Images in Immunotherapy and Precision Oncology: A Case Report of Neurofibromatosis-1.

Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disorder that primarily causes the growth of tumors along nerves. Additionally, the germline mutations involved in NF1 predispose patients to develop further malignancies. The mainstay initial treatment for these malignancies is surgical removal at diagnosis, although targeted therapies are under evaluation in the relapsed setting. We report a case of malignant peripheral nerve sheath tumor (MPNST), gastrointestinal stromal tumor (GIST), and pheochromocytoma in a patient with NF1 who presented with an infected right shoulder lesion that was confirmed to be spindle cell sarcoma via biopsy. She was treated with antibiotics; however, she rapidly deteriorated and opted for hospice care. NF1 germline mutations increase the risk of patients developing various types of cancer. Recent studies have shown that there is a role for using MEK inhibitors such as selumetinib for treating patients with NF1.

Navigating between Scylla and Charybdis: A roadmap to do better than Pola-RCHP in DLBCL.

In treating diffuse large B-cell lymphoma (DLBCL), oncologists have traditionally relied on the chemotherapy backbone of R-CHOP as standard of care. The two dangers that the hematologist must navigate between are the aggressive disease (Charybdis that in the absence of therapy systematically destroys all the ships) and the toxicity of the therapies (Scylla with its six monstrous heads that devours six crew members at a time), and hematologists have to navigate very carefully between both. Therefore, three different strategies were employed with the goal of improving cure rates: de-escalating regimens, escalating regimens, and replacement strategies. With a replacement strategy, a breakthrough in treatment was identified with polatuzumab vedotin (anti-CD79B antibody/drug conjugate) plus R-CHP. However, this regimen still did not achieve the elusive universal cure rate. Fortunately, advances in genomic and molecular technologies have allowed for an improved understanding of the heterogenous molecular nature of the disease to help develop and guide more targeted, precise, and individualized therapies. Additionally, new pharmaceutical technologies have led to the development of novel cellular therapies, such as chimeric antigen receptor (CAR) T-cell therapy, that could be more effective, while maintaining an acceptable safety profile. Thus, we aim to highlight the challenges of DLBCL therapy as well as the need to address therapeutic regimens eventually no longer tethered to a chemotherapy backbone. In the intersection of artificial intelligence and multi-omics (genomics, epigenomics, transcriptomics, proteomics, metabolomics), we propose the need to analyze multidimensional biologic datato launch a decisive attack against DLBCL in a targeted and individualized fashion.

Transcriptional control of leukemogenesis by the chromatin reader SGF29.

ABSTRACT: Aberrant expression of stem cell-associated genes is a common feature in acute myeloid leukemia (AML) and is linked to leukemic self-renewal and therapy resistance. Using AF10-rearranged leukemia as a prototypical example of the recurrently activated "stemness" network in AML, we screened for chromatin regulators that sustain its expression. We deployed a CRISPR-Cas9 screen with a bespoke domain-focused library and identified several novel chromatin-modifying complexes as regulators of the TALE domain transcription factor MEIS1, a key leukemia stem cell (LSC)-associated gene. CRISPR droplet sequencing revealed that many of these MEIS1 regulators coordinately controlled the transcription of several AML oncogenes. In particular, we identified a novel role for the Tudor-domain-containing chromatin reader protein SGF29 in the transcription of AML oncogenes. Furthermore, SGF29 deletion impaired leukemogenesis in models representative of multiple AML subtypes in multiple AML subtype models. Our studies reveal a novel role for SGF29 as a nononcogenic dependency in AML and identify the SGF29 Tudor domain as an attractive target for drug discovery.

Images in Immunotherapy and Precision Oncology: Angiosarcoma of the Spleen and Liver.

Primary splenic or hepatic angiosarcomas are ultra-rare and aggressive malignancies associated with poor prognosis. The mainstay treatments are surgical resection and chemotherapy. We report a case of angiosarcoma in a 50-year-old woman who presented with bruising, fatigue, ecchymosis, and hepatosplenomegaly. She was treated with the multi-kinase inhibitor sunitinib for 4 weeks before developing a splenic hemorrhage and succumbing. Recent studies have demonstrated the clinical benefit of immunotherapies in angiosarcomas. Additionally, sequencing techniques have showcased the diverse molecular aberrations involved in angiosarcomas, which offer opportunities for precision-matched targeted therapies such as inhibitors of the VEGF/VEGFR axis and PI3K/Akt/mTor pathway.

Examining the relationship between severe persistent mental illness and surgical outcomes in women undergoing mastectomy for breast cancer.

BACKGROUND: Severe persistent mental illness (SPMI) is associated with worse outcomes in cancer patients. Less is known about the relationship between SPMI and surgical outcomes after mastectomy for breast cancer. METHODS: We selected patients with breast cancer and SPMI from the National Inpatient Sample (2016-2018) and used propensity score matching. We then used multivariate analysis, Kruskal-Wallis tests, and conditional logistic regression to compare demographics and outcomes. RESULTS: The study sample consisted of 670 patients: 536 without SPMI and 134 with SPMI. SPMI was associated with bilateral mastectomy (bilateral: 53% vs. unilateral: 42.7%, p = 0.033) and decreased frequency of breast reconstruction (p < 0.001). SPMI was associated with more extended hospitalization (4 days vs. 2 days, p < 0.001) and increased risk of developing post-procedural infection and sepsis (OR 2.909). CONCLUSIONS: SPMI is associated with bilateral mastectomy, more extended hospitalization, and increased risk for post-procedural infection and sepsis - suggesting the need for increased use of standardized screening tools to identify SPMI in patients and inform perioperative management correctly.

Detection of TP53 Mutation in Acute Myeloid Leukemia by RT-PCR-Based Sanger Sequencing.

The TP53 gene is known to be one of the most frequently mutated genes in various human cancers. In de novo acute myeloid leukemia (AML), TP53 has been found to be mutated in ~10% of patients. Although the frequency of TP53 mutations in AML is substantially lower compared to other human cancers, TP53 mutations in AML are associated with poor response to chemotherapy and poor outcomes. Therefore, assessment of TP53 status is critical in clinical routines and research studies. In this chapter, we described the use of conventional RT-PCR for rapid detection of TP53 mutations by Sanger sequencing. We use AML cells as an example but provide sufficient details for usage in other cell types.

Analysis of Gender-Based Authorship Trends in Leading Pain-Medicine Journals Over 10 Years.

Authorship of peer-reviewed publications is important for academic rank, promotion, and national reputation. In pain medicine, limited information is available for authorship trends for women as compared with men. The objective of this study was to describe trends of female authorship data in the 5 pain journals with the highest impact factors over a 10-year period. We analyzed data for January, April, and October in 2009, 2014, and 2019. For each article, the following information was recorded: journal name, journal month, journal year, article title or article PMCID, total authors, total female authors, total male authors, total authors of unknown gender, presence or absence of a female first author, and presence or absence of a female last/senior author. Authorship for 924 articles was reviewed. When a man was senior author, women were first author on only 27.9% of articles (P<.001). A woman was 2 times as likely (57.2%) to be first author when a woman was the senior author (P<.001), pointing to the potential impact of female senior authors. An article with 50% or more female authors was 76.4% more likely to have a female senior author (P<.001). The results demonstrate the influence of a senior female author on the likelihood of an article's having a female first author. When men were the senior authors, women were half as likely to be first authors. The total number of female authors changed very little between 2009 and 2019.

Targeted and cellular therapies in lymphoma: Mechanisms of escape and innovative strategies.

The therapeutic landscape for lymphomas is quite diverse and includes active surveillance, chemotherapy, immunotherapy, radiation therapy, and even stem cell transplant. Advances in the field have led to the development of targeted therapies, agents that specifically act against a specific component within the critical molecular pathway involved in tumorigenesis. There are currently numerous targeted therapies that are currently Food and Drug Administration (FDA) approved to treat certain lymphoproliferative disorders. Of many, some of the targeted agents include rituximab, brentuximab vedotin, polatuzumab vedotin, nivolumab, pembrolizumab, mogamulizumab, vemurafenib, crizotinib, ibrutinib, cerdulatinib, idelalisib, copanlisib, venetoclax, tazemetostat, and chimeric antigen receptor (CAR) T-cells. Although these agents have shown strong efficacy in treating lymphoproliferative disorders, the complex biology of the tumors have allowed for the malignant cells to develop various mechanisms of resistance to the targeted therapies. Some of the mechanisms of resistance include downregulation of the target, antigen escape, increased PD-L1 expression and T-cell exhaustion, mutations altering the signaling pathway, and agent binding site mutations. In this manuscript, we discuss and highlight the mechanism of action of the above listed agents as well as the different mechanisms of resistance to these agents as seen in lymphoproliferative disorders.

Brexucabtagene autoleucel: a breakthrough in the treatment of mantle cell lymphoma.

In July 2020, the U.S. Food and Drug Administration (FDA) approved brexucabtagene autoleucel (BA), the first anti-CD19 chimeric antigen receptor (CAR) T-cell therapy for the treatment of relapsed/refractory mantle cell lymphoma (MCL). The pivotal ZUMA-2 trial led to the approval of BA in patients who experienced relapsed disease on prior therapies (chemotherapy and/or Bruton tyrosine kinase [BTK] inhibitors). The FDA approval of BA was based on excellent responses with this therapy in highly refractory patients with MCL, who conventionally had poor outcomes. Longer follow-up data from the ZUMA-2 study have been presented at recent international meetings. As is common with other CAR T-cell therapies in lymphomas, the main toxicities of BA therapy included cytokine release syndrome (CRS), infections, cytopenias and CAR-associated neurotoxicity. In this review, we provide a summary of the data in the development of BA and its impact on MCL patient survival and future directions.

Zanubrutinib in Treating Waldenström Macroglobulinemia, the Last Shall Be the First.

In Waldenström macroglobulinemia (WM), a lymphoplasmacytic lymphoma characterized by monoclonal immunoglobulin M (IgM) gammopathy, aberrant Bruton tyrosine kinase (BTK) signaling has been identified as one mechanism of pathogenesis. For this reason, selective BTK inhibiting therapies have emerged as an attractive option for treatment within the therapeutic landscape also comprising chemotherapy, monoclonal antibodies, proteasome inhibitors, and B-cell lymphoma 2 (BCL2) inhibitors. The first BTK inhibiting therapy, ibrutinib, showed great efficacy in treating WM. However, response rates were dependent on whether patients had the CXCR4 mutation, a molecular aberration that may confer resistance to BTK inhibitors. Furthermore, ibrutinib's toxicities, most notably hypertension and atrial arrhythmia, led to dose reductions or discontinuation. The toxicity profile of ibrutinib can be attributed to the inhibition of additional kinases that are structurally related to BTK. Therefore, the next-generation highly selective zanubrutinib was developed to address the concerns regarding toxicity and tolerance related to ibrutinib therapy. Based on the results of the randomized, open-label Phase 3 ASPEN (NCT03053440) trial, the Food and Drug Administration (FDA) approved zanubrutinib for treating WM. This trial directly compared zanubrutinib to ibrutinib in patients with treatment-naïve or relapsed/refractory WM, and the results showed stronger responses with zanubrutinib. More importantly, patients responded strongly to zanubrutinib therapy regardless of CXCR4 mutation status. Additionally, zanubrutinib was associated with fewer grade 3 or higher toxicities and was generally better tolerated. Another Phase 1/2 study has been conducted with just zanubrutinib in WM showcasing high efficacy with few toxicities as well. Even though zanubrutinib has been the third and last BTK inhibitor to currently penetrate the market for B-cell lymphoproliferative malignancies, we highlight the emergence of zanubrutinib as a key player in the forefront of the therapeutic landscape in WM.

Radiation and Chimeric Antigen Receptor T-cell Therapy in B-cell Non-Hodgkin Lymphomas.

OPINION STATEMENT: Chimeric antigen receptor T-cell therapy (CAR-T) is a revolutionary advancement in the management of chemotherapy refractory B-cell non-Hodgkin lymphomas representing a potentially curative therapy in scenarios that were previously only palliative. CAR-T cell therapy is associated with unique toxicities as well as practical challenges. One of those challenges is how to manage active lymphoma during the weeks-long CAR-T manufacturing process. Radiation therapy, steroids, and systemic therapy have all been used for what would be considered "bridging therapy" during this time frame. Radiation therapy is a particularly attractive strategy given its proven efficacy in chemotherapy refractory lymphomas; ability to stabilize patients, debulk disease, and palliate symptoms; as well as its potential to enhance the expansion and activity of CAR-T cells. Optimal dose, timing, and method of delivery are yet to be established though there is consensus that it should occur after apheresis if being used as a pre-treatment bridge. Another practical challenge is the management of patients in whom CAR-T cells fail. There is a potential emerging role for salvage radiation therapy, in select patients, for either palliation or as a means to get patients another potentially curative therapy. Collaborative well-designed prospective clinical trials are needed to definitively establish the role for radiation therapy (before or after CAR-T therapy) as well as define the impact on CAR-T cell activity/persistence and associated toxicity.

A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing.

Recent studies have reported that genome editing by CRISPR-Cas9 induces a DNA damage response mediated by p53 in primary cells hampering their growth. This could lead to a selection of cells with pre-existing p53 mutations. In this study, employing an integrated computational and experimental framework, we systematically investigated the possibility of selection of additional cancer driver mutations during CRISPR-Cas9 gene editing. We first confirm the previous findings of the selection for pre-existing p53 mutations by CRISPR-Cas9. We next demonstrate that similar to p53, wildtype KRAS may also hamper the growth of Cas9-edited cells, potentially conferring a selective advantage to pre-existing KRAS-mutant cells. These selective effects are widespread, extending across cell-types and methods of CRISPR-Cas9 delivery and the strength of selection depends on the sgRNA sequence and the gene being edited. The selection for pre-existing p53 or KRAS mutations may confound CRISPR-Cas9 screens in cancer cells and more importantly, calls for monitoring patients undergoing CRISPR-Cas9-based editing for clinical therapeutics for pre-existing p53 and KRAS mutations.

The ubiquitin ligase RNF5 determines acute myeloid leukemia growth and susceptibility to histone deacetylase inhibitors.

Acute myeloid leukemia (AML) remains incurable, largely due to its resistance to conventional treatments. Here, we find that increased abundance of the ubiquitin ligase RNF5 contributes to AML development and survival. High RNF5 expression in AML patient specimens correlates with poor prognosis. RNF5 inhibition decreases AML cell growth in culture, in patient-derived xenograft (PDX) samples and in vivo, and delays development of MLL-AF9-driven leukemogenesis in mice, prolonging their survival. RNF5 inhibition causes transcriptional changes that overlap with those seen upon histone deacetylase (HDAC)1 inhibition. RNF5 induces the formation of K29 ubiquitin chains on the histone-binding protein RBBP4, promoting its recruitment to and subsequent epigenetic regulation of genes involved in AML maintenance. Correspondingly, RNF5 or RBBP4 knockdown enhances AML cell sensitivity to HDAC inhibitors. Notably, low expression of both RNF5 and HDAC coincides with a favorable prognosis. Our studies identify an ERAD-independent role for RNF5, demonstrating that its control of RBBP4 constitutes an epigenetic pathway that drives AML, and highlight RNF5/RBBP4 as markers useful to stratify patients for treatment with HDAC inhibitors.

The role of the PZP domain of AF10 in acute leukemia driven by AF10 translocations.

Chromosomal translocations of the AF10 (or MLLT10) gene are frequently found in acute leukemias. Here, we show that the PZP domain of AF10 (AF10PZP), which is consistently impaired or deleted in leukemogenic AF10 translocations, plays a critical role in blocking malignant transformation. Incorporation of functional AF10PZP into the leukemogenic CALM-AF10 fusion prevents the transforming activity of the fusion in bone marrow-derived hematopoietic stem and progenitor cells in vitro and in vivo and abrogates CALM-AF10-mediated leukemogenesis in vivo. Crystallographic, biochemical and mutagenesis studies reveal that AF10PZP binds to the nucleosome core particle through multivalent contacts with the histone H3 tail and DNA and associates with chromatin in cells, colocalizing with active methylation marks and discriminating against the repressive H3K27me3 mark. AF10PZP promotes nuclear localization of CALM-AF10 and is required for association with chromatin. Our data indicate that the disruption of AF10PZP function in the CALM-AF10 fusion directly leads to transformation, whereas the inclusion of AF10PZP downregulates Hoxa genes and reverses cellular transformation. Our findings highlight the molecular mechanism by which AF10 targets chromatin and suggest a model for the AF10PZP-dependent CALM-AF10-mediated leukemogenesis.

A JAK/STAT-mediated inflammatory signaling cascade drives oncogenesis in AF10-rearranged AML.

Leukemias bearing fusions of the AF10/MLLT10 gene are associated with poor prognosis, and therapies targeting these fusion proteins (FPs) are lacking. To understand mechanisms underlying AF10 fusion-mediated leukemogenesis, we generated inducible mouse models of acute myeloid leukemia (AML) driven by the most common AF10 FPs, PICALM/CALM-AF10 and KMT2A/MLL-AF10, and performed comprehensive characterization of the disease using transcriptomic, epigenomic, proteomic, and functional genomic approaches. Our studies provide a detailed map of gene networks and protein interactors associated with key AF10 fusions involved in leukemia. Specifically, we report that AF10 fusions activate a cascade of JAK/STAT-mediated inflammatory signaling through direct recruitment of JAK1 kinase. Inhibition of the JAK/STAT signaling by genetic Jak1 deletion or through pharmacological JAK/STAT inhibition elicited potent antioncogenic effects in mouse and human models of AF10 fusion AML. Collectively, our study identifies JAK1 as a tractable therapeutic target in AF10-rearranged leukemias.

PopInf: An Approach for Reproducibly Visualizing and Assigning Population Affiliation in Genomic Samples of Uncertain Origin.

Germline genetic variation contributes to cancer etiology, but self-reported race is not always consistent with genetic ancestry, and samples may not have identifying ancestry information. In this study, we describe a flexible computational pipeline, PopInf, to visualize principal component analysis output and assign ancestry to samples with unknown genetic ancestry, given a reference population panel of known origins. PopInf is implemented as a reproducible workflow in Snakemake with a tutorial on GitHub. We provide a preprocessed reference population panel that can be quickly and efficiently implemented in cancer genetics studies. We ran PopInf on The Cancer Genome Atlas (TCGA) liver cancer data and identify discrepancies between reported race and inferred genetic ancestry. The PopInf pipeline facilitates visualization and identification of genetic ancestry across samples, so that this ancestry can be accounted for in studies of disease risk.

A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma.

Drug resistance and relapse remain key challenges in pancreatic cancer. Here, we have used RNA sequencing (RNA-seq), chromatin immunoprecipitation (ChIP)-seq, and genome-wide CRISPR analysis to map the molecular dependencies of pancreatic cancer stem cells, highly therapy-resistant cells that preferentially drive tumorigenesis and progression. This integrated genomic approach revealed an unexpected utilization of immuno-regulatory signals by pancreatic cancer epithelial cells. In particular, the nuclear hormone receptor retinoic-acid-receptor-related orphan receptor gamma (RORγ), known to drive inflammation and T cell differentiation, was upregulated during pancreatic cancer progression, and its genetic or pharmacologic inhibition led to a striking defect in pancreatic cancer growth and a marked improvement in survival. Further, a large-scale retrospective analysis in patients revealed that RORγ expression may predict pancreatic cancer aggressiveness, as it positively correlated with advanced disease and metastasis. Collectively, these data identify an orthogonal co-option of immuno-regulatory signals by pancreatic cancer stem cells, suggesting that autoimmune drugs should be evaluated as novel treatment strategies for pancreatic cancer patients.

Acute myeloid leukemia driven by the CALM-AF10 fusion gene is dependent on BMI1.

A subset of acute myeloid and lymphoid leukemia cases harbor a t(10;11)(p13;q14) translocation resulting in the CALM-AF10 fusion gene. Standard chemotherapeutic strategies are often ineffective in treating patients with CALM-AF10 fusions. Hence, there is an urgent need to identify molecular pathways dysregulated in CALM-AF10-positive leukemias which may lay the foundation for novel targeted therapies. Here we demonstrate that the Polycomb Repressive Complex 1 gene BMI1 is consistently overexpressed in adult and pediatric CALM-AF10-positive leukemias. We demonstrate that genetic Bmi1 depletion abrogates CALM-AF10-mediated transformation of murine hematopoietic stem and progenitor cells (HSPCs). Furthermore, CALM-AF10-positive murine and human AML cells are sensitive to the small-molecule BMI1 inhibitor PTC-209 as well as to PTC-596, a compound in clinical development that has been shown to result in downstream degradation of BMI1 protein. PTC-596 significantly prolongs survival of mice injected with a human CALM-AF10 cell line in a xenograft assay. In summary, these results validate BMI1 as a bona fide candidate for therapeutic targeting in AML with CALM-AF10 rearrangements.

Investigation of Genetic Dependencies Using CRISPR-Cas9-based Competition Assays.

Gene perturbation studies have been extensively used to investigate the role of individual genes in AML pathogenesis. For achieving complete gene disruption, many of these studies have made use of complex gene knockout models. While these studies with knockout mice offer an elegant and time-tested system for investigating genotype-to-phenotype relationships, a rapid and scalable method for assessing candidate genes that play a role in AML cell proliferation or survival in AML models will help accelerate the parallel interrogation of multiple candidate genes. Recent advances in genome-editing technologies have dramatically enhanced our ability to perform genetic perturbations at an unprecedented scale. One such system of genome editing is the CRISPR-Cas9-based method that can be used to make rapid and efficacious alterations in the target cell genome. The ease and scalability of CRISPR/Cas9-mediated gene-deletion makes it one of the most attractive techniques for the interrogation of a large number of genes in phenotypic assays. Here, we present a simple assay using CRISPR/Cas9 mediated gene-disruption combined with high-throughput flow-cytometry-based competition assays to investigate the role of genes that may play an important role in the proliferation or survival of human and murine AML cell lines.