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Putri Keumala Alisha
Identifikasi Metilasi Tumor Suppressor Genes (TSGs) pada Kanker Tiroid dengan Metode Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA) = Identification of Tumor Suppressor Genes (TSGs) Methylation in Thyroid Cancer using Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA)
"Metilasi DNA merupakan perubahan epigenetik yang umum terjadi sebagai penyebab inaktivasi gen pada tumor suppressor genes (TSGs). Metilasi pada promoter TSG memiliki asosiasi dengan pembentukan kanker tiroid. Metode methylation-specific multiplex ligation dependent-probe amplification (MS-MLPA) merupakan salah satu metode berbasis PCR yang dapat melakukan identifikasi metilasi pada beberapa gen dan analisis copy number variant secara simultan. Tujuan dari penelitian ini adalah untuk mengoptimasi metode MS-MLPA dan mengidentifikasi metilasi TSG pada kanker tiroid dengan metode MS-MLPA. Sebanyak 40 sampel fine needle aspiration biopsy (FNAB) dikumpulkan secara retrospektif di Rumah Sakit Kanker Dharmais. Sampel FNAB berasal dari pasien yang memiliki kelainan nodul tiroid. Metilasi TSG dianalisis dengan metode MS-MLPA menggunakan probemix Tumour Suppressor Mix 1 ME001-C2 (MRC-Holland). Sampel FNAB dibandingkan dengan reference sample berupa sampel darah yang berasal dari individu sehat. Penelitian ini berhasil mengoptimasi metode MS-MLPA dan mendeteksi metilasi pada 4 jenis tumor suppressor genes, yaitu gen RASSF1A, gen CASP8, gen FHIT, dan gen CHFR. Hasil identifikasi menunjukkan bahwa terdapat 20 sampel tumor ganas dan 2 sampel tumor jinak mengalami metilasi.
DNA methylation is a common epigenetic change that causes gene inactivation in tumor suppressor genes (TSGs). TSGpromoter methylation has an association with the formation of thyroid cancer. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) is a PCR-based method that can identify methylation in several genes and copy number variant simultaneously. The aim of this study is to optimize methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) and to identify tumor suppressor genes methylation of thyroid cancer using MS-MLPA. Retrospectively 40 Fine Needle Aspiration Biopsy samples were collected in Dharmais Cancer Hospital. FNAB samples were collected from patients with thyroid nodules abnormalities. Tumor suppressor genes methylation were analyzed using Tumour Suppressor Mix 1 ME001-C2 probemix (MRC-Holland) as MS-MLPA reagents. FNAB samples were compared with reference sample from blood that were collected from healthy people. This study has successfully optimizing MS-MLPA method and detecting 4 methylated tumor suppressor genes, RASSF1A, CAPS8, FHIT and CHFR. Methylation identification shows 20 malignant histopathology samples and 2 benign histopathology samples were methylated.
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Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2019
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Henny Fitria
Identifikasi Metilasi Mismatch Repair Gene (MMR) pada Kanker Kolon dengan Teknik Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA) = Identification of Mismatch Repair Gene (MMR) Methylation in Colon Cancer with Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA) techniques
"Metilasi DNA merupakan salah satu penyebab umum inaktivasi Mismatch Repair Gene (MMR). Gen MMR memperbaiki kesalahan penyisipan/penghapusan basa nukleotida pada proses sintesis DNA. Metilasi pada promoter gen MMR memiliki asosiasi dengan pembentukan kanker kolon, sehingga metilasi tersebut perlu diidentifikasi. Identifikasi gen MMR dapat dilakukan menggunakan teknik methylation-specific multiplex ligation-dependent probe amplification amplification (MS-MLPA). Prinsip dari teknik MS-MLPA yaitu amplifikasi probe yang menempel pada sekuens termetilasi. Tujuan dari penelitian ini yaitu untuk mengoptimasi teknik MS-MLPA dan mengidentifikasi metilasi gen MMR pada kanker kolon dengan teknik MS-MLPA. Penelitian ini menggunakan 27 sampel jaringan frozen kanker kolon yang telah tersedia di Biobank Rumah Sakit Kanker Dharmais (RSKD). Sampel tersebut dianalisis menggunakan probemix Mismatch Repair Gene [ME011-C1][C1-0518] yang telah didesain khusus untuk mendeteksi pada beberapa gen MMR yakni MLH1, PMS2, MSH6, dan MSH2. Hasil penelitian menunjukkan optimasi teknik MS-MLPA telah berhasil dilakukan, sehingga identifikasi metilasi pada gen MMR telah berhasil diperoleh pada 4 sampel pasien. Gen MMR tersebut yakni MLH1 dan MSH6, dengan persentase masing-masing 75% dan 25%.
DNA methylation is one of the most common causes of mismatch repair gene (MMR) inactivation. The MMR gene corrects errors in the insertion/deletion of nucleotide bases in the DNA synthesis process. MMR gene promoter methylation has an association with the formation of colon cancer, so the methylation needs to be identified. Identification of the MMR gene can be done using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) technique. The principle of the MS-MLPA technique is the amplification of the probe attached to the methylated sequence. The purpose of this study was to optimize the MS-MLPA technique and identify MMR gene methylation in colon cancer using the MS-MLPA technique. This study used 27 samples of frozen colon cancer tissue that were available at the Dharmais Cancer Hospital Biobank (RSKD). The samples were analyzed using the Mismatch Repair Gene probemix [ME011-C1][C1-0518] which has been specially designed to detect several MMR genes, namely MLH1, PMS2, MSH6, and MSH2. The results show that the optimization of the MS-MLPA technique has been successfully carried out, so that the identification of methylation in the MMR gene has been successfully obtained in 4 patient samples. The MMR genes are MLH1 and MSH6, with a percentage of 75% and 25%, respectively. analyzed using probemix Mismatch Repair Gene [ME011-C1][C1-0518] which has been specifically designed to detect several MMR genes namely MLH1, PMS2,
MSH6, and MSH2. The results showed that the optimization of the MS-MLPA technique was successful, so that identification of the methylation in the MMR gene was successfully obtained in 4 patient samples. The MMR genes are MLH1 and MSH6, with percentages of 75% and 25% respectively."
Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2020
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Rizka Arifah Iskandar
Identifikasi mutasi gen MLH1 dan MSH2 pada pasein kanker kolon menggunakan teknik Multiplex Ligation-Dependent Probe Amplification (MLPA) = Identification of MLH1 and MSH2 gene mutation in colon cancer patients using Multiplex Ligation-Dependent Probe Amplification (MLPA)
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Gen mismatch repair (MMR) merupakan gen yang berperan dalam mekanisme DNA repair. Gen MMR dapat memperbaiki kesalahan pasangan basa, perubahan nukleotida dan kesalahan dalam unit pengulangan pasangan basa (microsatellites) selama proses replikasi DNA. Mutasi pada MMR yang umum terjadi pada gen MLH1 dan MSH2 memiliki asosiasi dengan terjadinya Lynch Syndrome pada pasien kanker kolon. Lynch Syndrome (LS) atau Hereditary Non-Polyposis Colorectal Carcinoma (HNPCC) merupakan sindrom kanker kolon herediter yang paling umum diwariskan. LS dapat ditandai dengan mutasi gen MLH1 dan MSH2 berupa delesi dan duplikasi large genomic. Multiplex ligation-dependent probe amplification (MLPA) merupakan teknik kuantifikasi berbasis PCR yang dapat digunakan untuk mendeteksi perubahan copy number variant pada large genomic. Tujuan dari penelitian ini adalah untuk mengidentifikasi mutasi gen MLH1 dan MSH2 pada kanker kolon dengan teknik Multiplex Ligation-Dependent Probe Amplification (MLPA). Sebanyak 25 sampel darah pasien yang terdiagnosis kanker kolon yang dikumpulkan secara retrospektif di Rumah Sakit Kanker Dharmais dikoleksi dari tahun 2018-2019. Mutasi gen MLH1 dan MSH diidentifikasi pada sampel darah pasien yang terdiagnosis kanker kolon dengan teknik MLPA menggunakan Probemix P003-D1 MLH1/MSH2 (MRC-Holland). Penelitian ini berhasil melakukan optimalisasi penggunaan teknik MLPA dengan terpenuhinya kualitas fragmen kontrol MLPA, kualitas fragment analysis, dan comparative analysis pada perangkat lunak Coffalayser.Net. Hasil screening pada 25 sampel menunjukkan tidak ditemukan adanya pola mutasi gen MLH1 dan MSH2 pada sampel yang mengindikasikan tidak terjadinya Lynch Syndrome dan kanker kolon yang terjadi bersifat sporadis.

Mismatch repair genes (MMR) plays a role in the mechanism of DNA repair. The MMR genes correct base pair errors, nucleotide changes, and errors in base pair repeating units (microsatellites) during DNA replication. Mutations in MMR are common in MLH1 and MSH2 genes that have an association with the occurrence of Lynch Syndrome in colon cancer. Lynch Syndrome or Hereditary Non-Polyposis Colorectal Carcinoma (HNPCC) is the most common inherited hereditary colon cancer syndrome. LS is characterized by MLH1 and MSH2 gene mutations in the form of large genomic deletions and duplication. Multiplex ligation-dependent probe amplification (MLPA) is a PCRbased quantification technique that can detect changes in copy number variants in large genomics. The aim of the study was to identify MLH1 and MSH2 gene mutations in colon cancer with Multiplex Ligation-Dependent Probe Amplification (MLPA) technique. Twenty-five blood samples of patients diagnosed with colon cancer were collected in Dharmais Cancer Hospital collected in 2018-2019, retrospectively. Mutations in MLH1 and MSH2 genes were identified in blood samples of patients diagnosed with colon cancer by the MLPA technique using Probemix P003-D1 MLH1/MSH2 (MRC-Holland). This study succeeded in optimizing the use of MLPA technique by fulfilling the fragments quality control of MLPA, the quality of fragment analysis, and comparative analysis in Coffalayser.Net software. The results of 25 samples screening showed no pattern of MLH1 and MSH2 gene mutations in the sample. This data indicated that there was no Lynch Syndrome and the colon cancer was sporadic.

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Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2020
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Khalisha Sasikirana
Optimasi deteksi mutasi Gen HRAS, KRAS, NRAS dan BRAF pada kanker kolorektal menggunakan Metode Multiplex Ligation-Dependent Probe Amplification (MLPA) = The optimization of detecting HRAS, KRAS, NRAS, and BRAF Gene mutation in colorectal cancer using Multiplex Ligation-Dependent Probe Amplification Method
"Mutasi gen HRAS, KRAS, NRAS, dan BRAF telah dilaporkan terjadi pada kanker kolorektal. Multiplex Ligation-Dependent Probe Amplification (MLPA) merupakan metode yang mampu mendeteksi variasi copy number dari suatu gen spesifik dan memiliki kelebihan dibandingkan metode lain. Deteksi mutasi gen HRAS, KRAS, NRAS, dan BRAF pada kanker kolorektal menggunakan metode MLPA di Indonesia belum dilaporkan. Tujuan dari penelitian ini adalah untuk mengoptimasi metode MLPA dan mendeteksi mutasi gen HRAS, KRAS, NRAS, dan BRAF secara simultan pada kanker kolorektal menggunakan metode MLPA. Sampel penelitian berupa jaringan sebanyak 41 sampel yang berasal dari pasien kanker kolorektal di Rumah Sakit Kanker Dharmais. Sampel penelitian telah dikumpulkan sejak tahun 2017 dan disimpan dalam biobank. Mutasi gen HRAS, KRAS, NRAS, dan BRAF dianalisis dari sampel jaringan menggunakan metode MLPA dengan Kit SALSA MLPA Probemix P298-A1 BRAF-HRAS-KRAS- NRAS (MRC-Holland) kemudian dilakukan fragment Analysis menggunakan mesin Capillary Electrophoresis [3500xL genetic analyzer]. Data hasil fragment analysis selanjutnya dianalisis menggunakan perangkat lunak Coffalyser.Net. Hasil penelitian menunjukkan optimasi metode MLPA berhasil dilakukan serta mutasi gen HRAS, KRAS, NRAS, dan BRAF berhasil dideteksi dengan membandingkan perubahan jumlah copy number pada ratio chart sampel jaringan kanker dan sampel jaringan normal. Berdasarkan hasil yang diperoleh, metode MLPA berhasil dioptimasi dan mutasi pada gen HRAS, KRAS, NRAS, dan BRAF berhasil terdeteksi. Mutasi gen HRAS, KRAS, NRAS, dan BRAF terdeteksi dari seluruh 41 sampel dengan persentase masing-masing 17.07%, 26.82%, 2.43%, dan 19.51%. Mutasi yang terdeteksi adalah mutasi duplikasi dan delesi.
HRAS, KRAS, NRAS, and BRAF gene mutation has been reported in colorectal cancer. Multiplex Ligation-Dependent Probe Amplification (MLPA) is a method capable of detecting copy number variation of a specific gene. This method has advantages over other methods, however, the detection of gene mutation in colorectal cancer using MLPA in Indonesia has not been reported so far. The aim of this study is to optimize MLPA method and detect HRAS, KRAS, NRAS, and BRAF gene mutation simultaneously on colorectal cancer using the MLPA method. Research samples consist of 41 fresh colorectal cancer tissues collected from colorectal cancer patients in Dharmais Cancer Hospital. Research samples has been collected and stored in a biobank since 2017. HRAS, KRAS, NRAS, and BRAF gene mutation are analyzed from the research samples using the MLPA method with SALSA MLPA Probemix P298-A1 BRAF-HRAS-KRAS-NRAS (MRC-Holland) kit. Afterwards, fragment analysis is done using the Capillary Electrophoresis [3500xL genetic analyzer] machine. The results are then analyzed using the Coffalyser.Net software. This research succeeds in optimizing the detection of HRAS, KRAS, NRAS, and BRAF gene mutation on colorectal cancer using MLPA method and detecting the gene mutation of HRAS, KRAS, NRAS, dan BRAF by comparing the ratio chart of a normal and cancer tissue. The MLPA method was successfully optimized and the HRAS, KRAS, NRAS, and BRAF gene mutation successfully detected. The HRAS, KRAS, NRAS, and BRAF gene mutation successfully detected from 41 samples, with percentages of 17.07%; 26.82%; 2.43%; and 19.51%. The detected mutations are duplication and deletion."
Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2021
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Achmad Hudoyo
Inovasi metode deteksi kanker paru non-invasif menggunakan balon karet sebagai penampung napas-hembusan exhaled-breath terkondensasi, berbasis pemeriksaan metilasi dna dengan methylation-specific pcr dan analisis gas senyawa organik dengan gas chromatho = Simple latex baloon reservoir system to collect exhaled breathing condensate as novel non invasive lung cancer detection method based on dnamethylation with methylation specific pcr and volatyl organic compounds analysiswith gas chromatographymass spe
"Indonesia terdiri dari beribu pulau yang berpenghuni.Belum ada deteksi kanker paru yang non-invasif, sederhana, murah dan efektif sehingga diperlukan suatu inovasi. Deteksi metilasi DNA dengan sampel dalam kertas saring yang dapat dikirim melalui pos dan analisis kromatografi napas hembusan yang ditampung dalam balon karet adalah salah satu metode yang akan diujicoba dan diteliti. Penelitian ini bertujuan menemukan metode baru untuk deteksi kanker paru yang dapat dilakukan oleh tenaga kesehatan di berbagai daerah di seluruh Indonesia dengan mengirim sampel melalui pos.
Metode yang digunakan dalam penelitian berupa studi ekperimental dengan mendeteksi dan mengukur konsentrasi DNA serta menentukan status metilasi gen promoter spesifik APC RASSF1A dari sampel napas-hembusan pasien kanker paru yang ditampung dalam balon karet terkondensasi, dibandingkan dengan sampel-sampel sediaan sitologi, darah dan sputum menggunakan metode PCR-MSP, serta menganalisis sampel napas- hembusan menggunakan GCMS pasien kanker paru dengan kontrol orang normal.
Hasil penelitian ini membuktikan bahwa DNA dapat dideteksi, diamplifikasi dan diukur konsentrasinya dari napas-hembusan pasien kanker paru yang ditampung menggunakan balon karet. Konsentrasi DNA dari napas-hembusan secara statistik tidak berbeda bermakna dibanding konsentrasi DNA dalam sampel darah dan sputum, tetapi berbeda bermakna dibanding sediaan sitologi. Sebagian besar status metilasi gen APC RASSF1A adalah tidak termetilasi. Analisis uap napas menggunakan GCMS terbukti memperlihatkan senyawa-senyawa spesifik yang hanya dijumpai pada napas-hembusan pasien kanker paru.
Dari penelitian dapat disimpulkan bahwa DNA dapat dideteksi dari napas-hembusan pasien kanker paru yang ditampung dalam balon karet, dengan konsentrasi yang tidak berbeda bermakna dengan konsentrasi dalam darah dan sputum. Status metilasi gen APC RASSF1A tidak dapat dijadikan biomarker diagnosis kanker paru.Deteksi DNA sebagai sampel genetik dan analisis GCMS dari napas-hembusan yang ditampung dalam balon karet berpotensi dapat dijadikan metode deteksi kanker paru yang non-invasif.
Indonesia has more than 14,000 islands and access to health facilities has been challenging. Despite lung cancer is the leading cause of death, Indonesia has high prevalence of cigarette smokers and there has been no effective screening so far. Non invasive, simple, accurate and affordable tools for lung cancer detection is needed.
The method of this study is experimental study of which samples from sputum, blood, cytology and exhaled breath was analyzed using PCR MSP method to detect DNA methylation. In addition, exhaled breath samples were collected in latex balloons and profiled with GC MS.
The result of this study that DNA can be extracted, isolated and amplified from exhaled breath of lung cancer patients that had been collected in the latex balloons. Exhaled breath DNA concentration, statistically was not different with DNA concentration from blood and sputum, but lower and statistically different with tissue cytology samples. PCR MSP results revealed that the methylation status of APC and RASSF1A gene promoters were not methylated in the majority of samples. GC MS analyses showed that there were some chemical components specifically detected only in lung cancer patients and were absent in normal or healthty subjects.
The conclusion of this study that DNA can be extracted from exhaled breath with simple technique using balloons reservoir from lung cancer subjects and detection of methylation status of APC and RASSF1A promoter genes from this samples could be done. However, APC and RASSF1 methylation status may not be useful marker for lung cancer screening. On the other hand, analyses of chemical compounds obtained from exhaled breath in lung cancer patients had promising potential for new innovative detection of lung cancer with non invasive procedure."
Jakarta: Fakultas Kedokteran Universitas Indonesia, 2018
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Hariyono Winarto
Peran stres oksidatif terhadap ekspresi gen supresor tumor arid1a pada sel endometriosis dan kanker ovarium = The role of oxidative stress in on the expression of the tumor suppressor gene arid1a in endometriosis cells and ovarian cancer
"Pendahuluan: Endometriosis merupakan suatu kelainan jinak ginekologi yang dapat mengalami transformasi menjadi kanker. Stres oksidatif diduga berperan dalam perkembangan penyakit endometriosis. Gen supresor tumor ARID1A banyak ditemukan termutasi dan inaktif pada kanker ovarium yang berhubungan dengan endometriosis. Tujuan penelitian adalah untuk menganalisis peran stres oksidatif terhadap ekspresi gen supresor tumor ARID1A dalam transformasi endometriosis menjadi ganas.
Metoda: Penelitian dimulai dengan 10 sampel jaringan kanker ovarium, 10 sampel endometriosis dan3 jaringan endometrium eutopik sebagai kontrol yang diisolasi mRNA dan proteinnya. Analisis ekspresi gen ARID1A pada tingkat mRNA dilakukan dengan pemeriksaan RT-qPCR dan pada tingkat protein dengan ELISA. Pada sel endometriosis dan kanker ovarium dilakukan analisis stres oksidatif dengan pemeriksaan aktivitas antioksidan MnSOD dan pemeriksaan kadar MDA sebagai salah bukti kerusakan salah satu komponen sel. Setelah itu dilakukan uji eksperimental pada kultur sel endometriosis dan endometrium eutopik sebagai kontrol. Kedua sel kultur diinduksi dengan H2O2 konsentrasi 0 nM, 100 nM, dan 1000 nM. Analisis dilakukan terhadap ketahanan hidup sel, kadar ROS dan ekspresi gen ARID1A pada tingkat mRNA dan protein.
Hasil: Efek induksi H2O2 dalam menekan ekspresi gen ARID1A sel endometriosis dan sel endometrium eutopik pada tingkat mRNA dan protein, bermakna, meskipun pada kanker ovarium tidak bermakna pada penelitian ini.
Kesimpulan: Stres oksidatif berperan dalam menekan ekspresi gen supresor tumor ARID1A ditingkat mRNA dan protein pada endometriosis.
Introduction: Endometriosis as a gynecologic benign lesion, can transform itself into cancer. Oxidative stress is considered as an important factor in endometriosis development. Studies found that ARID1A as tumor suppressor gene, was frequently mutated and inactivated in endometriosis associated ovarian cancer. The aim of the study is to analyze the role of oxidative stress on ARID1A expresion in endometriosis malignant transformation.
Methods: This study started with ten samples of ovarian cancer, ten samples of endometriosis, and 3 samples of eutopic endometrioid tissues as control. They were analyzed for the expression of ARID1A by RT-qPCR and ELISA, then analyzed for the activity of MnSOD as antioxidant enzyme and level of malondialdehyde as one of the oxidative stress damage effect evidence on cell's components. The second part of the study was experimental study on cultured eutopic endometrial and endometriosis cells. They were induced by H2O2 of 0, 100, and 1000 nM concentration. Analysis of the expression of ARID1A by RTqPCR and ELISA, and the DCFH-DA for the level of Reactive oxygen species were done.
Result: The impact of the H2O2 induction in repressing ARID1A gene expression on the endometriosis as well on the eutopic endometrium cells are significant, but not on the ovarian cancer in this study.
Conclusion: Oxidative stress has a role in repressing the expression of ARID1A gene at the mRNA and protein levels on the endometriosis."
Jakarta: Fakultas Kedokteran Universitas Indonesia, 2014
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Andi Darma Putra
Pengaruh Konsentrasi MiR-21, MiR-145, Large Tumor Suppressor 1, dan Nuclear Factor Kappa B serta Usia terhadap Respons Kemoradiasi pada Pasien Kanker Serviks Uteri Stadium Lanjut Lokal = The Influence of MiR-21, MiR-145, Large Tumor Suppressor 1, Nuclear Factor Kappa B, and Age on Chemoradiation Response in Patients with Locally Advanced Stage Cervical Cancer.
"Kanker serviks merupakan salah satu kanker terbanyak pada perempuan dengan jumlah kasus dan kematian yang bermakna, terutama di negara-negara berkembang seperti Indonesia. Penelitian terbaru menyoroti peran mikroRNA (miRNA) dalam karsinogenesis, terutama miR-21 yang terlibat dalam berbagai jenis kanker pada perempuan, termasuk kanker serviks. Selain itu, miR-145, LATS1, dan NF-κB dipercaya memiliki peran dalam radioresistensi. Penelitian ini bertujuan untuk membuktikan pengaruh konsentrasi miR-21, miR-145, Large Tumor Suppressor 1 (LATS1), dan Nuclear Factor Kappa B (NF-kB) serta usia terhadap respons kemoradiasi pada pasien kanker serviks stadium lanjut lokal. Penelitian ini menggunakan desain potong lintang analitik yang dilakukan di Rumah Sakit Cipto Mangunkusumo dari bulan Juli 2017 sampai Juni 2023. Sampel jaringan dari biopsi serviks diambil dan diperiksa menggunakan real-time reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) untuk mendeteksi miR-21 dan miR-145, serta ELISA untuk mendeteksi konsentrasi LATS1 dan NF-kB sebelum pasien menerima terapi kemoradiasi. Pemeriksaan ultrasonografi kemudian dilakukan kembali untuk menilai respons radiasi dengan menggunakan kriteria RECIST 1.1. Dari 140 subjek, ditemukan gambaran histopatologi karsinoma sel skuamosa pada 119 (85%) sampel, dengan distribusi kanker serviks stadium IIIB pada 102 (72,9%) subjek dan stadium IVA pada 38 (27,1%) subjek. Ekspresi miR- 21 di atas cut-off lebih banyak ditemukan pada subjek yang radioresisten (p = 0,010; AUC = 67,6%). Ekspresi miR-145 dan LATS1 di atas cut-off lebih banyak ditemukan pada kelompok radioresisten, masing-masing dengan p = 0,132 (AUC = 38,8%) dan p = <0,001 (AUC = 32,7%). Ekspresi NF-kB di bawah cut-off ditemukan lebih banyak pada kelompok radioresisten (p = 0,009; AUC = 61%), dan usia di bawah cut-off juga lebih banyak ditemukan pada kelompok radioresisten (p = 0,138; AUC = 39,2%). Penelitian ini menunjukkan bahwa ekspresi miR-21 dan LATS1 pra-kemoradiasi yang tinggi serta ekspresi NF-κB yang rendah berhubungan dengan terjadinya radioresistensi. Sebaliknya, konsentrasi miR-145 dan usia tidak berhubungan dengan radioresistensi, sehingga dapat disimpulkan bahwa miR-21 memiliki potensi sebagai biomarker radioresisten pada pasien kanker serviks stadium lanjut lokal dan pemeriksaan kombinasi tidak disarankan.
Cervical cancer is one of the most common cancers in women with a significant number of cases and deaths, especially in developing countries such as Indonesia. Recent research highlights the role of microRNAs (miRNAs) in carcinogenesis, particularly miR-21, which is involved in various types of cancer in women, including cervical cancer. In addition, miR-145, LATS1 and NF-κB also considered to play a role in radioresistance. This study aims to determine the influence of miR- 21, miR-145, Large Tumor Suppressor 1 (LATS1), Nuclear Factor Kappa B (NF- κB), and age on chemoradiation response in locally advanced cervical cancer patients. This study used an analytical cross-sectional design conducted at Cipto Mangunkusumo Hospital from July 2017 to June 2023. Cervical biopsy tissue samples were collected and examined using real-time reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) to detect miR-21 and miR-145, and ELISA to measure LATS1 and NF-κB concentrations before patients underwent chemoradiation therapy. Ultrasound examination was then re-performed to assess radiation response using RECIST 1.1 criteria. This research obtained a total of 140 samples with histopathological subtype of squamous cell carcinoma found in 119 (85%) samples, with cervical cancer stage IIIB in 102 (72.9%) subjects and stage IVA in 38 (27.1%) subjects. Expression of miR-21 above the cut-off was more prevalent in radioresistant patients (p = 0.010; AUC = 67.6%). Expression of miR-145 and LATS1 above the cut-off were found to be higher in the radioresistant group with p = 0.132 (AUC = 38.8%) and p = <0.001 (AUC = 32.7%), respectively. NF-κB expression below the cut-off were found to be higher in the radioresistant group (p = 0.009; AUC = 61%), and age below the cut-off were also found to be higher in the radioresistant group (p = 0.138; AUC = 39.2%). This study showed that high expression of miR-21 and LATS1 pre-chemoradiation and low expression of NF-κB pre-chemoradiation were all associated with radioresistance, while miR- 145 concentration and age were not associated with radioresistance. This study concluded that miR-21 had the potential to be used as a radioresistant biomarker in patients with local advanced-stage cervical cancer and combination testing was not suggested."
Jakarta: Fakultas Kedokteran Universitas Indonesia, 2024
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Kamada, Rui
Tetramer stability and functional regulation of tumor suppressor protein p53
"This thesis presents the first report of the comprehensive and quantitative analysis of the effects of tumor-derived mutations on the tetrameric structure of tumor suppressor protein p53, which plays a central role in maintaining genomic integrity. Inactivation of p53 via mutation of its gene is a key step in tumorigenesis. Biophysical analyses revealed that the stability of the mutant peptides varied widely. Formation of a tetrameric structure is to be critical for protein–protein interactions, DNA binding, and the post-translational modification of p53. A small destabilization of the tetrameric structure therefore could result in dysfunction of tumor suppressor activity. This work suggests that the threshold for loss of tumor suppressor activity, in terms of the disruption of p53’s tetrameric structure, could be extremely low. Furthermore, functional control of p53 via tetramer formation was demonstrated, based on the structure–function analysis of mutant p53. The results disclosed that relatively small changes in tetramer formation, induced by the stabilization or inhibition of homo-tetramerization, could control p53 function."
Tokyo : Springer, 2012
e20406084
eBooks  Universitas Indonesia Library
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Muhammad Ikhsan
Uji Set Primer-Probe Deteksi Gen N1, N2, dan RdRp dari SARS-CoV-2 menggunakan Multiplex RT-qPCR = Primer-Probe Set Test for N1, N2, and RdRp Gene from SARS-CoV-2 Detection Using Multiplex RT-qPCR
"Pandemi COVID-19 bermula akibat infeksi virus SARS-CoV-2. Deteksi SARS-CoV-2 secara standar dilakukan dengan metode Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) yang mayoritas menarget gen N dan RdRp. Produk lokal untuk mendeteksi SARS-CoV-2 belum banyak tersedia dengan gen target baru berupa N2, RdRp, dan Orf1b. Tujuan dari penelitian ini adalah mengoptimasi reaksi multiplex RT-qPCR dengan dua pasang set primer yang masing-masing menarget gen N dan RdRp dengan gen RPP30 sebagai kontrol internal pengujian. Penelitian dilakukan dengan metode berupa pembuatan kultur Escherichia coli, ekstraksi plasmid Escherichia coli, ekstraksi RNA sel HepG2, PCR, RT-PCR, RT-qPCR, dan elektroforesis. Hasil penelitian di langkah awal memberikan keberhasilan ekstraksi plasmid dan RNA. Proses PCR terhadap plasmid yang menarget gen N dan RdRp dan RT-PCR terhadap RNA yang menarget gen RPP30 memberikan kemunculan pita berukutan mendekati 100 bp setelah dielektroforesis. RT-qPCR yang dilakukan menggunakan dua pasang set primer memberikan hasil positif dengan kemunculan grafik logaritmik pada plot RT-qPCR pada masing-masing primer. Hasil penelitian dapat disimpulkan berupa RT-qPCR telah berhasil dilakukan pada dua pasang set primer yang menarget gen N dan RdRp dengan kontrol internal berupa gen RPP30.
COVID-19 pandemic originated in December 2020 due to SARS-CoV-2 virus infection. Standardized SARS-CoV-2 detection is examined by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) with N and RdRp genes as the main target. Local SARS-CoV-2 detection product is not much available with only N2, RdRp, and Orf1b as gene target. This research aims to optimize multiplex RT-qPCR with two pairs of primer set targeting N and RdRp genes with RPP30 gene as internal control. The research is done by several methods: Escherichia coli culture production and plasmid extraction, HepG2 cell RNA extraction, PCR, RT-PCR, RT-qPCR, and electrophoresis. The result of the earlier steps is successful plasmid and RNA extraction. PCR on plasmid targeting N and RdRp genes and RT-PCR on RNA targeting RPP30 gene giving results of bands appearance with size around 100 bp after electrophoresis is done. RT-qPCR of two pairs of primer set generally giving positive results with appearance of logarithmic graph on RT-qPCR plots. Research results could be concluded with RT-qPCR are done successfully using two sets of primer that targeting N and RdRp genes with RPP30 gene as internal control."
Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2021
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Samosir, Yoshida Aussiana
Analisis deteksi molekuler tuberkulosis dari sampel urin menggunakan multiplex PCR dengan gen deteksi ESAT6, IS6110, dan MPT64 = Molecular detection of tuberculosis from urine specimens using multiplex PCR with detection genes ESAT6, IS6110, and MPT64
"Keberhasilan deteksi tuberkulosis (TB) relatif rendah pada negara berkembang dengan beban TB tinggi akibat kurangnya akurasi diagnosis. Penegakan diagnosis yang dilakukan dengan uji BTA dan TCM sebagai metode deteksi TB baku emas memiliki kelemahan dalam hal penggunaan spesimen sputum yang kemungkinan tidak tersedia pada pasien pediatrik, serta tidak representatif terhadap infeksi Mtb di luar jaringan paru. Urin dapat menjadi kandidat spesimen alternatif dikarenakan bersifat non-invasif. Deteksi antigen Mtb dalam urin menggunakan kit diagnostik Fujifilm SILVAMP TB LAM berhasil dilakukan pada populasi TB-HIV, namun deteksi gen Mtb secara langsung dalam urin belum banyak diteliti. Metode molekuler PCR telah digunakan dalam studi diagnostik karena memiliki nilai sensitivitas dan spesifisitas yang tinggi, sehingga dapat memberikan hasil diagnosis yang akurat. Tujuan penelitian adalah melalukan uji deteksi TB pada sampel urin populasi yang telah dinyatakan TB secara bakteriologis (kelompok Definite TB) dan populasi yang didiagnosa TB secara klinis namun tidak menunjukkan hasil laboratorium TB (kelompok Clinically TB) melalui metode multiplex PCR dengan gen target ESAT6, IS6110, dan MPT64 dan mengevaluasi potensi sampel urin sebagai spesimen alternatif diagnosis TB. Nilai positivity rate yang diperoleh adalah 71,43% (10/14) pada kelompok Definite TB dan 60,71% (17/28) pada kelompok Clinically TB. Metode multiplex PCR dengan spesimen urin dapat menjadi petunjuk pada kasus TB non-paru dan populasi yang tidak dapat mengeluarkan sputum berkualitas.
Tuberculosis (TB) screening and diagnostic accuracy is relatively low in developing countries, which has contributed to the high TB burden in such regions. The diagnostic gold standard is the acid-fast bacillus (AFB) smear and GeneXpert test. A major disadvantage for both tests is the utilisation of sputum specimens, which may not be available in paediatric cases and is not representative of extrapulmonary Mtb infection. Urine may be used as an adjunct specimen because of its non-invasive nature of collection. Previous studies have focused on detecting Mtb antigens in urine using the Fujifilm SILVAMP TB LAM diagnostic kit in TB-HIV populations, however direct Mtb DNA detection has not been intensively evaluated. In recent years, PCR techniques have been widely used due to high sensitivity and specificity values which provides rapid and accurate diagnoses. Therefore, the primary objective of this is to conduct a TB detection test in urine samples of two population groups previously tested with AFB smear and GeneXpert test; (1) definite bacteriological cases (Definite TB group), and (2) clinically diagnosed cases (Clinically TB group), using multiplex PCR with target genes ESAT6, IS6110, and MPT64. Specifically, the study aims to evaluate urine as an alternative specimen and supporting tool in TB diagnostics. Observed positivity rate of urine samples was 71.43% (10/14) in the Definite TB group and 60.71% (17/28) in the Clinically TB group. Multiplex PCR using urine specimens indicates effectiveness in rapid detection of extra-pulmonary TB and sputum-scarce cases."
Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2020
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