Journal: bioRxiv

Article Title: Three immunoregulatory signatures define non-productive HIV infection in CD4 + T memory stem cells

doi: 10.64898/2026.03.20.713012

Figure Lengend Snippet: (a) Mean-difference (MD) plot showing that no differentially expressed genes were found in CD4 + T SCM NE compared to Mock (|log 2 FC| >= 2 and FDR <= 0.01). (b) Volcano plot representing the relative expression of all genes in the CD4 + T SCM P vs mock comparison, with upregulated genes in red and downregulated genes in blue. (c) Venn diagram showing significantly upregulated genes in CD4 + T SCM NP compared to P, NE and mock (log 2 FC >= 2 and FDR <= 0.01). (d) Heatmap of CD4 + T SCM selected differentially expressed genes (Z-score is shown, row normalized considering only the displayed genes) across all sorted populations. (e) Boxplots representing transcript counts per million (CPM) detected by RNAseq in CD4 + T SCM for genes encoding for CCL22 , CCL17 , KYNU, IDO1 , BASP1 and TNFAIP2 in all sorted conditions (n=4). (f) Venn diagram of significantly upregulated genes in CD4 + T SCM harboring an integrated pMorpheus-V5 provirus (either NP or P compared to NE and mock, log 2 FC >= 2 and FDR <= 0.01). The six shared significantly upregulated genes are highlighted in the box below the Venn diagram. (g) Gene Ontology (GO) of Biological Processes (BP) of significantly upregulated genes in NP CD4 + T SCM , compared to P (left) and mock (right).

Article Snippet: Six hours before spinoculation, CCL22 100 ng/mL (MedChemExpress, # HY-P72790) or tryptophan 50 ug/mL (Sigma, # T8941) was added to the culture media.

Techniques: Expressing, Comparison, RNA sequencing

Journal: bioRxiv

Article Title: Three immunoregulatory signatures define non-productive HIV infection in CD4 + T memory stem cells

doi: 10.64898/2026.03.20.713012

Figure Lengend Snippet: (a) Expression of CCL22 and CCL17, (b) KYNU and IDO1, (c) BASP1 and TNFAIP2 mRNA in FACS-sorted total CD4 + T cells (Productively infected P, negative-exposed NE, mock unexposed mock, non-productively infected NP, compared to P) infected with HIV pMorpheus-V5 reporter virus (n=3). Significance was calculated on log-transformed fold-change values (normalized to P fold-change values, set as 1) using both one-way ANOVA with multiple comparisons (Dunnett’s multiple comparisons test, between NP, NE and mock) and one-sample t and Wilcoxon test (between single populations compared to P, only NP vs P t test significance is shown). *, P < 0.05: **, P < 0.01, ***, P < 0.001, ****, P < 0.0001, ns, not significant. Each dot represents a different donor.

Article Snippet: Six hours before spinoculation, CCL22 100 ng/mL (MedChemExpress, # HY-P72790) or tryptophan 50 ug/mL (Sigma, # T8941) was added to the culture media.

Techniques: Expressing, Infection, Virus, Transformation Assay

Journal: bioRxiv

Article Title: Three immunoregulatory signatures define non-productive HIV infection in CD4 + T memory stem cells

doi: 10.64898/2026.03.20.713012

Figure Lengend Snippet: (a) Uniform manifold approximation and projection (UMAP) of 43,112 naïve (TN) and memory (TM) CD4 + T cells from Cano-Gamez et al. (2020) . Cell type populations in the UMAP are colored according to the legend: naïve, central (T CM ) and effector (T EM ) memory cells, effector memory cells re-expressing CD45RA (T EMRA ), natural T regulatory (nTreg). (b) Dot plot showing the average gene expression per cell type and respective percentage of cells expressing each of 16 NP-upregulated genes, including chemokines ( CCL22, CCL17, CCL19, CXCL9, CXCL10, EBI3 ), tryptophan catabolic enzymes ( IDO1, IDO2, KYNU, IL4I1 ), and cytoskeletal regulators ( TNFAIP2, BASP1, FSCN1, MARCKS, PLEK, CYRIA ). (c) Heatmap displaying the expression levels of the 16 genes and corresponding UCell enrichment scores at the single-cell level in 2,756 CD4 + T cells (6.4%) in cells with detectable levels of CCL22 , CCL17 or CCL19 (marked by *). (d) UMAP of 1,821,725 human immune cells within the Human Immune Health Atlas (T cells, B cells, monocytes, natural killer (NK) cells, and 12 other subsets including dendritic cells (DC) and hematopoietic precursors) . Cell type populations in the UMAP are colored according to the legend. (e) Same as panel (b) but for the Human Immune Health Atlas . (f) Same as panel (c) but for the 448 cells (0.025%) with detectable CCL22 , CCL17 or CCL19 expression in the Human Immune Health Atlas (marked by *) .

Article Snippet: Six hours before spinoculation, CCL22 100 ng/mL (MedChemExpress, # HY-P72790) or tryptophan 50 ug/mL (Sigma, # T8941) was added to the culture media.

Techniques: Expressing, Gene Expression, Single Cell

Journal: bioRxiv

Article Title: Three immunoregulatory signatures define non-productive HIV infection in CD4 + T memory stem cells

doi: 10.64898/2026.03.20.713012

Figure Lengend Snippet: (a) Experimental outline of CD4 + T cells treated with either CCL22, Tryptophan or IL-2 (media control). CD4 + T cells were TCR activated for three days in the presence of IL-2. Six hours before spinoculation, CCL22 or tryptophan was added to the cells. After spinoculation, cells were kept in either CCL22, tryptophan or control media until FACS staining and analysis. (b through g) Bar graphs showing the percentages of NP and P cells in the conditions treated with CCL22, tryptophan or IL-2 (media control), in total CD4 + T cells (b), naïve (c), T SCM (d), T CM (e), T TM (f) and T EM (g, n=3), with the ratio between P and NP highlighted on each condition (P/NP).

Article Snippet: Six hours before spinoculation, CCL22 100 ng/mL (MedChemExpress, # HY-P72790) or tryptophan 50 ug/mL (Sigma, # T8941) was added to the culture media.

Techniques: Control, Staining

Journal: bioRxiv

Article Title: Three immunoregulatory signatures define non-productive HIV infection in CD4 + T memory stem cells

doi: 10.64898/2026.03.20.713012

Figure Lengend Snippet: (a) Representative contour plots gated on CD4 + T SCM population showing the percentage of CCL22 + IDO1 + cells in NP, P, NE and mock populations. (b) Representative contour plots gated on CD4 + T SCM population showing the percentage of single positive populations for either IDO1 or CCL22, in CD4 + T SCM NP, P, NE and Mock. (c through h) Bar graphs displaying the percentages of CCL22 + IDO1 + cells in every subset considered, in naïve (c), T SCM (d), T CM (e), T TM (f), T EM (g) and total CD4 + T cells (h, n=3). (i) Bar graph showing the percentage of CCL22 + IDO1 + in NP population across the CD4 + T cell subsets considered (n=3). Significance was calculated using Repeated Measures one-way ANOVA with multiple comparisons (Dunnett’s multiple comparisons test, between NP, P, NE and Mock). *, P < 0.05: **, P< 0.01, ***, P < 0.001, ****, P < 0.0001, ns, not significant. Data presented as the mean with SD.

Article Snippet: Six hours before spinoculation, CCL22 100 ng/mL (MedChemExpress, # HY-P72790) or tryptophan 50 ug/mL (Sigma, # T8941) was added to the culture media.

Techniques: