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Nakamura N, Kinami S, Fujita J, Kaida D, Tomita Y, Miyata T, Fujita H, Takamura H, Ueda N, Kosaka T. [A Case of Effective Disease Control of Advanced Gastric Cancer with Distant Lymph Node Metastases Following Nivolumab Treatment]. Gan To Kagaku Ryoho 2020; 47:1258-1260. [PMID: 32829368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A 66-year-old man was diagnosed with advanced gastric cancer(L, Less, Type 2, T4a[SE], N2, M1[LYM], H0, P0, cStage Ⅳ)and received treatment with S-1/cisplatin as first-line chemotherapy. This treatment resulted in partial response(PR) after 3 months, with reduction in the sizes of metastatic lymph nodes surrounding the pancreatic head and paraaortic lesion. However, the sizes of metastatic lymph nodes increased after 7 months of chemotherapy. Ramucirumab/nab-paclitaxel was then administered as second-line chemotherapy, and the diameter of the metastatic lymph nodes subsequently decreased after 4 months of the regimen. However, progressive disease was observed at 7 months, and blood transfusion was required because of bleeding from the primary gastric tumor. Therefore, nivolumab was initiated as third-line chemotherapy 14 months after the first treatment. After nivolumab administration, a 28% reduction in metastatic lymph nodes was achieved within 3 months, together with the regression of the primary gastric tumor and improvement in anemia within 6 months. PR was achieved after 12 months of nivolumab administration, and effective disease control was maintained for 16 months without any adverse reaction to nivolumab.
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Miyata T, Takamura H, Kin R, Nishiki H, Hashimoto A, Fujii Y, Miura S, Fujita J, Kaida D, Tomita Y, Nakamura N, Fujita H, Kinami S, Ueda N, Kosaka T. Pancreatic neuroendocrine tumor featuring growth into the main pancreatic duct and tumor thrombus within the splenic vein: a case report. J Surg Case Rep 2020; 2020:rjaa155. [PMID: 32699600 PMCID: PMC7365031 DOI: 10.1093/jscr/rjaa155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/29/2020] [Accepted: 05/14/2020] [Indexed: 11/13/2022] Open
Abstract
A 48-year-old woman was admitted to our hospital because of upper abdominal pain. Computer tomography showed an enhancing mass in the pancreatic body, dilation of the main pancreatic duct (MPD) and a filling defect within the splenic vein. On the basis of the preoperative diagnosis of pancreatic body cancer, distal pancreatectomy was scheduled. The pancreas was divided along the left edge of the gastroduodenal artery; however, frozen pathological examination of the pancreatic stump was tumor positive, and therefore a total pancreatectomy was performed. The lesion was a white expansive nodular mass that had spread into the MPD and protruded into the splenic vein. A pathological diagnosis of non-functioning neuroendocrine tumor (NET) was made. In general, imaging findings of disruption of the MPD and tumor vein thrombus are characteristics of pancreatic ductal adenocarcinoma, but are uncommon in NET. However, NET should be included in the differential diagnosis for such patients.
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Miyata T, Takamura H, Kin R, Nishiki H, Hashimoto A, Fujii Y, Miura S, Fujita J, Kaida D, Tomita Y, Nakamura N, Fujita H, Kinami S, Ueda N, Kosaka T. Spleen Volume as a Predictive Biomarker for Thrombocytopenia and Liver Dysfunction After Oxaliplatin-based Chemotherapy. Anticancer Res 2020; 40:3361-3370. [PMID: 32487632 DOI: 10.21873/anticanres.14319] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM We evaluated whether splenic volume (SV) predicts sinusoidal obstruction syndrome (SOS) in colorectal cancer (CRC) patients receiving capecitabine plus oxaliplatin (CapeOX) therapy. PATIENTS AND METHODS In this retrospective study, we measured SV in 41 patients receiving adjuvant CapeOX for CRC at five different time points. We compared the clinical data of the 18 patients who experienced ≥30% increases in SV immediately after vs. before CapeOX (group A) with data for the remaining 23 patients (group B). RESULTS Platelet numbers decreased and the levels of hepatobiliary enzymes increased significantly 1 year after CapeOX compared with before CapeOX in group A. However, in group B, significantly decreased platelet numbers and significantly increased aspartate transaminase levels were confirmed only immediately after CapeOX, with no significant subsequent changes. CONCLUSION SV was significantly associated with thrombocytopenia and liver dysfunction in CRC patients, and predicted SOS.
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Nakamura N, Kinami S, Fujita J, Kaida D, Tomita Y, Miyata T, Fujita H, Ueda N, Takamura H, Kosaka T. A Case of Advanced Gastroesophageal Junction Cancer with Bulky Lymph Node Metastases Treated with Nivolumab. Case Rep Oncol 2020; 13:702-707. [PMID: 32774260 PMCID: PMC7383216 DOI: 10.1159/000507955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/19/2022] Open
Abstract
A 71-year-old woman was diagnosed with advanced gastroesophageal junction cancer with bulky lymph nodes along the cardiac region and the lower mediastinum (GE-Circ type 3 T3 N3 M0 H0 stage III) and received treatment with S-1 and oxaliplatin (SOX) as first-line chemotherapy. After 3 cycles of SOX, severe anorexia and diarrhea were observed. We converted from this regimen of systemic chemotherapy to ramucirumab (RAM) monotherapy as second-line chemotherapy. This treatment resulted in a reduction in size of the metastatic lymph nodes along the cardiac region and the lower mediastinum. However, progression of lymph node metastasis and the primary tumor was observed following 7 months of RAM monotherapy. Therefore, nivolumab was initiated as third-line chemotherapy 14 months after the initial treatment. After 3 months of nivolumab administration, a 47% reduction in metastatic lymph nodes was achieved and a regression of the primary gastric tumor as seen on an enhanced computed tomography scan. After 7 months of nivolumab monotherapy, the diameter of the target lymph nodes had reduced by 81% from baseline, and there was no evidence of malignancy upon pathological assessment of the primary tumor site biopsy. The patient survived with nivolumab monotherapy for approximately 2 years after her first visit, without any adverse reaction to nivolumab.
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Nakamura N, Kinami S, Fujii Y, Miura S, Fujita J, Kaida D, Tomita Y, Miyata T, Fujita H, Ueda N, Iida Y, Kosaka T. The neutrophil/lymphocyte ratio as a predictor of peritoneal metastasis during staging laparoscopy for advanced gastric cancer: a retrospective cohort analysis. World J Surg Oncol 2019; 17:108. [PMID: 31238937 PMCID: PMC6593512 DOI: 10.1186/s12957-019-1651-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/19/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The use of staging laparoscopy (SL) has become widespread in patients with advanced gastric cancer (GC). This study aimed to evaluate the predictive value of the neutrophil/lymphocyte ratio (NLR) for the presence of peritoneal metastasis during staging laparoscopy in patients with advanced GC. METHODS This retrospective analysis was performed in 35 patients with advanced GC who underwent SL at Kanazawa Medical University Hospital between January 2009 and December 2017. Clinicopathological characteristics were examined and multivariate analyses were performed to identify preoperative laboratory parameters that were independently associated with the presence of peritoneal metastasis or cytological malignancy (P/CY positive) during SL. RESULTS A P/CY-positive result was confirmed during SL in 16 patients (45.7%). Patients with type 4 or diffuse type 3 tumors showed a significantly higher P/CY-positive rate than those with other tumor types (58.3% vs. 18.2%, P = 0.02). In the univariate analysis for preoperative laboratory parameters, NLR (P < 0.0001) and total protein (P = 0.03) and albumin (P = 0.04) levels were significantly correlated with a P/CY-positive result. On multivariate analysis, NLR was significantly correlated with a P/CY-positive result (P = 0.0002). In patients with type 4 or diffuse type 3 tumors, a high NLR (> 3.5) was associated with a significantly higher P/CY-positive rate than a low NLR (≤ 3.5) (83.3% vs. 33.3%, P = 0.01). Moreover, in patients without type 4 or diffuse type 3 tumors, the P/CY-positive rates were 100% and 0% in patients with NLR > 3.5 and NLR ≤ 3.5, respectively. CONCLUSIONS The preoperative NLR was a significant independent predictor of the presence of peritoneal metastasis during SL. Regardless of tumor type, patients with a high NLR could be reasonable candidates for SL. On the other hand, non-diffuse type tumor accompanied by a low NLR may not need to undergo SL.
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Nakamura N, Kinami S, Fujii Y, Miura S, Fujita J, Kaida D, Tomita Y, Miyata T, Fujita H, Ueda N, Kosaka T. A remarkable clinical response in advanced gastric cancer treated with trastuzumab plus capecitabine combination chemotherapy: A report of two cases. Clin Case Rep 2019; 7:714-718. [PMID: 30997070 PMCID: PMC6452495 DOI: 10.1002/ccr3.2056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/26/2019] [Indexed: 12/27/2022] Open
Abstract
When trastuzumab + capecitabine and cisplatin chemotherapy could not be conducted continuously because of severe adverse reactions to cisplatin, trastuzumab + capecitabine could be an alternative systemic chemotherapy options for metastatic or recurrent gastric cancer patients.
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Ohnishi T, Kinami S, Fujii Y, Miura S, Fujita J, Kaida D, Tomita Y, Fujita H, Nakano Y, Ueda N, Kosaka T. [Prognosis of Conversion Gastrectomy Cases for Stage IV Gastric Cancer]. Gan To Kagaku Ryoho 2017; 44:1799-1801. [PMID: 29394780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND We evaluated the efficacy of surgical resection following response to primary chemotherapy for prospective registered Stage IV gastric cancer patients. PATIENTS AND METHODS We analyzed the details and prognosis of 6 patients having advanced gastric cancer clinically diagnosed as resectable following primary chemotherapy between 2011 and 2015. RESULTS The reason for being diagnosed as unresectable before chemotherapy was metastasis to distant sites, including paraaortic lymph node metastasis in 3 cases, peritoneal metastasis in 2 cases, and liver metastasis in 1 case.Two patients were able to undergo R0 resection, and the remaining 4 patients were unable to undergo complete resection.The median survival time (MST)of the patients who underwent R0 resection was 567.5 days, and the MST of the patients who could not undergo R0 resection was 474 days. CONCLUSION Careful consideration of conversion gastrectomy may be important in inducing longterm survival in clinical Stage IV gastric cancer patients.
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Yoshimoto R, Kaida D, Furuno M, Burroughs AM, Noma S, Suzuki H, Kawamura Y, Hayashizaki Y, Mayeda A, Yoshida M. Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. RNA (NEW YORK, N.Y.) 2017; 23:47-57. [PMID: 27754875 PMCID: PMC5159648 DOI: 10.1261/rna.058065.116] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/03/2016] [Indexed: 05/27/2023]
Abstract
Spliceostatin A (SSA) is a methyl ketal derivative of FR901464, a potent antitumor compound isolated from a culture broth of Pseudomonas sp no. 2663. These compounds selectively bind to the essential spliceosome component SF3b, a subcomplex of the U2 snRNP, to inhibit pre-mRNA splicing. However, the mechanism of SSA's antitumor activity is unknown. It is noteworthy that SSA causes accumulation of a truncated form of the CDK inhibitor protein p27 translated from CDKN1B pre-mRNA, which is involved in SSA-induced cell-cycle arrest. However, it is still unclear whether pre-mRNAs are uniformly exported from the nucleus following SSA treatment. We performed RNA-seq analysis on nuclear and cytoplasmic fractions of SSA-treated cells. Our statistical analyses showed that intron retention is the major consequence of SSA treatment, and a small number of intron-containing pre-mRNAs leak into the cytoplasm. Using a series of reporter plasmids to investigate the roles of intronic sequences in the pre-mRNA leakage, we showed that the strength of the 5' splice site affects pre-mRNA leakage. Additionally, we found that the level of pre-mRNA leakage is related to transcript length. These results suggest that the strength of the 5' splice site and the length of the transcripts are determinants of the pre-mRNA leakage induced by SF3b inhibitors.
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Funaki H, Fujii Y, Miura S, Fujita J, Morioka E, Kaida D, Ohnishi T, Tomita Y, Noguchi M, Fujita H, Kinami S, Nakano Y, Ueda N, Kosaka T. [Treatment Outcomes of Advanced Gastric Cancer after Neoadjuvant Chemotherapy with S-1 and Cisplatin]. Gan To Kagaku Ryoho 2016; 43:1421-1423. [PMID: 28133010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
BACKGROUND The prognosis after neoadjuvant chemotherapy(NAC)is expected to improve in patients with resectable advanced gastric cancer who are at high risk of recurrence or those with unfavorable prognostic factors. PATIENTS AND METHODS This retrospective study examined treatment outcomes and survival of 25 patients with advanced gastric cancer who received NAC with S-1 and cisplatin(CDDP)between October 2008 and December 2015. RESULTS Among patients with clinical Stage II (4 patients)and III (21 patients)tumors, 13 had partial response(PR)and 12 had stable disease(SD). Neither complete response(CR)nor progressive disease(PD)was noted. CR of lymph node metastases was observed in 6 patients, PR in 9 patients, and SD in 7 patients. R0 resection was performed in 16 patients, R1 in 3 patients, and R2 in 6 patients. Histologic grades of primary tumors were Grade 0(1 patient), Grade 1a(16 patients), Grade 1b(5 patients), Grade 2(3 patients), and Grade 3(none). The 3-year survival rate after R0 resection was 46%, 3-year progression-free survival rate was 68%, and 3-year recurrence-free survival rate was 69%. Significant differences were observed for pathologic stages ypN0/1, 2, and 3(p=0.04), tumor down-stage(p=0.02), and overall tumor fStage I , II / III , and IV (p<0.01). CONCLUSION It is conceivable that R0 resection and downstaging after NAC will improve prognosis.
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Ueda N, Fujii Y, Miura S, Fujita J, Kaida D, Tomita Y, Ohnishi T, Funaki H, Fujita H, Kinami S, Nakano Y, Kosaka T. [Radical Resection of cT3a Gallbladder Cancer after Neoadjuvant Chemotherapy - A Case Report]. Gan To Kagaku Ryoho 2016; 43:1597-1599. [PMID: 28133069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report a case of a radical resection of cT3a gallbladder cancer after neoadjuvant chemotherapy(NAC). A 68-year-old man was referred to our hospital with a chief complaint of right hypochondralgia.Imaging findings were consistent with acute cholecystitis with a stone at the neck of the gallbladder, and advanced gallbladder cancer with infiltration into segments 4 and 5 from the fundus of the gallbladder, Gfb, cT3a(liver), cN1(8a), cM0, cStage III B, was diagnosed on staging laparoscopy. The patient received 3 courses of GEM plus CDDP NAC.The response to the treatment included reduction of the main tumor by 35%, diminished accumulation of FDG at the 8a lymph node, and decrease in serum CA19-9, from 163 U/mL to 75 U/mL. Cholecystectomy with the gallbladder bed and regional lymphadenectomy were performed.The histologic examination revealed extensive necrosis and degeneration of cancer cells in the infiltrating lesions, and the therapeutic effect was judged as Grade I b.The patient has now survived for 11 months without recurrence.
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Kaida D. The reciprocal regulation between splicing and 3'-end processing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:499-511. [PMID: 27019070 PMCID: PMC5071671 DOI: 10.1002/wrna.1348] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/05/2016] [Accepted: 02/22/2016] [Indexed: 12/14/2022]
Abstract
Most eukaryotic precursor mRNAs are subjected to RNA processing events, including 5′‐end capping, splicing and 3′‐end processing. These processing events were historically studied independently; however, since the early 1990s tremendous efforts by many research groups have revealed that these processing factors interact with each other to control each other's functions. U1 snRNP and its components negatively regulate polyadenylation of precursor mRNAs. Importantly, this function is necessary for protecting the integrity of the transcriptome and for regulating gene length and the direction of transcription. In addition, physical and functional interactions occur between splicing factors and 3′‐end processing factors across the last exon. These interactions activate or inhibit splicing and 3′‐end processing depending on the context. Therefore, splicing and 3′‐end processing are reciprocally regulated in many ways through the complex protein–protein interaction network. Although interesting questions remain, future studies will illuminate the molecular mechanisms underlying the reciprocal regulation. WIREs RNA 2016, 7:499–511. doi: 10.1002/wrna.1348 For further resources related to this article, please visit the WIREs website.
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Ueda N, Miura S, Morioka E, Kaida D, Tomita Y, Ohonishi T, Ohono Y, Noguchi M, Funaki H, Fujita H, Kinami S, Nakano Y, Kosaka T. [A Case of Gastric and Pancreatic Cancer Resected with Curative Intent while Preserving Organ Function]. Gan To Kagaku Ryoho 2015; 42:2343-2345. [PMID: 26805358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A 57-year-old woman was diagnosed with a pancreatic tumor. Abdominal computed tomography showed cStage Ⅳa pancreatic cancer with a 20×16 mm tumor near the base of the celiac artery. Since the tumor contacted the SMA at an angle of 90 degrees, it was judged as a borderline resectable tumor. In addition, cStage ⅠB gastric cancer was found in the corpus ventriculi. Since the patient had a respiratory complication, a distal pancreatectomy with celiac axis resection in combination with a total gastrectomy was considered too aggressive for this patient. Therefore, she received chemoradiotherapy prior to the surgery. Distal pancreatectomy with D2 lymphadenectomy and subtotal gastrectomy with lower left phrenic artery preservation was performed. This case involved a considerable extension of the disease and radical surgery; however, currently the patient's prognosis and QOL are good.
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Funaki H, Fujii Y, Fujita J, Morioka E, Kaida D, Ohonishi T, Tomita Y, Noguchi M, Fujita H, Kinami S, Nakano Y, Ueda N, Kosaka T. [Clinical Analysis of Esophageal Bypass Surgery with Nutritional Assessment in Patients with Unresectable Esophageal Cancer]. Gan To Kagaku Ryoho 2015; 42:1543-1546. [PMID: 26805090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND Esophageal bypass surgery is palliative surgery for unresectable esophageal cancer with esophageal stenosis, which often leads to poor nutrition. We investigated the clinical characteristics, nutritional status, and outcomes of patients who underwent esophageal bypass surgery. PATIENTS AND METHODS We reviewed 11 cases of esophageal bypass surgery for unresectable esophageal cancer performed in our hospital between 1992 and 2015, and we examined the surgical outcome along with preoperative nutritional assessment. RESULTS There were 1, 9, and 1 cases of cStage Ⅲ, Ⅳa, and Ⅳb, respectively. For the bypass, a gastric tube was used in 8 cases and colon reconstruction in 3. Postoperative complications were 1 case of recurrent laryngeal nerve palsy (9%), 4 cases of anastomotic leakage (36%), and 4 cases of pneumonia (36%). The preoperative nutritional status (total protein, albumin, and cholinesterase levels) in the esophageal bypass group (n=11) was significantly worse than that in the esophagectomy group (n=40). The median survival of all patients (n=11) was 5.7 months. Patients receiving induction chemoradiotherapy followed by bypass surgery (n=7) had a median survival of 15.2 months. CONCLUSION Since patients undergoing esophageal bypass surgery often present with malnutrition, attention to anastomotic leakage and infectious complications is necessary.
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Tomita Y, Fujii Y, Miura S, Fujita J, Morioka E, Kaida D, Ohonishi T, Ohono Y, Noguchi M, Funaki H, Fujita H, Kinami S, Nakano Y, Ueda N, Kosaka T, Sakata N. [A Successful Case of Treatment of Colonic Metastasis and Peritoneal Recurrence of Type 4 Gastric Cancer by Using Colectomy and Chemotherapy]. Gan To Kagaku Ryoho 2015; 42:1591-1593. [PMID: 26805106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a successful case of treatment of colonic metastasis and peritoneal recurrence of type 4 gastric cancer by using colectomy and chemotherapy. A 70-year-old woman with a diagnosis of type 4 advanced gastric cancer underwent distal gastrectomy. The final pathological diagnosis was LM, circ, type 4, sig, pT4a (SE), ly1, v1, pN1, M0, P0, CY0, pStage Ⅲa. Adjuvant chemotherapy was conducted with oral administration of S-1, though regrettably the chemotherapy was interrupted because of diarrhea, an adverse effect of S-1. Metastatic recurrence occurred on the transverse colon, for which she underwent transverse colectomy 2.9 years after the initial surgery. Another colonic metastasis in the ascending colon along with peritoneal recurrence was diagnosed 3.11 years after the initial surgery, and the patient underwent a palliative colostomy and received chemotherapy with S-1 plus docetaxel. She was successfully treated up to a clinical CR with chemotherapy, and she died 5.10 years after the initial surgery. In this case, a good prognosis was obtained through the combination of resection of the recurrence sites, palliative surgery for avoiding obstruction, and chemotherapy using S-1 plus docetaxel for metachronous multiple metastases.
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Koga M, Hayashi M, Kaida D. Splicing inhibition decreases phosphorylation level of Ser2 in Pol II CTD. Nucleic Acids Res 2015. [PMID: 26202968 PMCID: PMC4787822 DOI: 10.1093/nar/gkv740] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Phosphorylation of the C-terminal domain of the largest subunit of RNA polymerase II (Pol II), especially Ser2 and Ser5 residues, plays important roles in transcription and mRNA processing, including 5′ end capping, splicing and 3′ end processing. These phosphorylation events stimulate mRNA processing, however, it is not clear whether splicing activity affects the phosphorylation status of Pol II. In this study, we found that splicing inhibition by potent splicing inhibitors spliceostatin A (SSA) and pladienolide B or by antisense oligos against snRNAs decreased phospho-Ser2 level, but had little or no effects on phospho-Ser5 level. In contrast, transcription and translation inhibitors did not decrease phospho-Ser2 level, therefore inhibition of not all the gene expression processes cause the decrease of phospho-Ser2. SSA treatment caused early dissociation of Pol II and decrease in phospho-Ser2 level of chromatin-bound Pol II, suggesting that splicing inhibition causes downregulation of phospho-Ser2 through at least these two mechanisms.
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Matsunaga K, Hayashi R, Otsuka T, Kaida D, Ueda N, Kosaka T, Arisawa T. A case of IgG4-related disease complicated by duodenal bulbitis with IgG4-positive plasma cell infiltration. Endoscopy 2015; 46 Suppl 1 UCTN:E408-10. [PMID: 25314166 DOI: 10.1055/s-0034-1377397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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Hao Y, Colak R, Teyra J, Corbi-Verge C, Ignatchenko A, Hahne H, Wilhelm M, Kuster B, Braun P, Kaida D, Kislinger T, Kim PM. Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins. Cell Rep 2015. [PMID: 26146086 DOI: 10.1016/j.celrep.2015.06.031:183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Alternative splicing acts on transcripts from almost all human multi-exon genes. Notwithstanding its ubiquity, fundamental ramifications of splicing on protein expression remain unresolved. The number and identity of spliced transcripts that form stably folded proteins remain the sources of considerable debate, due largely to low coverage of experimental methods and the resulting absence of negative data. We circumvent this issue by developing a semi-supervised learning algorithm, positive unlabeled learning for splicing elucidation (PULSE; http://www.kimlab.org/software/pulse), which uses 48 features spanning various categories. We validated its accuracy on sets of bona fide protein isoforms and directly on mass spectrometry (MS) spectra for an overall AU-ROC of 0.85. We predict that around 32% of "exon skipping" alternative splicing events produce stable proteins, suggesting that the process engenders a significant number of previously uncharacterized proteins. We also provide insights into the distribution of positive isoforms in various functional classes and into the structural effects of alternative splicing.
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Hao Y, Colak R, Teyra J, Corbi-Verge C, Ignatchenko A, Hahne H, Wilhelm M, Kuster B, Braun P, Kaida D, Kislinger T, Kim PM. Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins. Cell Rep 2015; 12:183-9. [PMID: 26146086 DOI: 10.1016/j.celrep.2015.06.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 02/18/2015] [Accepted: 06/09/2015] [Indexed: 12/30/2022] Open
Abstract
Alternative splicing acts on transcripts from almost all human multi-exon genes. Notwithstanding its ubiquity, fundamental ramifications of splicing on protein expression remain unresolved. The number and identity of spliced transcripts that form stably folded proteins remain the sources of considerable debate, due largely to low coverage of experimental methods and the resulting absence of negative data. We circumvent this issue by developing a semi-supervised learning algorithm, positive unlabeled learning for splicing elucidation (PULSE; http://www.kimlab.org/software/pulse), which uses 48 features spanning various categories. We validated its accuracy on sets of bona fide protein isoforms and directly on mass spectrometry (MS) spectra for an overall AU-ROC of 0.85. We predict that around 32% of "exon skipping" alternative splicing events produce stable proteins, suggesting that the process engenders a significant number of previously uncharacterized proteins. We also provide insights into the distribution of positive isoforms in various functional classes and into the structural effects of alternative splicing.
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Masaki S, Yoshimoto R, Kaida D, Hata A, Satoh T, Ohno M, Kataoka N. Identification of the specific interactors of the human lariat RNA debranching enzyme 1 protein. Int J Mol Sci 2015; 16:3705-21. [PMID: 25671812 PMCID: PMC4346921 DOI: 10.3390/ijms16023705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/04/2015] [Indexed: 01/30/2023] Open
Abstract
In eukaryotes, pre-mRNA splicing is an essential step for gene expression. We have been analyzing post-splicing intron turnover steps in higher eukaryotes. Here, we report protein interaction between human Debranching enzyme 1 (hDbr1) and several factors found in the Intron Large (IL) complex, which is an intermediate complex of the intron degradation pathway. The hDbr1 protein specifically interacts with xeroderma pigmentosum, complementeation group A (XPA)-binding protein 2 (Xab2). We also attempted to identify specific interactors of hDbr1. Co-immunoprecipitation experiments followed by mass spectrometry analysis identified a novel protein as one of the specific interactors of hDbr1. This protein is well conserved among many species and shows the highest similarity to yeast Drn1, so it is designated as human Dbr1 associated ribonuclease 1 (hDrn1). hDrn1 directly interacts with hDbr1 through protein–protein interaction. Furthermore, hDrn1 shuttles between the nucleus and the cytoplasm, as hDbr1 protein does. These findings suggest that hDrn1 has roles in both the nucleus and the cytoplasm, which are highly likely to involve hDbr1.
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Ueda N, Kaida D, Tomita Y, Ohnishi T, Funaki H, Fujita H, Kinami S, Nakano Y, Kosaka T. [A patient with invasive carcinoma derived from IPMN who achieved long-term survival despite lymph node metastasis]. Gan To Kagaku Ryoho 2014; 41:2202-2204. [PMID: 25731470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A woman in her 70s was referred for examination of liver dysfunction. A cystic lesion with irregular contrast was observed at the pancreas head. The bile and pancreatic ducts were obstructed by the lesion. Part of the branch of the pancreatic duct at the pancreas head, continuous with the main pancreatic duct, was observed to be extended by using pancreatography. Pancreaticoduodenectomy was performed, and a diagnosis of invasive carcinoma from an intraductal papillary-mucinous neoplasm (IPMN) was made. Postoperative pathological diagnosis showed 16b1 inter-node metastasis. Liver and lung metastases were also detected after surgery; nevertheless, long-term survival was achieved for 5 years and 2 months by using various treatment modalities.
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Funaki H, Miura S, Morioka E, Kaida D, Ohnishi T, Ohno Y, Tomita Y, Noguchi M, Fujita H, Kinami S, Nakano Y, Ueda N, Kosaka T. [Evaluation of combination chemotherapy with docetaxel and nedaplatin in patients with advanced or recurrent esophageal cancer]. Gan To Kagaku Ryoho 2014; 41:2384-2386. [PMID: 25731531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND There is no standard regimen after failure of 5-fluorouracil and cisplatin-based first-line chemotherapy in patients with advanced or recurrent esophageal cancer. The feasibility of combination chemotherapy with docetaxel (DOC) and nedaplatin (CDGP) for these patients was retrospectively evaluated. METHODS Patients received DOC (30 mg/m² intra- venously) and CDGP (30-40 mg/m² intravenously) on days 1 and 15 of each 4-week period. The efficacy and toxicity of combination chemotherapy with DOC and CDGP in 13 patients was analyzed. RESULTS The patients received a median of 2 cycles of treatment(range, 1-23). The response and disease control rates were 8% and 54%, respectively. Grade 3 or 4 hematological toxicities were neutropenia, anemia, and thrombocytopenia, observed in 4(31%), 11(15%), and 2 patients (15%), respectively. Non-hematological toxicity, anorexia, was detected in only 1 patient(8%). No treatment-related death was observed. The median progression-free survival and overall survival were 3.2 and 11.6 months, respectively. CONCLUSIONS Combination chemotherapy with DOC and CDGP is considered a feasible regimen for refractory esophageal cancer.
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Koga M, Satoh T, Takasaki I, Kawamura Y, Yoshida M, Kaida D. U2 snRNP is required for expression of the 3' end of genes. PLoS One 2014; 9:e98015. [PMID: 24845214 PMCID: PMC4028248 DOI: 10.1371/journal.pone.0098015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/28/2014] [Indexed: 01/05/2023] Open
Abstract
Pre-mRNA in eukaryotes is subjected to mRNA processing, which includes capping, polyadenylation, and splicing. Transcription and mRNA processing are coupled, and this coupling stimulates mRNA processing; however, the effects of mRNA processing on transcription are not fully understood. In this study, we found that inhibition of U2 snRNP by a splicing inhibitor, spliceostatin A (SSA), or by an antisense oligonucleotide to U2 snRNA, caused gene-specific 3′-end down-regulation. Removal of SSA from the culture media restored expression of the 3′ ends of genes, suggesting that U2 snRNP is required for expression of the 3′ end of genes. Finally, we found that SSA treatment caused accumulation of Pol II near the 5′ end of 3′-end down regulated genes, such as CDK6, SMEK2 and EGFR, indicating that SSA treatment led to transcription elongation arrest on these genes. These findings suggest that U2 snRNP is important for production of full length mRNA probably through regulation of transcription elongation, and that a novel checkpoint mechanism prevents pre-mRNA from accumulating as a result of splicing deficiencies, and thereby prevents production of aberrant proteins that might be translated from pre-mRNAs through the arrest of transcription elongation.
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Koga M, Satoh T, Kaida D. U2 snRNP is required for the phosphorylation of Pol II CTD Ser2 and efficient transcription elongation (560.4). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.560.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Funaki H, Fujita J, Morioka E, Kaida D, Ohnishi T, Ohno Y, Tomita Y, Noguchi M, Fujita H, Kinami S, Nakano Y, Ueda N, Kosaka T. [Evaluation of conversion gastrectomy for treatment of Stage IV advanced gastric cancer]. Gan To Kagaku Ryoho 2013; 40:1615-1617. [PMID: 24393866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
BACKGROUND The standard treatment for Stage IV advanced gastric cancer (AGC) is systemic chemotherapy. Because patients who respond to induction chemotherapy seem to have a good prognosis, we converted the treatment strategy to gastrectomy( termed as conversion gastrectomy) in such patients. In this study, we estimated the outcomes of patients who underwent conversion gastrectomy for Stage IV AGC. METHODS We evaluated patients with Stage IV AGC who underwent conversion gastrectomy from October 2008 through September 2012 and retrospectively analyzed their clinicopathological variables and oncologic outcomes. RESULTS Twenty patients underwent conversion gastrectomy with an R0 resection rate of 45% (9/20). The median survival time (MST) was 18.0 months overall and did not differ significantly between patients with clinically stable disease( SD) and those with a partial response( PR)( 22.0 months vs 18.0 months, p=0.64). The MST was longer in patients with pathological Grade 1b-3 tumors than in those with Grade 1a tumors (47.8 months vs 16.3 months), and this difference was significant (p=0.04). Patients with R0 resection had a significantly longer MST than those with R1-2 ( 47.8 months vs 14.1 months ). CONCLUSIONS The present study provides evidence that patients with Stage IV AGC who undergo conversion gastrectomy with a histopathological response have a good prognosis and that R0 resection predicts longer survival.
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Ohnishi T, Kinami S, Fujita J, Morioka E, Kaida D, Ohno Y, Tomita Y, Noguchi M, Funaki H, Fujita H, Nakano Y, Ueda N, Kosaka T. [A case of jejnal cancer who was controlled peritoneal metastasis, successfully by combination therapy with docetaxel and S-1]. Gan To Kagaku Ryoho 2013; 40:1717-1719. [PMID: 24393899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The patient was a 60-year-old man who had been admitted to our hospital because of elevated serum CA19-9 levels. Endoscopy revealed a Borrmann type 2 tumor of the jejunum. Computed tomography (CT) revealed lymph node metastases and peritoneal seeding. Hence, he was diagnosed with advanced jejunal cancer with distant metastasis (T4N1M0 stage). We performed partial resection of the jejunum, and he underwent chemotherapy with docetaxel( DOC) and S-1 for the peritoneal seeding postoperatively. Follow-up CT revealed that the chemotherapy was effective, and the patient achieved complete remission following 9 months of treatment.
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