Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation

The development of dendritic cells (DCs), including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs), is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected Flt3L-driven DC differentiation using CRISPR-Cas9-based screening. Genome-wide screening identified multiple regulators of DC differentiation including subunits of TSC and GATOR1 complexes, which restricted progenitor growth but enabled DC differentiation by inhibiting mTOR signaling. An orthogonal screen identified the transcriptional repressor Trim33 (TIF-1γ) as a regulator of DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes or granulocytes. In particular, deletion of Trim33 caused rapid loss of DC progenitors, pDCs, and the cross-presenting cDC1 subset. Trim33-deficient Flt3+ progenitors up-regulated pro-inflammatory and macrophage-specific genes but failed to induce the DC differentiation program. Collectively, these data elucidate mechanisms that control Flt3L-driven differentiation of the entire DC lineage and identify Trim33 as its essential regulator.

Clonal barcoding of endogenous adult hematopoietic stem cells reveals a spectrum of lineage contributions

The hierarchical model of hematopoiesis posits that self-renewing, multipotent hematopoietic stem cells (HSCs) give rise to all blood cell lineages. While this model accounts for hematopoiesis in transplant settings, its applicability to steady-state hematopoiesis remains to be clarified. Here, we used inducible clonal DNA barcoding of endogenous adult HSCs to trace their contribution to major hematopoietic cell lineages in unmanipulated animals. While the majority of barcodes were unique to a single lineage, we also observed frequent barcode sharing between multiple lineages, specifically between lymphocytes and myeloid cells. These results suggest that both single-lineage and multilineage contributions by HSCs collectively drive continuous hematopoiesis, and highlight a close relationship of myeloid and lymphoid development.

Haplodeficiency of the 9p21 tumor suppressor locus causes myeloid disorders driven by the bone marrow microenvironment

The chromosome 9p21 locus comprises several tumor suppressor genes including MTAP, CDKN2A, and CDKN2B, and its homo- or heterozygous deletion is associated with reduced survival in multiple cancer types. We report that mice with germ line monoallelic deletion or induced biallelic deletion of the 9p21-syntenic locus (9p21s) developed a fatal myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN)-like disease associated with aberrant trabecular bone formation and/or fibrosis in the bone marrow (BM). Reciprocal BM transfers and conditional targeting of 9p21s suggested that the disease originates in the BM stroma. Single-cell analysis of 9p21s-deficient BM stroma revealed the expansion of chondrocyte and osteogenic precursors, reflected in increased osteogenic differentiation in vitro. It also showed reduced expression of factors maintaining hematopoietic stem/progenitor cells, including Cxcl12. Accordingly, 9p21s-deficient mice showed reduced levels of circulating Cxcl12 and concomitant upregulation of the profibrotic chemokine Cxcl13 and the osteogenesis- and fibrosis-related multifunctional glycoprotein osteopontin/Spp1. Our study highlights the potential of mutations in the BM microenvironment to drive MDS/MPN-like disease.

Transitional dendritic cells are distinct from conventional DC2 precursors and mediate proinflammatory antiviral responses

High-dimensional approaches have revealed heterogeneity amongst dendritic cells (DCs), including a population of transitional DCs (tDCs) in mice and humans. However, the origin and relationship of tDCs to other DC subsets has been unclear. Here we show that tDCs are distinct from other well-characterized DCs and conventional DC precursors (pre-cDCs). We demonstrate that tDCs originate from bone marrow progenitors shared with plasmacytoid DCs (pDCs). In the periphery, tDCs contribute to the pool of ESAM+ type 2 DCs (DC2s), and these DC2s have pDC-related developmental features. Different from pre-cDCs, tDCs have less turnover, capture antigen, respond to stimuli and activate antigen-specific naïve T cells, all characteristics of differentiated DCs. Different from pDCs, viral sensing by tDCs results in IL-1β secretion and fatal immune pathology in a murine coronavirus model. Our findings suggest that tDCs are a distinct pDC-related subset with a DC2 differentiation potential and unique proinflammatory function during viral infections.

Stem cell decoupling underlies impaired lymphoid development during aging

Mammalian aging is associated with multiple defects of hematopoiesis, most prominently with the impaired development of T and B lymphocytes. This defect is thought to originate in hematopoietic stem cells (HSCs) of the bone marrow, specifically due to the age-dependent accumulation of HSCs with preferential megakaryocytic and/or myeloid potential ("myeloid bias"). Here, we tested this notion using inducible genetic labeling and tracing of HSCs in unmanipulated animals. We found that the endogenous HSC population in old mice shows reduced differentiation into all lineages including lymphoid, myeloid, and megakaryocytic. Single-cell RNA sequencing and immunophenotyping (CITE-Seq) showed that HSC progeny in old animals comprised balanced lineage spectrum including lymphoid progenitors. Lineage tracing using the aging-induced HSC marker Aldh1a1 confirmed the low contribution of old HSCs across all lineages. Competitive transplantations of total bone marrow cells with genetically marked HSCs revealed that the contribution of old HSCs was reduced, but compensated by other donor cells in myeloid cells but not in lymphocytes. Thus, the HSC population in old animals becomes globally decoupled from hematopoiesis, which cannot be compensated in lymphoid lineages. We propose that this partially compensated decoupling, rather than myeloid bias, is the primary cause of the selective impairment of lymphopoiesis in older mice.

Tumor immunogenomic signatures improve a prognostic model of melanoma survival

Background

Tumor mutation burden (TMB) has been associated with melanoma immunotherapy (IT) outcomes, including survival. We explored whether combining TMB with immunogenomic signatures recently identified by The Cancer Genome Atlas (TCGA) can refine melanoma prognostic models of overall survival (OS) in patients not treated by IT.

Methods

Cox proportional-hazards (Cox PH) analysis was performed on 278 metastatic melanomas from TCGA not treated by IT. In a discovery and two validation cohorts Cox PH models assessed the interaction between TMB and 53 melanoma immunogenomic features to refine prediction of melanoma OS.

Results

Interferon-γ response (IFNγRes) and macrophage regulation gene signatures (MacReg) combined with TMB significantly associated with OS (p = 8.80E−14). We observed that patients with high TMB, high IFNγRes and high MacReg had significantly better OS compared to high TMB, low IFNγRes and low MacReg (HR = 2.8, p = 3.55E−08). This association was not observed in low TMB patients.

Conclusions

We report a model combining TMB and tumor immune features that significantly improves prediction of melanoma OS, independent of IT. Our analysis revealed that patients with high TMB, high levels of IFNγRes and MacReg had significantly more favorable OS compared to high TMB patients with low IFNγRes and low MacReg. These findings may substantially improve current melanoma prognostic models.

Novel blood-based biomarker predicting severe toxicity in melanoma anti-CTLA-4 immunotherapy treatment

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Background: Immune checkpoint inhibition (ICI) has improved clinical outcomes of metastatic melanoma (MM). However, 65-80% of treated patients experience immune-related adverse events (irAEs), urging for the availability of personalized and easy-access clinical biomarkers. We have previously shown that germline genetics related to host immunity affects ICI response and MM survival. In this study, we investigated if germline immune-related expression quantitative trait loci (ieQTLs) may predict ICI-induced irAEs in MM. Methods: Through a comprehensive interrogation of a healthy twin-cohort expression dataset (MuTHER), we identified 40 ieQTLs most significantly associated with the expression of 382 immune-related genes. These germline variants were genotyped using the MassARRAY system in anti-CTLA-4-treated MM patients, collected as part of a multi-institutional collaboration. Using multivariable logistic regression models, we tested the association of 40 ieQTLs with irAEs in a discovery cohort of 97 MM patients followed by a validation in additional cohort of 97 anti-CTLA-4 treated patients. Results: We found rs7036417 significantly associated with severe anti-CTLA-4 irAEs in the discovery (OR = 6.18; 95%CI = 1.61-23.74; p = 0.007) and validation (OR = 6.73, 95%CI = 1.42-31.86; p = 0.02) cohorts. Pooled analysis showed that carriers of two rs7036417 alternate alleles (TT) have a 6-fold increased risk of developing severe irAEs (OR = 6.11; 95% = 2.26-16.56;p = 0.0003). This association was not observed with ICI response or survival. The alternate allele of rs7036417 is associated with higher expression of SYK (spleen-associated tyrosine kinase), suggesting that elevated SYK contributes to developing severe irAEs. Conclusions: We report that rs7036417, an ieQTL in SYK, associates with an increased risk of severe irAEs, independent of ICI efficacy. SYK plays an important role in B-cell/T-cell expansion and increased pSYK has been reported in patients with rheumatoid arthritis or systemic lupus erythematosus. Based on our data, the over-expression of SYK likely explains the biological mechanisms of the association between rs7036417 and anti-CTLA4 irAEs. These findings propose a novel blood-based baseline biomarker stratifying the patients at increased risk of severe irAEs, with a clinical effect substantially surpassing those observed for currently available predictors. Our ongoing studies are currently investigating SYK eQTL as a novel target in toxicity-reducing therapies.

Undetected invasive lobular carcinoma of the breast: review of false-negative smears

Analysis of a series of 34 fine-needle aspirations (FNA) from 28 patients with invasive lobular carcinoma (ILC) was undertaken. The false-negative smears were reviewed to reveal the cause of such a relatively frequent error. This was a retrospective study and comparison between the cytological and pathological findings in a series of 34 FNA. Three cases were excluded without sufficient material. Twelve cases were positive, nine suspicious of malignancy, and 10 were considered false-negatives. In a second analysis of this later group, one was reclassified as carcinoma, two reconsidered without sufficient material for diagnosis, and the remaining seven, still considered negatives, constituted the core of this study. Of these seven, there were none with hypercellular smears and in six there was a predominance of fat-tissue fragments. The scarce epithelial component showed honeycomb-flat sheets in four, loose clusters in three, small and tight clusters with irregular limits in six, and more than 10% of isolated epithelial cells (noncohesive cells) in one case. "Staghorns" were undetected and myoepithelial cell nuclei were very scarce in all cases. Some nuclear enlargement was detected in one, angulated nuclear contour in three, and nuclear crowding was present in five. All seven had fine, homogeneous chromatin, without prominent nucleoli. Cytoplasmic limits were undefined in all but one (6/7) and occasional cytoplasmic vacuolization was detected in two. Hypocellular smears with few, small, and dense groups (but always with more than 10 groups in at least one smear) can be related with ILC. In these cases, further studies are recommended to exclude malignancy. The loose cluster and flat sheets identified in four cases represent a benign epithelial hyperplasia mixed with the ILC.

Rescreening of atypical cervicovaginal smears using PAPNET

BACKGROUND

Atypical squamous cells of undetermined significance (ASCUS) is a cytopathologic term used to describe cases without specific pathologic substratum. Between 10-60% of ASCUS cases correspond to squamous intraepithelial lesions (SIL).

METHODS

The objectives of this study were: 1) to detect the pathologic significance of ASCUS in study patients, 2) to determine whether PAPNET identifies these cases, and 3) to compare the results of PAPNET with those of a second conventional screening. One hundred and sixty-three consecutive patients with the cytologic diagnosis of ASCUS and adequate follow-up were selected. Of these, 111 patients had colposcopic lesions and biopsies were performed; in the remaining 52 cases colposcopy was negative, as were 3 consecutive annual Papanicolaou smears. In a blind review, all 163 cases were rescreened using PAPNET. A second manual screening was performed for comparison.

RESULTS

One hundred and twenty-six of the 163 cases (77.3%) showed no SIL on biopsy or follow-up. Of the 37 pathologic cases, the diagnosis was koilocytosis (flat condyloma) in 13 cases (8%), cervical intraepithelial neoplasia (CIN) type I in 11 cases (6.8%) low grade SIL [LSIL] in a total of 24 cases [14.8%]), and CIN II-III or high grade SIL (HSIL) in 11 cases (6.8%). In the review using PAPNET, 57 previous ASCUS cases were classified correctly as negative, and 7 of 13 koilocytosis cases (54%), 9 of 11 CIN I cases (82%), and 7 of 11 CIN II-III cases (64%) were diagnosed correctly. In the second conventional screening, 74 cases were negative and 77 cases were ASCUS; only 3 of 13 koilocytosis cases (23%), 4 of 11 CIN I cases (36.4%) and 5 of 11 CIN II-III cases (45.5%) were reclassified correctly.

CONCLUSIONS

Among 163 patients with ASCUS, 77.3% had no precancerous squamous lesions. Concordance with definitive diagnosis was more accurate in our study using PAPNET analysis (Kappa index [K] = 0.7158) than by second conventional screening (K = 0.4537). Furthermore, we reclassified 35% of smears as negative and 15% as SIL.