Biology subjects

Rosenwald, A.

Publications and source records attributed to Rosenwald, A..

11 recordsLinked to original sources

bioRxiv2026

Pharmacological arginine deprivation renders pancreatic cancer cells susceptible to senolysis and inhibition of the integrated stress response

Pancreatic ductal adenocarcinoma (PDAC) is almost inevitably fatal and largely resistant to current chemotherapy regimens. Senolysis, i. e. the selective elimination of senescent cells, and the targeting of cancer specific cellular metabolism are two novel treatment approaches that have proven to be effective for a variety of cancer types in pre-clinical studies. We now demonstrate that pharmacological depletion of arginine with pegylated recombinant human arginase 1 (PEG-rhARG1) induced senescence and activated the integrated stress response (IRS) in PDAC cells. Cells treated in such a manner were strikingly susceptible towards senolysis with ABT-263 (navitoclax) and also sensitive towards inhibition of the IRS. These results demonstrate a novel mechanism for an induced sensitivity of PDAC cells that could be exploited for cancer therapy.

cancer biology↗

bioRxiv2025

An immunobiliary single-cell atlas resolves crosstalk of type 2 cDCs and γδT cells in cholangitis

Background and aimsThe immunobiliary niche serves as a reservoir of tissue-resident immune cells, yet the role of unconventional T cells during cholangitis remains poorly understood. Here, we connect cell state dynamics of type 2 conventional dendritic cells (cDC2) in cholangitis with site-specific{gamma}{delta} T17 responses in liver and draining lymph nodes (LN). MethodsThe 0.1% Diethoxycarbonyl-1,4-Dihydrocollidine (DDC) diet was used to generate an immunobiliary DC- and{gamma}{delta} T-enriched mouse liver and LN single-cell RNA-sequencing (scRNA-seq) atlas covering temporal disease dynamics, resolution and cDC2B depletion. cDC2 trajectories were inferred using VarID2 and{gamma}{delta} T cell transcription factor (TF) regulon activity was predicted by SCENIC. The human biliary niche was resolved by integrating human liver scRNA-seq data with available spatial transcriptomics data. Functional studies were conducted using Tcrd knockout, Il17a/f knockout and Tcrd reporter mice. ResultsA disease trajectory of Mgl2+ cDC2B was identified connecting DC maturation, homing and the expression of Il17-inducing genes. Disease progression was associated with numeric exhaustion of mature cDC2B and recruitment of DC precursors.{gamma}{delta} T cells were the main Il17 producers and were subtyped into Il17ahigh Scart1+ V{gamma}6+ and Il17low Scart2+ V{gamma}4+ populations exhibiting cDC2-directed communication and divergent TF regulon activity. Spatial proximity and conserved molecular interactions of cDC2 and{gamma}{delta} T cells were confirmed in human cholangitis. Il17-deficiency resulted in reduced liver fibrosis in mice, while cDC2B depletion attenuated{gamma}{delta} T17 cell states. ConclusionsIn cholangitis, a profibrogenic function of{gamma}{delta} T cells is contingent on the induction by peribiliary cDC2B, thereby highlighting relevant disease determinants within the immunobiliary and liver-draining LN niche. Impact and ImplicationsThe immunobiliary niche contains rare immune cells such as conventional dendritic cells and unconventional T cells, however, the function of these cell types in liver inflammation remains poorly understood. Mirroring human biliary diseases such as primary sclerosing cholangitis, we induced experimental cholangitis in a mouse model to generate a site-specific single-cell sequencing atlas resource resolving underexplored cell populations. Our data capture a profibrotic hepatic disease state trajectory of Mgl2+ cDC2B inducing a{gamma}{delta} T cell-specific Il17-response, which is attenuated upon cDC2B depletion and in DC precursors, which are characterized by reduced genomic accessibility of{gamma}{delta} T cell-interacting genes. These results highlight the importance of portal niche residing underexplored immune cell populations and the necessity to further resolve immunobiliary niche responses and crosstalk in inflammatory settings such as in cholangitis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/664083v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d21193org.highwire.dtl.DTLVardef@7ff3dcorg.highwire.dtl.DTLVardef@630c78org.highwire.dtl.DTLVardef@c79f9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Transient YAP/TAZ inhibition exposes therapeutic vulnerabilities in advanced cancers

YAP and TAZ, key effectors of the Hippo pathway, are frequently hyperactivated in cancer, where they drive tumor progression and resistance to therapy. Their oncogenic activity relies on interaction with TEAD transcription factors, making the TEAD-YAP/TAZ complex an attractive therapeutic target. Using translational mouse models, we demonstrate that sustained systemic YAP/TAZ depletion leads to severe side effects. However, even transient YAP/TAZ inhibition alone is sufficient to suppress tumor growth in advanced stages. Mechanistically, YAP/TAZ activity promotes T cell exclusion from the tumors by inducing target genes involved in tissue remodeling. Consequentially, YAP/TAZ inhibition induces immune infiltration, but the infiltrating T cells rapidly become exhausted. Combining YAP/TAZ inhibition with immune checkpoint blockade (ICB) overcomes this exhaustion and sensitizes previously resistant tumors to immunotherapy.

cancer biology↗

bioRxiv2024

Towards routine proteome profiling of FFPE tissue: Insights from a 1,200 case pan-cancer study

Proteome profiling of formalin-fixed paraffin-embedded (FFPE) specimens has gained traction for the analysis of cancer tissue for the discovery of molecular biomarkers. However, reports so far focused on single cancer entities, comprised relatively few cases and did not assess the long-term performance of experimental workflows. Here, we did so by analyzing 1,220 tumors from six cancer entities processed over the course of three years. Key findings include the need for a new normalization method ensuring equal and reproducible sample loading for LC-MS/MS analysis across cohorts, showing that tumors can, on average, be profiled to a depth of >4,000 proteins and discovering that current software fails to process such large data sets. We report the first comprehensive pan-cancer proteome expression resource for FFPE material comprising 11,000 proteins which is of immediate utility to the scientific community by way of a web resource. It enables a range of analysis including quantitative comparisons of proteins between patients or cohorts or the discovery of protein fingerprints representing the tissue of origin, or proteins enriched in certain cancer entities.

pathology↗

bioRxiv2023

Proteomic profiling identifies Serpin B9 as mediator of resistance to CAR T-cell and bispecific antibody treatment in B-cell lymphoma

Although T-cell-engaging therapies are highly effective in patients with relapsed and/or refractory B-cell non-Hodgkin lymphoma (B-NHL), responses are often not durable. To identify tumor-intrinsic drivers of resistance, we quantified in-vitro response to CD19-directed chimeric antigen receptor T-cells (CD19-CAR) and bispecific antibodies (BsAb) across 46 B-NHL cell lines and measured their proteomic profiles at baseline. Among the proteins associated with poor in-vitro response was Serpin B9, an endogenous granzyme B inhibitor. Knock-out of SERPINB9 in cell lines with high intrinsic expression rendered them more susceptible to CD19-CAR and CD19-BsAb. Overexpression in cell lines with low intrinsic expression attenuated responses. Polatuzumab, vorinostat, lenalidomide, or checkpoint inhibitors improved response to CD19-CAR, although independently of Serpin B9 expression. Besides providing an important resource of therapy response and proteomic profiles, this study refines our understanding of resistance in T-cell engaging therapies, and suggests clinically relevant combination regimes.

cancer biology↗

bioRxiv2022

A new type of transcriptional reprogramming by an IRF4 mutation in lymphoma

SUMMARY PARAGRAPHDisease-causing mutations in genes encoding transcription factors (TFs) are a recurrent finding in hematopoietic malignancies and might involve key regulators of lineage adherence and cellular differentiation1-3. Such mutations can affect TF-interactions with their cognate DNA-binding motifs4, 5. Whether and how TF-mutations impact upon the nature of binding to TF composite elements (CE) and influence their interaction with other TFs is unclear. Here, we report a new mechanism of TF alteration in human lymphomas with perturbed B cell identity. It is caused by a recurrent somatic missense mutation c.295T>C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cell-differentiation and -activation6, 7. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF composite elements (CEs). Furthermore, IRF4-C99R thoroughly modifies IRF4 function, by blocking IRF4-dependent plasma cell induction, and up-regulating disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single arginine mutation creates a complex switch of TF specificity and gene regulation. These data open the possibility of designing specific inhibitors to block the neomorphic, disease-causing DNA-binding activities of a mutant transcription factor.

cancer biology↗

bioRxiv2022

T cell landscape definition by multi-omics identifies Galectin-9 as novel immunotherapy target in chronic lymphocytic leukemia

Failure of cancer immunotherapy is linked to T cell exhaustion. To decipher the underlying mechanisms, we explored the T cell landscape in blood, bone marrow and lymph node samples of patients with chronic lymphocytic leukemia (CLL), and spleen samples of a CLL mouse model. By single-cell RNA-sequencing, mass cytometry (CyTOF), and multiplex image analysis of tissue microarrays, we identified a disease-specific accumulation of distinct regulatory T cell subsets and T cell exhaustion stages and their trajectories in CLL lymph nodes. Integration of T cell receptor sequencing data revealed a clonal expansion of CD8+ precursor exhausted T cells (TPEX), suggesting their CLL reactivity. Interactome analyses identified the TIM3 ligand Galectin-9 as a novel immunoregulatory molecule in CLL. Blocking of Galectin-9 in CLL-bearing mice slowed down disease development and reduced the number of TIM3-expressing T cells. Galectin-9 expression correlated with shorter survival of patients with CLL, renal cell carcinoma or glioma. Statement of significanceOur findings for the first time define the T cell landscape in CLL lymph nodes and reshape the current understanding of T cell exhaustion in this malignancy. They further introduce Galectin-9 as novel immune checkpoint with a high potential to overcome resistance to PD1 targeting drugs in CLL and beyond.

cancer biology↗

bioRxiv2021

Preclinical models of human multiple myeloma subgroups

Multiple myeloma (MM), a tumor of germinal center (GC)-experienced plasma cells, comprises distinct genetic subgroups, such as the t(11;14)/CCND1 and the t(4;14)/MMSET subtype. We have generated subgroup-specific MM models by the GC B cell-specific co-activation of Ccnd1 or MMSET with a constitutively active Ikk2 mutant, mimicking the secondary NF{kappa}B activation frequently seen in human MM. Ccnd1/Ikk2ca and MMSET/Ikk2ca mice developed a pronounced, clonally restricted plasma cell outgrowth with age, accompanied by serum M spikes, bone marrow insufficiency and bone lesions. The transgenic plasma cells could be propagated in vivo and showed transcriptional profiles resembling their human counterparts. Thus, we show that Ccnd1 and MMSET cooperate with NF{kappa}B in MM pathogenesis, considering for the first time the genetic heterogeneity of MM for the generation of preclinical models.

cancer biology↗

bioRxiv2021

NOTCH1 drives immune-escape mechanisms in B cell malignancies

NOTCH1 is a recurrently mutated gene in Chronic Lymphocytic Leukemia (CLL) and Mantle Cell Lymphoma (MCL). Functional studies to investigate its role have been hampered by the inability to genetically manipulate primary human lymphoma cells, attributed to low transduction-efficacy and procedure-associated toxicity. To overcome these limitations, we have developed a novel method to retrovirally transfer genes into malignant human B cells. We generated isogenic human tumor cells from patients with CLL and MCL, differing only in their expression of NOTCH1. Our data demonstrate that NOTCH1 facilitates immune-escape of malignant B cells by up-regulating PD-L1, partly dependent on autocrine interferon-{gamma} signaling. In addition, NOTCH1 causes silencing of the entire HLA-class II locus via suppression of the transcriptional co-activator CIITA. These NOTCH1-mediated immune escape mechanisms are associated with the expansion of CD4+ T cells in vivo, further contributing to the poor clinical outcome of NOTCH1-mutated CLL and MCL.

cancer biology↗

bioRxiv2017

Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education

Bioinformatics, a discipline that combines aspects of biology, statistics, and computer science, is increasingly important for biological research. However, bioinformatics instruction is rarely integrated into life sciences curricula at the undergraduate level. To understand why, the Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE, \"nibbles\") recently undertook an extensive survey of life sciences faculty in the United States. The survey responses to open-ended questions about barriers to integration were subjected to keyword analysis. The barrier most frequently reported by the ~1,260 respondents was lack of faculty training. Faculty at associates-granting institutions report the least training in bioinformatics and the least integration of bioinformatics into their teaching. Faculty from underrepresented minority groups (URMs) in STEM reported training barriers at a higher rate than others, although the number of URM respondents was small. Interestingly, the cohort of faculty with the most recently awarded PhD degrees reported the most training but were teaching bioinformatics at a lower rate than faculty who earned their degrees in previous decades. Other barriers reported included lack of student interest in bioinformatics; lack of student preparation in mathematics, statistics, and computer science; already overly full curricula; and limited access to resources, including hardware, software, and vetted teaching materials. The results of the survey, the largest to date on bioinformatics education, will guide efforts to further integrate bioinformatics instruction into undergraduate life sciences education.

scientific communication and education↗

bioRxiv2017

DNA copy number gains of TCF4 (E2-2) are associated with poor outcome and the activated B-cell-like subtype of diffuse large B-cell lymphoma

The activated B-cell (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) is characterized by the chronic activation of signaling initiated by immunoglobulin- (IgM). By analyzing DNA copy profiles of 1,000 DLBCLs, we identified gains of 18q21.2 as the most frequent genetic alteration in ABC-like DLBCL. We show that these alterations target the TCF4 (E2-2) transcription factor, and that over-expression of TCF4 leads to its occupancy on immunoglobulin gene enhancers and increased expression of IgM at the transcript and protein level. The TCF4 gene is one of the top BRD4-regulated genes in DLBCL. Using a BET proteolysis-targeting chimera (PROTAC) we show that TCF4 and IgM expression can be extinguished, and ABC-like DLBCL cells can be killed in vitro and in vivo. This highlights a novel genetic mechanism for promoting immunoglobulin signaling in ABC-like DLBCL and provides a functional rationale for the use of BET inhibitors in this disease.

genomics↗