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Hello everyone,

Great working group yesterday! I will work on scheduling a follow-up Rapamycin Working Group Meeting. Here is a summary from today’s, January 17, 2023, meeting:

Eric Verdin from the Buck Institute provided background and updates on rapamycin in aging. mTOR signaling is the target of rapamycin. mTOR signaling in T cells involves metabolic cues, antigen recognition, and immunologic cues. Rapamycin can inactivate the mTORC1 complex more predominantly; however, the mTORC2 complex is inhibited with chronic rapamycin treatment. Rapamycin has been routinely used in the aging field because there is evidence that rapamycin treatment increases life span in mice  (ex: lifespan in mice can increase from 9% to 26% in almost all experiments and sometimes ranges from 30-100% increase).

Testing rapamycin in humans has not been as successful. They found that rapamycin tricks the body into thinking that there is not enough energy coming in and begins the fasting mode (even if you eat, your body thinks you are fasting). This can cause humans to lose weight and muscle. When you have high glucose levels, then insulin secretion and mTORC1 activation is triggered. There is no evidence that rapamycin works in decreasing the aging process in humans and is a drug for immunosuppression. However, there are some positive studies with primates, mice, and dogs. There is growing evidence that inactivating mTORC2 leads to side effects, whereas mTORC1 targeting may be desirable. Humans that are taking it once a week have more inhibition of mTORC1 and not mTORC2 (no side effects with 1x/week). The half-life of the drug is 36 hrs. How does it affect the lifespan of cells? In vitro replicative lifespan is generally used as a test for viability. This has not been tested in the Verdin lab, but Eric guessed that if you add rapamycin it might stop the replication of the cells. Telomere length can also be preserved.

Papers that were discussed:

Rapamycin Reduces CCR5 Density Levels on CD4 T Cells, and This Effect Results in Potentiation of Enfuvirtide (T-20) against R5 Strains of Human Immunodeficiency Virus Type 1 In Vitro.

FOXO1 promotes HIV latency by suppressing ER stress in T cells.

Regulation of stem cell function and neuronal differentiation by HERV-K via mTOR pathway

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

Rapamycin limits CD4+ T cell proliferation in simian immunodeficiency virus-infected rhesus macaques on antiretroviral therapy.

This last study looks at the suppression of ART after 31 days and then administering rapamycin. Administered anti-CD3 in animals with rapamycin. Tim Henrick commented that monkey studies had really high concentrations of rapamycin (compared to his human studies). This may be because monkeys have higher levels of exposure than humans. The tissue and plasma concentrations in NHPs were way above that in humans treated long-term.

Avi Nath discusses his study: Regulation of stem cell function and neuronal differentiation by HERV-K via mTOR pathway. They showed the mTOR pathway is activated by interactions between the envelope protein of HERV-K and CD98 heavy chain. They also showed a novel interaction between mTOR and LPCAT-1 which regulates histone 4 deacetylation. In the context of human endogenous retroviruses (HERVs), there is a small number of transcription factors. HML-2 LTR can regulate the expression of host genes as promoters and enhancers. He shared some data from the paper: Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. They are interested in brain studies. If you over-express in stem cells, they will produce tumors, and the expression of neurons leads to motor neuron disease. The study shares the different effects of HML-2 expression.

Hello HOPEians,

Happy Holidays!

During the RF1 meeting on Dec 19, 2022, we discussed some weaknesses from the SAB report and heard a lecture from Helena Reyes-Gopar (Nixon Lab) at the Instituto Nacional De Medicina Genómica about “Stellarscope quantifies the expression of transposable elements at locus resolution in single cells.” To summarize, Helena shared that they created a tool to set in motion single-cell retrotranscriptomics; they are characterizing HERV transcription in single PBMCs, and stellarscope uses a scRNA-seq alignment and your annotation to provide a matrix that includes counts for your elements (e.g HERVs).

Down the line, the Nixon Lab plans to look at more than one donor, sort T cells and monocytes, and create a small list of TEs that are expressed. Michael Corley suggested looking at methylation/chromatin data from sorted cells to orthogonally validate and also distinguish self-expressed TEs from those co-transcribed with host genes. Ulrike mentioned that they are working with bulk and mapping to HERV by taking different public datasets and found CD4 signatures. ATAC data is generally less recalcitrant to mapping because they often overlap TE and uniquely mapping flanking sequences.

One of the weaknesses that was discussed was:

“The aims of RF1 were not all totally compelling. Testing for synergy of repressive factors might be helpful but probably not groundbreaking. Looking to HERVs as models for chromatin based repression may or may not pay off – they are mostly repressed by DNA methylation in mature cells, which allows for shutoff of embryonic ZNF genes. Perhaps this is suggesting a focus on DNA methylation, though. Not sure studying tat-independent virus will be helpful.”

In the next SAB meeting, we could do better explaining the big points in the presentations and describing the physiology in more detail. We could try to understand how different HERVs located in different loci are expressed differently and look for targeted M-seq and HERV classes.

In an upcoming Scientific Working Group – HERV & HIV on January 23rd from 10-11 am PT, Cedric, Ulrike, and Zichong are working on screening zinc finger proteins for silencers and Zichong already received some good results that will be discussed further in the next meeting.

Actions for the next meeting:

• Susana Valente – Schedule meeting with Cedric to go over PITCH approach for HERVs

• Roan Lab – Look for DUX4 expression in single-cell RNAseq tonsil datasets (+/- HIV)

• (In progress) Luisa Mori, Ana Leda, and Susana Valente considering writing a review/summary of all the HIV latency models

Announcements:

• The HOPE Collaboratory-Wide Meeting is on Tuesday, January 17, 2023, 12-1 pm PT

• There is a Scientific Working Group – HERV & HIV on January 23rd from 10-11 am PT

• The next RF1 standing meeting will be in February: Date TBD and we will discuss new HERV projects

• Please Acknowledge HOPE & the NIH in any publications or presentations and notify the Program Manager. Here are some examples of what you can include.

“Research reported in this publication was supported by the NIAID of the National Institutes of Health under award number UM1AI164559, with co-funding support from NIDA, NIMH, NHLBI, the NIDDK, and the NINDS. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”

“This research was supported by NIAID award number UM1AI164559, co-funded by NHLBI, NIDA, NIMH, NINDS, and NIDDK.”

Hello HOPEians,

During the RF1 meeting on October 17th, 2022 we discussed the new RF/Collaboratory wide format and who would submit abstracts for the HIV Persistence meeting in Miami. Attached are the Management & Operations Updates.

HIV Persistence – International Workshop Miami

Abstracts are due TODAY (by 3pm PT/ 6pm ET)

Please send me your abstracts, so we can decide who will present during the flask talks. Here is a list of individuals that are submitting abstracts (please contact me if I missed someone):

• Julie Frouard, Zichong Li, Ulrike Lange, Ursula Schulze-Gahmen, Daniela Boehm, Luisa Mori, Sonia Mediouni Jablonski, Michael Corley (2x), Alina Pang, Chuan Li, Priti Kumar

A reminder that the abstracts that you submit will likely get published if chosen. You can have max 10 authors. CROI has some rules about presenting abstracts that have already been presented:

“If study data are accepted for publication or presentation after the abstract submission to CROI, and that publication or presentation is expected to take place before CROI, the presenting author must contact the conference manager at CROIabstracts@iasusa.org to provide details as soon as the presentation is accepted for review, presentation, or publication in another venue or outlet. Please be aware that, while publication in these circumstances will not necessarily prevent presentation of the research at CROI, our strong preference is that any additional publication or presentation happens either simultaneous to or following presentation at CROI. Requests to publish or present research accepted for presentation at CROI prior to its presentation at CROI will be evaluated on a case-by-case basis. Failure to notify the conference promptly regarding plans to publish or present a CROI-accepted abstract prior to CROI may result in the removal of the study from the conference program.”

Here is some language you can use to Acknowledge HOPE & the NIH:

“Research reported in this publication was supported by the NIAID of the National Institutes of Health under award number UM1AI164559, with co-funding support from NIDA, NIMH, NHLBI, the NIDDK, and the NINDS. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”

“This research was supported by NIAID award number UM1AI164559, co-funded by NHLBI, NIDA, NIMH, NINDS, and NIDDK.”

New RF Structure

The RF meeting structure will change beginning in November.  For the rest of October, each RF will hold its monthly meeting.  In November, a larger group meeting will take place in lieu of the individual RF meetings.  These will alternate every month.

Hello HOPEians,

Here is a quick update on the RF1 meeting from July 18th, 2022.

During the RF1 meeting, Cedric Feschotte (Cornell University) shared updates that Sabrina Leddy has started working in his lab on HERV expression in HIV elite controllers and Julius Judd who was previously working on zinc fingers is leaving his lab soon. Susana Valente (University of Florida) explained her research with DUX4, FUBP3, dCA-resistant viruses, and how p32 interacts with Tat’s basic domain.

Zichong Li (Greene Lab at Gladstone) discussed different epigenetic modifiers and the effects of new SPAs and the nucleosomal modification mechanisms for silencing HIV.  Martin Kinisu (Greene Lab) also shared his work on CRISPRoffV2 combining DNA and H3K9 methylation, the optimization of KRAB domain for HIV silencing, and exploring inducible expression systems using the piggyback technology. In his early findings, Martin found that ETRs transiently silence HIV reactivation in 30-70% of cells. Melanie Ott and Daniela Boehm (Gladstone) resubmitted their SYMD5 paper and performed the SMYD5 rescue experiment in 5A8 J-Lat cells. Their findings show that SYMD5 is highly expressed in CD4+ T cells and is a positive regulator of HIV transcription.  SYMD5 also methylates histones and Tat in vitro.

Actions for next meeting:

• Susana Valente – Schedule a meeting with Cedric to go over DUX4 data

• Chuan Li – Give MNase-Seq protocol to Zichong Li

• Roan Lab – Look for DUX4 expression in single-cell RNAseq tonsil datasets (+/- HIV)

• (In progress) Luisa Mori, Ana Leda, and Susana Valente considering writing a review/summary of all the HIV latency models

Announcements:

• August 15th HOPE – PAVE Guest Speaker: Dr. Persaud

• The next standing meeting is on Sept 19 – Bharath Sreekumar will give a refresher on their data on transducing T cells.  Cedric Feschotte and Sabrina Leddy will give updates on HERV expression in HIV-1 elite controllers.

• Call for nominations for the HOPE 2022 Awards (Instructions attached)

• Please Acknowledge HOPE & the NIH in any publications or presentations and notify the Program Manager. Here are some examples of what you can include.

“Research reported in this publication was supported by the NIAID of the National Institutes of Health under award number UM1AI164559, with co-funding support from NIDA, NIMH, NHLBI, the NIDDK, and the NINDS. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”

“This research was supported by NIAID award number UM1AI164559, co-funded by NHLBI, NIDA, NIMH, NINDS, and NIDDK.”

Hello HOPEians,

Here is a quick update on the RF1 meeting from 5/16.  

During the RF1 meeting, Sonia Jablonski, a Staff Scientist in the Valente lab discussed transcriptional crosstalk between DUX4-FL and HIV-1. Martin Kinisu from the Greene lab discussed recent work on vetting CRISPR-off (7kb) as a latency promoting factor and testing variable KRAB domains. Zichong Li from the Greene lab discussed three factors that can play a role in the efforts to block & lock HIV outside of the 30 synergies identified among 10 silencing factors. Bharath Sreekumar from the Ott Lab gave an update on transducing t-cells. Thomas Premeaux shared information from the Johnathan Karn paper on The Glucocorticoid Receptor Is a Critical Regulator of HIV Latency in Human Microglial Cells. Melanie led a discussion of new ETRs including BRECiB.

 Actions for next meeting:

• Cedric – Share data on ZNF579 with Susana
• Roan lab – look for DUX4 expression in single-cell RNAseq tonsil datasets (+/- HIV)

Long-Term Actions:

• Luisa Mori, Ana Leda, and Susana considering writing a review/summary of all the HIV latency models 
• (T-TRACE) Discuss whether it would make sense to apply T-TRACE when we test block-and-lock agents in humanized mice 
• (Systems to test spironolactone in, and which concentrations) Roan lab to collect samples to look at XPB and send to Valente Lab
• (Aim 2) Keep the discussion open on the use of PICh or other methods

At the next meeting on June 29th, we will have a guest speaker, Dr. Mathias Lichterfeld.

Hello HOPEians,

Here is a quick update on the RF1 meeting from 4/18.  

In today’s meeting, we discussed HIV and HERVs integration sites, with an overview from Doug, Ulrike, Matthew, and Manu. The slides will be in the RF1 Dropbox later. 

Actions for next meeting:

• Sydney/Doug – Schedule HIV and HERVs Integration site subgroup meeting
• Melanie – Follow up if any members of the AIDS malignancy consortium at UCSF/Gladstone. Attempt to identify HIV infected subjects on 2-deoxy-glucose treatment
• Cedric – Share data on ZNF579 with Susana
• Susana – Share list of ChAP-MS interactors with Cedric

Long-Term Actions:

• Luisa Mori, Ana Leda, and Susana considering writing a review/summary of all the HIV latency models 
• (T-TRACE) Discuss whether it would make sense to apply T-TRACE when we test block-and-lock agents in humanized mice 
• (Systems to test spironolactone in, and which concentrations) Roan lab to collect samples to look at XPB and send to Valente Lab
• (Aim 2) Keep the discussion open on the use of PICh or other methods

The next meeting is May 16th and RF1 leaders will follow up with a topic and agenda.

Hello HOPEians,

Here is a quick update on the RF1 meeting from 3/21.  

In today’s meeting we got updates from:

• Feschotte Lab: Julius presented data on ZNF579. ZNF579 interacts with TRIM22 and the PDH complex, potentially interesting for regulation of HIV latency.
• Greene Lab: Zichong showed preliminary data that overexpressing BCL7C, KANSL2, and SIRT2 enhance HIV latency. 
• Valente Lab: Updates on p32 regulating HIV transcription. 
• Ott Lab: Bharath is continuing to collaborate with Ulrike to generate a telomerase immortalized primary T cell with HIV integrated into the BACH2 locus. Daniela is finalizing SMYD5 paper as well as continuing to work with the Toronto group to develop SMYD5 inhibitors (RF2).

Announcements:

• The next meeting is April 18th – Discuss integration sites of HIV and HERVs and more lab updates

Actions for next meeting:

• Melanie – Follow up if any members of the AIDS malignancy consortium at UCSF/Gladstone. Attempt to identify HIV infected subjects on 2-deoxy-glucose treatment
• Cedric – Share data on ZNF579 with Susana
• Susana – Share list of ChAP-MS interactors with Cedric
• Subgroup meeting on ZNF579
  • Attendees: Cedric, Julius, Eric, Melanie, Susana, Warner
  • Discuss potential involvement on metabolism and interaction with components of PDH complex
• Melanie and Susana meet to discuss potentially generating a crystal structure of p32 and Tat (Susana, Melanie, Ursula, Chuan)

Long-Term Actions:

• Luisa Mori, Ana Leda, and Susana considering writing a review/summary of all the HIV latency models 
• (T-TRACE) Discuss whether it would make sense to apply T-TRACE when we test block-and-lock agents in humanized mice 
• (Systems to test spironolactone in, and which concentrations) Roan lab to collect samples to look at XPB and send to Valente Lab
• (Aim 2) Keep the discussion open on the use of PICh or other methods

​​Hello HOPEians,

Here is a quick update on the RF1 meeting from 1/18. Ana Leda from the Valente Lab (Scripps) gave a presentation on “Mechanisms of Tat-independent HIV replication”. There was a great discussion on dCA- resistant viruses. We also discussed action items and a new format/structure for RF1 meetings (see below). Please reach out to Warner of Susana if you have any questions or concerns. If interested, please email Danielle or Sydney to get the Zoom recording of the meeting. 

Announcements:

• We will be changing the time for RF1 meetings to 1 hr 15 min with the goal of finishing in 1 hour. The meeting will consist of one 10-15 minute presentation; action items; and 2 minute round-table lab updates.
• Next meetings: 
  • February 25, 1-2:15 pm PT (4-5:15 pm ET) Presenting: Zichong Li from the Greene Lab (Gladstone)
  • March 21, 9-10:15am PT (12-1:15pm ET) Presenting: TBD from the Feschotte Lab (Cornell) 
• Updated new RF1 dates in the calendar (Rescheduled due to Monday Holidays)

• Feb 25, 1-2:15 pm PT (4-5:15 pm ET)
• Jun 29, 10-11:15 am PT (1-2:15 pm ET)

**If you are having issues with HOPE meeting updates, please check with your IT department about calendar syncing and look out for our reminder emails.

Actions for next meeting:

• Melanie – Follow up if any members of the AIDS malignancy consortium at UCSF/Gladstone. Attempt to identify HIV infected subjects on 2-deoxy-glucose treatment

• Aim 1

• Nicolas/Eric – Set a subgroup meeting for metabolism and tonsil model (Verdin, Valente, Roan, Nixon, Furler, Ott)

• Aim 2
• Doug –  (in progress) Create subgroup meeting in February to discuss HERVs and HIV integration sites (Verdin, Nixon, Valente, Ott, Greene, Ndhvolu, Lange, and Feschotte) 

Long-Term Actions:

• Luisa Mori and Susana considering writing a review/summary of all the HIV latency models 
• (T-TRACE) Discuss whether it would make sense to apply T-TRACE when we test block-and-lock agents in humanized mice 
  • RF2 Subgroup meeting to discuss cryo-preserving humanized mouse tissue for single-cell experiments with Lish, Nadia, Priti and Susana, and Danielle. Jan 31st 12-1pm ET (9-10am PT) – On the HOPE Calendar
• (Systems to test spironolactone in, and which concentrations) Roan lab to collect samples to look at XPB and send to Valente Lab
• (Aim 2) Keep the discussion open on the use of PICh or other methods

Hello HOPEians,

 

Here is a list of actions Danielle and I gathered from the RF1 meeting yesterday. Please reach out to Warner of Susana if you have any questions or concerns.

 

Date: Nov 15, 2021

 

Actions for next meeting:

• Melanie – Follow up if any members of the AIDS malignancy consortium at UCSF/Gladstone. Attempt to identify HIV infected subjects on 2-deoxy-glucose treatment
• Lish – Check with Last Gift, Uganda, Brazil, natural history cohort, etc. if there may be any participants on metabolic drugs
• Aim 1
  • Eric – Set a subgroup meeting for metabolism and tonsil model (Verdin, Valente, Roan, Nixon, Furler, and Ott)
• Aim 2
  • Doug –  (in progress) Create subgroup meeting to discuss HERVs and HIV integration sites (Verdin, Nixon, Valente, Ott, Greene, Ndhvolu, Lange, and Feschotte)

Long-Term Actions:

• Luisa Mori and Susana considering writing a review/summary of all the HIV latency models
• (T-TRACE) Discuss whether it would make sense to apply T-TRACE when we test block-and-lock agents in humanized mice
• (Systems to test spironolactone in, and which concentrations) Roan lab to collect samples to look at XPB and send to Valente Lab
• (Aim 2) Determine the use of PICh or other methods Valente Lab, Greene Lab, and Feschotte lab

Announcements:

• Subgroup meeting on latency models Nov 17th, 9-10am PT (12-1pm ET)
• Sydney – Updated new RF1 dates in the calendar (Rescheduled due to Monday Holidays)
  • Jan 18, 1:30-3:15 pm PT (4:30-6:15 pm ET)
  • Feb 25, 1-2:45 pm PT (4-5:45 pm ET)
  • Jun 29, 10-11:45 am PT (1-2:45 pm ET)
• We are canceling the RF1 Dec 20th meeting because it is so close to the holidays.

Hello HOPEians,

Here is a list of actions Danielle and I gathered from the RF1 meeting last week. Please let us know if you have any questions or concerns.

• Warner – Set a meeting with Nadia and Susana – Finalize how and when to use t-trace for block and lock.
• Nadia – Send samples to Susana to look at the degradation of XPB protein.

• Aim 1
  • Susana can share Jurkat D6 Wild Type HIV cell line. Reach out to her if interested
  • Luisa Mori will create a summary of all the HIV latency models (Done)
    • Take a look at the PowerPoint and let us know if you have any comments to add (Dropbox)
    • Luisa considering writing a review on the latency models 
  • Revisit transcriptional profiling methods – 
    • Michael Corley – Share data/protocol for HiC 
      • Add the protocols to the slack (Michael- create PDF)
  • Systematically create silencing models so we have a battery of tools (recommend CRISPRi) and observe the long-term effects of silencing
    • Warner to set a sub meeting for those that would use the models (Ott Lab, Greene Lab, Valente Lab, Roan Lab, Feschotte Lab)
    • Warner to share CRISPRi vectors following sub-meeting as needed
• Aim 2
  • Susana to set a sub meeting to discuss PICh or other methods with Valente Lab, Greene Lab, and Feschotte lab
• Aim 4
  • We need to test established latency in patient samples using an in vitro system, using single-cell sequencing methods before going to in vivo models
    • Nadia – Set sub meeting will be set with Valente lab, Roan lab, Greene Lab, Ndhlovu Lab, and Ott Lab to discuss different potential models

Reminder for ALL to start spending down their budgets.

Upcoming Meetings:

November 15th, 2021: Verdin, Ott

December 20th, 2021: Ndhvolu, and TBD