Long-term real-world data of ustekinumab in Crohn's disease: the Stockholm ustekinumab study

Background

Ustekinumab is used to treat inflammatory bowel disease mainly in patients failing anti-tumour necrosis factor (TNF)-agents.

Objectives

To provide real-world data in unselected patients with Crohn's disease (CD), treated with ustekinumab.

Design

Longitudinal retrospective study at four hospitals in Stockholm, Sweden.

Methods

Disease activity (Harvey-Bradshaw index and physician global assessment), laboratory parameters, endoscopic findings and drug persistence were assessed. Follow-up data were obtained in patients that stopped ustekinumab.

Results

In total, 322 patients (median age 38 years, 48% women) were included. All had luminal disease and 22% also fistulizing disease. A total of 271 (84%) had failed ⩾1 and 148 (46%) ⩾2 anti-TNF drugs; 34% failed vedolizumab. At inclusion, 93% had active disease; 28% were on oral corticosteroids and 18% on thiopurines. The median follow-up on treatment was 13.5 months; overall 67% were followed at least 24 months. By intention to treat analysis, response rate at 3 and 12 months was 43% and 42%, respectively. Among patients with ongoing ustekinumab, 19% were in steroid-free remission at 3 months and 64% at 12 months. The median faecal calprotectin level decreased from 460 µg/g at baseline to 156 µg/g at 3 months and was 182 µg/g at 12 months. C-reactive protein remained stable at 4 mg/L whereas serum albumin increased slightly. About 31% of patients were withdrawn during the first 12 months, mainly due to persisting disease activity 21%, adverse events 5%, bowel surgery 0.6% or malignancy 0.3%. The overall persistence on ustekinumab was 88%, 51%, 34% and 20% at 3, 12, 24 and 36 months, respectively. Within 12 months following withdrawal of ustekinumab in 121 patients, 64% had active disease most of the time, 68% needed another biologic and 24% underwent surgery.

Conclusion

Among difficult-to-treat patients with CD, ustekinumab was effective in the majority, with high drug persistence at 12 and 24 months in combination with a favourable safety profile.

Rapid weight gain in infliximab treated Crohn's disease patients is sustained over time: real-life data over 12 months

BACKGROUND

Infliximab (IFX) is used in active Crohn's disease for induction and maintenance of remission. There are scanty data on weight gain in IBD-patients under anti-TNF treatment. We investigated changes in weight and blood chemistry in anti-TNF-naïve Crohn's disease patients during their first course of IFX.

METHODS

Retrospective analysis of 110 patients (77 men, 33 women) aged 34 years (range 14-73), 54 with luminal and 56 with fistulising disease, given at least 3 infusions of IFX (range 3-11). Data regarding body weight, height, C-reactive protein (CRP), haemoglobin and S-albumin at baseline, before the third infusion, at three months and at 12 months were collected.

RESULTS

At 6 weeks, 65 (59%) increased in weight, 73% and 76% at three and 12 months, respectively. There was an increase in median weight (1.7 kg, IQR = 3.1 kg) and BMI (0.5 kg/m², IQR = 1.2 kg/m²) at 6 weeks, which persisted at three and 12 months (all p < .001). There was no difference between men and women. Young patients, patients with underweight or fistulising disease increased most in weight. Disease activity assessed by PGA and SES-CD decreased at all time points (p < .05). Increases in weight and BMI correlated with an increase in serum albumin and a decrease in CRP.

CONCLUSION

Approximately 60% of Crohn's disease patients experience weight gain within the first six weeks of infliximab treatment. The weight increment correlates with improvements in inflammatory markers and disease activity. The causes of weight gain may be related to treatment induced metabolic changes and reduced inflammatory burden.

Suppression of Aiolos and Ikaros expression by lenalidomide reduces human ILC3-ILC1/NK cell transdifferentiation

The Ikaros family of transcription factors (TFs) are important regulators of lymphocyte function. However, their roles in human innate lymphoid cell (ILC) function remain unclear. Here, we found that Ikaros (IKZF1) is expressed by all ILC subsets, including NK cells, in blood, tonsil, and gut, while Helios (IKZF2) is preferentially expressed by ILC3 in tonsil and gut. Aiolos (IKZF3) followed the expression pattern of T-bet and Eomes, being predominantly expressed by ILC1 and NK cells. Differentiation of IFN-γ-producing ILC1 and NK cells from ILC3 by IL-1β plus IL-12-stimulation was associated with upregulation of T-bet and Aiolos. Selective degradation of Aiolos and Ikaros by lenalidomide suppressed ILC1 and NK cell differentiation and expression of ILC1 and NK cell-related transcripts (LEF1, PRF1, GRZB, CD244, NCR3, and IRF8). In line with reduced ILC1/NK cell differentiation, we observed an increase in the expression of the ILC3-related TF Helios, as well as ILC3 transcripts (TNFSF13B, IL22, NRP1, and RORC) and in the frequency of IL-22 producing ILC3 in cultures with IL-1β and IL-23. These data suggest that suppression of Aiolos and Ikaros expression inhibits ILC1 and NK cell differentiation while ILC3 function is maintained. Hence, our results open up for new possibilities in targeting Ikaros family TFs for modulation of type 1/3 immunity in inflammation and cancer.

Heterogeneity in differentiation capacity among ILC precursors in human peripheral blood and tissues

Background

The origin of human Innate Lymphoid Cells (ILCs) remains less well characterised compared to mice. Single-cell RNA-sequencing recently revealed a population of ILC precursors (ILCP) expressing CD62L and CD45RA, which shows diversity in frequencies among blood, tonsil and intestine.

Objective

We set out to determine the differentiation capacity and epigenetic landscape of blood, tonsil and intestinal ILCP.

Methods

Blood, tonsil and intestinal ILCP were sort-purified on the basis of CD62L and CD45RA (CD62L+/−CD45RA+/−) and cultured on OP9-DL1 stromal cells under specific cytokine conditions. Additionally, genome-wide chromatin accessibility was measured using ATAC-sequencing.

Results

We show that all ILCP subsets in blood and tonsil were able to differentiate to IFN-γ-producing ILC1/NK cells. Whereas all blood ILCP subsets readily differentiated to IL-13-producing ILC2, no or very few ILC2 were generated from tonsil ILCP. In contrast, tonsil ILCP subsets showed higher ability to generate IL-22-producing ILC3, compared to blood ILCP. These data indicate that ILCP in blood are poised towards ILC1/ILC2 while ILCP in tonsil favours ILC1/ILC3 differentiation. To further dissect their development, we are currently analysing global epigenetic information of tonsil ILCP, aiming to delineate their chromatin landscape. Finally, we investigated the ILCP in intestinal samples and detected accumulation of CD62L−CD45RA+ ILCP in the inflamed mucosa of patients with inflammatory bowel disease (IBD) as compared to the non-inflamed tissue. We are currently analysing the potency of those cells.

Conclusion

Heterogeneity in ILC differentiation in blood and tissues could further reveal novel targets for IBD treatment.

Suppression of Aiolos and Ikaros expression by lenalidomide reduces human ILC3–ILC1/NK cell transdifferentiation

The Ikaros family of transcription factors (TFs) are important regulators of lymphocyte function. However, their roles in human innate lymphoid cell (ILC) function remain unclear. Here, we found that Ikaros (IKZF1) is expressed by all ILC subsets, including NK cells, in blood, tonsil and gut, while Helios (IKZF2) is preferentially expressed by ILC3 in tonsil and gut. Aiolos (IKZF3) followed the expression pattern of T-bet and Eomes, being predominantly expressed by ILC1 and NK cells. Differentiation of IFN-γ-producing ILC1 and NK cells from ILC3 by IL-1β plus IL-12-stimulation was associated with upregulation of T-bet and Aiolos. Selective degradation of Aiolos and Ikaros by lenalidomide suppressed ILC1 and NK cell differentiation and expression of ILC1 and NK cell-related transcripts (LEF1, PRF1, GRZB, CD244, NCR3, IRF8). In line with reduced ILC1/NK cell differentiation we observed an increase in the expression of the ILC3-related TF Helios, as well as ILC3 transcripts (TNFSF13B, IL22, NRP1 and RORC) and in the frequency of IL-22 producing ILC3 in cultures with IL-1β and IL-23. These data suggest that suppression of Aiolos and Ikaros expression inhibits ILC1 and NK cell differentiation while ILC3 function is maintained. Hence, our results open up for new possibilities in targeting Ikaros family TFs for modulation of type 1/3 immunity in inflammation and cancer.

Distinct Alterations in the Composition of Mucosal Innate Lymphoid Cells in Newly Diagnosed and Established Crohn's Disease and Ulcerative Colitis

BACKGROUND AND AIMS

Innate lymphoid cells [ILC] have been suggested to play a role in inflammatory bowel disease [IBD]. Here, we investigated the ILC compartment in intestinal biopsies and blood from distinct patient groups with Crohn's disease [CD] and ulcerative colitis [UC], either newly diagnosed or with disease established for at least 1 year. This approach allowed us to simultaneously investigate temporal, disease-specific, and tissue-specific changes in ILC composition in IBD.

METHODS

ILC subset frequencies, phenotype, and transcription factor profile in blood and intestinal biopsies were investigated by multi-parameter flow cytometry analysis. Endoscopic disease severity was judged using the ulcerative colitis endoscopic index of severity and the simple endoscopic score for Crohn's disease.

RESULTS

The frequency of NKp44+ILC3 was decreased in inflamed tissue, both in patients with CD and those with UC, already at the time of diagnosis, and correlated with disease severity. Simultaneously, the frequency of ILC1 was increased in patients with CD, whereas the frequency of ILC2 was increased in patients with UC. However, in patients with established UC or CD, both ILC1 and ILC2 were increased. In contrast to the ILC composition in inflamed tissue, ILC in non-inflamed tissue or blood were unchanged compared with non-IBD controls. Finally, in patients undergoing treatment with an anti-α4β7 antibody the frequencies of ILC in peripheral blood remained unchanged.

CONCLUSIONS

We report both shared and distinct changes in ILC composition depending on diagnosis and disease duration. The alterations in ILC composition in IBD occur selectively at inflamed sites in the gut.

Flt3 ligand expands bona fide innate lymphoid cell precursors in vivo

A common helper-like innate lymphoid precursor (CHILP) restricted to the innate lymphoid cells (ILC) lineage has been recently characterized. While specific requirements of transcription factors for CHILPs development has been partially described, their ability to sense cytokines and react to peripheral inflammation remains unaddressed. Here, we found that systemic increase in Flt3L levels correlated with the expansion of Lineage (Lin)^negα4β7⁺ precursors in the adult murine bone marrow. Expanded Lin^negα4β7⁺ precursors were bona fide CHILPs as seen by their ability to differentiate into all helper ILCs subsets but cNK in vivo. Interestingly, Flt3L-expanded CHILPs transferred into lymphopenic mice preferentially reconstituted the small intestine. While we did not observe changes in serum Flt3L during DSS-induced colitis in mice or plasma from inflammatory bowel disease (IBD) patients, elevated Flt3L levels were detected in acute malaria patients. Interestingly, while CHILP numbers were stable during the course of DSS-induced colitis, they expanded following increased serum Flt3L levels in malaria-infected mice, hence suggesting a role of the Flt3L-ILC axis in malaria. Collectively, our results indicate that Flt3L expands CHILPs in the bone marrow, which might be associated with specific inflammatory conditions.

Systemic Chemokine Levels with "Gut-Specific" Vedolizumab in Patients with Inflammatory Bowel Disease-A Pilot Study

Vedolizumab, a gut-specific biological treatment for inflammatory bowel disease (IBD), is an antibody that binds to the α₄β₇ integrin and blocks T-cell migration into intestinal mucosa. We aimed to investigate chemokine levels in serum of IBD-patients treated with vedolizumab. In this pilot study, we included 11 IBD patients (8 Crohn’s disease, 3 ulcerative colitis) previously non-respondent to anti-tumor necrosis factor (TNF)-agents. Patients received vedolizumab at week 0, 2 and 6 and were evaluated for clinical efficacy at week 10. Clinical characteristics and routine laboratory parameters were obtained and patients were classified as responders or non-responders. Expression of 21 chemokines in serum was measured using Proximity Extension Assay and related to clinical outcome. At week 10, 6 out of 11 patients had clinically responded. Overall expression of CCL13 increased after treatment. In non-responders, expression of CCL13 and CXCL8 increased after treatment, and CCL20 and CXCL1 expressions were higher compared to responders. In responders, CCL28 decreased after treatment. C-reactive protein (CRP) correlated negatively with 6 chemokines before therapy, but not after therapy. Systemic CCL13 expression increases in IBD-patients after vedolizumab therapy and several chemokine levels differ between responders and non-responders. An increased CCL13-level when starting vedolizumab treatment, might indicate potential prognostic value of measuring chemokine levels when starting therapy with vedolizumab. This study provides new information on modulation of systemic chemokine levels after vedolizumab treatment.

Vitamin D downregulates the IL-23 receptor pathway in human mucosal group 3 innate lymphoid cells

BACKGROUND

Vitamin D deficiency is a risk factor for inflammatory bowel disease (IBD). The IL-23-driven tissue-resident group 3 innate lymphoid cells (ILC3s) play essential roles in intestinal immunity, and targeting IL-23/12 is a promising approach in IBD therapy.

OBJECTIVE

We set out to define the role of 1α,25-dihydroxy vitamin D3 (1,25D) in regulating functional responses of human mucosal ILC3s to IL-23 plus IL-1β stimulation.

METHODS

Transcriptomes of sorted tonsillar ILC3s were assessed by using microarray analysis. ILC3 cytokine production, proliferation, and differentiation were determined by means of flow cytometry, ELISA, and multiplex immunoassay. Intestinal cell suspensions and ILC3s sorted from gut biopsy specimens of patients with IBD were also analyzed along with plasma 25-hydroxy vitamin D3 (25D) detection.

RESULTS

ILC3s stimulated with IL-23 plus IL-1β upregulated the vitamin D receptor and responded to 1,25D with downregulation of the IL-23 receptor pathway. Consequently, 1,25D suppressed IL-22, IL-17F, and GM-CSF production from tonsillar and gut ILC3s. In parallel, 1,25D upregulated genes linked to the IL-1β signaling pathway, as well as the IL-1β-inducible cytokines IL-6, IL-8, and macrophage inflammatory protein 1α/β. The 1,25D-triggered skewing in ILC3 function was not accompanied or caused by changes in viability, proliferation, or phenotype. Finally, we confirmed low 25D plasma levels in patients with IBD with active inflammation.

CONCLUSION

In light of the beneficial targeting of IL-23/12 in patients with IBD, 1,25D appears as an interesting therapeutic agent that inhibits the IL-23 receptor pathway, providing a novel mechanism for how ILC3s could be manipulated to regulate intestinal inflammation.

Different evolutionary behavior of structurally related, repetitive sequences occurring in the same Balbiani ring gene in Chironomus tentans

The Balbiani ring 2 (BR 2) gene in Chironomus tentans is highly internally repeated. Two types of related repeat units-the alpha and beta types-are tandemly arranged in separate blocks, which together are likely to form the major part of the gene. Every repeat unit has one constant region and one subrepeat region. Here we analyze the length and sequence of a number of repeat units of both types and compare the units within and between the blocks. The approximately 100 alpha repeat units are essentially invariant regarding length and sequence. In contrast, when the approximately 70 beta repeat units are compared, six length variants are found, four of which have been sequenced. The length variations reside in the subrepeat regions and are due to different numbers of whole or half subrepeats. Furthermore, the subrepeat regions differ by several base-pair substitutions, many of which change the amino acid sequence. On the other hand, all beta-type constant regions are of equal length and are virtually homogeneous in sequence. The observed length distributions in combination with analysis of the basepair substitutions in the alpha-and beta-type constant and subrepeat regions suggest that the alpha and beta blocks are of different age, that seemingly homologous repeated regions may play different functional roles at the protein level, and that sequence correction mechanisms are likely to operate to different extents on the constant and subrepeat regions within the beta block.

Disruption of pairing and synapsis of chromosomes causes stage-specific apoptosis of male meiotic cells

During meiosis, DNA replication is followed by two successive rounds of chromosome segregation (meiosis I and II), which give rise to genetically diverse haploid gametes. The prophase of the first meiotic division is highly regulated and alignment and synapsis of the homologous chromosomes during this stage are mediated by the synaptonemal complex. Incorrect assembly of the synaptonemal complex results in cell death, impaired meiotic recombination and aneuploidy. Oocytes with meiotic defects often survive the first meiotic prophase and give rise to aneuploid gametes. Similarly affected spermatocytes, on the other hand, almost always undergo apoptosis at a male-specific meiotic checkpoint, located specifically at epithelial stage IV during spermatogenesis. Many examples of this stage IV-specific arrest have been described for several genetic mouse models in which DNA repair or meiotic recombination are abrogated. Interestingly, in C. elegans, meiotic recombination and synapsis are monitored by two separate checkpoint pathways. Therefore we studied spermatogenesis in several knockout mice (Sycp1(-/-), Sycp3(-/-), Smc1beta(-/-) and Sycp3/Sycp1 and Sycp3/Smc1beta double-knockouts) that are specifically defective in meiotic pairing and synapsis. Like for recombination defects, we found that all these genotypes also specifically arrest at epithelial stage IV. It seems that the epithelial stage IV checkpoint eliminates spermatocytes that fail a certain quality check, being either synapsis or DNA damage related.

Low level chromosome instability in embryonic cells of primary aneuploid mice

Karyotypic analyses of Down syndrome patients have identified a low level of chromosome mosaicism, suggesting that the primary aneuploid status of the cells promotes further chromosomal segregation errors. Sycp3-null female mice produce aneuploid oocytes, which after fusion with normal haploid sperm, result in offspring with systemic whole chromosome, aneuploid embryo cells. Using the Sycp3-null female as a model, we observe an increase in the number of embryonic cells at E7.0 that exhibit abnormal chromosomal bridges at the anaphas estage of mitosis. This result suggests that global changes in gene expression patterns resulting from primary aneuploidy can affect mitotic chromosome segregation, resulting in a low level of chromosomal instability. The increased level of chromosomal instability could in the absence of mitotic checkpoints, lead to chromosomal mosaicism within the adult organism, as seen in Down syndrome patients.

[Capsule endoscopy is better than other methods. 66 examinations performed at Sodersjukhuset prove a high diagnostic yield]

Capsule endoscopy is a non-invasive method to investigate the small intestine by means of a swallowable videocapsule that takes pictures during its passage throughout the gut. The method has been proven to have a high diagnostic yield in obscure GI bleeding and suspected small bowel Crohn's disease in cases where traditional methods have failed. In 63 patients consecutively evaluated by capsule endoscopy pathological lesions were found in 39 (62%), of which angiodysplasias were the most common (33%). Inflammatory changes including Crohn's disease constituted 40% of the findings. Malignant tumors were found in two patients (5%). Half of the patients with patological findings were either medically treated or referred to surgery. Capsule endoscopy is a new method for small bowel examination that has a great potential to replace some older methods with lower diagnostic yield.

Differential expression of multiple alternative spliceforms of the Men1 tumor suppressor gene in mouse

The multiple endocrine neoplasia type 1 gene (MEN1) is a tumor suppressor gene associated with the development of tumors in the parathyroids, the pituitary, and the pancreas and has also been linked to impaired germ cell production. The murine ortholog, Men1, is highly homologous to the human counterpart both at DNA and protein levels. The present study was undertaken to further approach the function of Men1 and its encoded protein menin. By 5' RACE and RT-PCR four alternative splice variants were identified, indicating a 5' heterogeneity of Men1 similar to the human counterpart. By mRNA in situ hybridization of embryonal and adult mouse tissues, all four splice variants were shown to be expressed, albeit at varying timepoints and levels in the different tissues. However, a putative isoform postulated from the DNA sequence, which would elongate the reading frame by 15 bases at the exon 2/intron 2 junction, was not found to occur in mouse. The strongest expression was detected in testis, both at the mRNA and protein level and was therefore further characterized by protein analysis of cells isolated from different stages of the spermatogenesis. Western blotting revealed a single protein of approximately 70 kDa detected in total testis, isolated pachytene spermatocytes and in haploid spermatids. Notably, no menin expression was detectable in the extracts from epididymis where the maturation of sperms is almost completed, suggesting that menin plays a crucial role during spermatogenesis.

A meiotic chromosomal core consisting of cohesin complex proteins recruits DNA recombination proteins and promotes synapsis in the absence of an axial element in mammalian meiotic cells

The behavior of meiotic chromosomes differs in several respects from that of their mitotic counterparts, resulting in the generation of genetically distinct haploid cells. This has been attributed in part to a meiosis-specific chromatin-associated protein structure, the synaptonemal complex. This complex consist of two parallel axial elements, each one associated with a pair of sister chromatids, and a transverse filament located between the synapsed homologous chromosomes. Recently, a different protein structure, the cohesin complex, was shown to be associated with meiotic chromosomes and to be required for chromosome segregation. To explore the functions of the two different protein structures, the synaptonemal complex and the cohesin complex, in mammalian male meiotic cells, we have analyzed how absence of the axial element affects early meiotic chromosome behavior. We find that the synaptonemal complex protein 3 (SCP3) is a main determinant of axial-element assembly and is required for attachment of this structure to meiotic chromosomes, whereas SCP2 helps shape the in vivo structure of the axial element. We also show that formation of a cohesin-containing chromosomal core in meiotic nuclei does not require SCP3 or SCP2. Our results also suggest that the cohesin core recruits recombination proteins and promotes synapsis between homologous chromosomes in the absence of an axial element. A model for early meiotic chromosome pairing and synapsis is proposed.

Oligosaccharides display both rigidity and high flexibility in water as determined by 13C NMR relaxation and 1H,1H NOE spectroscopy: evidence of anti-phi and anti-psi torsions in the same glycosidic linkage

The trisaccharide beta-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe has been investigated by molecular dynamics (MD) simulations and NMR experiments in water. 13C spin-lattice (T1) and spin-spin (T2) relaxation times, together with 1H,13C NOE data were measured at two magnetic field strengths (9.4 and 14.1 T) in a 277 K D2O solution. Relaxation data interpreted by means of the model-free formalism revealed a rigid (S2 approximately 0.9) oligosaccharide tumbling in solution. 1H,1H Cross-relaxation rates were determined at 600 MHz by 1D DPFGSE NOESY and T-ROESY experiments, which provided high quality data and subsequently proton-proton distances within the trisaccharide. The presence of anti conformers at both torsions of a glycosidic linkage is demonstrated for the first time. MD simulations were carried out to facilitate analysis of the NOE data. In total, 15 simulations-starting from five different conformational states--were performed, with production runs of up to 10 ns, resulting in 83 ns of oligosaccharide dynamics in water. anti Conformers were populated to different degrees in the simulations, especially at the phi2 torsion angle. By combining the results from the NOE experiments and the MD simulations, the anti conformers at the (1-->2)-linkage were quantified as 7% anti-phi2 and 2% anti-psi2, revealing a highly flexible trisaccharide in which large conformational changes occur. From the MD simulations, interresidue hydrogen bonding, from HO2" to O2 or O3, was significantly populated (approximately 40%) in both of the anti conformational states. The contentious issue over rigidity versus flexibility in oligosaccharides has thus been thoroughly examined, showing that the dynamics should be taken into account for a relevant description of the molecular system.

Conformational investigation of a cyclic enterobacterial common antigen employing NMR spectroscopy and molecular dynamics simulations

The three-dimensional structure of a cyclic enterobacterial common antigen (ECA) having four trisaccharide repeating units has been investigated by NMR spectroscopy and molecular dynamics simulations. Three different NMR parameters were determined: (a) (1)H,(1)H cross-relaxation rates from NOE experiments were used for determination of proton-proton distances; (b) trans-glycosidic (3)J(C,H) scalar coupling constants analyzed via a Karplus-type relationship provided information on torsion angles; and (c) (1)H,(13)C one-bond dipolar couplings obtained in a dilute liquid-crystalline medium were interpreted in terms of the orientational order and molecular conformations. The molecular dynamics simulations of the dodecasaccharide were performed with explicit water and counterions, which are important factors that strongly influence molecular conformation. Subsequently, the results from computer simulation were used to generate a three-dimensional structure of the cyclic ECA which is consistent with the experimental NMR parameters.

Characterisation of the human APC1, the largest subunit of the anaphase-promoting complex

Accurate segregation of sister chromatids during mitosis is necessary to avoid the aneuploidy found in many cancers. The spindle checkpoint, which monitors the metaphase to anaphase transition, has been shown to be defective in cancers with chromosomal instability. This checkpoint regulates the anaphase-promoting complex or cyclosome (APC/C), a cell cycle ubiquitin ligase regulating among other things sister chromatid separation. We have previously investigated the mouse Apc1 protein (previously also called Tsg24), the largest subunit of the APC/C. We have now sequenced a full-length human APC1 cDNA, mapped its chromosomal location, and analysed its intron-exon boundaries. We have also investigated the RNA and protein expression of the Apc1 and other APC/C components in normal and cancer cells and the relative occurrence of expressed sequence tags (ESTs) representing APC subunits from different tissues. The different APC/C subunits are expressed in most tissues and cell types at fairly constant levels relative to each other, suggesting that they perform their functions as part of a complex. A difference from this pattern is however seen for the APC6, which in some cases is more strongly expressed, suggesting a special function for this protein in certain tissues and cell types.

The spatial and temporal expression of Tekt1, a mouse tektin C homologue, during spermatogenesis suggest that it is involved in the development of the sperm tail basal body and axoneme

Tektins comprise a family of filament-forming proteins that are known to be coassembled with tubulins to form ciliary and flagellar microtubules. Recently we described the sequence of the first mammalian tektin protein, Tekt1 (from mouse testis), which is most homologous with sea urchin tektin C. We have now investigated the temporal and spatial expression of Tekt1 during mouse male germ cell development. By in situ hybridization analysis TEKT1 RNA expression is detected in spermatocytes and in round spermatids in the mouse testis. Immunofluorescence microscopy analysis with anti-Tekt1 antibodies showed no distinct labeling of any subcellular structure in spermatocytes, whereas in round spermatids anti-Tekt1 antibodies co-localize with anti-ANA antibodies to the centrosome. At a later stage, elongating spermatids display a larger area of anti-Tektl staining at their caudal ends; as spermiogenesis proceeds, the anti-Tekt1 staining disappears. Together with other evidence, these results provide the first intraspecies evidence that Tekt1 is transiently associated with the centrosome, and indicates that Tekt1 is one of several tektins to participate in the nucleation of the flagellar axoneme of mature spermatozoa, perhaps being required to assemble the basal body.

A visual intracellular classification strategy for uncharacterized human proteins

The human cDNA and genomic sequencing projects will result in the identification and isolation of some 140,000 genes, the majority of which lack predicted functions and for which the cellular localizations are not known. The identification and characterization of protein components of specific cell structures and machineries are essential steps not only toward defining functions of genes but also toward understanding cell function and regulation. We describe here a new approach, termed PROLOC, which uses full-length cDNAs for systematic classification of novel proteins as a functional pointer. We have PCR-amplified 25 uncharacterized human genes and expressed the encoded proteins as GFP fusions in a human cell line. This pilot project has identified novel proteins associated with the nucleolus, mitochondria, the ER, the ER-Golgi-intermediate compartment (ERGIC), the GC, the plasma membrane, and cytoplasmic foci. This visual classification approach may be scaled up to handle a large number of novel genes and permit the generation of a global cellular protein localization map. Such information should be valuable for many aspects of functional genomics and cell biology.

High-throughput protein expression of cDNA products as a tool in functional genomics

A proteomics approach has been developed aimed to allow high throughput analysis of protein products expressed from cDNA fragments (expressed sequence tags, ESTs). The concept relies on expression of gene products to generate specific antibodies for protein analysis, such as immunolocalization of the proteins on cellular and subcellular level. To evaluate the system, 55 cDNA clones with predominantly unknown function were selected from a mouse testis cDNA-library. A bacterial expression system was designed that allowed robust expression and easy purification. Protein levels between 15 and 80 mg l(-1) were obtained for 49 of the clones. Five clones were selected for immunization and all yielded functional antibodies that gave specific staining in Western blot screening of samples from various cell types. Furthermore, extensive immunolocalization information on subcellular level was obtained for three of the five clones. All generated data were stored in a relational database, and are made available through a web-interface (http://www.biochem.kth.se/multiscale/), which also provides relevant links and allows homology searches from the original sequences. The possibility to allow analysis of gene products from whole genomes using this 'localization proteomics' approach is discussed.

Molecular dynamics simulation and nuclear magnetic resonance studies of the terminal glucotriose unit found in the oligosaccharide of glycoprotein precursors

The trisaccharide alpha-d-Glcp-(1 --> 2)-alpha-d-Glcp-(1 --> 3)-alpha-d-Glcp-OMe, a model for the terminal glucotriose in Glc(3)Man(9)GlcNAc(2) in glycoprotein precursors, has been investigated by computer simulations and NMR spectroscopy. Molecular dynamics simulations were performed for 1 ns in aqueous solution and 20 ns in vacuo using the CHARMM-based force fields PARM22 and CHEAT95. An additional Monte Carlo simulation with the HSEA force field was also carried out. Experimental NMR data in water solution was obtained from measurement of long-range (1)H,(13)C heteronuclear trans-glycosidic coupling constants, (3)J(H,C), using one-dimensional Hadamard spectroscopy. Calculation of the (3)J(H,C) values from the simulations showed a varying degree of agreement to experimental data. It could be shown from simulation that the &phi; torsion angles differed, which was corroborated by the NMR measurements. Analyses were done of radial distribution functions and of hydrogen bonds. It was suggested that intermolecular hydrogen bonds were present, but in contrast to simulation the results from NMR spectroscopy did not support any major contribution. Hence, their influence on the conformation of the trisaccharide is rather small. Comparison of (1)H NMR chemical shifts for the trisaccharide and the glucotriose in Glc(3)Man(8)GlcNAc revealed high similarity. However, the derived conformation of the model substance in this work differed at one glycosidic torsion angle compared to the glucotriose on a large oligosaccharide.

The murine SCP3 gene is required for synaptonemal complex assembly, chromosome synapsis, and male fertility

During meiosis, the homologous chromosomes pair and recombine. An evolutionarily conserved protein structure, the synaptonemal complex (SC), is located along the paired meiotic chromosomes. We have studied the function of a structural component in the axial/lateral element of the SC, the synaptonemal complex protein 3 (SCP3). A null mutation in the SCP3 gene was generated, and we noted that homozygous mutant males were sterile due to massive apoptotic cell death during meiotic prophase. The SCP3-deficient male mice failed to form axial/lateral elements and SCs, and the chromosomes in the mutant spermatocytes did not synapse. While the absence of SCP3 affected the nuclear distribution of DNA repair and recombination proteins (Rad51 and RPA), as well as synaptonemal complex protein 1 (SCP1), a residual chromatin organization remained in the mutant meiotic cells.

Recovery of upstream cDNA sequences by a PCR-based biotin-capture method

The world-wide, large-scale sequencing efforts have generated an abundance of partial cDNA sequences, i.e., expressed sequence tags (ESTs), accessible in the public databases. To enable functional characterization of these partial cDNA sequences, general and robust methods for recovery of upstream full-coding cDNA sequences are needed. Here, a novel biotin- and PCR-assisted capture method was used directly on poly(A)+ RNA for the purpose of generating a full-coding sequence of a gene with only partially known sequence and for which a full-length clone of the gene was not found in existing cDNA libraries. The presented method involves linear extension by reverse transciptase from a biotinylated primer annealing in a region with known sequence. After capture of the generated single-stranded cDNA onto paramagnetic beads, unspecifically annealing primers, i.e., arbitrary primers, were used to generate cDNA fragments that could be amplified by PCR and thereafter directly sequenced without subcloning. By using the presented strategy, which is to be seen as a complement to rapid amplification of cDNA ends (RACE)-related methods, we were able to recover full-coding sequence versions of two potential splice variants of the target gene. The general applicability of the novel method for recovery and sequencing of cDNA sequences is discussed.

Characterization of a novel nucleolar protein that transiently associates with the condensed chromosomes in mitotic cells

We report the isolation and characterization of a murine gene encoding a conserved mammalian nucleolar protein. The protein, called Tsg118, has a predicted molecular mass of 59.4 kDa and a high content of basic amino acids. A homologous human gene was localized to chromosome 16p12.3. The Tsg118 protein is predominantly expressed in proliferating somatic cells and in male germ cells. Indirect immunofluorescence microscopy analysis using an affinity-purified anti-Tsg118 serum shows colocalization of Tsg118 and a known nucleolar protein, fibrillarin, to the dense fibrillar component of the nucleolus. The nucleolar localization of the Tsg118 protein appears to be temporally restricted to the interphase stages of the somatic cell cycle and to the meiotic phase of spermatogenesis. We find that the Tsg118 protein localizes to the nucleolus in both proliferating and serum-starved cells. Interestingly, as the nucleolar signal disappears in mitotic cells, the Tsg118 protein instead becomes associated with the surface of the condensed chromosomes.

Expression of ciliary tektins in brain and sensory development

Many types of neural tissues and sensory cells possess either motile or primary cilia. We report the first mammalian (murine testis) cDNA for tektin, a protein unique to cilia, flagella, and centrioles, which we have used to identify related proteins and genes in sensory tissues. Comparison with the sequence database reveals that tektins are a gene family, spanning evolution from Caenorhabditis elegans (in which they correlate with touch receptor cilia) and Drosophila melanogaster, to Mus musculus and Homo sapiens (in which they are found in brain, retina, melanocytes, and at least 13 other tissues). The peptide sequence RPNVELCRD, or a variant of it, is a prominent feature of tektins and is likely to form a functionally important protein domain. Using the cDNA as a probe, we determined the onset, relative levels, and locations of tektin expression in mouse for several adult tissues and embryonic stages by Northern blot analysis and in situ hybridization. Tektin expression is significant in adult brain and in the choroid plexus, the forming retina (primitive ependymal zone corresponding to early differentiating photoreceptor cells), and olfactory receptor neurons of stage embryonic day 14 embryos. There is a striking correlation of tektin expression with the known presence of either motile or primary cilia. The evolutionary conservation of tektins and their association with tubulin in cilia and centriole formation make them important and useful molecular targets for the study of neural development.

The synaptonemal complex protein SCP3 can form multistranded, cross-striated fibers in vivo

The synaptonemal complex protein SCP3 is part of the lateral element of the synaptonemal complex, a meiosis-specific protein structure essential for synapsis of homologous chromosomes. We have investigated the fiber-forming properties of SCP3 to elucidate its role in the synaptonemal complex. By synthesis of SCP3 in cultured somatic cells, it has been shown that SCP3 can self-assemble into thick fibers and that this process requires the COOH-terminal coiled coil domain of SCP3, as well as the NH2-terminal nonhelical domain. We have further analyzed the thick SCP3 fibers by transmission electron microscopy and immunoelectron microscopy. We found that the fibers display a transversal striation with a periodicity of approximately 20 nm and consist of a large number of closely associated, thin fibers, 5-10 nm in diameter. These features suggest that the SCP3 fibers are structurally related to intermediate filaments. It is known that in some species the lateral elements of the synaptonemal complex show a highly ordered striated structure resembling that of the SCP3 fibers. We propose that SCP3 fibers constitute the core of the lateral elements of the synaptonemal complex and function as a molecular framework to which other proteins attach, regulating DNA binding to the chromatid axis, sister chromatid cohesion, synapsis, and recombination.

MMC and LD simulations of alpha-D-Manp-(1-->2)-beta-D-Glcp-OMe: comparison to long-range heteronuclear NMR coupling constants and to the crystal structure

The conformational flexibility and the dynamics of alpha-D-Manp(1-->2)-beta-D-Glcp-OMe have been investigated by Metropolis Monte Carlo (MMC) and Langevin dynamics (LD) simulations. The two simulation techniques employ different force fields, namely the HSEA force field and a CHARMm-based force field. The former shows less conformational flexibility than the latter, in which a multiple energy minima conformational space is sampled. Long-range heteronuclear nuclear magnetic resonance (NMR) coupling constants have been measured by selective excitations of the carbons at the glycosidic linkage. Calculated 3J(C,H) values from MMC and LD simulations show excellent agreement to those from NMR experiments. The X-ray crystal structure has a conformation within a region of the conformational space populated in both force fields.

A subunit of the anaphase-promoting complex is a centromere-associated protein in mammalian cells

Sister chromatids in early mitotic cells are held together mainly by interactions between centromeres. The separation of sister chromatids at the transition between the metaphase and the anaphase stages of mitosis depends on the anaphase-promoting complex (APC), a 20S ubiquitin-ligase complex that targets proteins for destruction. A subunit of the APC, called APC-alpha in Xenopus (and whose homologs are APC-1, Cut4, BIME, and Tsg24), has recently been identified and shown to be required for entry into anaphase. We now show that the mammalian APC-alpha homolog, Tsg24, is a centromere-associated protein. While this protein is detected only during the prophase to the anaphase stages of mitosis in Chinese hamster cells, it is constitutively associated with the centromeres in murine cells. We show that there are two forms of this protein in mammalian cells, a soluble form associated with other components of the APC and a centromere-bound form. We also show that both the Tsg24 protein and the Cdc27 protein, another APC component, are bound to isolated mitotic chromosomes. These results therefore support a model in which the APC by ubiquitination of a centromere protein regulates the sister chromatid separation process.

Presence of synaptonemal complex protein 1 transversal filament-like protein in human primary spermatocytes

The synaptonemal complex (SC) is involved in the pairing of chromosomes during meiosis. We found that antibodies raised against a protein component (P1) of the mouse synaptonemal complex, mouse SCP1, also identified the SC in human primary spermatocytes. Biopsies from 18 men presented with infertility were evaluated by light-field microscopy and grouped into five categories: normal spermatogenesis, Sertoli cell-only syndrome, meiotic disturbances, spermiogenic (i.e. differentiation) disturbances, and other combined disturbances. In all the normal subjects the SCP1 antibody distinctly stained the synaptonemal complexes of primary spermatocytes, whereas Sertoli cells, spermatogonia or spermatids were never stained. In three of the groups, which had germ cells but showed spermatogenic disturbances, the staining was similar to that seen in normal subjects. In sharp contrast to this, in sections from men with Sertoli cell-only syndrome no specific staining was seen. This study demonstrates that a SCP1-related protein is also conserved in the synaptonemal complex in meiotic cells from man. Further studies will reveal to what extent the absence or the non-functionality of SCP1 contributes to male infertility.

The transcriptional and translational control of diazepam binding inhibitor expression in rat male germ-line cells

The diazepam binding inhibitor [DBI, also known as acyl-CoA-binding protein, (ACBP), or endozepine] is a 10-kD protein that has been suggested to be involved in the regulation of several biological processes such as acyl-CoA metabolism, steroidogenesis, insulin secretion, and gamma-aminobutyric acid type A (GABA(A))/benzodiazepine receptor modulation. DBI has been cloned from vertebrates, insects, plants, and yeasts. In mammals, DBI is expressed in almost all the tissues studied. Nevertheless, DBI expression is restricted to specific cell types. Here we have studied DBI gene expression in the germ-line cells of rat testis. The DBI gene was intensively transcribed in postmeiotic round spermatids from stages VI to VIII of the seminiferous epithelial cycle. A prominent, spermatid-specific upstream transcription initiation site was identified in addition to the multiple common transcriptional initiation sites found in the somatic tissues. However, no DBI protein was detected in round spermatids, suggesting that the DBI transcripts were translationally arrested. The DBI protein was detected in the late spermatogenic stages starting from elongating spermatids from step 18 (stage VI) onward. The DBI protein was also detected in mature spermatozoa and in ejaculated human sperms. The majority of DBI was located at the middle piece of the spermatozoons tail enriched with mitochondria. On the basis of this observation and the well-established role of DBI in acyl-CoA metabolism, we propose that DBI expression in spermatozoa reflects the usage of fatty acids as a primary energy source by spermatozoa. The biological function of DBI in spermatozoa could thus be related to the motility function of sperm.

Expression of the meiosis-specific synaptonemal complex protein 1 in a heterologous system results in the formation of large protein structures

The synaptonemal complex is a meiosis-specific structure essential for synapsis of homologous chromosomes. The synaptonemal complex protein 1 (SCP1) is a major constituent of the transversal filament, a fibrous structure that connects the central element of the synaptonemal complex with the two lateral elements. The SCP1 protein forms filamentous dimers with the two molecules that have the same polarity, with the C-termini being anchored in the lateral elements and the N-termini reaching into the central element. We investigated whether the SCP1 protein can take part in the formation of higher order protein structures by expressing it in a heterologous system. We find that expression of SCP1 in Swiss-3T3 fibroblast cells results in the formation of large protein structures. These protein structures resemble a higher order protein structure produced by overexpression of a yeast transversal filament protein in meiotic cells. Our results show that SCP1 is a structural protein and that it most likely is directly involved in the assembly of the synaptonemal complex.

Identification of BIME as a subunit of the anaphase-promoting complex

The initiation of anaphase and exit from mitosis require the activation of a proteolytic system that ubiquitinates and degrades cyclin B. The regulated component of this system is a large ubiquitin ligase complex, termed the anaphase-promoting complex (APC) or cyclosome. Purified Xenopus laevis APC was found to be composed of eight major subunits, at least four of which became phosphorylated in mitosis. In addition to CDC27, CDC16, and CDC23, APC contained a homolog of Aspergillus nidulans BIME, a protein essential for anaphase. Because mutation of bimE can bypass the interphase arrest induced by either nimA mutation or unreplicated DNA, it appears that ubiquitination catalyzed by APC may also negatively regulate entry into mitosis.

Localization of the N-terminus of SCP1 to the central element of the synaptonemal complex and evidence for direct interactions between the N-termini of SCP1 molecules organized head-to-head

The synaptonemal complex (SC) is a meiosis-specific, tripartite structure essential for synapsis of homologous chromosomes; it contains a central element positioned between two lateral elements and transversal filaments connecting the lateral elements. In mammals, a major constituent of the transversal filament is known: the SCP1 protein. It contains a long central coiled-coil motif and the molecules are probably organized as dimers, each forming a coiled-coil fiber. We have now developed a new sensitive procedure for immunoelectron microscopy of synaptonemal complex proteins and determined the exact localization of the two nonhelical ends of the SCP1 protein within the mouse synaptonemal complex. We found that the N-terminal end of the SCP1 protein is located within the central element of the synaptonemal complex, whereas the C-terminal end is close to or within the lateral element of the synaptonemal complex. This result supports the notion that SCP1 is an extended filamentous protein and that the two molecules of the putative SCP1 dimer are likely to have the same polarity. The observation that the N-termini are confined to the central element indicated that SCP1 dimers, anchored in opposite lateral elements, could establish contact with each other in the central element via their N-termini. To test this possibility we used the yeast two-hybrid system and found that the N-terminal end of the SCP1 protein indeed strongly interacted with itself, but not with other protein domains tested. We therefore suggest that a transversal filament consists of one or more pairs of SCP1 dimers, each pair being organized in a head-to-head arrangement with the C-termini anchored in the lateral elements and the two N-termini being joined in the central element.

A general bacterial expression system for functional analysis of cDNA-encoded proteins

A general system for functional analysis of cDNA-encoded proteins is described. The basic concept involves the expression in Escherichia coli of selected portions of cDNAs in an approach toward the understanding of the function of the corresponding proteins. A selected cDNA is expressed as part of a fusion protein used for immunization to elicit antibodies, and a corresponding fusion protein, having the cDNA-encoded portion in common, for purification of target protein-specific antibodies. This antiserum could be used for functional analysis of the cDNA-encoded protein, e.g., by immunohistology. Two general expression vector systems for E. coli have been constructed, both (i) designed with multiple cloning sites in three different reading frames, (ii) having their protein production controlled by the tightly regulated T7 promoter, and (iii) enabling affinity purification of the expressed target proteins by fusions to IgG-binding domains derived from staphylococcal protein A or a serum albumin-binding protein derived from streptococcal protein G, respectively. This novel system has been evaluated by expressing five cDNAs, isolated from prepubertal mouse testis by a differential cDNA library screening strategy. All five clones could be expressed intracellularly in E. coli as fusion proteins with high production levels, ranging from 4 to 500 mg/liter, and affinity purification yielded essentially full-length products. Characterization of affinity-purified antibodies revealed that there exists no cross-reactivity between the two fusion systems and that such antibodies indeed could be used for immunohistology. The implications for the described system for large-scale functional analysis of cDNA libraries are discussed.

The murine Ki-67 cell proliferation antigen accumulates in the nucleolar and heterochromatic regions of interphase cells and at the periphery of the mitotic chromosomes in a process essential for cell cycle progression

We have isolated the murine homologue of the human Ki-67 antigen. The Ki-67 antigen is used as a marker to assess the proliferative capacity of tumour cells; however, its cellular function is not known. The murine Ki-67 cDNA sequence (TSG126) was found to contain 13 tandem repeats, making up more than half of the total protein size. A comparison of this repetitive sequence block to its human counterpart, which contains 16 consecutive repeat units, revealed several conserved sequence motifs, including one motif frequently observed in proteins interacting with DNA. An antiserum developed against the product of the TSG126 cDNA clone identified a protein with an apparent molecular mass of 360 kDa, mainly expressed in proliferating cells. The TSG126 protein begins to accumulate during the late G1 stage of the cell cycle and is first seen as numerous small granules evenly distributed throughout the nucleus. During the S and the G2 phases, larger foci that overlap with the nucleoli and the heterochromatic regions are formed. At the onset of mitosis the TSG126 protein undergoes a dramatic redistribution process and becomes associated with the surface of the condensed chromosomes. The relative absence of the TSG126 protein from G1 interphase cells strongly argues against a model where the association of the TSG126 protein with mitotic chromosomes merely reflects a mechanism for the symmetrical distribution of nucleolar proteins between daughter cells. Instead, the intracellular distribution of the TSG126 protein during the cell cycle suggests that it could have a chromatin-associated function in both interphase and mitotic cells. Microinjection of anti-TSG126 antibodies into proliferating Swiss-3T3 fibroblasts was found to delay cell cycle progression, indicating that the TSG126 protein has an essential nuclear function.

Expression of a large number of novel testis-specific genes during spermatogenesis coincides with the functional reorganization of the male germ cell

Structural and functional changes, essential for the formation of mature male germ cells, are known to take place at specific stages of the mammalian spermatogenic process. To identify novel genes that are involved in this developmental process, we have initiated a large-scale cDNA sequencing project (Hoog+, Nucleic Acids Res. 19: 93-98, 1991; Starborg et al., Mol. Reprod. Dev. 33: 243-251, 1992; Yuan et al., Biol. Reprod., 1995). Five-hundred and forty cDNAs have been isolated from testicular cDNA libraries and partially sequenced, 355 of which were found to represent genes previously not described in the literature. In addition, a number of cDNAs was found to be related to genes previously identified only in lower eukaryotes, suggesting that these murine genes encode functions that are evolutionary conserved. One of these murine cDNAs was related to the Aspergillus nidulans BimE gene, a putative cell cycle checkpoint regulator (Starborg et al., J. Biol. Chem., 1994). Southern blot analysis revealed that the murine BimE-related gene is strongly conserved in mammals. RNA blotting experiments of 361 novel murine cDNAs have identified 52 cDNAs that are expressed only during spermatogenesis, 36 of which are expressed only in spermatids, and 16 cDNAs that are expressed in both spermatocytes and spermatids. A survey of the literature revealed 40 mammalian genes that have previously been shown to be expressed mainly during spermatogenesis, and together with our results, they define three dominating temporal patterns of gene expression during spermatogenesis, each pattern coinciding with known functional or structural changes occurring during this differentiation process.

Haploid gene expression: temporal onset and storage patterns of 13 novel transcripts during rat and mouse spermiogenesis

The temporal and spatial expression of thirteen novel spermatid-specific genes corresponding to cDNA clones isolated from an adult mouse testis library was analyzed. Northern analysis of RNA from seminiferous tubules at defined stages of the rat and mouse seminiferous epithelial cycle and in situ hybridization of testis sections revealed that these mRNAs were expressed in a stage-specific manner. The expression of all mRNAs was first detected in early round spermatids, and it increased to abundance during stages VII-VIII of the epithelial cycle. Twelve out of thirteen mRNAs were found not only in round spermatids but also in transcriptionally inactive elongated spermatids, suggesting that they are stored and regulated at the translational level. The variation in the length of the poly(A) tail was detected for four of the transcripts, represented by cDNA clones MTEST70, MTEST627, MTEST641, and MTEST643 at defined stages of the cycle. Similarity in the stage-specific expression pattern displayed by this group of haploid-specific genes strongly suggests the presence of common regulatory mechanisms that act during spermiogenesis, and these genes also provide a means for further studies of these mechanisms.

A murine replication protein accumulates temporarily in the heterochromatic regions of nuclei prior to initiation of DNA replication

We have analyzed the expression of the murine P1 gene, the mammalian homologue of the yeast MCM3 protein, during the mitotic cell cycle. The MCM3 protein has previously been shown to be of importance for initiation of DNA replication in Saccharomyces cerevisiae. We found that the murine P1 protein was present in the nuclei of mammalian cells throughout interphase of the cell cycle. This is in contrast to the MCM3 protein, which is located in the nuclei of yeast cells only between the M and the S phase of the cell cycle. Detailed analysis of the intranuclear localization of the P1 protein during the cell cycle revealed that it accumulates transiently in the heterochromatic regions towards the end of G1. The accumulation of the P1 protein in the heterochromatic regions prior to activation of DNA replication suggests that the mammalian P1 protein is also of importance for initiation of DNA replication. The MCM2-3.5 proteins have been suggested to represent yeast equivalents of a hypothetical replication licensing factor initially described in Xenopus. Our data support this model and indicate that the murine P1 protein could function as replication licensing factor. The chromosomal localization of the P1 gene was determined by fluorescence in situ hybridization to region 6p12 in human metaphase chromosomes.

Rapid cDNA sequencing in combination with RNA expression studies in mice identifies a large number of male germ cell-specific sequence tags

A large number of cDNA clones were isolated from an adult mouse testis cDNA library and partially sequenced. Sequence comparisons revealed that many of them displayed similarities to genes previously identified only in invertebrates and lower eukaryotes, including, e.g., one cDNA clone related to the Drosophila melanogaster suppressor of forked gene. Other cDNA clones were found to be related, but not identical, to rodent genes involved in a variety of cellular activities, e.g., signal transduction and tumor development. The RNA expression patterns of 258 cDNA clones were analyzed through use of Northern blot methodology. Forty-two novel cDNA clones were found to be expressed only in male germ cells, the majority of them during spermiogenesis. One male germ cell-specific mouse cDNA clone was found to be similar to tektin A1, a protein known to interact with the flagellar microtubules of sea urchin sperm.

A novel murine gene encoding a 216-kDa protein is related to a mitotic checkpoint regulator previously identified in Aspergillus nidulans

We describe the isolation and characterization of a novel mouse gene, tsg24, which displays striking sequence similarities to the Aspergillus nidulans bimE gene. The bimE gene has been shown to be a mitotic checkpoint regulator, negatively regulating entry into mitosis in A. nidulans. The tsg24 gene was found to contain a long open reading frame of 1944 amino acids, encoding a polypeptide with a calculated molecular mass of 216,087 Da. We have developed an antibody directed against the product of the tsg24 gene and identified a protein with a molecular mass of approximately 200 kDa. This protein was found to be uniformly expressed throughout interphase of the cell cycle, whereas the level of this protein was lower in protein extracts prepared from mitotic cells.

Analysis of the expression of a large number of novel genes isolated from mouse prepubertal testis

The analysis of genes expressed in a restricted temporal and spatial manner during spermatogenesis has given insights into different gene-regulatory mechanisms active in germ cells. However, very few genes have so far been described that are predominantly active in spermatogonia and the early meiotic cell types of testis. To isolate a battery of such genes, more than 100 different mRNA molecules were isolated from a mouse prepubertal testicular cDNA library, and their expression patterns in different tissues analyzed. Thirty mRNAs, 26 of them previously not described in the literature, were found to be predominantly expressed in mouse testis. A detailed analysis of their expression patterns identified a number of mRNA molecules differentially expressed in testicular cell types, including both germ cells and somatic cell types. Characterization of these mRNAs also revealed five distinct temporal phases of gene expression during prepubertal germ cell development. Three different genes, mainly active in the spermatogonial and the early meiotic cell types of testis, were isolated and will be used to characterize further stage-specific gene expression during germ cell differentiation.

Balbiani ring 1 gene in Chironomus tentans. Sequence organization and dynamics of a coding minisatellite

Balbiani ring (BR) genes in diptera encode large secretory proteins and are classical model systems for studies of gene expression. In Chironomus tentans, four closely related BR genes, BR 1, BR 2.1, BR 2.2 and BR 6 form a gene family. The BR genes have been partially characterized and are known to contain long arrays of tandemly arranged repeat units with an hierarchical repeat organization. Here, we report the sequence organization of the complete transcribed part of the BR 1 gene in C. tentans. The gene contains five exons and four introns. Three of the introns are located at the 5' end and the fourth at the 3' end of the gene. Exon 4 is approximately 35,000 bases long and is built completely from tandemly organized repeats. We show that this long repeat block contains two types of related repeat units, beta and gamma. Each type forms a large uninterrupted array, a 5' beta array and a 3' gamma array with a sharp border between them. In the hierarchical repeat structure in each repeat array, all repeats are virtually identical at one level of repetition, but shown differences at the next level. The whole repeat block in the BR 1 gene fluctuates in size between different alleles, but not by more than 10%. In contrast, within the block, the beta and gamma arrays vary in length between 8000 and 29,000 bases in an inverse fashion, together keeping the overall length requirement. We propose that the length of exon 4 is conserved by selection of cross-over products of a given length, and that the internal hierarchical sequence organization in the BR 1 gene is a consequence of the combined action of several different sequence turnover mechanisms, all dependent on the unequal pairing of homologous sequences at different, competing levels of repetition.

Isolation of a large number of novel mammalian genes by a differential cDNA library screening strategy

As part of the ongoing human and mouse genome projects, the aim of this study was to isolate novel, previously uncharacterized, genes from mouse testis. Two approaches were compared for their effectiveness in isolating novel genes: random, vs differential, complementary DNA (cDNA) cloning methods. In the differential approach, only the cDNA clones containing rare sequences (as determined by preliminary clone hybridization) are further analyzed; in the random approach, cDNA clones are isolated at random from the cDNA library. More than two hundred cDNA clones altogether were analyzed, using a PCR-mediated amplification and sequencing strategy. A comparison of these sequences to nucleic acid and protein sequence databases, revealed that 84% of the isolated rare cDNA clones represented new, previously uncharacterized mouse genes. In contrast, less than 63% of the cDNA clones isolated at random from cDNA libraries, contained novel genes. Thus, the probability of isolating new, previously uncharacterized, mammalian genes from cDNA libraries can be markedly improved by focusing efforts on clones containing rare sequences.

Analysis of a murine male germ cell-specific transcript that encodes a putative zinc finger protein

A cDNA species, corresponding to a gene with testis-specific expression (TSGA), was isolated from a testis cDNA library. The temporal and spatial expression of TSGA was studied by in situ hybridization as well as RNA filter hybridization. In tissue sections, the TSGA sequence was confined to cells within the seminiferous tubules. For filter hybridization, RNA was isolated from testis of prepubertal rats of different ages as well as from enriched populations of various germ cell types. It was found that TSGA is expressed only in male germ cells and that the steady-state level of TSGA transcripts reaches a maximum during the meiotic and the postmeiotic stages of germ cell development, suggesting a meiotic or postmeiotic function for the encoded protein. TSGA encodes a putative protein having 1,214 amino acids and contains a zinc finger, a structure that previously has been shown to mediate binding to nucleic acids.