Accession	GSE165705
Status	2021/9/3
Title	Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV (ChIP-Seq)
Organism	Homo sapiens
Experiment type	Genome binding/occupancy profiling by high throughput sequencing
Summary	Persons living with HIV (PLWH) are at increased risk of tuberculosis (TB). HIV-associated TB is mainly the result of recent infection with Mycobacterium tuberculosis (Mtb) followed by rapid progression to disease. Alveolar macrophages (AM) are the first cells of the innate immune system that engage Mtb, but how HIV and antiretroviral therapy (ART) impact on the anti-mycobacterial response of AM is not known. In this study AM were challenged in vitro with Mtb, and their epigenetic and transcriptomic responses were determined for PLWH receiving ART, control subjects who were HIV-free (HC) and subjects who received pre-exposure prophylaxis (PrEP) with ART to prevent HIV infection. Compared to HC subjects’ response to Mtb, we showed that AM isolated from PLWH and PrEP subjects displayed substantially weaker transcriptomic response and no significant changes in their chromatin state. These findings revealed a previously unknown adverse effect of ART.
Samples	GSM ID Sample info Characteristics Description GSM5048539 ChIP-Seq Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (1987);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1005;prescription drugs: Genvoya;active ingredient: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir;art start year: 2002;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2018/02/07;mtb challenged: yes;fragments in clean bam: 2 Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048518 ChIP-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 29;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1091;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/01/11;mtb challenged: no;fragments in clean bam: 1 Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048540 ChIP-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 41;medical.history: HIV (2014);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1267;prescription drugs: Viread, Tivicay, Edurant;active ingredient: Tenofovir_DF, Dolutegravir, Rilpivirine;art start year: 2015;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/02/07;mtb challenged: no;fragments in clean bam: 2 Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048541 ChIP-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 41;medical.history: HIV (2014);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1267;prescription drugs: Viread, Tivicay, Edurant;active ingredient: Tenofovir_DF, Dolutegravir, Rilpivirine;art start year: 2015;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/02/07;mtb challenged: yes;fragments in clean bam: 2 Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048519 ChIP-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 29;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1091;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/01/11;mtb challenged: yes;fragments in clean bam: 1 Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048542 ChIP-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 62;medical.history: HIV (2012);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 650;prescription drugs: Truvada, Tivicay;active ingredient: Emtricitabine, Tenofovir_DF, Dolutegravir;art start year: 2012;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/06/20;mtb challenged: no;fragments in clean bam: 2 Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048543 ChIP-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 62;medical.history: HIV (2012);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 650;prescription drugs: Truvada, Tivicay;active ingredient: Emtricitabine, Tenofovir_DF, Dolutegravir;art start year: 2012;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/06/20;mtb challenged: yes;fragments in clean bam: 2 Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048520 ChIP-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1263;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/12/13;mtb challenged: no;fragments in clean bam: 1 Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048544 ChIP-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 33;medical.history: HIV (2017);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 633;prescription drugs: Genvoya;active ingredient: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir;art start year: 2017;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/07/11;mtb challenged: no;fragments in clean bam: 1 Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048545 ChIP-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 33;medical.history: HIV (2017);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 633;prescription drugs: Genvoya;active ingredient: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir;art start year: 2017;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/07/11;mtb challenged: yes;fragments in clean bam: 1 Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048521 ChIP-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1263;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/12/13;mtb challenged: yes;fragments in clean bam: 1 Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048522 ChIP-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: F;age: 31;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 871;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/12/12;mtb challenged: no;fragments in clean bam: 2 Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048523 ChIP-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: F;age: 31;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 871;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/12/12;mtb challenged: yes;fragments in clean bam: 2 Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048524 ChIP-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: F;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1023;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2017/12/20;mtb challenged: no;fragments in clean bam: 2 Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048546 ChIP-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 60;medical.history: HIV (2006);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 906;prescription drugs: Atripla;active ingredient: Emtricitabine, Tenofovir_DF, Efavirenz;art start year: 2007;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/07/04;mtb challenged: no;fragments in clean bam: 2 Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048547 ChIP-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 60;medical.history: HIV (2006);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 906;prescription drugs: Atripla;active ingredient: Emtricitabine, Tenofovir_DF, Efavirenz;art start year: 2007;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/07/04;mtb challenged: yes;fragments in clean bam: 2 Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048525 ChIP-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: F;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1023;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2017/12/20;mtb challenged: yes;fragments in clean bam: 2 Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048526 ChIP-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (2002);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1172;prescription drugs: Biktarvy;active ingredient: Emtricitabine, Tenofovir_AF, Bictegravir;art start year: 2002;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2019/12/04;mtb challenged: no;fragments in clean bam: 1 Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048527 ChIP-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (2002);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1172;prescription drugs: Biktarvy;active ingredient: Emtricitabine, Tenofovir_AF, Bictegravir;art start year: 2002;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2019/12/04;mtb challenged: yes;fragments in clean bam: 1 Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048528 ChIP-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (2002);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 536;prescription drugs: Truvada, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Raltegravir;art start year: 2004;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/10/11;mtb challenged: no;fragments in clean bam: 1 Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048529 ChIP-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (2002);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 536;prescription drugs: Truvada, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Raltegravir;art start year: 2004;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/10/11;mtb challenged: yes;fragments in clean bam: 1 Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048530 ChIP-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 50;medical.history: HIV (1997);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 439;prescription drugs: Complera;active ingredient: Emtricitabine, Tenofovir_DF, Rilpivirine;art start year: 1999;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2017/11/29;mtb challenged: no;fragments in clean bam: 1 Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048531 ChIP-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 50;medical.history: HIV (1997);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 439;prescription drugs: Complera;active ingredient: Emtricitabine, Tenofovir_DF, Rilpivirine;art start year: 1999;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2017/11/29;mtb challenged: yes;fragments in clean bam: 1 Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048532 ChIP-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: F;age: 54;medical.history: HIV (1994);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 716;prescription drugs: Complera, Reyataz, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Rilpivirine, Atazanavir, Raltegravir;art start year: 1994;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/12/06;mtb challenged: no;fragments in clean bam: 1 Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048533 ChIP-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: F;age: 54;medical.history: HIV (1994);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 716;prescription drugs: Complera, Reyataz, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Rilpivirine, Atazanavir, Raltegravir;art start year: 1994;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/12/06;mtb challenged: yes;fragments in clean bam: 1 Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048534 ChIP-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 57;medical.history: HIV (1996);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 983;prescription drugs: Kivexa, Reyataz, Norvir;active ingredient: Abacavir, Lamivudine, Atazanavir, Ritonavir;art start year: 1997;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/12/06;mtb challenged: no;fragments in clean bam: 1 Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048535 ChIP-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 57;medical.history: HIV (1996);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 983;prescription drugs: Kivexa, Reyataz, Norvir;active ingredient: Abacavir, Lamivudine, Atazanavir, Ritonavir;art start year: 1997;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/12/06;mtb challenged: yes;fragments in clean bam: 1 Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048536 ChIP-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 51;medical.history: HIV x (2003);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 468;prescription drugs: Triumeq;active ingredient: Abacavir, Dolutegravir, Lamivudine;art start year: 2004;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/01/24;mtb challenged: no;fragments in clean bam: 2 Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library GSM5048537 ChIP-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 51;medical.history: HIV x (2003);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 468;prescription drugs: Triumeq;active ingredient: Abacavir, Dolutegravir, Lamivudine;art start year: 2004;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/01/24;mtb challenged: yes;fragments in clean bam: 2 Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library GSM5048538 ChIP-Seq Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (1987);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1005;prescription drugs: Genvoya;active ingredient: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir;art start year: 2002;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2018/02/07;mtb challenged: no;fragments in clean bam: 2 Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Platform	GPL24676  : Illumina NovaSeq 6000 (Homo sapiens)
Literature	34473646
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