Molecular and Clinical Determinants of Acquired Resistance and Treatment Duration for Targeted Therapies in Colorectal Cancer

PURPOSE

Targeted therapies have improved outcomes for patients with metastatic colorectal cancer, but their impact is limited by rapid emergence of resistance. We hypothesized that an understanding of the underlying genetic mechanisms and intrinsic tumor features that mediate resistance to therapy will guide new therapeutic strategies and ultimately allow the prevention of resistance.

EXPERIMENTAL DESIGN

We assembled a series of 52 patients with paired pre-treatment and progression samples who received therapy targeting EGFR (n=17), BRAF V600E (n=17), KRAS G12C (n=15), or amplified HER2 (n=3) to identify molecular and clinical factors associated with time on treatment (TOT).

RESULTS

All patients stopped treatment for progression and TOT did not vary by oncogenic driver (p=0.5). Baseline disease burden (≥3 versus <3 sites, p=0.02), the presence of hepatic metastases (p=0.02), and gene amplification on baseline tissue (p=0.03) were each associated with shorter TOT. We found evidence of chromosomal instability (CIN) at progression in patients with baseline MAPK pathway amplifications and those with acquired gene amplifications. At resistance, copy number changes (p=0.008) and high number (≥5) of acquired alterations (p=0.04) were associated with shorter TOT. Patients with hepatic metastases demonstrated both higher number of emergent alterations at resistance and enrichment of mutations involving receptor tyrosine kinases.

CONCLUSIONS

Our genomic analysis suggests that high baseline CIN or effective induction of enhanced mutagenesis on targeted therapy underlies rapid progression. Longer response appears to result from a progressive acquisition of genomic or chromosomal instability in the underlying cancer or from the chance event of a new resistance alteration.

Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation

Liver metastasis (LM) confers poor survival and therapy resistance across cancer types, but the mechanisms of liver-metastatic organotropism remain unknown. Here, through in vivo CRISPR-Cas9 screens, we found that Pip4k2c loss conferred LM but had no impact on lung metastasis or primary tumor growth. Pip4k2c-deficient cells were hypersensitized to insulin-mediated PI3K/AKT signaling and exploited the insulin-rich liver milieu for organ-specific metastasis. We observed concordant changes in PIP4K2C expression and distinct metabolic changes in 3,511 patient melanomas, including primary tumors, LMs and lung metastases. We found that systemic PI3K inhibition exacerbated LM burden in mice injected with Pip4k2c-deficient cancer cells through host-mediated increase in hepatic insulin levels; however, this circuit could be broken by concurrent administration of an SGLT2 inhibitor or feeding of a ketogenic diet. Thus, this work demonstrates a rare example of metastatic organotropism through co-optation of physiological metabolic cues and proposes therapeutic avenues to counteract these mechanisms.

Intratumoral TREX1 induction promotes immune evasion by limiting type I interferon

Chromosomal instability is a hallmark of human cancer that is associated with aggressive disease characteristics. Chromosome mis-segregations help fuel natural selection, but they risk provoking a cGAS-STING immune response through the accumulation of cytosolic DNA. The mechanisms of how tumors benefit from chromosomal instability while mitigating associated risks, such as enhanced immune surveillance, are poorly understood. Here, we identify cGAS-STING-dependent upregulation of the nuclease TREX1 as an adaptive, negative feedback mechanism that promotes immune evasion through digestion of cytosolic DNA. TREX1 loss diminishes tumor growth, prolongs survival of host animals, increases tumor immune infiltration, and potentiates response to immune checkpoint blockade selectively in tumors capable of mounting a type I interferon response downstream of STING. Together, these data demonstrate that TREX1 induction shields chromosomally unstable tumors from immune surveillance by dampening type I interferon production and suggest that TREX1 inhibitors might be used to selectively target tumors that have retained the inherent ability to mount an interferon response downstream of STING.

Micronuclei and Cancer

Chromosome-containing micronuclei are a feature of human cancer. Micronuclei arise from chromosome mis-segregation and characterize tumors with elevated rates of chromosomal instability. Although their association with cancer has been long recognized, only recently have we broadened our understanding of the mechanisms that govern micronuclei formation and their role in tumor progression. In this review, we provide a brief historical account of micronuclei, depict the mechanisms underpinning their creation, and illuminate their capacity to propel tumor evolution through genetic, epigenetic, and transcriptional transformations. We also posit the prospect of leveraging micronuclei as biomarkers and therapeutic targets in chromosomally unstable cancers.

SIGNIFICANCE

Micronuclei in chromosomally unstable cancer cells serve as pivotal catalysts for cancer progression, instigating transformative genomic, epigenetic, and transcriptional alterations. This comprehensive review not only synthesizes our present comprehension but also outlines a framework for translating this knowledge into pioneering biomarkers and therapeutics, thereby illuminating novel paths for personalized cancer management.

The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance

In this study, the impact of the apolipoprotein B mRNA-editing catalytic subunit-like (APOBEC) enzyme APOBEC3B (A3B) on epidermal growth factor receptor (EGFR)-driven lung cancer was assessed. A3B expression in EGFR mutant (EGFRmut) non-small-cell lung cancer (NSCLC) mouse models constrained tumorigenesis, while A3B expression in tumors treated with EGFR-targeted cancer therapy was associated with treatment resistance. Analyses of human NSCLC models treated with EGFR-targeted therapy showed upregulation of A3B and revealed therapy-induced activation of nuclear factor kappa B (NF-κB) as an inducer of A3B expression. Significantly reduced viability was observed with A3B deficiency, and A3B was required for the enrichment of APOBEC mutation signatures, in targeted therapy-treated human NSCLC preclinical models. Upregulation of A3B was confirmed in patients with NSCLC treated with EGFR-targeted therapy. This study uncovers the multifaceted roles of A3B in NSCLC and identifies A3B as a potential target for more durable responses to targeted cancer therapy.

Risk of Radiation-Associated Secondary Malignancies among Patients with Breast Cancer Harboring TP53 Germline Variants

PURPOSE/OBJECTIVE(S)

Radiation-associated malignancies are rare and poorly understood. TP53 encodes a multifunctional protein that maintains genome integrity and is the most common somatically mutated gene in cancer. Germline pathogenic variants of TP53 predispose carriers to several cancers comprising the Li-Fraumeni syndrome. It is hypothesized that carriers are also at increased risk of radiotherapy (RT)-associated secondary malignancies; however, reports are mixed. We evaluated the risk of secondary malignancies after breast RT among patients with Li-Fraumeni syndrome.

MATERIALS/METHODS

This multi-institutional cohort study included carriers of TP53 germline variants who underwent surgical treatment for breast cancer between 1980 and 2020. Patients were stratified based on germline TP53 classification (pathogenic variants [PV] vs variants of uncertain significance [VUS]). The primary outcome of interest was the cumulative incidence risk of developing an in-field secondary cancer after radiotherapy for primary breast carcinoma.

RESULTS

Ninety-one patients (57 PV and 34 VUS) were evaluated with a median age of 36 years (interquartile range [IQR] 31, 42) and a median follow up of 7.9 years (IQR 4.7, 14.4). Among those with PV who received RT (n = 22), 4 secondary non-breast cancers developed in the radiation field (15-year cumulative incidence 19% [95% CI: 4-43%]), whereas, among those with PV who did not receive RT (n = 35), 0 secondary non-breast cancers were observed in the treated breast (15-year cumulative incidence 0%; p = 0.043). We observed 3 radiation-associated sarcomas among patients with PV who received RT (15-year risk 12% [95% CI 2-33%]) compared with 0 among those who did not receive RT (p = 0.08). No RT-associated sarcomas were observed among 18 patients with TP53 VUS who received RT. RT was not associated with overall survival, despite higher T and N breast cancer stage among those receiving RT (p = 0.33). As expected, patients with PV were more likely than those with VUS to develop any secondary cancer following breast cancer treatment (15-year risk: 54% [95% CI: 33-72%] vs. 14% [95% CI: 3-36%]).

CONCLUSION

Carriers of pathogenic variants of TP53 are at elevated risk of developing secondary malignancies after breast cancer treatment. This population is at particular risk of developing in-field secondary cancers following RT. This iatrogenic risk must be weighed against the anticipated therapeutic benefit of tumor control. Shared decision making is crucial in the radiotherapeutic management of breast cancer patients harboring the Li-Fraumeni syndrome.

Non-cell-autonomous cancer progression from chromosomal instability

Chromosomal instability (CIN) is a driver of cancer metastasis1-4, yet the extent to which this effect depends on the immune system remains unknown. Using ContactTracing-a newly developed, validated and benchmarked tool to infer the nature and conditional dependence of cell-cell interactions from single-cell transcriptomic data-we show that CIN-induced chronic activation of the cGAS-STING pathway promotes downstream signal re-wiring in cancer cells, leading to a pro-metastatic tumour microenvironment. This re-wiring is manifested by type I interferon tachyphylaxis selectively downstream of STING and a corresponding increase in cancer cell-derived endoplasmic reticulum (ER) stress response. Reversal of CIN, depletion of cancer cell STING or inhibition of ER stress response signalling abrogates CIN-dependent effects on the tumour microenvironment and suppresses metastasis in immune competent, but not severely immune compromised, settings. Treatment with STING inhibitors reduces CIN-driven metastasis in melanoma, breast and colorectal cancers in a manner dependent on tumour cell-intrinsic STING. Finally, we show that CIN and pervasive cGAS activation in micronuclei are associated with ER stress signalling, immune suppression and metastasis in human triple-negative breast cancer, highlighting a viable strategy to identify and therapeutically intervene in tumours spurred by CIN-induced inflammation.

The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity

The cell-autonomous balance of immune-inhibitory and -stimulatory signals is a critical process in cancer immune evasion. Using patient-derived co-cultures, humanized mouse models, and single-cell RNA-sequencing of patient melanomas biopsied before and on immune checkpoint blockade, we find that intact cancer cell-intrinsic expression of CD58 and ligation to CD2 is required for anti-tumor immunity and is predictive of treatment response. Defects in this axis promote immune evasion through diminished T cell activation, impaired intratumoral T cell infiltration and proliferation, and concurrently increased PD-L1 protein stabilization. Through CRISPR-Cas9 and proteomics screens, we identify and validate CMTM6 as critical for CD58 stability and upregulation of PD-L1 upon CD58 loss. Competition between CD58 and PD-L1 for CMTM6 binding determines their rate of endosomal recycling over lysosomal degradation. Overall, we describe an underappreciated yet critical axis of cancer immunity and provide a molecular basis for how cancer cells balance immune inhibitory and stimulatory cues.

Epigenetic dysregulation from chromosomal transit in micronuclei

Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers1-4, but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei5,6 and subsequent rupture of the micronuclear envelope7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer.

Mitotic clustering of pulverized chromosomes from micronuclei

Complex genome rearrangements can be generated by the catastrophic pulverization of missegregated chromosomes trapped within micronuclei through a process known as chromothripsis1-5. As each chromosome contains a single centromere, it remains unclear how acentric fragments derived from shattered chromosomes are inherited between daughter cells during mitosis6. Here we tracked micronucleated chromosomes with live-cell imaging and show that acentric fragments cluster in close spatial proximity throughout mitosis for asymmetric inheritance by a single daughter cell. Mechanistically, the CIP2A-TOPBP1 complex prematurely associates with DNA lesions within ruptured micronuclei during interphase, which poises pulverized chromosomes for clustering upon mitotic entry. Inactivation of CIP2A-TOPBP1 caused acentric fragments to disperse throughout the mitotic cytoplasm, stochastically partition into the nucleus of both daughter cells and aberrantly misaccumulate as cytoplasmic DNA. Mitotic clustering facilitates the reassembly of acentric fragments into rearranged chromosomes lacking the extensive DNA copy-number losses that are characteristic of canonical chromothripsis. Comprehensive analysis of pan-cancer genomes revealed clusters of DNA copy-number-neutral rearrangements-termed balanced chromothripsis-across diverse tumour types resulting in the acquisition of known cancer driver events. Thus, distinct patterns of chromothripsis can be explained by the spatial clustering of pulverized chromosomes from micronuclei.

Targeting the undruggable

Journey through basic biology reveals a way to treat chromosomally unstable cancers.

Innate immune signaling drives late cardiac toxicity following DNA-damaging cancer therapies

Late cardiac toxicity is a potentially lethal complication of cancer therapy, yet the pathogenic mechanism remains largely unknown, and few treatment options exist. Here we report DNA-damaging agents such as radiation and anthracycline chemotherapies inducing delayed cardiac inflammation following therapy due to activation of cGAS- and STING-dependent type I interferon signaling. Genetic ablation of cGAS-STING signaling in mice inhibits DNA damage-induced cardiac inflammation, rescues late cardiac functional decline, and prevents death from cardiac events. Treatment with a STING antagonist suppresses cardiac interferon signaling following DNA-damaging therapies and effectively mitigates cardiac toxicity. These results identify a therapeutically targetable, pathogenic mechanism for one of the most vexing treatment-related toxicities in cancer survivors.

Abstract IA026: Chromosomal instability as a driver of cancer metastasis

Chromosomal instability (CIN) is a hallmark of human cancer that is associated with metastasis and immune evasion. Yet, how CIN shapes the tumor microenvironment (TME) to facilitate tumor progression remains poorly understood. We undertook a systems level approach to better define the impact of CIN on cancer cell states as well as TME phenotypes and found that cancer cell CIN engenders a pro-metastatic TME that is markedly enriched for immune-suppressive macrophages, a granulocytic infiltrate, and dysfunctional T cells. We then developed a novel computational tool to infer conditionally dependent cell-cell interactions from single cell RNA sequence data to define tumor-derived factors that shape the TME and promote metastatic dissemination. This work led to the identification of novel therapeutic targets in chromosomally unstable tumors and sheds light on key mechanisms by which CIN cooperates with the immune system to drive disease progression.

Citation Format: Samuel F. Bakhoum. Chromosomal instability as a driver of cancer metastasis [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr IA026.

Ovarian cancer mutational processes drive site-specific immune evasion

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability1-4 patterned by distinct mutational processes5,6, tumour heterogeneity7-9 and intraperitoneal spread7,8,10. Immunotherapies have had limited efficacy in HGSOC11-13, highlighting an unmet need to assess how mutational processes and the anatomical sites of tumour foci determine the immunological states of the tumour microenvironment. Here we carried out an integrative analysis of whole-genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumour sites from 42 treatment-naive patients with HGSOC. Homologous recombination-deficient HRD-Dup (BRCA1 mutant-like) and HRD-Del (BRCA2 mutant-like) tumours harboured inflammatory signalling and ongoing immunoediting, reflected in loss of HLA diversity and tumour infiltration with highly differentiated dysfunctional CD8+ T cells. By contrast, foldback-inversion-bearing tumours exhibited elevated immunosuppressive TGFβ signalling and immune exclusion, with predominantly naive/stem-like and memory T cells. Phenotypic state associations were specific to anatomical sites, highlighting compositional, topological and functional differences between adnexal tumours and distal peritoneal foci. Our findings implicate anatomical sites and mutational processes as determinants of evolutionary phenotypic divergence and immune resistance mechanisms in HGSOC. Our study provides a multi-omic cellular phenotype data substrate from which to develop and interpret future personalized immunotherapeutic approaches and early detection research.

cGAS-STING and the deadly CIN: how chronic inflammation represents a therapeutic vulnerability in chromosomally unstable cancers

Chromosomal instability (CIN) is a key genomic driver of human cancer. CIN generates genomic copy-number heterogeneity and tumor-derived inflammation. In a recent paper, Hong et al. identify the cGAS-STING innate immune pathway as a crucial dependency in cancer cells with CIN and pinpoint the IL6/STAT3 axis as a therapeutic vulnerability in these difficult-to-treat tumors.

Dissecting the treatment-naive ecosystem of human melanoma brain metastasis

Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma; yet, our understanding of the underlying salient biology is rudimentary. Here, we performed single-cell/nucleus RNA-seq in 22 treatment-naive MBMs and 10 extracranial melanoma metastases (ECMs) and matched spatial single-cell transcriptomics and T cell receptor (TCR)-seq. Cancer cells from MBM were more chromosomally unstable, adopted a neuronal-like cell state, and enriched for spatially variably expressed metabolic pathways. Key observations were validated in independent patient cohorts, patient-derived MBM/ECM xenograft models, RNA/ATAC-seq, proteomics, and multiplexed imaging. Integrated spatial analyses revealed distinct geography of putative cancer immune evasion and evidence for more abundant intra-tumoral B to plasma cell differentiation in lymphoid aggregates in MBM. MBM harbored larger fractions of monocyte-derived macrophages and dysfunctional TOX+CD8+ T cells with distinct expression of immune checkpoints. This work provides comprehensive insights into MBM biology and serves as a foundational resource for further discovery and therapeutic exploration.

Abstract 2164: Chromosomal instability as a mediator of anti-tumor immunity in pancreatic cancer

Chromosomal instability (CIN) is a hallmark of solid cancers and an established driver of dis-ease progression, therapy resistance, metastasis and on the whole poor patient outcome. Pancreatic cancer, in particular, is defined by dismal survival rates with many patients presenting with metastatic disease upon diagnosis and 5-year survival only reaching ~10%. Recent efforts to improve prognosis for pancreatic cancer patients involved immunotherapies alone and in combination with other therapeutics, however, progress remains limited. Despite CIN’s established role as a driver of disease progression, we have made the paradoxical observation that chromosomally unstable, murine pancreatic cancer cells elicit an anti-tumor immune response. CIN was induced in a chromosomally stable, metastatic model using piggyBac mutagenesis to increase chromosome segregation errors and simultaneously express the diphtheria toxin receptor, thymidine kinase, firefly luciferase and blue fluorescence protein transgenes. Modeling metastatic dissemination by injection of cells into the tail vein of mice led to robust tumor formation in the lungs where CINlow cells formed many small lesions while CINhigh cells formed fewer but larger tumors. We investigated if the tumors were infiltrated differentially by immune cells by immunofluorescence and found that CINhigh tumors were more readily infiltrated by effector T-cells. This observation motivated us to test immunotherapy response in CINlow and CINhigh tumors. Subcutaneously implanted tumor cells were treated with an immune checkpoint inhibitor and isotype control antibody which revealed that CINhigh cells responded to immunotherapy while CINlow cells did not. However, this response could easily be explained by the expression of ectopic antigens in CINhigh cells as a result of the piggyBac mutagenesis, therefore, we derived isogenic single cell clones from the CINhigh population and probed chromosome segregation fidelity and anti-tumor immunity in a more controlled system. Indeed, we were able to isolate CINlow and CINhigh subclones and found that these displayed similar lung engraftment to original CINlow and CINhigh cells as demonstrated by in vivo bioluminescence imaging. Importantly, this difference in engraftment efficiency was alleviated in immunocompromised mice supporting our notion that CIN mediates an anti-tumor immune response in this setting. In summary, our data implicates CIN as a determinant of therapeutic and genetic anti-tumor immunity in a preclinical model of pancreatic cancer. The utility of this model is illustrated by the isogenic nature of cells that only differ in CIN levels and their expression of in vitro and in vivo selection markers. Currently, we are determining the mechanistic underpinnings of our observation using a combination of transcriptomics and genetic manipulations by CRISPR/Cas9.

Citation Format: Daniel Bronder, Roshan K. Sriram, Samuel F. Bakhoum. Chromosomal instability as a mediator of anti-tumor immunity in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2164.

Abstract 2553: Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability patterned by distinct mutational processes, a high degree of tumor heterogeneity and intraperitoneal spread. As immunotherapies have thus far proven ineffective in this disease, we sought to establish the determinants of immune recognition, avoidance and evasion in disease natural history to gain insight into the co-evolutionary processes underlying malignant progression and host immunity. Accordingly we linked mutational processes and anatomic sites of tumor foci as determinants of tumor microenvironment (TME) cellular phenotypes within and between patients using genome-based stratification of homologous recombination proficient (HRP) and deficient (HRD) disease subtypes, and profiling single cell phenotypes from ~1 million cells including cancer cells, T cells, myeloid cells and fibroblasts derived from single cell RNA sequencing, and in situ spatial profiling of histopathology, cancer cell, T cell and macrophage states of 160 tumor sites obtained from 42 treatment-naive patients. Mutational processes in HRD-Dup (BRCA1 mutant-like) tumors were associated with cancer cell-intrinsic JAK/STAT signaling and predominance of highly-differentiated dysfunctional CD8+ T cells in the TME; HRD-Del (BRCA2 mutant-like) tumors were associated with cancer cell-intrinsic NF-κB and TNFα signaling and expansion of M2-type macrophages; and foldback inversion (FBI, HRP) tumors were associated with cancer cell-intrinsic TGFβ signaling and overall immune exclusion, with a predominance of naive/central memory-like T cells. Increased neoantigen burden and HLA loss of heterozygosity (LOH) were defining genomic features of the HRD, but not FBI tumors. These mechanisms of escape from immune predation, with distinct signalling activity and losses of HLA allelic diversity in HRD tumors, connect evolutionary selection with immunological phenotypic states. Multi-region sampling revealed substantial spatial variation, highlighting site-specific properties of the ovary and fallopian tube as putative “immune-privileged” sites. These results establish that in patients with widespread intraperitoneal disease, the local properties of organ sites may determine malignant cell selection and immune pruning. Furthermore, we observed that spatial cellular topology is a major determinant of tumor-immune interactions by in situ protein measurements, revealing ubiquitous PD1-PDL1 interactions in HRD tumors. Together, our findings yield mechanistic insights for how distinct mutational processes in HGSOC lead to diverse patterns of within- and between- patient variation in immune resistance, which can be exploited to optimize future immuno-therapeutic treatment strategies.

Citation Format: Ignacio Vázquez-García, Florian Uhlitz, Nicholas Ceglia, Jamie L. Lim, Michelle Wu, Neeman Mohibullah, Arvin Eric B. Ruiz, Kevin M. Boehm, Viktoria Bojilova, Christopher J. Fong, Tyler Funnell, Diljot Grewal, Eliyahu Havasov, Samantha Leung, Arfath Pasha, Druv M. Patel, Maryam Pourmaleki, Nicole Rusk, Hongyu Shi, Rami Vanguri, Marc J. Williams, Allen W. Zhang, Vance Broach, Dennis S. Chi, Arnaud Da Cruz Paula, Ginger J. Gardner, Sarah H. Kim, Matthew Lennon, Kara Long Roche, Yukio Sonoda, Oliver Zivanovic, Ritika Kundra, Agnes Viale, Yonina Bykov, Fatemeh N. Derakhshan, Luke Geneslaw, Ana Maroldi, Andrea Schietinger, Travis J. Hollmann, Samuel F. Bakhoum, Robert A. Soslow, Lora H. Ellenson, Nadeem Abu-Rustum, Carol Aghajanian, Claire F. Friedman, Andrew McPherson, Britta Weigelt, MSK SPECTRUM Consortium, Dmitriy Zamarin, Sohrab P. Shah. Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2553.

Abstract 3768: Epigenetic dysregulation from chromosomal transit in micronuclei

Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers, yet whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei, and subsequent micronuclear envelope rupture profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice as well as cancer and nontransformed cells. Some of the changes to histone PTMs occur due to micronuclear envelope rupture whereas others are inherited from mitotic abnormalities prior to micronucleus formation. Using orthogonal techniques, we show that micronuclei exhibit extensive differences in chromatin accessibility with a strong positional bias between promoters and distal or intergenic regions. Finally, we show that inducing CIN engenders widespread epigenetic dysregulation and that chromosomes which transit in micronuclei experience durable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, in addition to genomic copy number alterations, CIN can serve as a vehicle for epigenetic reprogramming and heterogeneity in cancer.

Citation Format: Albert S. Agustinus, Ramya Raviram, Bhargavi Dameracharla, Jens Luebeck, Stephanie Stransky, Lorenzo Scipioni, Robert M. Myers, Melody Di Bona, Mercedes Duran, Britta Weigelt, Shira Yomtoubian, Eleonore Toufektchan, Paul S. Mischel, Vivek Mittal, Sohrab Shah, John Maciejowski, Enrico Gratton, Peter Ly, Mathieu F. Bakhoum, Dan Landau, Vineet Bafna, Simone Sidoli, Yael David, Samuel F. Bakhoum. Epigenetic dysregulation from chromosomal transit in micronuclei [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3768.

Abstract 981: A genetic-metabolic axis of metastatic liver organotropism

Genomic and adaptive determinants of organ-specific metastasis are poorly understood. A model of sequential acquisition of divergent somatic mutations is insufficient to explain metastasis. Liver metastasis (LM) occurs frequently and is associated with a poor prognosis and reduced therapy response in several cancers, including in patients with melanoma and lung cancer. To identify drivers of metastatic niches, we used a syngeneic mouse melanoma model which recapitulates genomic, metastatic and therapy response patterns seen in patients. We performed a large-scale in vivo CRISPR-Cas9 knockout screen and identified perturbations that promote LM, but not primary tumor growth or metastasis to other organs (e.g. lung). The “top hit” in this screen associated with LM was loss Pip4k2c. We generated Pip4k2cKO cells and show that in otherwise isogenic melanoma cell lines, loss of Pip4k2c led to increased baseline and insulin-induced activation of the PI3K/AKT pathway, and increased invasive capacity. Rescuing Pip4k2cKO with full-length (Pip4k2cRec) or allosteric domain deficient (Pip4k2cAD) Pip4k2c ORFs, we show that hyperactivation of the PI3K/AKT pathway in is mediated by loss of the allosteric domain function, and not loss of the kinase domain of Pip4k2c. Treatment with different PI3K inhibitors effectively abrogated the pathway, but was partly bypassed in the presence of insulin in Pip4k2cKO and Pip4k2cAD, but not parental or Pip4k2cRec cells. Upon tail vein injection, Pip4k2cKO cells produced a significantly increased LM burden compared to parental cells, and this effect was rescued in Pip4k2cRec but not Pip4k2cAD, further affirming that loss of allosteric domain was required for this phenotype. We reasoned that Pip4k2cKO cells preferentially colonized the liver by co-opting the insulin-rich milieu in this organ. To test this, we used shRNA targeted against the insulin receptor (Insr) generated Pip4k2cKO/InsrshIR and showed that Insr was required but not sufficient to enhance LM burden. Given the promising in vitro activity of PI3K inhibitors, we next tested whether these could abrogate LM in vivo. Surprisingly, we found a substantial increase in LM burden in mice with Pip4k2cKO-bearing LM treated with PI3K inhibition compared to vehicle treated animals. We show that this paradoxical observation was due to host-mediated increased in glucose and insulin in response to PI3K inhibitor, which promoted a forward loop of increased liver metastasis. Breaking this loop with either ketogenic diet or treatment with a SGLT2 inhibitor in turn rescued increased these host responses and resulted in reduced LM burden in combination with PI3K inhibition. In summary, we identify a novel mechanism of metastatic liver organotropism and pharmacological and dietary combinations to reduced liver metastatic burden. Given the expanding use of PI3K inhibitors, our findings may have important clinical implications.

Citation Format: Meri Rogava, Johannes C. Melms, Stephanie Davis, Clemens Hug, Bryan Ngo, Michael J. Lee, Patricia Ho, Amit Dipak Amin, Yiping Wang, Sean Chen, William Ge, David Liu, Thomas Tüting, Martin Röcken, Thomas K. Eigentler, Samuel F. Bakhoum, Andrei Molotkov, Akiva Mintz, Lewis C. Cantley, Peter K. Sorger, Benjamin Izar. A genetic-metabolic axis of metastatic liver organotropism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 981.

Abstract 1589: Unraveling the mechanisms underlying micronuclear rupture, a seminal event in cancer progression

Chromosomal instability is a hallmark of aggressive human cancers and it is often associated with metastasis, immune evasion, and therapeutic resistance. Chromosomally unstable tumors often contain rupture-prone micronuclei, which harbor mis-segregated chromosomes. Rupture of micronuclear envelopes represents a critical event in the evolution of chromosomally unstable tumors given its ability to catalyze the formation of genomic rearrangements known as chromothripsis, and to trigger the cytosolic DNA-sensing cGAS-STING inflammatory pathway, whose aberrant and chronic activation was found to promote metastatic progression [1]. Despite its central role in tumor progression, how micronuclear membranes collapse and why membrane repair mechanisms, which are functional at the primary nucleus, fail to restore micronuclear integrity, remains poorly understood. Here we show that the answer to these fundamental questions lays in mitochondria proximity to micronuclei: by means of advanced microscopy and cellular and molecular biology techniques, our results demonstrate that ruptured micronuclei are more heavily embedded in the mitochondrial matrix than the intact ones, and that ROS are the main cause of micronuclear rupture. We used a combination of ROS-inducing drugs on a variety of cell lines to show an increase in collapsed micronuclei, while using ROS-scavengers we reduced the physiological basal amount of micronuclear rupture.

Nuclear membrane catastrophe has recently been identified as the main outcome of unrestrained activity of the ESCRT-III nuclear membrane repair complex, of which CHMP7 is the scaffolding protein [2]. We showed that cells under oxidative stress display an increase in CHMP7 content in micronuclei whose membrane is not yet collapsed, implicating a causative role of CHMP7 in micronuclear envelope rupture. Furthermore, by means of genetic manipulation we demonstrate a central role for CHMP7 in ROS-induced rupture, with evidences pointing towards a non-canonical role for CHMP7 in this process. We thus provide a mechanistic insight into a fundamental hub in advanced cancers metastatic onset: by understanding the players involved into micronuclear collapse, this work can bring to light new untapped drug targets that are specific for those cells that will undergo metastatic transformation. In conclusion, our study has the potential to develop new and more effective therapies for the treatment of aggressive chromosomally unstable cancers.

1. Bakhoum, S.F., et al., Chromosomal instability drives metastasis through a cytosolic DNA response. Nature, 2018. 553(7689): p. 467-472.

2. Vietri, M., et al., Unrestrained ESCRT-III drives micronuclear catastrophe and chromosome fragmentation. Nat Cell Biol, 2020. 22(7): p. 856-867

Citation Format: Melody Di Bona, Albert Agustinus, Yanyang Chen, Lorenzo Scipioni, Daniel Bronder, Samuel F. Bakhoum. Unraveling the mechanisms underlying micronuclear rupture, a seminal event in cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1589.

Abstract 1514: Examining the impact of chromosomal instability on mucosal melanoma tumor infiltrate and responses to PD-1 based therapy

Mucosal melanoma (McM) is a rare subtype of melanoma arising from melanocytes of mucosal surfaces that comprises less than 2% of all melanomas in the US. Although PD-1 based checkpoint inhibition is standard initial therapy, McM has been shown to respond less often than cutaneous melanoma. We explored the hypothesis of this resistance being due to a lower tumor mutational burden (TMB) and high levels of chromosomal instability resulting in the formation of micronuclei, a greater than average fraction of genome altered (FGA) as defined by the MSK-IMPACT hybridization capture based NGS platform, and decreased immune infiltration. We utilized MSK-IMPACT data, to collect TMB and FGA data from 112 mucosal melanoma patients of which 56 had received frontline PD-1 based immunotherapy (28 a-PD-1 nivolumab/pembrolizumab, 28 nivolumab + ipilimumab). This population had a median follow-up time of 92 months, median progression free survival (PFS) of 13 months and median overall survival (OS) of 47 months. Dichotomized TMB was not associated with PFS or OS. However, higher than median FGA was associated with a significantly worse PFS (median 16 months vs. not reached [NR]) and OS (median 38months vs. NR). We then explored the association to traditional markers of chromosomal instability using multiplex immunofluorescence (IF) in tumor samples taken from 18 patients within the treatment cohort. We quantified cGMP-AMP synthase (cGAS) positive micronuclei present and found that FGA correlated directly with the number of micronuclei in the tumor, supporting that FGA is a reasonable indicator of chromosomal instability. As expected, there was no such association with micronuclei and TMB. Using multiplex IF we quantified CD8+ and CD8xPD1 co-positive cells at the tumor invading margin. Tumors with higher FGA had lower infiltration of CD8+ cells and CD8xPD1 co-positive cells. The same relationship was found when directly comparing number of micronuclei to CD8+ and CD8xPD1 co-positive cells. Our data suggests that patients with McM that harbor higher levels of chromosomal instability characterized by presence of micronuclei and resultant higher fraction of genome altered on MSK-IMPACT have fewer PD1+/CD8+ T cells in the tumor microenvironment and have inferior progression-free and overall survival with standard PD-1 blockade. This immunosuppressive mechanism may represent a uniquely poor prognosis group that may benefit from altering the downstream signaling resultant of chromosomal instability.

Citation Format: Emma Armstrong, Lee Gottesdiener, Nikolaus Schultz, Samuel F. Bakhoum, Travis J. Hollmann, Alexander Shoushtari. Examining the impact of chromosomal instability on mucosal melanoma tumor infiltrate and responses to PD-1 based therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1514.

Chromosomal instability as a source of genomic plasticity

Chromosomal instability (CIN) is a hallmark of the most aggressive malignancies. Features of these tumors include complex genomic rearrangements, the presence of mis-segregated chromosomes in micronuclei, and extrachromosomal DNA (ecDNA) formation. Here, we review the development of CIN, and examine CIN in the context of cancer evolution, tumor genomic evolution, and therapeutic resistance. We also discuss the role of whole-genome duplications, breakage-fusion-bridge cycles, ecDNA or double minutes in gene amplification promoting tumor evolution.

The pleiotropic roles of cGAS-STING signaling in the tumor microenvironment

Cytosolic DNA is prevalent in cells constituting the tumor microenvironment (TME) and can activate the cyclic guanosine monophosphate–adenosine monophosphate synthase (cGAS)–stimulator of interferon genes (STING) innate immune pathway. The initiation, transmission, and execution of the cGAS–STING pathway can take place among different cell types within the TME and thus cGAS–STING may play opposing roles in driving tumor progression in addition to its tumor cell-intrinsic role. Herein, we review recent advances in the cGAS–STING field with a focus on its crosstalk with other signaling pathways in the TME. Future efforts to depict a more detailed picture of the roles of cGAS–STING signaling in the TME will help design a better cancer treatment regime by targeting the cGAS–STING pathway more precisely.

Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

Metastatic progression is the main cause of death in cancer patients, whereas the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we assembled MSK-MET, a pan-cancer cohort of over 25,000 patients with metastatic diseases. By analyzing genomic and clinical data from this cohort, we identified associations between genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma, and HR+/HER2+ breast ductal carcinoma, but not in others, including colorectal cancer and high-grade serous ovarian cancer, where copy-number alteration patterns may be established early in tumor development. We also identified somatic alterations associated with metastatic burden and specific target organs. Our data offer a valuable resource for the investigation of the biological basis for metastatic spread and highlight the complex role of chromosomal instability in cancer progression.

APOBEC3 as a driver of genetic intratumor heterogeneity

Our recent study revealed that APOBEC3B is upregulated during the preinvasive stages of non-small cell lung cancer and breast cancer. In addition to its role in mediating single nucleotide variants, we propose that APOBEC3 promotes copy number intratumor heterogeneity prior to invasion, providing a substrate for cancer evolution.

Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution

APOBEC3 enzymes are cytosine deaminases implicated in cancer. Precisely when APOBEC3 expression is induced during cancer development remains to be defined. Here we show that specific APOBEC3 genes are upregulated in breast ductal carcinoma in situ, and in preinvasive lung cancer lesions coincident with cellular proliferation. We observe evidence of APOBEC3-mediated subclonal mutagenesis propagated from TRACERx preinvasive to invasive non-small cell lung cancer (NSCLC) lesions. We find that APOBEC3B exacerbates DNA replication stress and chromosomal instability through incomplete replication of genomic DNA, manifested by accumulation of mitotic ultrafine bridges and 53BP1 nuclear bodies in the G1 phase of the cell cycle. Analysis of TRACERx NSCLC clinical samples and mouse lung cancer models revealed APOBEC3B expression driving replication stress and chromosome missegregation. We propose that APOBEC3 is functionally implicated in the onset of chromosomal instability and somatic mutational heterogeneity in preinvasive disease, providing fuel for selection early in cancer evolution. SIGNIFICANCE: This study reveals the dynamics and drivers of APOBEC3 gene expression in preinvasive disease and the exacerbation of cellular diversity by APOBEC3B through DNA replication stress to promote chromosomal instability early in cancer evolution.This article is highlighted in the In This Issue feature, p. 2355.

A molecular single-cell lung atlas of lethal COVID-19

Respiratory failure is the leading cause of death in patients with severe SARS-CoV-2 infection^1,2, but the host response at the lung tissue level is poorly understood. Here we performed single-nucleus RNA sequencing of about 116,000 nuclei from the lungs of nineteen individuals who died of COVID-19 and underwent rapid autopsy and seven control individuals. Integrated analyses identified substantial alterations in cellular composition, transcriptional cell states, and cell-to-cell interactions, thereby providing insight into the biology of lethal COVID-19. The lungs from individuals with COVID-19 were highly inflamed, with dense infiltration of aberrantly activated monocyte-derived macrophages and alveolar macrophages, but had impaired T cell responses. Monocyte/macrophage-derived interleukin-1β and epithelial cell-derived interleukin-6 were unique features of SARS-CoV-2 infection compared to other viral and bacterial causes of pneumonia. Alveolar type 2 cells adopted an inflammation-associated transient progenitor cell state and failed to undergo full transition into alveolar type 1 cells, resulting in impaired lung regeneration. Furthermore, we identified expansion of recently described CTHRC1⁺ pathological fibroblasts³ contributing to rapidly ensuing pulmonary fibrosis in COVID-19. Inference of protein activity and ligand-receptor interactions identified putative drug targets to disrupt deleterious circuits. This atlas enables the dissection of lethal COVID-19, may inform our understanding of long-term complications of COVID-19 survivors, and provides an important resource for therapeutic development.

The clinical and molecular significance associated with STING signaling in breast cancer

STING signaling in cancer is a crucial component of response to immunotherapy and other anti-cancer treatments. Currently, there is no robust method of measuring STING activation in cancer. Here, we describe an immunohistochemistry-based assay with digital pathology assessment of STING in tumor cells. Using this novel approach in estrogen receptor-positive (ER+) and ER- breast cancer, we identify perinuclear-localized expression of STING (pnSTING) in ER+ cases as an independent predictor of good prognosis, associated with immune cell infiltration and upregulation of immune checkpoints. Tumors with low pnSTING are immunosuppressed with increased infiltration of "M2"-polarized macrophages. In ER- disease, pnSTING does not appear to have a significant prognostic role with STING uncoupled from interferon responses. Importantly, a gene signature defining low pnSTING expression is predictive of poor prognosis in independent ER+ datasets. Low pnSTING is associated with chromosomal instability, MYC amplification and mTOR signaling, suggesting novel therapeutic approaches for this subgroup.

Deep learning predicts chromosomal instability from histopathology images

Chromosomal instability (CIN) is a hallmark of human cancer yet not readily testable for patients with cancer in routine clinical setting. In this study, we sought to explore whether CIN status can be predicted using ubiquitously available hematoxylin and eosin histology through a deep learning-based model. When applied to a cohort of 1,010 patients with breast cancer (Training set: n = 858, Test set: n = 152) from The Cancer Genome Atlas where 485 patients have high CIN status, our model accurately classified CIN status, achieving an area under the curve of 0.822 with 81.2% sensitivity and 68.7% specificity in the test set. Patch-level predictions of CIN status suggested intra-tumor heterogeneity within slides. Moreover, presence of patches with high predicted CIN score within an entire slide was more predictive of clinical outcome than the average CIN score of the slide, thus underscoring the clinical importance of intra-tumor heterogeneity.

Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis

Cytosolic DNA is characteristic of chromosomally unstable metastatic cancer cells, resulting in constitutive activation of the cGAS-STING innate immune pathway. How tumors co-opt inflammatory signaling while evading immune surveillance remains unknown. Here, we show that the ectonucleotidase ENPP1 promotes metastasis by selectively degrading extracellular cGAMP, an immune-stimulatory metabolite whose breakdown products include the immune suppressor adenosine. ENPP1 loss suppresses metastasis, restores tumor immune infiltration, and potentiates response to immune checkpoint blockade in a manner dependent on tumor cGAS and host STING. Conversely, overexpression of wild-type ENPP1, but not an enzymatically weakened mutant, promotes migration and metastasis, in part through the generation of extracellular adenosine, and renders otherwise sensitive tumors completely resistant to immunotherapy. In human cancers, ENPP1 expression correlates with reduced immune cell infiltration, increased metastasis, and resistance to anti-PD-1/PD-L1 treatment. Thus, cGAMP hydrolysis by ENPP1 enables chromosomally unstable tumors to transmute cGAS activation into an immune-suppressive pathway. SIGNIFICANCE: Chromosomal instability promotes metastasis by generating chronic tumor inflammation. ENPP1 facilitates metastasis and enables tumor cells to tolerate inflammation by hydrolyzing the immunotransmitter cGAMP, preventing its transfer from cancer cells to immune cells.This article is highlighted in the In This Issue feature, p. 995.

The Evolution of STING Signaling and Its Involvement in Cancer

The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway has been primarily characterized as an inflammatory mechanism in higher eukaryotes in response to cytosolic double-stranded DNA (dsDNA). Since its initial discovery, detailed mechanisms delineating the dynamic subcellular localization of its different components and downstream signaling have been uncovered, leading to attempts to harness its proinflammatory properties for therapeutic benefit in cancer. Emerging evidence, however, indicates that a crucial primordial function of STING is to promote autophagy, and that downstream interferon (IFN) signaling emerged recently in its evolutionary history. Furthermore, studies suggest that this pathway is a crucial regulator of cellular metabolism that potentially couples inflammation to nutrient availability. We focus on the evolutionarily conserved functions of STING, and we discuss how a broader understanding of this pathway can help us to better appreciate its potential role in cancer and harness it for therapeutic benefit.

Re-awakening Innate Immune Signaling in Cancer: The Development of Highly Potent ENPP1 Inhibitors

Activation of innate immune signaling in the tumor microenvironment is central to a successful anti-tumor immune response, and it is in large part mediated by cytosolic double-stranded DNA sensing. Here, Carozza et al. (2020b) report potent and selective inhibitors of ENPP1, a negative regulator of innate immune signaling, which are shown to potentiate anti-tumor immune responses.

Pervasive chromosomal instability and karyotype order in tumour evolution

Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.

Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition

A hallmark of metastasis is the adaptation of tumor cells to new environments. Metabolic constraints imposed by the serine and glycine-limited brain environment restrict metastatic tumor growth. How brain metastases overcome these growth-prohibitive conditions is poorly understood. Here, we demonstrate that 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the rate-limiting step of glucose-derived serine synthesis, is a major determinant of brain metastasis in multiple human cancer types and preclinical models. Enhanced serine synthesis proved important for nucleotide production and cell proliferation in highly aggressive brain metastatic cells. In vivo, genetic suppression and pharmacologic inhibition of PHGDH attenuated brain metastasis, but not extracranial tumor growth, and improved overall survival in mice. These results reveal that extracellular amino acid availability determines serine synthesis pathway dependence, and suggest that PHGDH inhibitors may be useful in the treatment of brain metastasis. SIGNIFICANCE: Using proteomics, metabolomics, and multiple brain metastasis models, we demonstrate that the nutrient-limited environment of the brain potentiates brain metastasis susceptibility to serine synthesis inhibition. These findings underscore the importance of studying cancer metabolism in physiologically relevant contexts, and provide a rationale for using PHGDH inhibitors to treat brain metastasis.This article is highlighted in the In This Issue feature, p. 1241.

Morphology-Predicted Large-Scale Transition Number in Circulating Tumor Cells Identifies a Chromosomal Instability Biomarker Associated with Poor Outcome in Castration-Resistant Prostate Cancer

Chromosomal instability (CIN) increases a tumor cell's ability to acquire chromosomal alterations, a mechanism by which tumor cells evolve, adapt, and resist therapeutics. We sought to develop a biomarker of CIN in circulating tumor cells (CTC) that are more likely to reflect the genetic diversity of patient's disease than a single-site biopsy and be assessed rapidly so as to inform treatment management decisions in real time. Large-scale transitions (LST) are genomic alterations defined as chromosomal breakages that generate chromosomal gains or losses of greater than or equal to10 Mb. Here we studied the relationship between the number of LST in an individual CTC determined by direct sequencing and morphologic features of the cells. This relationship was then used to develop a computer vision algorithm that utilizes CTC image features to predict the presence of a high (9 or more) versus low (8 or fewer) LST number in a single cell. As LSTs are a primary functional component of homologous recombination deficient cellular phenotypes, the image-based algorithm was studied prospectively on 10,240 CTCs in 367 blood samples obtained from 294 patients with progressing metastatic castration-resistant prostate cancer taken prior to starting a standard-of-care approved therapy. The resultant computer vision-based biomarker of CIN in CTCs in a pretreatment sample strongly associated with poor overall survival times in patients treated with androgen receptor signaling inhibitors and taxanes. SIGNIFICANCE: A rapidly assessable biomarker of chromosomal instability in CTC is associated with poor outcomes when detected in men with progressing mCRPC.

Abstract 5712: Nutrient scarcity confers breast cancer brain metastasis sensitivity to serine synthesis pathway inhibition

The metabolic milieu of the brain is severely deprived of nutrients, including the amino acids serine and its catabolite glycine. The metabolic rewiring required for tumor cells to survive in the nutrient-limited environment of the brain and the metabolic vulnerabilities this confers are poorly understood.

Here we demonstrate that cell-intrinsic de novo serine synthesis is a major determinant of triple-negative breast cancer (TNBC) brain metastasis. Whole proteome comparison of TNBC cells that differ in their capacity to colonize the brain reveals that 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the rate-limiting step of glucose-derived serine synthesis, is the most significantly upregulated protein in cells that efficiently metastasize to the brain. Expression of catalytically active PHGDH in a non-brain trophic cell line promoted brain metastasis. Furthermore, genetic silencing or pharmacological inhibition of PHGDH attenuated brain metastasis burden in mice.

These findings indicate that nutrient availability determines serine synthesis pathway dependence in brain metastasis, and suggest that PHGDH inhibitors may be useful in the treatment of patients with cancers that have spread to the brain.

Citation Format: Bryan Ngo, Eugenie Kim, Sophia Doll, Sophia Bustraan, Alba Luengo, Shawn M. Davidson, Ahmed Ali, Gino Ferraro, Diane Kang, Jing Ni, Roger Liang, Ariana Plasger, Edward R. Kastenhuber, Roozbeh Eskandari, Sarah Bacha, Roshan Sriram, Benjamin D. Stein, Samuel F. Bakhoum, Edouard Mullarky, Matija Snuderl, Nello Mainolfi, Vipin Suri, Adam Friedman, Mark Manfredi, David M. Sabatini, Drew Jones, Min Yu, Jean J. Zhao, Rakesh K. Jain, Matthew G. Vander Heiden, Matthias Mann, Lewis C. Cantley, Michael E. Pacold. Nutrient scarcity confers breast cancer brain metastasis sensitivity to serine synthesis pathway inhibition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5712.

Breast Radiation Therapy Under COVID-19 Pandemic Resource Constraints-Approaches to Defer or Shorten Treatment From a Comprehensive Cancer Center in the United States

Purpose

Breast radiation therapy accounts for a significant proportion of patient volume in contemporary radiation oncology practice. In the setting of anticipated resource constraints and widespread community infection with SARS-CoV-2 during the COVID-19 pandemic, measures for balancing both infectious and oncologic risk among patients and providers must be carefully considered. Here, we present evidence-based guidelines for omitting or abbreviating breast cancer radiation therapy, where appropriate, in an effort to mitigate risk to patients and optimize resource utilization.

Methods and Materials

Multidisciplinary breast cancer experts at a high-volume comprehensive cancer center convened contingency planning meetings over the early days of the COVID-19 pandemic to review the relevant literature and establish recommendations for the application of hypofractionated and abbreviated breast radiation regimens.

Results

Substantial evidence exists to support omitting radiation among certain favorable risk subgroups of patients with breast cancer and for abbreviating or accelerating regimens among others. For those who require either whole-breast or postmastectomy radiation, with or without coverage of the regional lymph nodes, a growing body of literature supports various hypofractionated approaches that appear safe and effective.

Conclusions

In the setting of a public health emergency with the potential to strain critical healthcare resources and place patients at risk of infection, the parsimonious application of breast radiation therapy may alleviate a significant clinical burden without compromising long-term oncologic outcomes. The judicious and personalized use of immature study data may be warranted in the setting of a competing mortality risk from this widespread pandemic.

A CINful way to overcome addiction: how chromosomal instability enables cancer to overcome its oncogene addiction

Oncogene-addicted tumors present a valuable target for therapeutic intervention and an opportunity to achieve a wide therapeutic window. Nonetheless, resistance to targeted therapies is frequently observed and it arises through multiple mechanisms, including mutations in the target gene. Chromosomal instability, a defining feature of human cancer, has been linked to targeted therapy resistance, but the mechanism underlying this association is poorly understood. In the current issue of EMBO Molecular Medicine, Salgueiro et al show that chromosomal instability can lead to the generation of alternative oncogenic drivers, thereby providing the ability for cancer cells to overcome the oncogene withdrawal bottleneck. Importantly, this study shows that, by generating de novo genomic diversity, chromosomal instability serves as an adaptive response to therapeutic insult.

Regenerative lineages and immune-mediated pruning in lung cancer metastasis

Developmental processes underlying normal tissue regeneration have been implicated in cancer, but the degree of their enactment during tumor progression and under the selective pressures of immune surveillance, remain unknown. Here, we show that human primary lung adenocarcinomas are characterized by the emergence of regenerative cell types typically seen in response to lung injury, and by striking infidelity amongst transcription factors specifying most alveolar and bronchial epithelial lineages. In contrast, metastases are enriched for key endoderm and lung-specifying transcription factors, SOX2 and SOX9, and recapitulate more primitive transcriptional programs spanning stem-like to regenerative pulmonary epithelial progenitor states. This developmental continuum mirrors the progressive stages of spontaneous outbreak from metastatic dormancy in a mouse model and exhibits SOX9-dependent resistance to Natural Killer (NK) cells. Loss of developmental stage-specific constraint in macrometastases triggered by NK cell depletion suggests a dynamic interplay between developmental plasticity and immune-mediated pruning during metastasis.

The Cytosolic DNA-Sensing cGAS-STING Pathway in Cancer

The recognition of DNA as an immune-stimulatory molecule is an evolutionarily conserved mechanism to initiate rapid innate immune responses against microbial pathogens. The cGAS-STING pathway was discovered as an important DNA-sensing machinery in innate immunity and viral defense. Recent advances have now expanded the roles of cGAS-STING to cancer. Highly aggressive, unstable tumors have evolved to co-opt this program to drive tumorigenic behaviors. In this review, we discuss the link between the cGAS-STING DNA-sensing pathway and antitumor immunity as well as cancer progression, genomic instability, the tumor microenvironment, and pharmacologic strategies for cancer therapy. SIGNIFICANCE: The cGAS-STING pathway is an evolutionarily conserved defense mechanism against viral infections. Given its role in activating immune surveillance, it has been assumed that this pathway primarily functions as a tumor suppressor. Yet, mounting evidence now suggests that depending on the context, cGAS-STING signaling can also have tumor and metastasis-promoting functions, and its chronic activation can paradoxically induce an immune-suppressive tumor microenvironment.

Cancer Evolution: No Room for Negative Selection

In this issue of Cell, Martincorena et al. and Campbell et al. interrogated the selection dynamics during tumor evolution using large-scale genomics datasets. They found that somatic mutations in cancer are largely neutral, highlighting a near-complete absence of negative selection. Neutral evolution enables tolerance of hypermutation, which defines a surprisingly large fraction of adult cancer.

Expanding the Role of STING in Cellular Homeostasis and Transformation

The cytosolic DNA-sensing cGAS-STING pathway was originally characterized as a key innate immune mediator responsible for the induction of antiviral genes in response to foreign DNA species in the cytosol. Mounting evidence, however, points to a complex role for cGAS and STING in cancer. Two recent reports, by Ranoa et al. (Cancer Research, 2018;https://doi.org/10.1158/0008-5472.CAN-18-1972) and Nassour et al. (Nature 2019;565:659-663), dissect the function of this pathway during the early steps of cellular transformation and shed light on the complexity and context-dependence of cGAS-STING signaling in cancer.

A Markov chain for numerical chromosomal instability in clonally expanding populations

Cancer cells frequently undergo chromosome missegregation events during mitosis, whereby the copies of a given chromosome are not distributed evenly among the two daughter cells, thus creating cells with heterogeneous karyotypes. A stochastic model tracing cellular karyotypes derived from clonal populations over hundreds of generations was recently developed and experimentally validated, and it was capable of predicting favorable karyotypes frequently observed in cancer. Here, we construct and study a Markov chain that precisely describes karyotypic evolution during clonally expanding cancer cell populations. The Markov chain allows us to directly predict the distribution of karyotypes and the expected size of the tumor after many cell divisions without resorting to computationally expensive simulations. We determine the limiting karyotype distribution of an evolving tumor population, and quantify its dependency on several key parameters including the initial karyotype of the founder cell, the rate of whole chromosome missegregation, and chromosome-specific cell viability. Using this model, we confirm the existence of an optimal rate of chromosome missegregation probabilities that maximizes karyotypic heterogeneity, while minimizing the occurrence of nullisomy. Interestingly, karyotypic heterogeneity is significantly more dependent on chromosome missegregation probabilities rather than the number of cell divisions, so that maximal heterogeneity can be reached rapidly (within a few hundred generations of cell division) at chromosome missegregation rates commonly observed in cancer cell lines. Conversely, at low missegregation rates, heterogeneity is constrained even after thousands of cell division events. This leads us to conclude that chromosome copy number heterogeneity is primarily constrained by chromosome missegregation rates and the risk for nullisomy and less so by the age of the tumor. This model enables direct integration of karyotype information into existing models of tumor evolution based on somatic mutations.

Chromosomal instability (CIN) is a hallmark of cancer and it results from persistent chromosome segregation errors during cell division. CIN has been shown to play a key role in drug resistance and tumor metastasis. While our understanding of CIN on the cellular level has grown over the past decade, our ability to predict the behavior of tumors containing billions of cells remains limited due to the paucity of adequate mathematical models. Here, we develop a Markov-chain model that is capable of providing exact solutions for long-term chromosome copy number distributions during tumor growth. Using this model we confirm the presence of optimal chromosome missegregation rates that balance genomic heterogeneity required for tumor evolution and survival. Interestingly, we show that chromosome copy number heterogeneity is primarily influenced by the rate of chromosome segregation errors rather than the age of the tumor. At chromosome missegregation rates frequently observed in cancer, tumors can acquire maximal genomic heterogeneity after a few hundred cell divisions. This model enables the integration of selection imparted by CIN into existing models of tumor evolution based on somatic mutations to explore their mutual effects.

The Multifaceted Role of Chromosomal Instability in Cancer and Its Microenvironment

Chromosomal instability (CIN) is a hallmark of human cancer, and it is associated with poor prognosis, metastasis, and therapeutic resistance. CIN results from errors in chromosome segregation during mitosis, leading to structural and numerical chromosomal abnormalities. In addition to generating genomic heterogeneity that acts as a substrate for natural selection, CIN promotes inflammatory signaling by introducing double-stranded DNA into the cytosol, engaging the cGAS-STING anti-viral pathway. These multipronged effects distinguish CIN as a central driver of tumor evolution and as a genomic source for the crosstalk between the tumor and its microenvironment, in the course of immune editing and evasion.