Novel anti-GARP antibody DS-1055a augments anti-tumor immunity by depleting highly suppressive GARP+ regulatory T cells.

Regulatory T (Treg) cells, which are essential for maintaining self-tolerance, inhibit anti-tumor immunity, consequently hindering protective cancer immunosurveillance, and hampering effective anti-tumor immune responses in tumor-bearing hosts. Here, we show that depletion of Treg cells via targeting glycoprotein A repetitions predominant (GARP) induces effective anti-tumor immune responses. GARP was specifically expressed by highly suppressive Treg cells in the tumor microenvironment (TME) of multiple cancer types in humans. In the periphery, GARP was selectively induced in Treg cells, but not in effector T cells, by polyclonal stimulation. DS-1055a, a novel afucosylated anti-human GARP monoclonal antibody, efficiently depleted GARP+ Treg cells, leading to the activation of effector T cells. Moreover, DS-1055a decreased FoxP3+CD4+ T cells in the TME and exhibited remarkable anti-tumor activity in humanized mice bearing HT-29 tumors. We propose that DS-1055a is a new Treg-cell-targeted cancer immunotherapy agent with augmentation of anti-tumor immunity.

Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance.

BACKGROUND: PSI-BLAST, an extremely popular tool for sequence similarity search, features the utilization of Position-Specific Scoring Matrix (PSSM) constructed from a multiple sequence alignment (MSA). PSSM allows the detection of more distant homologs than a general amino acid substitution matrix does. An accurate estimation of the weights for sequences in an MSA is crucially important for PSSM construction. PSI-BLAST divides a given MSA into multiple blocks, for which sequence weights are calculated. When the block width becomes very narrow, the sequence weight calculation can be odd. RESULTS: We demonstrate that PSI-BLAST indeed generates a significant fraction of blocks having width less than 5, thereby degrading the PSI-BLAST performance. We revised the code of PSI-BLAST to prevent the blocks from being narrower than a given minimum block width (MBW). We designate the modified application of PSI-BLAST as PSI-BLASTexB. When MBW is 25, PSI-BLASTexB notably outperforms PSI-BLAST consistently for three independent benchmark sets. The performance boost is even more drastic when an MSA, instead of a sequence, is used as a query. CONCLUSIONS: Our results demonstrate that the generation of narrow-width blocks during the sequence weight calculation is a critically important factor that restricts the PSI-BLAST search performance. By preventing narrow blocks, PSI-BLASTexB upgrades the PSI-BLAST performance remarkably. Binaries and source codes of PSI-BLASTexB (MBW = 25) are available at https://github.com/kyungtaekLIM/PSI-BLASTexB .

Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

Protein database search for public databases is a fundamental step in the target selection of proteins in structural and functional genomics and also for inferring protein structure, function, and evolution. Most database search methods employ amino acid substitution matrices to score amino acid pairs. The choice of substitution matrix strongly affects homology detection performance. We earlier proposed a substitution matrix named MIQS that was optimized for distant protein homology search. Herein we further evaluate MIQS in combination with LAST, a heuristic and fast database search tool with a tunable sensitivity parameter m, where larger m denotes higher sensitivity. Results show that MIQS substantially improves the homology detection and alignment quality performance of LAST across diverse m parameters. Against a protein database consisting of approximately 15 million sequences, LAST with m = 105 achieves better homology detection performance than BLASTP, and completes the search 20 times faster. Compared to the most sensitive existing methods being used today, CS-BLAST and SSEARCH, LAST with MIQS and m = 106 shows comparable homology detection performance at 2.0 and 3.9 times greater speed, respectively. Results demonstrate that MIQS-powered LAST is a time-efficient method for sensitive and accurate homology search.

Alterations in rRNA-mRNA interaction during plastid evolution.

Translation initiation depends on the recognition of mRNA by a ribosome. For this to occur, prokaryotes primarily use the Shine-Dalgarno (SD) interaction, where the 3'-tail of small subunit rRNA (core motif: 3'CCUCC) forms base pairs with a complementary signal sequence in the 5'-untranslated region of mRNA. Here, we examined what happened to SD interactions during the evolution of a cyanobacterial endosymbiont into modern plastids (including chloroplasts). Our analysis of available complete plastid genome sequences revealed that the majority of plastids retained SD interactions but with varying levels of usage. Parallel losses of SD interactions took place in plastids of Chlorophyta, Euglenophyta, and Chromerida/Apicomplexa lineages, presumably related to their extensive reductive evolution. Interestingly, we discovered that the classical SD interaction (3'CCUCC/5'GGAGG [rRNA/mRNA]) was replaced by an altered SD interaction (3'CCCU/5'GGGA or 3'CUUCC/5'GAAGG) through coordinated changes in the sequences of the core rRNA motif and its paired mRNA signal. These changes in plastids of Chlorophyta and Euglenophyta proceeded through intermediate stages that allowed both the classical and altered SD interactions. This coevolution between the rRNA motif and the mRNA signal demonstrates unexpected plasticity in the translation initiation machinery.

Pregnancy Outcomes and Risk Factors for Uterine Rupture After Laparoscopic Myomectomy: A Single-Center Experience and Literature Review.

STUDY OBJECTIVE: To evaluate pregnancy outcomes after laparoscopic myomectomy (LSM), focusing on the risk of uterine rupture. DESIGN: Retrospective cohort study (Canadian Task Force classification III). SETTING: University hospital. PATIENTS: Of 676 women who visited the obstetrics department for a pregnancy after undergoing LSM performed at the same center between 1994 and 2012, we included the 523 women who had follow-up through the end of pregnancy. INTERVENTIONS: All patients underwent LSM, and their medical charts were retrospectively reviewed. MEASUREMENTS AND MAIN RESULTS: Multiple myomas were removed in 35.2% of cases, intramural-type lesions occurred in 46.5% of cases, and the mean myoma diameter was 4.9 cm. Pregnancy outcomes after LSM included 400 (76.5%) full-term deliveries and 100 (19.1%) vaginal deliveries, with other adverse outcomes being no different than the general population. The mean interval between LSM and pregnancy was 14 months, and only 3 (0.6%) cases of uterine rupture occurred during pregnancy. In analysis, by reviewing the published cases of uterine rupture, we found that the mean diameter, myoma number and type, and the rate of uterine suture were similar between the ruptured cases and all of our cases of LSM. CONCLUSION: LSM can be safely used in women of reproductive age who want to become pregnant. Uterine rupture occurs in rare cases, regardless of myoma features, but further large-scale studies are required to ascertain the detailed effects of various surgical techniques.

A multicenter study of the importance of systemic chemotherapy for patients with small-cell neuroendocrine carcinoma of the uterine cervix.

AIMS: We investigated the prognosis of patients with small-cell neuroendocrine carcinoma of the uterine cervix (SCNEC) in relation to treatment modalities. METHODS: We retrospectively reviewed the medical records and pathological reports of 102 patients who were histologically diagnosed with SCNEC at 5 different institutes. Time to progression (TTP) and overall survival (OS) were analyzed for each treatment modality. RESULTS: Of the patients with early-stage [International Federation of Obstetrics and Gynecology (FIGO) stage IB2 or below] SCNEC, 57.8 and 79.3% underwent radical hysterectomy followed by adjuvant therapy. In advanced-stage SCNEC, concurrent chemoradiation therapy was given to 51.4% of the patients. The overall recurrence rate was 51.6%. In early- and advanced-stage SCNEC, the TTP was not different (22.3 vs. 13.3 months, p = 0.104), but the OS was different (40.7 vs. 21.4 months, p = 0.029). Parametrial involvement and lymph vascular space invasion were found to be associated with an unfavorable prognosis. Interestingly, survival was the most unfavorable in patients with early-stage SCNEC who had never received chemotherapy. FIGO stage and use of chemotherapy were identified as independent prognostic factors in SCNEC patients. CONCLUSIONS: SCNEC requires systemic chemotherapy as part of the initial treatment, along with surgery or radiation, even in patients with early-stage disease.

Distribution and perinatal transmission of bacterial vaginal infections in pregnant women without vaginal symptoms.

BACKGROUND: We evaluated the distribution and vertical transmission of bacterial vaginal infections in asymptomatic pregnant women. METHODS: We performed multiplex PCR on secretions collected on cervical swabs from pregnant women at over 36 weeks of gestation and on oral secretions collected from their neonates immediately after delivery. We detected sexually transmitted infections (STIs) with the following 6 species: Trichomonas vaginalis, Mycoplasma hominis, Mycoplasma genitalium, Chlamydia trachomatis, Neisseria gonorrhoeae, and Ureaplasma urealyticum. RESULTS: Infectious agents were detected in 64 of 455 pregnant women (14.1%) and in 11 neonates (2.4%). The rate of vertical transmission was 17.2% and all the infectious agents detected in neonates were concordant with those found in their mothers. U. urealyticum was the most frequently detected in the maternal genitalia, followed by M. hominis. Women who were in labor for a longer period of time had a higher risk of vertically transmitting STI agents to their neonates. CONCLUSIONS: Vertical transmission of bacterial STIs from mothers to their infants is possible at delivery and influenced by the duration of labor. STIs should be diagnosed in pregnant women to prevent vertical transmission from the mother to the infant at the time of delivery.

Large variations in bacterial ribosomal RNA genes.

Ribosomal RNA (rRNA) genes, essential to all forms of life, have been viewed as highly conserved and evolutionarily stable, partly because very little is known about their natural variations. Here, we explored large-scale variations of rRNA genes through bioinformatic analyses of available complete bacterial genomic sequences with an emphasis on formation mechanisms and biological significance. Interestingly, we found bacterial genomes in which no 16S rRNA genes harbor the conserved core of the anti-Shine-Dalgarno sequence (5'-CCTCC-3'). This loss was accompanied by elimination of Shine-Dalgarno-like sequences upstream of their protein-coding genes. Those genomes belong to 1 or 2 of the following categories: primary symbionts, hemotropic Mycoplasma, and Flavobacteria. We also found many rearranged rRNA genes and reconstructed their history. Conjecturing the underlying mechanisms, such as inversion, partial duplication, transposon insertion, deletion, and substitution, we were able to infer their biological significance, such as co-orientation of rRNA transcription and chromosomal replication, lateral transfer of rRNA gene segments, and spread of rRNA genes with an apparent structural defect through gene conversion. These results open the way to understanding dynamic evolutionary changes of rRNA genes and the translational machinery.

Magnetic resonance imaging and intraoperative frozen sectioning for the evaluation of risk factors associated with lymph node metastasis in endometrial cancer.

INTRODUCTION: To analyze the accuracy of magnetic resonance imaging (MRI) and intraoperative frozen sectioning (IFS) for predicting the low- and high-risk patients and risk factors associated with lymph node (LN) metastasis in patients with surgically staged endometrial cancer. METHODS: The medical records of 175 patients with endometrial cancer who underwent comprehensive surgical staging including pelvic and para-aortic LN dissection between January 2008 and July 2011 were retrospectively analyzed. Results of MRI and IFS of the uterus for the evaluation of risk factors were correlated with final pathology. RESULTS: Our results showed a high specificity and negative predictive value of MRI and IFS for the evaluation of myometrial invasion and cervical stromal invasion. Of the 41 patients identified as low risk by both MRI and IFS, none had pelvic or para-aortic LN metastases in the final pathology. CONCLUSIONS: The results indicate that MRI and IFS may be useful for the evaluation of risk factors associated with LN metastasis in patients with endometrial cancer. Magnetic resonance imaging and IFS can be used to accurately identify low-risk patients who do not need comprehensive surgical staging and may prevent unnecessary lymphadenectomy.

Lymphovascular space invasion is highly associated with lymph node metastasis and recurrence in endometrial cancer.

BACKGROUND: Lymphovascular space invasion (LVSI) has been evaluated as a predictor for nodal metastasis or poor survival in endometrial adenocarcinoma. AIMS: To evaluate whether LVSI is a prognostic factor for lymph node metastasis and relapse of disease in endometrial adenocarcinoma. MATERIALS & METHODS: We retrospectively analysed the medical records of 438 women with endometrial adenocarcinoma treated by surgical staging, including pelvic and paraaortic lymph node dissection, between January 1996 and July 2011. RESULTS: One hundred sixty-three women (37.2%) were LVSI-positive and 275 (62.8%) were negative. LVSI-positive women were significantly older and showed more advanced stage, poorer differentiation, and a higher frequency of non-endometrioid histology type, myometrial invasion, and positive peritoneal cytology than LVSI-negative women. Surgeries by laparotomy rather than laparoscopy and more adjuvant therapies were conducted in LVSI-positive women. The median number of pelvic and paraaortic lymph nodes removed were not different, but LVSI-positive patients showed more lymph node metastases. The LVSI-positive group also showed a higher recurrence of disease and lower survival rates than the LVSI-negative group. Negative predictive values of LVSI for lymph node metastasis and recurrence of disease were 96.4 and 97.1%, respectively. In multivariate analysis, LVSI did not influence overall or disease-free survival after adjusting for several confounding factors. CONCLUSIONS: In the cases that the nodal status has not been assessed in endometrial adenocarcinoma, the presence of LVSI may be a reasonable surrogate in addition to other risk factors, in determining the need for adjuvant therapy.