Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy

Embryonic development is dictated by tight regulation of DNA replication, cell division and differentiation. Mutations in DNA repair and replication genes disrupt this equilibrium, giving rise to neurodevelopmental disease characterized by microcephaly, short stature and chromosomal breakage. Here, we identify biallelic variants in two components of the RAD18-SLF1/2-SMC5/6 genome stability pathway, SLF2 and SMC5, in 11 patients with microcephaly, short stature, cardiac abnormalities and anemia. Patient-derived cells exhibit a unique chromosomal instability phenotype consisting of segmented and dicentric chromosomes with mosaic variegated hyperploidy. To signify the importance of these segmented chromosomes, we have named this disorder Atelís (meaning - incomplete) Syndrome. Analysis of Atelís Syndrome cells reveals elevated levels of replication stress, partly due to a reduced ability to replicate through G-quadruplex DNA structures, and also loss of sister chromatid cohesion. Together, these data strengthen the functional link between SLF2 and the SMC5/6 complex, highlighting a distinct role for this pathway in maintaining genome stability

Reciprocal specialization in ecological networks

Theories suggest that food webs might consist of groups of species forming ‘blocks’, ‘compartments’ or ‘guilds’. We consider ecological networks – subsets of complete food webs – involving species at adjacent trophic levels. Reciprocal specializations occur when (say) a pollinator (or group of pollinators) specializes on a particular flower species (or group of such species) and vice versa. Such specializations tend to group species into guilds. We characterize the level of reciprocal specialization for both antagonistic interactions – particularly parasitoids and their hosts – and mutualistic ones – such as insects and the flowers that they pollinate. We also examine whether trophic patterns might be ‘palimpsests’ – that is, there might be reciprocal specialization within taxonomically related species within a network, but these might be obscured when these relationships are combined. Reciprocal specializations are rare in all these systems when tested against the most conservative null model.Peer reviewe

Karyogram of LX-2 cell.

<p>Representative numbers and appearance of chromosomes that was found in one LX-2 cell as obtained after Giemsa stain in lightmicroscopic analysis. The karyotype was determined to 74, XYY, +del(1)(q4?1), der(2;10)(p10;p10), +del(3)(q25)x2, +der(4)add(4)(q31), der(5)?t(5;9)(q35;q34)?del(5)(p15), der(5)add(5)(p1?3), +der(5)add(5)(p1?3)x2, +6,del(7)(p1?3), +del(7)(p1?3), +der(9)(11q23->11q21::14q32->14q11.2::9p13->9qter)x3, +i(10)(q10), −11, del(11)(p11.2), +del(12)(pter->q12::q15->q22::q24.2->qter), −13, −14, +15, +der(16)t(16;17)(q11.1;q11.2), +der(18)(18pter->18q11.2::1q25->1q32::7q22->7qter), +20, +20, +21, +21, der(22)?t(22;?)(q11.2;?), +11mar, respectively. Please note that a characteristic derivative of chromosome 18, i.e. +der(18)(18pter->18q11.2::1q25->1q32::7q22->7qter), is marked with an arrow in this figure. A characteristic derivative of chromosome 18 that contains part of chromosomes 1 and 7 was seen in three karyograms and is marked by a black arrow.</p

Expression analysis.

<p>Cell extracts were prepared from hMFB, LX-2, HepG2, Hep3B, HUVEC and Wi-38 VA-13 subline 2RA and analysed in Western blot for expression of (i) extracellular matrix proteins (fibronectin, collagen IV, collagen I), (ii) receptors of TGF-β (endoglin, TβRII, TβRI), (iii) HSC/MFB markers (vimentin, desmin, α-SMA, CTGF, Id2, p21), and (iv) SV40 large T-antigen and β-actin. We used two parenchymatic (HepG2, Hep3B) and other cell entities (hMFB, HUVEC, and WI-38) as controls because they are well characterized for the expression of tested genes and served as positive or negative controls in this analysis.</p

Median appearance of chromosome regions per cell based upon SKY analysis of eight metaphases from human LX-2 cell line.

<p>The average copy numbers per cell of each human chromosome region are shown in correspondence to their chromosome ideogram based on summary SKY analysis.</p

Chromosomal imbalances detected in the LX-2 cell line using a SNP 6.0 Array.

<p>Gains and losses are shown by red and blue triangles, respectively.</p

Complete SKYGRAM of LX-2 cells based on eight cells.

<p>Characters above rearranged chromosome ideograms are for numbers of metaphases with this aberration. Rearrangements recognized only once in SKY analysis are ignored. Based on this analysis, the complete SKYGRAM of LX-2 was determined to 64∼83, XXY, −1, del(1)(q11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Herrmann1" target="_blank">[3]</a>, del(2)(q11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Herrmann1" target="_blank">[3]</a>, +del(3)(p11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Tacke1" target="_blank">[2]</a>, del(6)(p11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Tacke1" target="_blank">[2]</a>, del(7)(p11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Xu1" target="_blank">[4]</a>, del(7)(q11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Tacke1" target="_blank">[2]</a>, del(7)(p15) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Tacke1" target="_blank">[2]</a>, +der(7)t(7;18)(p11;p11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Herrmann1" target="_blank">[3]</a>, der(8)t(5;8)(q11;q11)t(5;14)(q31;q23) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Xu1" target="_blank">[4]</a>, der(9)t(9;14)(p12;q11)t(11;14)(q14;q24)del(11)(q12) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Wasmuth1" target="_blank">[7]</a>, del(10)(q22) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Xu1" target="_blank">[4]</a>,i(10)(q10) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Tacke1" target="_blank">[2]</a>, der(11)del(11)(p11)del(11)(q22)x2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Tacke1" target="_blank">[2]</a>, del(12)(q11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Tacke1" target="_blank">[2]</a>, +del(13)(q21) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Tacke1" target="_blank">[2]</a>,-14,-14, +del(17)(p11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone.0075692-Tacke1" target="_blank">[2]</a>,+20[cp8], respectively. More detailed SKYGRAM data for LX-2 cells were deposited in the SKY/M-FISH & CGH database located at the National Center for Biotechnology Information that can be found at: <a href="http://www.ncbi.nlm.nih.gov/sky/skyquery.cgi" target="_blank">http://www.ncbi.nlm.nih.gov/sky/skyquery.cgi</a>.</p

Spectral karyogram (SKY) of the hepatic stellate cell line LX-2.

<p>Shown is a representative image of LX-2 cells hybridized with a 24-color SKY probe (<i>upper left panel</i>). The chromosomes were counterstained with DAPI (<i>upper right panel</i>). The spectral images of hybridized metaphases were acquired using a cytogenetic workstation and grouped with the SkyView software (<i>lower panel</i>). Based on this analysis, the karyotype of this LX-2 metaphase is determined to: 73<3n+>, XXXYY, ish +der(1)t(1;18)(p11;q21)t(1;7)(q42;p12), der(2)t(2;10)(p11;q11), del(2)(q11), +der(3)t(3;6)(qter;q11), der(3)t(3;5)(p11;q23)t(3;5)(q24;q23)del(5)(q14), −5, +del(6)(p11), der(6)t(6;14)(p11;q11), der(6)t(6;11)(q11;q12), der(7)t(7;18)(p11;p11), del(7)(q21), +der(8)t(8;5)(q11;q11)t(5;14)(q31;q23), der(8)t(4;8)(q32;p12), +der(9)t(3;9)(p22;qter)del(9)(p11), der(9)t(9;14)(p12;q11)t(14;11)(q24;q14)del(11)(q12), +der(10)del(10)(p12)del(10)(q23), der(10)t(5;10)(p12;p11), del(11)(p14), der(11)del(11)(p14)del(11)(q23)x2, der(12)t(12;22)(q13;q12), −13, −14x2,+i(15)(p10), +der(15)t(15;20)(q15;q11), der(16)t(16;17)(p11;q11), del(17)(p11), −19, −20, −21, der(21)t(21;13)(p11;q11), del(X)(q24), del(X)(q25), del(X)(q21). Please note that the derivative that contains parts of chromosomes 1, 18 and 7 (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075692#pone-0075692-g001" target="_blank">Figure 1</a>) were also seen in this analysis.</p

Effects of liberal vs restrictive transfusion thresholds on survival and neurocognitive outcomes in extremely low-birth-weight infants: the ETTNO randomized clinical trial

Importance Red blood cell transfusions are commonly administered to infants weighing less than 1000 g at birth. Evidence-based transfusion thresholds have not been established. Previous studies have suggested higher rates of cognitive impairment with restrictive transfusion thresholds. Objective To compare the effect of liberal vs restrictive red blood cell transfusion strategies on death or disability. Design, Setting, and Participants Randomized clinical trial conducted in 36 level III/IV neonatal intensive care units in Europe among 1013 infants with birth weights of 400 g to 999 g at less than 72 hours after birth; enrollment took place between July 14, 2011, and November 14, 2014, and follow-up was completed by January 15, 2018. Interventions Infants were randomly assigned to liberal (n = 492) or restrictive (n = 521) red blood cell transfusion thresholds based on infants’ postnatal age and current health state. Main Outcome and Measures The primary outcome, measured at 24 months of corrected age, was death or disability, defined as any of cognitive deficit, cerebral palsy, or severe visual or hearing impairment. Secondary outcome measures included individual components of the primary outcome, complications of prematurity, and growth. Results Among 1013 patients randomized (median gestational age at birth, 26.3 [interquartile range {IQR}, 24.9-27.6] weeks; 509 [50.2%] females), 928 (91.6%) completed the trial. Among infants in the liberal vs restrictive transfusion thresholds groups, respectively, incidence of any transfusion was 400/492 (81.3%) vs 315/521 (60.5%); median volume transfused was 40 mL (IQR, 16-73 mL) vs 19 mL (IQR, 0-46 mL); and weekly mean hematocrit was 3 percentage points higher with liberal thresholds. Among infants in the liberal vs restrictive thresholds groups, the primary outcome occurred in 200/450 (44.4%) vs 205/478 (42.9%), respectively, for a difference of 1.6% (95% CI, −4.8% to 7.9%; P = .72). Death by 24 months occurred in 38/460 (8.3%) vs 44/491 (9.0%), for a difference of −0.7% (95% CI, −4.3% to 2.9%; P = .70), cognitive deficit was observed in 154/410 (37.6%) vs 148/430 (34.4%), for a difference of 3.2% (95% CI, −3.3% to 9.6%; P = .47), and cerebral palsy occurred in 18/419 (4.3%) vs 25/443 (5.6%), for a difference of −1.3% (95% CI, −4.2% to 1.5%; P = .37), in the liberal vs the restrictive thresholds groups, respectively. In the liberal vs restrictive thresholds groups, necrotizing enterocolitis requiring surgical intervention occurred in 20/492 (4.1%) vs 28/518 (5.4%); bronchopulmonary dysplasia occurred in 130/458 (28.4%) vs 126/485 (26.0%); and treatment for retinopathy of prematurity was required in 41/472 (8.7%) vs 38/492 (7.7%). Growth at follow-up was also not significantly different between groups. Conclusions and Relevance Among infants with birth weights of less than 1000 g, a strategy of liberal blood transfusions compared with restrictive transfusions did not reduce the likelihood of death or disability at 24 months of corrected age