Edhyana Sahiratmadja

Genetic Association and Expression Studies Indicate a Role of Toll-Like Receptor 8 in Pulmonary Tuberculosis

Despite high rates of exposure, only 5–10% of people infected with Mycobacterium tuberculosis will develop active tuberculosis (TB) disease, suggesting a significant role for genetic variation in the human immune response to this infection. Here, we studied TB association and expression of 18 genes involved in the Toll-like receptor (TLR) pathways. Initially, we genotyped 149 sequence polymorphisms in 375 pulmonary TB patients and 387 controls from Indonesia. We found that four polymorphisms in the TLR8 gene on chromosome X showed evidence of association with TB susceptibility in males, including a non-synonymous polymorphism rs3764880 (Met1Val; P = 0.007, odds ratio (OR) = 1.8, 95% c.i. = 1.2–2.7). We genotyped these four TLR8 polymorphisms in an independent collection of 1,837 pulmonary TB patients and 1,779 controls from Russia and again found evidence of association in males (for rs3764880 P = 0.03, OR = 1.2, 95% c.i. = 1.02–1.48). Combined evidence for association is P = 1.2×10−3–6×10−4. In addition, a quantitative PCR analysis indicated that TLR8 transcript levels are significantly up-regulated in patients during the acute phase of disease (P = 9.36×10−5), relative to baseline levels following successful chemotherapy. A marked increase in TLR8 protein expression was also observed directly in differentiated macrophages upon infection with M. bovis bacille Calmette-Guérin (BCG). Taken together, our results provide evidence, for the first time, of a role for the TLR8 gene in susceptibility to pulmonary TB across different populations.

Genome-Wide Expression Profiling Identifies Type 1 Interferon Response Pathways in Active Tuberculosis

Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), remains the leading cause of mortality from a single infectious agent. Each year around 9 million individuals newly develop active TB disease, and over 2 billion individuals are latently infected with M.tb worldwide, thus being at risk of developing TB reactivation disease later in life. The underlying mechanisms and pathways of protection against TB in humans, as well as the dynamics of the host response to M.tb infection, are incompletely understood. We carried out whole-genome expression profiling on a cohort of TB patients longitudinally sampled along 3 time-points: during active infection, during treatment, and after completion of curative treatment. We identified molecular signatures involving the upregulation of type-1 interferon (α/β) mediated signaling and chronic inflammation during active TB disease in an Indonesian population, in line with results from two recent studies in ethnically and epidemiologically different populations in Europe and South Africa. Expression profiles were captured in neutrophil-depleted blood samples, indicating a major contribution of lymphocytes and myeloid cells. Expression of type-1 interferon (α/β) genes mediated was also upregulated in the lungs of M.tb infected mice and in infected human macrophages. In patients, the regulated gene expression-signature normalized during treatment, including the type-1 interferon mediated signaling and a concurrent opposite regulation of interferon-gamma. Further analysis revealed IL15RA, UBE2L6 and GBP4 as molecules involved in the type-I interferon response in all three experimental models. Our data is highly suggestive that the innate immune type-I interferon signaling cascade could be used as a quantitative tool for monitoring active TB disease, and provide evidence that components of the patient’s blood gene expression signature bear similarities to the pulmonary and macrophage response to mycobacterial infection.

A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians

BackgroundThere is reason to expect strong genetic influences on the risk of developing active pulmonary tuberculosis (TB) among latently infected individuals. Many of the genome wide linkage and association studies (GWAS) to date have been conducted on African populations. In order to identify additional targets in genetically dissimilar populations, and to enhance our understanding of this disease, we performed a multi-stage GWAS in a Southeast Asian cohort from Indonesia.MethodsIn stage 1, we used the Affymetrix 100 K SNP GeneChip marker set to genotype 259 Indonesian samples. After quality control filtering, 108 cases and 115 controls were analyzed for association of 95,207 SNPs. In stage 2, we attempted validation of 2,453 SNPs with promising associations from the first stage, in 1,189 individuals from the same Indonesian cohort, and finally in stage 3 we selected 251 SNPs from this stage to test TB association in an independent Caucasian cohort (n = 3,760) from Russia.ResultsOur study suggests evidence of association (P = 0.0004-0.0067) for 8 independent loci (nominal significance P < 0.05), which are located within or near the following genes involved in immune signaling: JAG1, DYNLRB2, EBF1, TMEFF2, CCL17, HAUS6, PENK and TXNDC4.ConclusionsMechanisms of immune defense suggested by some of the identified genes exhibit biological plausibility and may suggest novel pathways involved in the host containment of infection with TB.

Polymorphisms in autophagy genes and susceptibility to tuberculosis.

Recent data suggest that autophagy is important for intracellular killing of Mycobacterium tuberculosis, and polymorphisms in the autophagy gene IRGM have been linked with susceptibility to tuberculosis (TB) among African-Americans, and with TB caused by particular M. tuberculosis genotypes in Ghana. We compared 22 polymorphisms of 14 autophagy genes between 1022 Indonesian TB patients and 952 matched controls, and between patients infected with different M. tuberculosis genotypes, as determined by spoligotyping. The same autophagy polymorphisms were studied in correlation with ex-vivo production of TNF, IL-1β, IL-6, IL-8, IFN-γ and IL-17 in healthy volunteers. No association was found between TB and polymorphisms in the genes ATG10, ATG16L2, ATG2B, ATG5, ATG9B, IRGM, LAMP1, LAMP3, P2RX7, WIPI1, MTOR and ATG4C. Associations were found between polymorphisms in LAMP1 (p = 0.02) and MTOR (p = 0.02) and infection with the successful M. tuberculosis Beijing genotype. The polymorphisms examined were not associated with M. tuberculosis induced cytokines, except for a polymorphism in ATG10, which was linked with IL-8 production (p = 0.04). All associations found lost statistical significance after correction for multiple testing. This first examination of a broad set of polymorphisms in autophagy genes fails to show a clear association with TB, with M. tuberculosis Beijing genotype infection or with ex-vivo pro-inflammatory cytokine production.

HPV Genotyping Linear Assay Test Comparison in Cervical Cancer Patients: Implications for HPV Prevalence and Molecular Epidemiology in a Limited-resource Area in Bandung, Indonesia

BACKGROUND Persistent infection with high risk human papillomavirus (hrHPV) is strongly associated with cervical cancer. Normal cervical cells may also harbor hrHPV, and detection of early hrHPV infection may minimize risk of cervical cancer development. This study aimed to compare two commercial HPV genotyping assays that may affordable for early screening in a limited-resource setting in Bandung, Indonesia. MATERIALS AND METHODS DNA from cervical biopsies with histologically confirmed as squamous cell cervical cacinoma were HPV genotyped by Linear Assay 1 (Roche Diagnostics, Mannheim, Germany) or Linear Assay 2 (Digene HPV Genotyping RH Test, Qiagen Gaithersburg, MD). In a subset of samples of each group, HPV genotype results were then compared. RESULTS Of 28 samples genotyped by linear assay 1, 22 (78.6%) demonstrated multiple infections with HPV-16 and other hrHPV types 18, 45 and/or 52. In another set of 38 samples genotyped by linear assay 2, 28 (68.4%) were mostly single infections by hrHPV type 16 or 18. Interestingly, 4 samples that had been tested by both kits showed discordant results. CONCLUSIONS In a limited-resource area such as in Indonesia, country with a high prevalence of HPV infection a reliable cervical screening test in general population for early hrHPV detection is needed. Geographical variation in HPV genotyping result might have impacts for HPV prevalence and molecular epidemiology as the distribution in HPV genotypes should give clear information to assess the impact of HPV prophylactic vaccines.

Polymorphisms in SP110 are not associated with pulmonary tuberculosis in Indonesians.

Despite being high transmissible, Mycobacterium tuberculosis (M. tuberculosis) infection causes active disease in only 5-10% of disease-susceptible individuals. This has instigated interest in studying potentially underlying genetic host factors and mechanisms in tuberculosis (TB). The recent identification of the Intracellular pathogen resistance 1 (Ipr1) gene, which plays a major role in controlling M. tuberculosis susceptibility and infection severity in mice (Pan et al., 2005), has prompted studies on its human homolog; SP110 in humans. Association of SP110 SNPs with pulmonary TB were first reported in a study on West African families (Tosh et al., 2006). Subsequent attempts to replicate these findings in other populations, including another West African (Ghanaian) cohort (Thye et al., 2006), however, were unsuccessful. Here we have genotyped 20 SNPs located in the SP110 gene, including the previously TB associated variants; rs2114592 and rs3948464, for the first time in a South East Asian cohort from Indonesia. Our study did not reveal any statistically significant associations between SP110 SNPs and pulmonary TB. In addition, a meta-analysis of the two previously TB associated SNPs revealed that these are not associated with TB, further confirming the lack of convincing evidence for SP110 to be implicated in TB susceptibility, as yet in humans.

The influence of influenza virus infections on the development of tuberculosis

Recently, it was shown that interferon-γ mediated immune responses, which play a major role in the control of infection with Mycobacterium tuberculosis (Mtb), can be inhibited by type I interferons. Since type I interferons are abundantly induced during viral infections, we hypothesized that infections with influenza viruses might play a role in the development of active TB disease either directly after exposure to Mtb or through reactivation of latent Mtb infection. To explore this hypothesis we investigated in a retrospective study whether newly diagnosed adult tuberculosis patients from Indonesia had had recent influenza infection. Plasma samples from TB patients and controls were assayed for antibodies against two subtypes of at that time relevant, seasonal influenza A viruses. Overall, no correlation was observed with the presence of antibodies and manifest tuberculosis. Still, antibody titers against circulating A/H3N2 influenza virus were slightly enhanced in tuberculosis patients as compared to controls, and highest in cases of advanced tuberculosis. This suggests that tuberculosis patients were recently infected with influenza, before clinical manifestation of the disease. Alternatively, the production of antibodies and susceptibility to tuberculosis may be influenced by a common confounding factor, for example the ability of patients to induce interferon-α. We conclude that in an endemic country like Indonesia, an influenza virus infection is not a major determinant for developing clinically manifest tuberculosis.

Low Hemoglobin among Pregnant Women in Midwives Practice of Primary Health Care, Jatinangor, Indonesia: Iron Deficiency Anemia or β-Thalassemia Trait?

Low hemoglobin (Hb) or anemia is common among pregnant women in developing countries which may cause adverse pregnancy outcomes and maternal deaths. Our study aimed to assess Hb level measured by midwives in primary health care facility at rural area of Jatinangor, Indonesia, and to explore whether the anemia was due to iron deficiency (IDA) or β-thalassemia trait (β-TT). Pregnant women (n = 105) had finger prick test for Hb level during a regular antenatal care examination from October to November 2016. Hb level by finger prick test was compared with venous blood, measured by complete blood count (CBC). Indices including MCV and MCH and indices of Shine & Lal, Mentzer, Srivastava, Engels & Frase, Ehsani, and Sirdah were analyzed to differentiate anemia due to IDA and anemia due to suspect β-TT. HbA2 was measured to confirm β-TT. Anemic pregnant women were found in 86.7% by finger prick test compared to 21.9% (n = 23) by CBC. The prevalence of β-TT in our study was 5.7%. Hb measurement among pregnant women in low resource area is highly important; however, finger prick test in this study showed a high frequency of anemia which may lead to iron oversupplementation. A standard CBC is encouraged; MCV and MCH would help midwives to identify β-TT.

Human Papillomavirus Genotypes Profile in Cervical Cancer Patients at Dr. Hasan Sadikin General Hospital, Bandung, Indonesia

BACKGROUND As in other developing countries, cervical cancer is the most frequent gynecologic malignancy in Indonesia. Persistent high risk genotypes of human papillomavirus (HPV) that infect the cervical tissue have been established as the etiology of cervical cancer. This study aimed to explore the profile of cervical cancer patients and the infected HPV genotypes at Dr. Hasan Sadikin General Hospital-Bandung. MATERIALS AND METHODS During the year 2010, 554 cervical cancer patients were registered. In a subset of the patients during July-November 2010, 40 randomized fresh biopsies were tested for HPV genotype after obtained informed consent. The distribution of HPV genotypes and the association to risk factors were analysed. RESULTS The result showed that 62.5% of the tested biopsies were infected by multiple HPV infections, with HPV-16 found in most of the cervical cancer patients (90%). Marriage at age younger than 16 years old was statistically significant in relation to multiple HPV infection (p=0.003), but not parity more than three times (p=0.59). CONCLUSIONS Although high paritiy in our study was not associated with multiple HPV infection, good family planning programs and reproductive health education need to be emphasized in Indonesia as high parity and marriage at young age might increase the chance of cervical cancer development.

Status Asetilator Gen NAT2 pada Pasien Tuberkulosis dan Tuberkulosis dengan Diabetes Melitus di Kupang, Nusa Tenggara Timur

Indonesia adalah negara dengan jumlah penderita tuberkulosis (TB) terbanyak kedua di dunia. Diabetes melitus (DM) merupakan salah satu komorbid TB. Arylamine N-acetyltransferase 2 (NAT2) adalah enzim yang berfungsi memetabolisir isoniazid (INH) yang disandi oleh gen NAT2 . Gen NAT2 memiliki sejumlah polimorfisme dan dapat menentukan kemampuan seseorang untuk memetabolisir obat yang disebut status asetilator. Pada individu dengan status asetilator lambat, INH dimetabolisir dengan lambat sehingga memungkinkan terjadi intoksikasi hati. Pada TB dengan DM (TBDM) status asetilator lambat dapat membuat pengobatan TB maupun DM menjadi kurang optimal. Penelitian ini bertujuan mengeksplorasi status asetilator pasien TBDM di RSUD Prof. WZ Johannes Kupang periode Juni–November 2011. Pada penelitian potong lintang ini DNA dari darah 122 pasien TB diisolasi dan gen NAT2 kemudian diamplifikasi dan disekuensing untuk diketahui status asetilatornya. Hasil penelitian menunjukkan terdapat 5 pasien yang memiliki glukosa serum >200 mg/dL yang dikategorikan sebagai pasien TBDM. Pada pasien TBDM didapatkan seorang dengan status asetilator cepat (NAT2*4/NAT2*4), 2 orang dengan status asetilator sedang (NAT2*13A/NAT2*6J), dan 2 orang dengan status asetilator lambat (NAT2*5/NAT2*5G, NAT2*6A/ NAT2*6A, NAT2*7B/ NAT2*7B). Pada pasien TB yang dipilih secara random berdasar usia dan jenis kelamin serupa dengan TBDM didapatkan 2 orang dengan status asetilator cepat (NAT2*4/NAT2*4) dan 3 orang dengan asetilator sedang (NAT2*4/NAT2*6A, NAT2*13A/NAT2*6J). TBDM yang memiliki status asetilator lambat berpotensi memiliki masalah ganda dalam terapi, selain dapat terjadi toksisitas hati akibat terapi dengan INH, juga dapat mengakibatkan pengobatan DM menjadi tidak optimal. Perlu dilakukan peneltian lebih lanjut terkait farmakogenetik pada TBDM. [ MKB. 2016;49(1):61–6] Kata kunci : Asetilator, isoniazid, NAT2 , farmakogenetik, tuberkulosis NAT2 Gene Acetylator Status of Tuberculosis and Tuberculosis with Diabetes Mellitus Patients in Kupang, Nusa Tenggara Timur Indonesia is the second highest country with TB patients in the world. Diabetes mellitus (DM) is a comorbid of TB. Arylamine N-acetyltransferase 2 (NAT2), encoded by the NAT2 gene, is an enzyme that metabolizes isoniazid (INH). NAT2 gene has some polimorphysims that may play a role in INH acetylating process. Those who are slow acetylators may develop liver intoxication as a consequence of slow INH metabolism process. Slow acetylator TBDM patients may complicate both TB and DM treatment, causing them to be less optimal. The aim of this study was to explore the acetylator status of TBDM patients in Kupang, Indonesia. A cross-sectional study was conducted by obtaining DNA of 122 TB patients in Kupang in June–November 2011. NAT2 gene was amplified and sequenced to determine the acetylator status. There were 5 TB patients who had a glucose serum level of >200mg/dL and was catagorized as TBDM. Result showed that there was 1 TBDM patient who was a rapid acetylator (NAT2*4/NAT2*4), 2 patients as intermediate acetylators (NAT2*13A/NAT2*6J), and 2 patients as slow acetylators (NAT2*5/NAT2*5G, NAT2*6A/ NAT2*6A, NAT2*7B/ NAT2*7B). Meanwhile, there were 2 TB patients who was rapid acetylators (NAT2*4/NAT2*4) and 3 patients as intermediate acetylators (NAT2*4/NAT2*6A, NAT2*13A/NAT2*6J). Slow NAT2 acetylator TBDM patients potentially face more problems during therapy. As INH may cause liver intoxication, these patients may also experience unoptimum DM treatment. Therefore, it is strongly recommended to do a study on the role of pharmacogenomics in TBDM. [ MKB. 2016;49(1):61–6] Key words: Acetylator, isoniazid, NAT2 , pharmacogenetics, tuberculosis