Inter-assay variability of next-generation sequencing-based gene panels

BACKGROUND: Tumor heterogeneity has been known to cause inter-assay discordance among next-generation sequencing (NGS) results. However, whether preclinical factors such as sample type, sample quality and analytical features of gene panel can affect the concordance between two different assays remains largely unexplored. METHODS: Replicate sets of DNA samples extracted from formalin-fixed paraffin-embedded tissues (FFPE) (n = 20) and fresh frozen (FF) tissues (n = 10) were herein analyzed using a tumor-only (TO) and paired tumor-normal (TN) gene panel in laboratories certified by the Clinical Laboratory Improvement Amendment. Reported variants from the TO and TN panels were then compared. Furthermore, additional FFPE samples were sequentially sliced from the same FFPE block and submitted to another TN panel assay. RESULTS: Substantial discordance (71.8%) was observed between the results of the two panels despite using identical DNA samples, with the discordance rate being significantly higher for FFPE samples (p < 0.05). Among the 99 variants reported only in the TO panel, 32.3% were consistent with germline variants, which were excluded in the TN panel, while 30.3% had an allele frequency of less than 5%, some of which were highly likely to be artificial calls. The comparison of two independent TN panel assay results from the same FFPE block also showed substantial discordance rate (55.3%). CONCLUSIONS: In the context of clinical settings, our comparative analysis revealed that inter-NGS assay discordance commonly occurred due to sample types and the different analytical features of each panel

Experimental model for the irradiation-mediated abscopal effect and factors influencing this effect

Radiotherapy (RT) is the primary treatment for cancer. Ionizing radiation from RT induces tumor damage at the irradiated site, and, although clinically infrequent, may cause regression of tumors distant from the irradiated site-a phenomenon known as the abscopal effect. Recently, the abscopal effect has been related to prolongation of overall survival time in cancer patients, though the factors that influence the abscopal effect are not well understood. The aim of this study is to clarify the factors influencing on abscopal effect. Here, we established a mouse model in which we induced the abscopal effect. We injected MC38 (mouse colon adenocarcinoma) cells subcutaneously into C57BL/6 mice at two sites. Only one tumor was irradiated and the sizes of both tumors were measured over time. The non-irradiated-site tumor showed regression, demonstrating the abscopal effect. This effect was enhanced by an increase in the irradiated-tumor volume and by administration of anti-PD1 antibody. When the abscopal effect was induced by a combination of RT and anti-PD1 antibody, it was also influenced by radiation dose and irradiated-tumor volume. These phenomena were also verified in other cell line, B16F10 cells (mouse melanoma cells). These findings provide further evidence of the mechanism for, and factors that influence, the abscopal effect in RT

Effects of psychotherapy for middle-aged individuals with anxiety disorders in a general medicine practice

Background: Anxiety disorders are mental disorders that cause somatic symptoms for which patients may seek care from generalmedicine departments. We focused on anxiety disorders in middle-aged patients and examined the effect of a psychotherapeuticintervention.Materials and Methods: The participants were 14 middle-aged patients diagnosed with an anxiety disorder. Patients receivedpretreatment assessments and were randomly assigned to a pharmacotherapy group (n = 8) or a pharmacotherapy and psychotherapygroup (n = 6). The duration of the study was three months. Pre-and post-treatment, the Medical Outcomes Study 36-ItemShort-Form Health Survey (SF-36), State-Trait Anxiety Inventory (STAI), and a visual analog scale (VAS) were administered. Inthe pharmacotherapy and psychotherapy group, salivary cortisol was collected pre- and post-psychotherapy at the first and finalpsychotherapy sessions.Result: Four patients in the pharmacotherapy group withdrew from the study. There were no significant differences in the totalscores of the SF-36 or STAI between groups. Improvement was seen in the pharmacotherapy and psychotherapy group pre- andpost- treatment. SF-36 subscales of bodily pain (p = 0.02) and mental health (p = 0.04) were significantly higher than posttreatment.The state anxiety score on the STAI improved post-treatment (p = 0.03). On the VAS, the pharmacotherapy and psychotherapygroup’s symptoms were significantly improved (p = 0.02).Conclusion: This suggests that psychotherapy for middle-aged individuals contributes to the improvement of anxiety states andHRQoL in general medicine departments. It promotes the recognition of curative effects and prevents doctor shopping

Is the Importance of Achieving Stable Disease Different between Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors and Cytotoxic Agents in the Second-Line Setting for Advanced Non-small Cell Lung Cancer?

BackgroundIt is controversial whether achieving stable disease leads to a survival benefit and whether the importance of achieving stable disease differs between cytotoxic agents and molecular targeted agents. To examine these questions, the authors retrospectively reviewed phase II and III studies in the second-line setting for advanced non-small cell lung cancer using epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) and cytotoxic agents separately.MethodsThe authors chose 45 trials for the chemotherapy group and nine for the EGFR TKI group by searching the PubMed database. All nine trials in the EGFR TKI group concern gefitinib and erlotinib.ResultsThe median survival time increased 0.0375 month with each 1% increase in stable disease rate (p = 0.039), and each 1% increase in response rate resulted in 0.0744 (p < 0.001) month of median survival time in the analysis combined with both cytotoxic agents and EGFR TKIs. Main and interaction terms for EGFR TKI treatment were not statistically significant. With respect to time to progression, only response rate showed a statistically significant relationship with survival.ConclusionsTo obtain response seems to be more important than to achieve stable disease for both cytotoxic agents and EGFR TKIs, although achieving stable disease is still valuable. The relationship between survival and response or stable disease appears similar for cytotoxic agents and EGFR TKIs

Comprehensive genomic profiling for patients with chemotherapy‐naïve advanced cancer

Comprehensive genomic profiling (CGP) testing by next-generation sequencing has been introduced into clinical practice as part of precision cancer medicine to select effective targeted therapies. However, whether CGP testing at the time of first-line chemotherapy could be clinically useful is not clear. We conducted this single-center, prospective, observational study to investigate the feasibility of CGP testing for chemotherapy-naïve patients with stage III/IV gastrointestinal cancer, rare cancer, and cancer of unknown primary, using the FoundationOne® companion diagnostic (F1CDx) assay. The primary outcome was the detection rate of at least one actionable/druggable cancer genomic alteration. Actionable/druggable cancer genomic alterations were determined by the F1CDx report. An institutional molecular tumor board determined the molecular-based recommended therapies. A total of 197 patients were enrolled from October 2018 to June 2019. CGP success rate was 76.6% (151 of 197 patients), and median turnaround time was 19 days (range: 10-329 days). Actionable and druggable cancer genomic alterations were reported in 145 (73.6%) and 124 (62.9%) patients, respectively. The highest detection rate of druggable genomic alterations in gastrointestinal cancers was 80% in colorectal cancer (48 of 60 patients). Molecular-based recommended therapies were determined in 46 patients (23.4%). CGP testing would be a useful tool for the identification of a potentially effective first-line chemotherapy

髄膜癌腫症による頭蓋内圧亢進症に対する脳室腹腔短絡術の有用性

　髄膜癌腫症は，がんの集学的治療の進歩による生存期間の延長に伴い，診断される機会も増加している．髄膜癌腫症は患者のQuality of life(QOL) を著しく低下させ，生命予後に直結することが多い．神経症状の軽減によるQOL の改善を考えると，髄膜癌腫症に対する外科治療の介入を検討し直す必要があると思われる．　我々は，髄膜癌腫症に対し外科治療を施行した３症例経験した．外科治療の適応に関し，過去の症例も交え，文献的考察を加え報告する．　【症例１】56歳男性．肺癌を原発とする多発脳転移を伴う髄膜癌腫症と診断された．全脳照射後に全身化学療法を行うも，意識障害をきたし，全身化学療法の継続が困難となった．髄液排除によりPerformance Status（PS）が改善したため，脳室腹腔短絡術を施行した．術後，意識障害は改善し，治療を再開した．PS は改善し，比較的良好な日常生活を送れQOL は改善したと考えられたが，Nivolumab の副作用により，全身状態は悪化し，術後３か月で死亡した．　【症例２】55歳女性．肺腺癌と診断され，頭痛が出現し，髄膜癌腫症と診断された．EGFR-TKIを含む全身化学療法を行い，症状は改善傾向であった．その後，頭痛，嘔気が増悪しPS は低下した．脳室ドレナージ術により，PS は改善し，嘔気・疼痛のコントロールが可能となったため，脳室腹腔短絡術を施行した．術後，緩和医療に移行し，残された時間を有意義に過ごすことができ，QOL は改善したと考えられたが，全身状態の悪化により術後４か月で死亡した．　【症例３】66歳女性．頭痛が出現し，肺癌に伴う，髄膜癌腫症と診断された．疼痛コントロールが困難であり，PS も低下していたため，脳室ドレナージ術を施行したところ，疼痛コントロールが可能となった．PS の改善に伴い，Erlotinib による治療を開始することができた．しかし，間質性肺炎による全身状態の悪化により，脳室腹腔短絡術は施行できず，脳室ドレナージ術から44日で死亡した．　The incidence of leptomeningeal carcinomatosis is increasing with the extension of the survival because of the advances in cancer treatment. This condition significantly deteriorates the patients\u27 quality of life (QOL) and worsens the prognosis. Because the reduction of neurological symptoms can be expected to improve the QOL, it is necessary to reexamine the indications for surgical treatment of leptomeningeal carcinomatosis. We report three cases of surgically treated leptomeningeal carcinomatosis, and we review the literature, including past cases, with regard to the indications for surgical treatment.　Case 1: A 56-year-old man was diagnosed with leptomeningeal carcinomatosis with multiple brain metastases from lung cancer. Whole-brain irradiation was performed, followed by systemic chemotherapy, which was discontinued because of the development of a consciousness disorder. As the patient’s performance status (PS) improved after ventricular drainage, ventriculoperitoneal (VP) shunt was performed. Postoperatively, the consciousness disorder improved, and treatment was restarted. The patient’s PS and QOL improved; he was able to live a relatively good daily life. However, he died 3 months after the surgery because of deterioration of his general condition resulting from the side effects of nivolumab.　Case 2: A 55-year-old woman diagnosed with lung adenocarcinoma complained of headaches. She was diagnosed with leptomeningeal carcinomatosis and underwent systemic chemotherapy, including epidermal growth factor receptor tyrosine kinase inhibitors. Her symptoms initially improved; however, after a while, the headaches and nausea worsened and her PS deteriorated. The ventricular drainage improved her PS; therefore, VP shunt was performed. Postoperatively, her PS and QOL improved and she was switched to palliative care as the nausea and pain became controllable. However, she died because of deterioration of her general condition 4 months after the surgery.　Case 3: A 66-year-old woman complaining of headaches was diagnosed with leptomeningeal carcinomatosis associated with lung cancer. Because pain control was difficult and her PS was reduced, ventricular drainage was performed. Postoperatively, pain control became possible and her PS improved. Although treatment with erlotinib was started, the patient could not undergo VP shunt because of deterioration of her general condition resulting from an interstitial pneumonia, and she died 44 days after the ventricular drainage

破裂脳動脈瘤の発症12日目に別の未破裂脳動脈瘤が破裂した1例

　67歳女性．以前より左中大脳動脈・脳底動脈本幹・左海綿静脈洞部内頚動脈に未破裂脳動脈瘤を指摘されていた．突然に激しい頭痛・嘔気が出現し，その5日後に他院でsubarachnoid hemorrhage（SAH）を指摘されたため，当院紹介となった．CT で左シルビウス裂・左大脳半球脳溝を中心にSAH を認めるも，脳幹周囲には認めなかった．緊急DSA では，左中大脳動脈瘤は4.9mm でbleb を伴っていたが，脳底動脈瘤は6.5mm，左内頚動脈瘤は2.9mm で，いずれもblebはなかった．左中大脳動脈瘤の破裂と考え，緊急で同部位にコイル塞栓術を施行し，ほぼ完全閉塞された．しかし，第12病日に突然昏睡状態となり，CT で橋腹側を中心に新たなSAH を認めた．脳底動脈瘤の破裂と診断し，緊急コイル塞栓術を行った．術後意識状態は改善し，NPH に対しVP シャントを追加し，mRS1で自宅退院となった．短期間で2個の動脈瘤が破裂した比較的稀な症例と考えられ，報告する．　We report a rare case of recurrent bleeding caused by another cerebral aneurysm during the subacute phase of aneurymal subarachnoid hemorrhage (SAH). A 67-yearold woman developed severe headache and visited our hospital on the 5th day from the onset. Her computed tomography (CT) confirmed SAH, and her angiography revealed three intracranial aneurysms: a 4.9-mm left middle cerebral artery aneurysm (MCA An) with bleb formation, a 6.5-mm basilar trunk aneurysm (BA trunk An) without bleb, and a 2.9-mm internal carotid cavernous sinus aneurysm without bleb. As the SAH was present mostly in the left cerebral hemisphere and left Sylvian fissure without the involvement of the basal cistern. MCA An was thought to bleed. Subsequently, she underwent coil embolization and recovered well. However, she suddenly became comatose on the 12th day from the onset. Her CT showed diffuse SAH localized around the prepontine cistern. Second angiography demonstrated the expanded BA trunk An. Coil embolization was then successfully performed. VP shunt insertion was added for hydrocephalus secondary to SAH, and left our hospital with favorable outcome

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target