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RF1 Actions 10/17/22

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.

RF1 Actions 7/18/22

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.”

RF1 Actions 5/16/22

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.

RF1 Actions 4/18/22

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.

RF1 Actions 3/21/22

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

RF1 Actions 1/18/22

​​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

RF1 Actions 11/15/21

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.

RF1 Actions 10/18/21

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

RF1 Actions 9/20/21

Actions: 

  • Aim 1
    • Susana can share Jurkat D6 Wild Type HIV cell line used in Takata latency model. Reach out to her if interested 
    • Luisa Mori will create a summary of all the HIV latency models (including pros and cons) to be emailed before the next RF1 meeting
    • Revisit transcriptional profiling methods – 
      • Danielle – Create a slack channel for discussions on transcriptional profiling
      • Michael Corley – Share data/protocol for HiC 
    • 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
      • After the latency models are circulated from Aim 1: Sub meeting will be set with Valente lab, Roan lab, Greene Lab, Ndhlovu Lab, and Ott Lab to discuss different potential models