorinated dibenzofurans (PCDFs) (p = 0.002), dioxins-like PCBs (p = 0.001), hexachlorobenzene (HCB) (p < 0.001) and p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE) (p = 0.002) were decreased between the studied time. In contrast, the serum concentrations of medium chain chlorinated paraffins showed an increasing trend between 2007 and 2009 and 2019 (p = 0.019). Our findings report a particular concern of emerging contaminant medium chain chlorinated paraffin exposure to humans. Future observational studies with repeated measurements of chlorinated paraffins in general populations worldwide and large sample size are warranted.

Retrospective cell lineage reconstruction in humans by using short tandem repeats.

Cell lineage analysis aims to uncover the developmental history of an organism back to its cell of origin. Recently, novel in vivo methods utilizing genome editing enabled important insights into the cell lineages of animals. In contrast, human cell lineage remains restricted to retrospective approaches, which still lack resolution and cost-efficient solutions. Here, we demonstrate a scalable platform based on short tandem repeats targeted by duplex molecular inversion probes. With this human cell lineage tracing method, we accurately reproduced a known lineage of DU145 cells and reconstructed lineages of healthy and metastatic single cells from a melanoma patient who matched the anatomical reference while adding further refinements. This platform allowed us to faithfully recapitulate lineages of developmental tissue formation in healthy cells. In summary, our lineage discovery platform can profile informative somatic mutations efficiently and provides solid lineage reconstructions even in challenging low-mutation-rate healthy single cells.

Interleukin-6 trans-signaling is a candidate mechanism to drive progression of human DCCs during clinical latency.

Although thousands of breast cancer cells disseminate and home to bone marrow until primary surgery, usually less than a handful will succeed in establishing manifest metastases months to years later. To identify signals that support survival or outgrowth in patients, we profile rare bone marrow-derived disseminated cancer cells (DCCs) long before manifestation of metastasis and identify IL6/PI3K-signaling as candidate pathway for DCC activation. Surprisingly, and similar to mammary epithelial cells, DCCs lack membranous IL6 receptor expression and mechanistic dissection reveals IL6 trans-signaling to regulate a stem-like state of mammary epithelial cells via gp130. Responsiveness to IL6 trans-signals is found to be niche-dependent as bone marrow stromal and endosteal cells down-regulate gp130 in premalignant mammary epithelial cells as opposed to vascular niche cells. PIK3CA activation renders cells independent from IL6 trans-signaling. Consistent with a bottleneck function of microenvironmental DCC control, we find PIK3CA mutations highly associated with late-stage metastatic cells while being extremely rare in early DCCs. Our data suggest that the initial steps of metastasis formation are often not cancer cell-autonomous, but also depend on microenvironmental signals.

Pre- and post-diagnostic blood profiles of perfluoroalkyl acids in type 2 diabetes mellitus cases and controls.

BACKGROUND: Studies exploring the associations between perfluoroalkyl acids (PFAAs) and type 2 diabetes mellitus (T2DM) are rather limited and have reported conflicting results. All studies to date, including prospective ones, have relied on a single blood sample to study this association. Similarly, studies investigating how T2DM status may influence the longitudinal changes in PFAA concentrations have not been previously performed. As PFAA concentrations in humans have changed considerably over the last two decades, and as individuals diagnosed with T2DM usually undergo lifestyle changes that could influence these concentrations, a single blood sample may not necessarily reflect the life-time exposure to PFAA concentrations. Hence, repeated measurements from the same individuals will extend our understanding of how PFAAs are associated with T2DM. The present study, therefore, aimed to explore associations between pre- and post-diagnostic PFAA blood profiles and T2DM and assess factors associated with longitudinal changes in PFAAs in T2DM cases and controls. METHODS: Questionnaire data and blood samples from women participating in the Norwegian Women and Cancer study were used to conduct a nested case-control study among 46 T2DM cases matched to 85 non-diabetic controls. PFAAs were measured in blood samples collected prior to (2001/02) and after (2005/6) T2DM diagnosis. We investigated the association between PFAAs and incident and prevalent T2DM using conditional logistic regression. We assessed the longitudinal changes in PFAA concentrations within and between matched cases and controls using t-tests and linear regression models. RESULTS: We observed no significant associations between pre-diagnostic PFAA concentrations and T2DM incidence. Similar results were observed for the post-diagnostic PFAA concentrations and T2DM prevalence. Decrease over time in PFAA concentrations were observed for PFOA and ∑PFOS concentrations, whereas increase over time were observed for PFNA, PFDA and PFUnDA concentrations. Longitudinal trends in PFAA concentrations among T2DM cases were similar to the changes observed in controls. CONCLUSIONS: The study did not find evidence of association between PFAAs and incident or prevalent T2DM. The longitudinal changes in PFAAs concentrations were not influenced by T2DM status.

Recruitment of Host Nuclear Pore Components to the Vicinity of Theileria Schizonts.

Parasitic protozoans of the genus Theileria are intracellular pathogens that induce the cellular transformation of leukocytes, causing uncontrolled proliferation of the infected host cell. The transforming stage of the parasite has a strictly intracellular lifestyle and ensures its distribution to both daughter cells during host cell cytokinesis by aligning itself across the metaphase plate and by binding tightly to central spindle and astral microtubules. Given the importance of the parasite surface in maintaining interactions with host microtubules, we analyzed the ultrastructure of the host-parasite interface using transmission electron microscopy combined with high-resolution fluorescence microscopy and live-cell imaging. We show that porous membranes, termed annulate lamellae (AL), closely associate with the Theileria surface in infected T cells, B cells, and macrophages and are not detectable in noninfected bovine cell lines such as BL20 or BoMACs. AL are membranous structures found in the cytoplasm of fast-proliferating cells such as cancer cells, oocytes, and embryonic cells. Although AL were first observed more than 60 years ago, the function of these organelles is still not known. Indirect immunofluorescence analysis with a pan-nuclear pore complex antibody, combined with overexpression of a panel of nuclear pore proteins, revealed that the parasite recruits nuclear pore complex components close to its surface. Importantly, we show that, in addition to structural components of the nuclear pore complex, nuclear trafficking machinery, including importin beta 1, RanGAP1, and the small GTPase Ran, also accumulated close to the parasite surface.IMPORTANCETheileria schizonts are the only known eukaryotic organisms capable of transforming another eukaryotic cell; as such, probing of the interactions that occur at the host-parasite interface is likely to lead to novel insights into the cell biology underlying leukocyte proliferation and transformation. Little is known about how the parasite communicates with its host or by what route secreted parasite proteins are translocated into the host, and we propose that nuclear trafficking machinery at the parasite surface might play a role in this. The function of AL remains completely unknown, and our work provides a basis for further investigation into the contribution that these porous, cytomembranous structures might make to the survival of fast-growing transformed cells.

Perfluoroalkyl substances in adolescents in northern Norway: Lifestyle and dietary predictors. The Tromsø study, Fit Futures 1.

Perfluoroalkyl substances (PFASs) are environmentally persistent chemicals widely used in many consumer products due to water and oil proofing and fire-resistant properties. Several PFASs are recognized as environmental pollutants. This study investigated serum concentrations of 18 different PFASs and their associations with diet and lifestyle variables in 940 adolescents (age 15-19 years) who participated in the Fit Futures 1 study in the Troms arctic district of Norway. Serum concentrations of PFASs were analyzed by ultrahigh pressure liquid chromatography coupled to a triple quadrupole mass spectrometer (UHPLC-MS/MS). The most abundant PFASs in this population were perfluorooctane sulfonate (PFOS), perfluorooctanoate (PFOA), perfluorohexane sulfonate (PFHxS), perfluorononanoate (PFNA) and perfluorodecanoate (PFDA) that were found in 99% of the participants. Perfluoroheptane sulfonate (PFHpS) was found in 98% of the participants. Median concentrations were: PFOS 6.20 ng/mL, PFOA 1.92 ng/mL, PFHxS 0.71 ng/mL, PFNA 0.50 ng/mL, PFDA 0.21 ng/mL and PFHpS 0.15 ng/mL. Median of PFASs sum concentration (∑PFAS) was 10.7 ng/mL, the concentration range was 2.6-200.8 ng/mL. Intake of fat fish, fish liver, seagull eggs, reindeer meat and drinks with sugar were the main dietary predictors of several PFASs. Intake of junk food (pizza, hamburger, sausages) was positively associated with PFNA, intake of canned food was positively associated with PFHxS. Intake of fruits and vegetables, milk products, snacks and candy was not associated with PFASs concentrations. Lean fish intake was positively associated with PFUnDA, but not with other PFASs. There was a positive association of ∑PFAS, PFHxS, PFOA, PFNA and PFDA with chewed tobacco use.

Identification and characterisation of a Theileria annulata proline-rich microtubule and SH3 domain-interacting protein (TaMISHIP) that forms a complex with CLASP1, EB1, and CD2AP at the schizont surface.

Theileria annulata is an apicomplexan parasite that modifies the phenotype of its host cell completely, inducing uncontrolled proliferation, resistance to apoptosis, and increased invasiveness. The infected cell thus resembles a cancer cell, and changes to various host cell signalling pathways accompany transformation. Most of the molecular mechanisms leading to Theileria-induced immortalization of leukocytes remain unknown. The parasite dissolves the surrounding host cell membrane soon after invasion and starts interacting with host proteins, ensuring its propagation by stably associating with the host cell microtubule network. By using BioID technology together with fluorescence microscopy and co-immunoprecipitation, we identified a CLASP1/CD2AP/EB1-containing protein complex that surrounds the schizont throughout the host cell cycle and integrates bovine adaptor proteins (CIN85, 14-3-3 epsilon, and ASAP1). This complex also includes the schizont membrane protein Ta-p104 together with a novel secreted T. annulata protein (encoded by TA20980), which we term microtubule and SH3 domain-interacting protein (TaMISHIP). TaMISHIP localises to the schizont surface and contains a functional EB1-binding SxIP motif, as well as functional SH3 domain-binding Px(P/A)xPR motifs that mediate its interaction with CD2AP. Upon overexpression in non-infected bovine macrophages, TaMISHIP causes binucleation, potentially indicative of a role in cytokinesis.

Organic pollutants in compost and digestate. Part 2. Polychlorinated dibenzo-p-dioxins, and -furans, dioxin-like polychlorinated biphenyls, brominated flame retardants, perfluorinated alkyl substances, pesticides, and other compounds.

Compost and digestate are important recycling fertilizers and have beneficial effects on soil parameters. However, they can contain significant amounts of organic pollutants. Here, the first comprehensive data set on dibenzo-p-dioxins and -furans (PCDD/F), dioxin-like polychlorinated biphenyls (DL-PCB), brominated flame retardants, perfluorinated alkyl substances (PFAS), pesticides, phthalates, nonylphenol and chlorinated paraffins (CP) in source-separated compost and digestate from Switzerland is presented (n = 3-18). The median summation 17PCDD/F and summation 12DL-PCB concentrations were at 3.2 ng I-TEQ kg(-1)dry weight (dw) and 3.0 ng WHO-TEQ kg(-1)dw, respectively. Brominated diphenyl ether 209 (BDE 209) accounted for 72% of the total polyBDE content (10 microg kg(-1)dw). Hexabromocyclododecane (HBCD) and tetrabromobisphenol A (TBBPA) levels were at 100 and 0.51 microg kg(-1)dw, respectively. PFAS were identified for the first time in compost and digestate (median concentration 6.3 microg kg(-1)dw, summation 21compounds). Out of 269 pesticides analysed, 30 fungicides, 14 herbicides, eight insecticides and one acaricide were detected. Di-(2-ethylhexyl)phthalate (DEHP) median concentration accounted for 280 microg kg(-1)dw and nonylphenol was below the detection limit of 1 mg kg(-1)dw. The sum of short and medium chain CP was between 90 and 390 microg kg(-1)dw. The concentrations observed were at or above the levels found in background soils, which are the main recipient of compost and digestate. Where actually applied, compost can contribute considerably to the total input of organic pollutants to the soil. However, on a total Swiss agricultural area base, inputs seem to be limited.