Trends in Oncology

Hepatocellular carcinoma (HCC) is one of the most prevalent types of liver cancer, and it usually develops in patients with underlying cirrhosis or chronic liver disease and metabolic syndrome.^[1] HCC can spread to other body parts and affect patients' survival rates and outcomes severely. In this blog post, we will provide essential insights into HCC metastases and delve into the therapeutic options.

Over 60% of patients with HCC are diagnosed in advanced stages, leading to an overall 5-year survival rate of 21%. However, this rate is between 60% and 70% in patients with early diagnosis who undergo liver transplants.^[2] Patients diagnosed with advanced-stage HCC, defined by the presence of vascular invasion or extrahepatic metastases, have a poor prognosis with a median survival of less than 1 year. ^[3] Early detection of HCC is vital in increasing therapeutic opportunities and improving patients’ outcomes, and new diagnostic biomarkers are under investigation to enhance HCC screening.^[4]

Available treatments for HCC metastases depend on the tumor's location, the extent of the cancer, and the patient's general condition. Surgical resection, liver transplant, radiofrequency, and microwave ablation are all first-line treatments for tumors that have not spread to other body parts. Chemoembolization is commonly used and improves survival in asymptomatic patients with multifocal regional disease. ^[5]

Systemic therapies, such as sorafenib and lenvatinib have been shown to be effective in prolonging survival rates and outcomes in patients with advanced HCC. These agents are multikinase inhibitors that block tyrosine kinases involved in angiogenesis, cancer development and growth, and tumor microenvironment regulation. They are used as first-line therapy in advanced HCC with contraindications to VEGF and immune checkpoint inhibitors. Immune checkpoint inhibitors are instead used together with bevacizumab in patients without contraindication. Alternative tyrosine kinase inhibitors, such as regorafenib, cabozantinib, and ramucirumab are used as second-line treatments.^[6]

Scientists are also researching new therapies for advanced HCC, including novel molecular-targeted therapies (such as STAT3 and CDK4 inhibitors) and immunotherapies to use as single agents or in combination. Several clinical trials are currently underway to investigate the efficacy and safety of these new therapies for advanced and metastatic HCC.^[7]

Hepatocellular carcinoma is a critical concern for clinicians and patients, given the cancer progression and severity. Validating new diagnostic biomarkers and developing new therapeutic approaches to overcome drug resistance will be paramount in improving patients’ survival and quality of life.

Human epidermal growth factor receptor 2 (HER2; ERBB2) has been shown to induce oncogenesis in several cancers, particularly breast and gastric cancers. HER2 is estimated to be overexpressed in ~20% of all breast cancers, and outcomes for these breast cancers were poor before HER2-targeted therapies^[1]. Our understanding of mechanisms by which HER2 drives tumor growth and metastasis led to one of the first targeted therapies for treating HER2+ breast cancers. Here we highlight what is known about HER2 and oncogenesis. and how this information can be applied to the development of new targeted therapies.

Gene amplification of the ERRB2 oncogene is one of the most common genetic defects detected in HER2+ tumors and typically causes overexpression of HER2 at the cell membrane^[2]. HER2 proteins more readily dimerize with other HER2 proteins to form homodimers or with other ERRB members to form heterodimers. These complexes induce oncogenic signaling cascades, including MAPK and PI3K/AKT/mTOR, which cause cellular proliferation, angiogenesis, and resistance to apoptosis^[3]. Due to the dominant role of HER2 in breast cancer, anti-HER2 antibodies were developed as one of the first targeted therapies. In 2006, clinical trial results of breast cancer patients treated with the anti-HER2 antibody trastuzumab showed significant improvements in progression-free survival and overall survival^[4],[5]. Unfortunately, ~20-25% of metastatic breast cancer patients develop resistance to anti-HER2 therapies. More recent studies have focused on engineering new forms of anti-HER2 antibodies or developing HER1/2 inhibitors that can be used alone or in combination with other targeted therapies.

The current standard of care for HER2+ breast cancer includes chemotherapy with adjuvant HER2-targeted therapies and endocrine therapy as indicated. Advances in targeted therapies are further improving treatment protocols. The next-generation anti-HER2 monoclonal antibody margetuximab targets the same HER2 epitope as trastuzumab and is modified in its Fc domain to improve antibody-dependent cellular cytotoxicity.^[6] Margetuximab was approved by the FDA in December 2020 for the treatment of metastatic breast cancer in patients who had received prior HER2 therapies^[7]. Two different bispecific antibodies have also been developed and are in clinical trials: ZW25 is a bispecific antibody that targets two different HER2 epitopes, and PRS-343 is a bispecific antibody that targets a HER2 epitope and the 4-1BB costimulatory immunoreceptor^[8]. Bispecific antibodies are under development for breast cancer and other cancers because they exploit the property that antibodies have two epitope binding sites and can be engineered to better target a single molecule or crosslink multiple molecules, like HER2 and immune checkpoint molecules.

Antibody-drug conjugates have also been evaluated as novel therapeutics that target HER2. Trastuzumab deruxtecan is an anti-HER2 antibody conjugated to a cytotoxic payload that is linked by a cleavable drug linker^[9]. This treatment has been recently approved by the FDA and it shows superior targeting of cytotoxic drugs to HER2+ tumor cells and shows efficacy on individuals who have been treated previously with anti-HER2 mAbs.

HER2-specific tyrosine kinase inhibitors have also been successful in treating HER2+ tumors, especially brain metastases because these drugs can cross the blood-brain barrier. Lapatinib, neratinib, pyrotinib, and tucatinib are four HER2-specific tyrosine kinase inhibitors used to treat HER2+ breast cancers. Lapatinib is an oral, irreversible small molecule HER1/HER2/HER4 TKI that was first approved in 2007 for the treatment of metastatic breast cancer^[10]. Neratinib is a similar, orally available irreversible small molecule HER1/HER2/HER4 TKI that showed better efficacy against EGFR mutants and has been approved for use as an adjuvant therapy following trastuzumab treatment^[11]. The development of resistance is also a problem for HER2-targeted TKIs, and pyrotinib is an experimental HER1/HER2/HER4 TKI under investigation as a potential new drug that is less prone to resistance^[12]. Tucatinib is a TKI that is highly selective for HER2 approved for use in combination with trastuzumab and capecitabine in HER2+ breast and colorectal cancers, including patients with metastases and who have received previous anti-HER2 treatment^[13].

HER2+ breast cancers continue to be challenging to treat due to resistance and metastasis. Combination therapies with antibodies and targeted inhibitors have dramatically improved survival in HER2+ breast cancer patients, but individuals who relapse continue to be faced with limited treatment options. New antibody-drug conjugates, bispecific antibodies, and targeted inhibitors are under investigation and hold the promise of better, more durable treatment options for patients.

^[1] Hudis CA. Trastuzumab--mechanism of action and use in clinical practice. N. Engl. J. Med. 2007 Jul 5;357(1):39-51.

^[2] Slamon DJ, Clark GM, Wong SG, Levin WJ, Ullrich A, McGuire WL. Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science. 1987 Jan 9;235(4785):177-82.

^[3] Moasser MM. The oncogene HER2: its signaling and transforming functions and its role in human cancer pathogenesis. Oncogene. 2007 Oct 4;26(45):6469-87.

^[4] Romond EH, Perez EA, Bryant J, Suman VJ, Geyer Jr CE, Davidson NE, Tan-Chiu E, Martino S, Paik S, Kaufman PA, Swain SM. Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N. Engl. J. Med. 2005 Oct 20;353(16):1673-84.

^[5] Smith I, Procter M, Gelber RD, Guillaume S, Feyereislova A, Dowsett M, Goldhirsch A, Untch M, Mariani G, Baselga J, Kaufmann M. 2-year follow-up of trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer: a randomised controlled trial. Lancet. 2007 Jan 6;369(9555):29-36.

^[6] Rugo HS, Im SA, Cardoso F, Cortés J, Curigliano G, Musolino A, Pegram MD, Wright GS, Saura C, Escrivá-de-Romaní S, De Laurentiis M. Efficacy of margetuximab vs trastuzumab in patients with pretreated ERBB2-positive advanced breast cancer: a phase 3 randomized clinical trial. JAMA Oncol. 2021 Apr 1;7(4):573-84

^[7] https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-margetuximab-metastatic-her2-positive-breast-cancer.

^[8] Kunte S, Abraham J, Montero AJ. Novel HER2-targeted therapies for HER2-positive metastatic breast cancer. Cancer. 2020 Oct 1;126(19):4278-4288.

^[9] Doi T, Shitara K, Naito Y, Shimomura A, Fujiwara Y, Yonemori K, Shimizu C, Shimoi T, Kuboki Y, Matsubara N, Kitano A, Jikoh T, Lee C, Fujisaki Y, Ogitani Y, Yver A, Tamura K. Safety, pharmacokinetics, and antitumour activity of trastuzumab deruxtecan (DS-8201), a HER2-targeting antibody-drug conjugate, in patients with advanced breast and gastric or gastro-oesophageal tumours: a phase 1 dose-escalation study. Lancet Oncol. 2017 Nov;18(11):1512-1522.

^[10] Ryan Q, Ibrahim A, Cohen MH, Johnson J, Ko CW, Sridhara R, Justice R, Pazdur R. FDA drug approval summary: lapatinib in combination with capecitabine for previously treated metastatic breast cancer that overexpresses HER-2. Oncologist. 2008 Oct;13(10):1114-9.

^[11] Minami Y, Shimamura T, Shah K, LaFramboise T, Glatt KA, Liniker E, Borgman CL, Haringsma HJ, Feng W, Weir BA, Lowell AM, Lee JC, Wolf J, Shapiro GI, Wong KK, Meyerson M, Thomas RK. The major lung cancer-derived mutants of ERBB2 are oncogenic and are associated with sensitivity to the irreversible EGFR/ERBB2 inhibitor HKI-272. Oncogene. 2007 Jul 26;26(34):5023-7.

^[12] Li Q, Guan X, Chen S, Yi Z, Lan B, Xing P, Fan Y, Wang J, Luo Y, Yuan P, Cai R, Zhang P, Li Q, Zhong D, Zhang Y, Zou J, Zhu X, Ma F, Xu B. Safety, Efficacy, and Biomarker Analysis of Pyrotinib in Combination with Capecitabine in HER2-Positive Metastatic Breast Cancer Patients: A Phase I Clinical Trial. Clin. Cancer Res. 2019 Sep 1;25(17):5212-5220.

^[13] Murthy RK, Loi S, Okines A, Paplomata E, Hamilton E, Hurvitz SA, Lin NU, Borges V, Abramson V, Anders C, Bedard PL, Oliveira M, Jakobsen E, Bachelot T, Shachar SS, Müller V, Braga S, Duhoux FP, Greil R, Cameron D, Carey LA, Curigliano G, Gelmon K, Hortobagyi G, Krop I, Loibl S, Pegram M, Slamon D, Palanca-Wessels MC, Walker L, Feng W, Winer EP. Tucatinib, Trastuzumab, and Capecitabine for HER2-Positive Metastatic Breast Cancer. N Engl J Med. 2020 Feb 13;382(7):597-609.

Prostate cancer is one of the most common forms of cancer that affects the prostate gland in the male urogenital tract. Most prostate cancers are slow growing and are usually detected in individuals older than age 50. Although environmental factors contribute to the development of prostate cancer, risk is significantly associated with incidence among first-degree relatives. In recent years, several inherited and spontaneously mutated genes have been linked to prostate cancer. Here we highlight these findings and how they provide insight into the development of targeted prostate cancer therapies.

Prostate cancer tumors are typically characterized by a wide range of genomic aberrations including somatic copy number alterations (SCNAs), structural rearrangements, and point mutations. Metastatic prostate tumors may have hundreds of these aberrations throughout the genome, but recent studies of primary prostate tumors have been critical to defining mutations associated with tumor development. Most primary prostate tumors have SCNAs, typically in the form of deletions that target a small area of the genome¹. Deletions are often seen in the tumor suppressor genes BRCA2, NKX3.1, PTEN, and RB1².

Structural rearrangements are another source of genomic variation observed in primary prostate tumors, for which the TMPRSS2:ERG rearrangement is most common and causes the androgen-responsive TMPRSS2 serine protease to drive expression of the ERG oncogene³. Other rearrangements have been linked to prostate cancer, including TMPRSS2 fusions with other ETS family members beyond ERG (ETV1 and ETV4)⁴. Some studies have suggested a link between ERG rearrangements and SCNA incidence, although it is not yet clear if rearrangements lead to destabilization of the genome and increased occurrence of SCNAs¹.

Somatic mutations occur on relatively high frequency primary prostate tumors, and this has been linked to mutations DNA mismatch repair proteins, tumor suppressors and oncogenes. The tumor suppressor TP53 is consistently identified as mutated in prostate tumors⁵. Mutations in the tumor suppressor genes BRCA1 and BRCA2 are well known for their association with breast and ovarian cancer but have also been linked to prostate cancer, and recent studies have shown that certain BRCA2 pathogenic sequence variants are associated with an elevated risk for aggressive prostate cancer^6,7. PALB2 is a protein that interacts with BRCA2, and a recent study indicated that individuals who have certain PALB2 variants are more predisposed to aggressive forms of prostate cancer⁸. In addition, mutations in genes associated with DNA mismatch repair (MMR), such as MSH2, MSH6, and MLH1, are associated with greater prostate cancer risk⁹, and individuals with Lynch syndrome, which is caused by a germline mutation in one of these MMR genes, are also at greater risk of developing an aggressive form of prostate cancer¹⁰.

One of the most important genes involved in prostate cancer progress is the gene expressing the androgen receptor (AR). Dozens of somatic mutations have been identified in the AR, and many of these mutations target the ligand binding domain¹¹. Some prostate cancers can be treated successfully with drugs that inhibit AR signaling, such as enzalutamide, but resistance frequently occurs and is associated with worse outcomes. AR promotes prostate cancer cell survival by regulating several cellular programs. Although AR activity inhibition through androgen deprivation therapy (ADT) results in the suppression of AR-related pathways and durable clinical remission¹², the disease may recur as castration-resistant prostate cancer (CRPC), typically with reactivated AR signaling. In this case, patients are treated with second-generation AR pathway inhibitors such as enzalutamide and abiraterone. Unfortunately, durable complete responses under these treatments are rare, and a substantial number of CRPC tumors progress under treatment despite loss of AR signaling. CRPC with AR-null phenotype are classified as tumors with diffuse small cell or neuroendocrine (NE) characteristics (SCNPC) or as double-negative (DNPC) phenotype that lacks both NE and AR activity¹³. A recently described genome-wide CRISPR-Cas9 screen was used to identify kinases that could be inhibited in the presence of enzalutamide. BRAF or downstream MAPK signaling molecules were identified as targets that could be co-inhibited with enzalutamide to improve overall therapeutic effects of these drugs¹⁴.

Genomic alterations in prostate cancer are highly variable and can impact many critical cellular processes. By understanding which genes drive disease progression, potential therapeutic targets can be identified, and disease outcomes under different treatment regimens can be better predicted.

[1] Taylor BS, Schultz N, Hieronymus H, et al. Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010 Jul 13;18(1):11-22.

[2] Wallis CJ, Nam RK. Prostate Cancer Genetics: A Review. EJIFCC. 2015 Mar 10;26(2):79-91.

[3] Tomlins SA, Rhodes DR, Perner S et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. 2005 Oct 28;310(5748):644-8.

[4] Rubin MA, Maher CA, Chinnaiyan AM. Common gene rearrangements in prostate cancer. J. Clin. Oncol. 2011 Sep 20;29(27):3659-68.

[5] Ecke TH, Schlechte HH, Schiemenz K et al. TP53 gene mutations in prostate cancer progression. Anticancer Res. 2010 May 1;30(5):1579-86.

[6] Patel VL, Busch EL, Friebel TM, et al. Association of Genomic Domains in BRCA1 and BRCA2 with Prostate Cancer Risk and Aggressiveness. Cancer Res. 2020 Feb 1;80(3):624-638.

[7] Oh M, Alkhushaym N, Fallatah S, et al. The association of BRCA1 and BRCA2 mutations with prostate cancer risk, frequency, and mortality: A meta-analysis. Prostate. 2019 Jun;79(8):880-895.

[8] Wokołorczyk D, Kluźniak W, Stempa K, Rusak B, Huzarski T, Gronwald J, Gliniewicz K, Kashyap A, Morawska S, Dębniak T, Jakubowska A. PALB2 mutations and prostate cancer risk and survival. Br. J. Cancer. 2021 May 18:1-7.

[9] Ritch E, Fu SY, Herberts C, Wang G, et al. Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer. Clin. Cancer Res. 2020 Mar 1;26(5):1114-25.

[10] Haraldsdottir S, Hampel H, Wei L, et al. Prostate cancer incidence in males with Lynch syndrome. Genet. Med. 2014 Jul;16(7):553-7.

[11] Ferraldeschi R, Welti J, Luo J, Attard G, de Bono JS. Targeting the androgen receptor pathway in castration-resistant prostate cancer: progresses and prospects. Oncogene. 2015 Apr 2;34(14):1745-57.

[12] Heinlein CA, Chang C. Androgen receptor in prostate cancer. Endocr Rev. 2004;25(2):276–308.

[13] Bluemn EG, Coleman IM, Lucas JM et al. Androgen receptor pathway-independent prostate cancer is sustained through FGF signaling. Cancer Cell. 2017;32(4):474–489.

[14] Palit SAL, van Dorp J, Vis D, Lieftink C, Linder S, Beijersbergen R, Bergman AM, Zwart W, van der Heijden MS. A kinome-centered CRISPR-Cas9 screen identifies activated BRAF to modulate enzalutamide resistance with potential therapeutic implications in BRAF-mutated prostate cancer. Sci. Rep. 2021 Jul 1;11(1):13683.

Preclinical oncology research is a critical component in the development of new cancer therapeutics, and it is essential that drug candidates are carefully screened before they are tested in human clinical trials. One valuable tool in preclinical oncology research is the use of cell line-derived xenograft (CDX) models. In this blog post, we will explore the benefits of CDX models for preclinical oncology screening and how they can be used to improve our understanding of cancer and the development of new treatments.

CDX models are created by implanting human cancer cells into immunocompromised mice. These cells develop into tumors that resemble their human counterparts and can be used to study the biology of cancer and test new treatments. One significant advantage of CDX models is that they are relatively easy and fast to establish, making them a cost-effective alternative to other preclinical screening models.^[1]

CDX models allow researchers to study the response of tumors to treatments in vivo, replicating the conditions of human cancer. Additionally, they can be used to evaluate the pharmacodynamics and pharmacokinetics (PD/PK) of candidate drugs. These models allow researchers to evaluate how drugs impact tumor growth over time, and how the drug is distributed throughout the body. This information is critical in determining the optimal dosing regimen for cancer patients.^[2-4]

CDX models have been widely used in preclinical research for several decades and can provide valuable insights into the underlying biology of cancer. Tumors grown in CDX models can be analyzed in depth to identify biological markers that can inform the development of targeted therapies. The use of CDX models can help researchers better understand the complexity of cancer and identify new therapeutic targets.^[5-6]

In conclusion, CDX models offer several advantages for preclinical oncology screening, including their ease of establishment, ability to replicate human conditions, and ability to provide insights into the biology of cancer. By incorporating CDX models into their preclinical screening strategies, researchers can more accurately predict the efficacy of cancer drugs and improve the development of new cancer therapies.

1.    Long Y, Xie B, Shen HC, Wen D. Translation Potential and Challenges of In Vitro and Murine Models in Cancer Clinic. Cells. 2022 Nov 30;11(23):3868. doi: 10.3390/cells11233868. PMID: 36497126; PMCID: PMC9741314.

2.    Qin L, Wang L, Zhang J, Zhou H, Yang Z, Wang Y, Cai W, Wen F, Jiang X, Zhang T, Ye H, Long B, Qin J, Shi W, Guan X, Yu Z, Yang J, Wang Q, Jiao Z. Therapeutic strategies targeting uPAR potentiate anti-PD-1 efficacy in diffuse-type gastric cancer. Sci Adv. 2022 May 27;8(21):eabn3774. doi: 10.1126/sciadv.abn3774. Epub 2022 May 25. PMID: 35613265; PMCID: PMC9132454.

3.    Chen Y, Chen HN, Wang K, Zhang L, Huang Z, Liu J, Zhang Z, Luo M, Lei Y, Peng Y, Zhou ZG, Wei Y, Huang C. Ketoconazole exacerbates mitophagy to induce apoptosis by downregulating cyclooxygenase-2 in hepatocellular carcinoma. J Hepatol. 2019 Jan;70(1):66-77. doi: 10.1016/j.jhep.2018.09.022. Epub 2018 Oct 1. PMID: 30287340.

4.    Kendsersky NM, Lindsay J, Kolb EA, Smith MA, Teicher BA, Erickson SW, Earley EJ, Mosse YP, Martinez D, Pogoriler J, Krytska K, Patel K, Groff D, Tsang M, Ghilu S, Wang Y, Seaman S, Feng Y, Croix BS, Gorlick R, Kurmasheva R, Houghton PJ, Maris JM. The B7-H3-Targeting Antibody-Drug Conjugate m276-SL-PBD Is Potently Effective Against Pediatric Cancer Preclinical Solid Tumor Models. Clin Cancer Res. 2021 May 15;27(10):2938-2946. doi: 10.1158/1078-0432.CCR-20-4221. Epub 2021 Feb 22. PMID: 33619171; PMCID: PMC8127361.

5.    Oduwole OO, Poliandri A, Okolo A, Rawson P, Doroszko M, Chrusciel M, Rahman NA, Serrano de Almeida G, Bevan CL, Koechling W, Huhtaniemi IT. Follicle-stimulating hormone promotes growth of human prostate cancer cell line-derived tumor xenografts. FASEB J. 2021 Apr;35(4):e21464. doi: 10.1096/fj.202002168RR. PMID: 33724574.

6.    Tang N, Cheng C, Zhang X, Qiao M, Li N, Mu W, Wei XF, Han W, Wang H. TGF-β inhibition via CRISPR promotes the long-term efficacy of CAR T cells against solid tumors. JCI Insight. 2020 Feb 27;5(4):e133977. doi: 10.1172/jci.insight.133977. PMID: 31999649; PMCID: PMC7101140.

Signal transduction networks are essential to normal cell growth and function, but signaling abnormalities, such as those caused by spontaneous mutations in signaling components, are the leading causes of tumor growth. The extracellular signal-regulated kinase (ERK) signaling pathway contributes to normal cell proliferation, differentiation, and survival, but components of the ERK pathway are upregulated in many tumor types, including those associated with melanoma, lung, colon and pancreatic cancers.

The critical role of the ERK pathway in cancer has resulted in the development of drugs and therapeutics that can inhibit overactivation of ERK signaling molecules or target aberrant signaling pathways upstream of ERK. The emergence of precision medicine-driven cancer treatments has advanced the ERK pathway inhibitor field. Breakthroughs in cancer genomics has enabled researchers to analyze tumor sequences derived from patient data and identify novel targets in the ERK pathway. This type of computational analysis coupled with large scale in vitro screening is essential to narrowing down which novel inhibitors are studied further during preclinical development.

The use of patient-derived xenograft (PDX) mouse models is critical to the discovery of next-generation ERK inhibitors. PDX models involve the use of mice that are engrafted with tumor tissue derived from patient samples. These mice typically have suppressed immune systems in order to tolerate tumor grafts and can be engineered to express other components of the human immune system, such as immune checkpoint inhibitors. PDX models that use tumors with mutations in ERK signaling, such as a colorectal tumor with a V600-mutated BRAF molecule, can be used in the preclinical screening of novel ERK pathway inhibitors. Novel inhibitors can be screened simultaneously in different PDX models, and the safety and efficacy of these molecules can also be assessed in combination with other therapeutics.

We are entering an era when cancer patients will have access to precision medicine treatments informed by the genetic analysis of their tumors, and the strategic deployment of new and improved ERK pathway inhibitors in patients with specific ERK mutations will improve treatment efficacy and overall survival. PDX models are essential to the development of these new ERK pathway inhibitors and many other novel immunotherapies.

The quality of data received from clinical specialty testing labs is largely dependent on the integrity of the samples tested. One critical aspect of this is the proper isolation of PBMCs - peripheral blood mononuclear cells - often used in high-complexity flow cytometry research. To get the best quality results, researchers must use the most optimal tubes to isolate these cells. Three main types of tubes are commonly used: SepMate tubes, CPT tubes, and Manual Ficoll Gradient tubes. Each of these tubes has advantages and disadvantages that researchers must consider carefully. In this blog post, we will look at the pros and cons of each tube type and what you should consider before selecting one for your clinical trial.

SepMate Tubes:

SepMate tubes come in different sizes that enable researchers to isolate PBMCs from different numbers of tubes at once. These tubes work by using an inserted plastic separation technology that helps remove unwanted clumps of cells. One of the most significant advantages of these tubes is that they can be used for small to medium-sized samples with ease. The technology also separates cells significantly, making it easy to measure the concentration of cells after the separation procedure accurately. Furthermore, the tube also allows for rapid and consistent layering and easy collection of PBMCs, making it ideal for research. However, obtaining a high percentage of neutrophils is not possible, as they would be trapped below the barrier inside the tube. SepMate tubes are disposable, which makes them less financially sensible in the long run.

CPT Tubes:

CPT tubes are anticoagulant-based layered tubes that allow for the collection directly to cell separation without any additional processing. CPT tubes simplify the separation process and reduce the risk of contamination. They offer a more robust PBMC isolation process, and specific manufacturers produce four types to suit different research needs regarding testing human cells. The tubes generate high PBMC yields with high cell viability, making them an optimal option where quality is paramount. The primary disadvantage of CPT tubes is that they are quite expensive when compared to other tube types for PBMC isolation.

Manual Ficoll Gradient Tubes:

Manual Ficoll Gradient tubes require manual handling and processing, so they aren't automated. Due to this, the individual processing of Ficoll gradient tubes can cause variability in the manual layering steps, leading to variation in the final cell yield. The biggest issue with this type of isolation tube is that it takes longer to obtain the actual PBMCs than using SepMate or CPT tubes, which may create more significant delays in your research. Additionally, due to the manual nature of this type of PBMC isolation, final PBMC recovery rates are usually dependent on the experience of the researcher.

In conclusion, the right tube type will depend on your primary requirements for your research. Regardless of your choice, there is still a need to make sure you select a tube type that meets the technical requirements of your studies and delivers high-quality results. Champions Oncology has expertise in GCLP-compliant PBMC isolation using SepMate, CPT, and manual Ficoll Gradient tube types and can advise the best choice for your upcoming clinical trial.

Sarcomas are a group of aggressive heterogeneous tumors for which more than 100 histological subtypes have been defined¹. Sarcomas are found in a variety of solid tissues, including bone and gastrointestinal stromal cells. Current treatment options include radiotherapy, surgical resection, targeted therapies, and chemotherapy, but these treatments have had limited efficacy on intermediate to high-grade tumors. Investigations into the molecular and cellular mechanisms that drive sarcomas have helped identify potential biomarkers that can serve as potential therapeutic targets. In addition, recent studies have also focused on the tumor microenvironment (TME) within sarcomas and the roles of different immune cell subsets creating an immunosuppressive microenvironment. These observations directly inform novel immunotherapeutic approaches that are being examined in preclinical and clinical studies.

Sarcoma TME and Immune Checkpoint Blockade

In general, sarcoma TMEs are highly immunosuppressive environments, and a recent analysis of the Ewing’s sarcoma family of tumors (ESFT) showed poor overall survival correlated with tumors that had a TME with elevated expression of hypoxia-inducible factor 1-α and were enriched with immunosuppressive M2 macrophages and neutrophils². The presence of tumor-associated macrophages has also been linked to sarcoma growth and metastasis, and elevated expression of the immune checkpoint molecule PD-L1 also correlated with metastasis and poor overall survival^3,4. These observations led to clinical trials that evaluated the efficacy of immune checkpoint blockade for treating sarcomas, but treatments that targeted PD-1/PD-L1 or CTLA-4 showed limited clinical efficacy and did not meet primary endpoints for overall survival^5,6.

Targeted Therapies

Genomic studies of sarcomas have been critical to identifying mutations associated with tumor growth, angiogenesis, and metastasis. These findings led to clinical trials examining the efficacy of tyrosine kinase inhibitors or inhibitors that target vascular endothelial growth factor or insulin-like growth factor-1, but most of these trials failed to meet overall survival endpoints^7,8. More recent genomic studies have indicated that mutations associated with different tumors occur in the same genes as some of the targeted therapies, but the mutations differ sufficiently to render these therapies ineffective⁹.

Cellular Immunotherapy

Cell-based immunotherapies have shown great promise in treating hematologic malignancies and are being explored for solid tumors. Chimeric antigen receptor (CAR) T cells have been of particular interest as they are patient-derived T cells engineered to express a tumor-specific receptor and thus can target tumors without being detected as foreign cells. Preclinical studies suggested that sarcoma-specific CAR T cells may be effective, but clinical trials have failed due to poor penetration and function of CAR T cells in the immunosuppressive TME¹⁰.

Recent and ongoing studies are exploring the effects of multi-CAR T cell strategies that target different tumor antigens, as well as the effects of using modified dendritic cells or natural killer cells or combining treatment modalities¹¹.

Effective and lasting treatment options for sarcomas continue to be elusive but advances in genomic analysis and immune-based treatments are slowly improving outcomes. Like other cancers, clinical studies exploring treatment combinations are also showing promise and may provide critical breakthroughs for some of the most aggressive sarcomas.

 ¹ Doyle LA. Sarcoma classification: an update based on the 2013 World Health Organization Classification of Tumors of Soft Tissue and Bone. Cancer. 2014 Jun 15;120(12):1763-74.

 ² Stahl D, Gentles AJ, Thiele R, Gütgemann I. Prognostic profiling of the immune cell microenvironment in Ewing’s Sarcoma Family of Tumors. Oncoimmunology. 2019 Dec 2;8(12):e1674113.

³ Xiao W, Klement JD, Lu C, Ibrahim ML, Liu K. IFNAR1 controls autocrine type I IFN regulation of PD-L1 expression in myeloid-derived suppressor cells. J. Immunol. 2018 Jul 1;201(1):264-77.

⁴ Zhu Z, Jin Z, Zhang M, Tang Y, Yang G, Yuan X, Yao J, Sun D. Prognostic value of programmed death-ligand 1 in sarcoma: a meta-analysis. Oncotarget. 2017 Aug 29;8(35):59570.

⁵ Maki RG, Jungbluth AA, Gnjatic S, Schwartz GK, D’Adamo DR, Keohan ML, Wagner MJ, Scheu K, Chiu R, Ritter E, Kachel J. A pilot study of anti-CTLA4 antibody ipilimumab in patients with synovial sarcoma. Sarcoma. 2013 Oct;2013.

⁶ Zuo W and Lingdi Z. Recent advances and application of PD-1 blockade in sarcoma." Oncotargets and Therapy 2019; 12:6887.

⁷ Ray-Coquard IL, Domont J, Tresch-Bruneel E, Bompas E, Cassier PA, Mir O, Piperno-Neumann S, Italiano A, Chevreau C, Cupissol D, Bertucci F. Paclitaxel given once per week with or without bevacizumab in patients with advanced angiosarcoma: a randomized phase II trial. J. Clin. Oncol. 2015 Sep 1;33(25):2797-802.

⁸ Tap WD, Demetri G, Barnette P, Desai J, Kavan P, Tozer R, Benedetto PW, Friberg G, Deng H, McCaffery I, Leitch I. Phase II study of Ganitumab, a fully human anti–type-1 insulin-like growth factor receptor antibody, in patients with metastatic ewing family tumors or desmoplastic small round cell tumors. J. Clin. Oncol. 2012 May 20;30(15):1849-56.

⁹ Trédan O, Wang Q, Pissaloux D, Cassier P, de la Fouchardière A, Fayette J, Desseigne F, Ray-Coquard I, de la Fouchardière C, Frappaz D, Heudel PE. Molecular screening program to select molecular-based recommended therapies for metastatic cancer patients: analysis from the ProfiLER trial. Ann. Oncol. 2019 May 1;30(5):757-65.

₁₀ Thanindratarn P, Dean DC, Nelson SD, Hornicek FJ, Duan Z. Chimeric antigen receptor T (CAR-T) cell immunotherapy for sarcomas: From mechanisms to potential clinical applications. Cancer Treatment Reviews. 2020 Jan 1; 82:101934.

¹¹ Patel S, Burga RA, Powell AB, Chorvinsky EA, Hoq N, McCormack SE, Van Pelt SN, Hanley PJ, Cruz CR. Beyond CAR T cells: other cell-based immunotherapeutic strategies against cancer. Front. Onc. 2019 Apr 10; 9:196.

Ovarian cancer remains one of the leading causes of mortality for women with gynecological cancers and continues to be associated with stubbornly low 5-year survival rates. Depending on the stage or type of ovarian cancer, localized treatments including surgical resection or radiation may be sufficient. Treatment of metastatic ovarian cancer may include surgery and radiation combined with chemotherapy. Hormone therapy is also typically combined with chemotherapy for targeted reduction of estrogen and/or stimulation of progesterone for the targeted treatment of ovarian stromal tumors that produce high levels of estrogen. Nonetheless, many of these treatments have limited efficacy for treating metastatic ovarian cancer.

Advances in targeted ovarian cancer treatments have been facilitated by identification of cellular replication machinery in some cancer subtypes, including defects in the breast cancer-associated protein (BRCA)1 and BRCA2 genes, which play critical roles in DNA repair and transcription regulation^[1]. Poly (ADP-ribose) polymerases (PARP) are a family of enzymes that can repair single strand DNA breaks through the base excision repair pathway^[2]. PARPs can work together with normal BRCA1/2 to repair double strand DNA breaks by the homologous recombination (HR) pathway. Preclinical studies have shown that PARP inhibitors are effective in cells with BRCA1/2 mutations because these mutations combined with PARP inhibition cause synthetic lethality due to blockade of multiple DNA repair pathways.

Olaparib was the first PARP inhibitor approved for the treatment of germline BRCA1/2-mutated metastatic ovarian cancer in 2014^[3]. This treatment was recommended for patients who had undergone three or more rounds of chemotherapy. Olaparib was later approved as a first-line maintenance therapy for germline or somatic BRCA1/2 mutations as well for the treatment of advanced ovarian cancers that have partial or complete responses to first-line platinum-based chemotherapies. Two other PARP inhibitors are also currently approved for different ovarian cancer diagnoses including rucaparib, which is approved for the treatment of germline BRCA1/2 mutations following two rounds of chemotherapy and for maintenance therapy following platinum-based therapies regardless of BRCA mutation status. Similarly, niraparib is approved to treat ovarian cancers with BRCA1/2 mutations or genomic instability and disease progression following platinum-based chemotherapies.

Like many other targeted therapies, some patients are completely unresponsive to treatment or develop resistance to PARP inhibitor monotherapy. Recent studies have described promising results associated with combined treatments, including PARP inhibitors combined with anti-angiogenic drugs like bevacizumab^[4] or immune check point inhibitors like pembrolizumab^[5]. There are currently three ongoing phase III first-line trials comparing the efficacy of combining PARP inhibitors and immune checkpoint blockade with VEGF inhibitors. Several thousand women are being enrolled in these studies with a goal of trying to determine if these combinations improve outcomes^[6].

PARP inhibitors continue to be effective for treating hormone receptor-negative tumors but are less effective in treating hormone-receptor-positive ovarian tumors. Current trials are exploring the use of hormone inhibitors to disrupt hormone receptor signaling in ovarian tumors and render them sensitive to PARP inhibition^[7].

PARP inhibitors have provided clinical benefits to ovarian cancer patients who previously had limited treatment options. Future studies will likely improve the efficacy of PARP inhibition as a monotherapy or in combination with other targeted therapies.

[1] Venkitaraman AR. Functions of BRCA1 and BRCA2 in the biological response to DNA damage. J Cell Sci. 2001 Oct;114(Pt 20):3591-8.

[2] D'Amours D, Desnoyers S, D'Silva I, Poirier GG. Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem J. 1999 Sep 1;342 ( Pt 2)(Pt 2):249-68.

[3] Franzese E, Centonze S, Diana A, Carlino F, Guerrera LP, Di Napoli M, De Vita F, Pignata S, Ciardiello F, Orditura M. PARP inhibitors in ovarian cancer. Cancer Treatment Reviews. 2019 Feb 1;73:1-9.

[4] Ray-Coquard I, Pautier P, Pignata S, Pérol D, González-Martín A, Berger R, Fujiwara K, Vergote I, Colombo N, Mäenpää J, Selle F. Olaparib plus bevacizumab as first-line maintenance in ovarian cancer. New England Journal of Medicine. 2019 Dec 19;381(25):2416-28.

[5] Konstantinopoulos PA, Waggoner S, Vidal GA, Mita M, Moroney JW, Holloway R, Van Le L, Sachdev JC, Chapman-Davis E, Colon-Otero G, Penson RT, Matulonis UA, Kim YB, Moore KN, Swisher EM, Färkkilä A, D'Andrea A, Stringer-Reasor E, Wang J, Buerstatte N, Arora S, Graham JR, Bobilev D, Dezube BJ, Munster P. Single-Arm Phases 1 and 2 Trial of Niraparib in Combination with Pembrolizumab in Patients With Recurrent Platinum-Resistant Ovarian Carcinoma. JAMA Oncol. 2019 Aug 1;5(8):1141-1149.

[6] Elyashiv, Osnat, Yien Ning Sophia Wong, and Jonathan A. Ledermann. "Frontline Maintenance Treatment for Ovarian Cancer." Current Oncology Reports 23.8 (2021): 1-10.m

[7] Matulonis UA, Wulf GM, Barry WT, Birrer M, Westin SN, Farooq S, Bell-McGuinn KM, Obermayer E, Whalen C, Spagnoletti T, Luo W. Phase I dose escalation study of the PI3kinase pathway inhibitor BKM120 and the oral poly (ADP ribose) polymerase (PARP) inhibitor olaparib for the treatment of high-grade serous ovarian and breast cancer. Annals of Oncology. 2017 Mar 1;28(3):512-8.

With advances in next-generation sequencing (NGS) technologies, gene expression analysis has become an increasingly popular area of research. Two common methods used for this purpose are RNA sequencing (RNAseq) and whole transcriptome sequencing (WTS). Both techniques provide valuable insights into the molecular mechanisms of individual cells and organisms. However, when should one use RNAseq versus WTS for gene expression analysis? In this post, we will explore the advantages and disadvantages of both methods and provide guidance on which one to use.

RNAseq

RNAseq is a method of sequencing RNA molecules and measuring the abundance of each transcript. This method is capable of identifying all types of RNA, including messenger RNA (mRNA), noncoding RNA, and small RNA. It requires high-quality RNA and can detect alternative splicing, fusion genes, and post-transcriptional modifications. RNAseq is particularly useful for identifying novel transcripts and quantifying gene expression levels in low-abundance genes^[1].

However, RNAseq has some disadvantages. Its high sensitivity may lead to high levels of noise when dealing with lowly expressed genes. The method can also be expensive, and the data analysis process can be complex. Additional bioinformatic tools are required to accurately quantify gene expression levels, identify differential expression, and perform pathway analysis^[1].

Whole Transcriptome Sequencing

WTS is a newer approach that can comprehensively analyze the transcriptome of an organism without relying on annotation. This method sequences the entire complement of RNA sequences, including both known and unknown transcripts. WTS can provide greater resolution for splice variants and more accurate gene expression quantification compared to RNAseq^[2].

WTS has several advantages, including the elimination of the need for gene annotation. The technique is also cost-effective since the sequencing depth can be adjusted based on the number of samples analyzed. The method is flexible and can be used in a variety of applications such as identifying regulatory noncoding RNAs and studying alternative splicing events^[2].

However, WTS comes with a few drawbacks. The technique requires higher sequencing depth for accurate gene expression quantification, which can increase the cost of the experiment. Additionally, WTS can detect unexpected transcripts or splice variants, creating new challenges for data analysis and interpretation^[2].

When to use RNAseq versus WTS

Choosing between RNAseq and WTS depends on the goals of the experiment, the type of RNA to be analyzed, and the available resources. Researchers should consider the complexity of their sample and the genotypic variation, as WTS is better suited for samples with a higher degree of variability. RNAseq is a better choice for studies involving differential expression of known protein-coding genes. In contrast, WTS can identify novel transcripts and regulatory noncoding RNA without relying on a predetermined set of annotated transcripts^[3-4].

In conclusion, RNAseq and WTS are both powerful techniques for gene expression analysis. RNAseq is better suited for identifying differentially expressed genes in complex samples with low-abundance genes, while WTS is more effective when searching for novel transcripts and studying alternative splicing events. Both techniques require careful experimental design and bioinformatic analysis for accurate results. Ultimately, researchers should choose the method that aligns with their experimental goals and available resources. Understanding the advantages and disadvantages of each method can help optimize experimental design and result interpretation.

At Champions Oncology, we offer both RNAseq and WTS. We use an enrichment-based RNAseq method when the input RNA is of high quality, while we opt for a depletion-based WTS method when the input RNA quality is lower, with an integrity score as low as 2.0. This approach allows us to utilize different methods in different situations to obtain gene expression results from a broader range of samples.

[1] Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet. 2011 Sep 7;12(10):671-82. doi: 10.1038/nrg3068. PMID: 21897427.

[2] Jobanputra V, Wrzeszczynski KO, Buttner R, Caldas C, Cuppen E, Grimmond S, Haferlach T, Mullighan C, Schuh A, Elemento O. Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology. Semin Cancer Biol. 2022 Sep;84:23-31. doi: 10.1016/j.semcancer.2021.07.003. Epub 2021 Jul 10. PMID: 34256129.

[3] Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, Khaitovich P. Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics. 2009 Apr 16;10:161. doi: 10.1186/1471-2164-10-161. PMID: 19371429; PMCID: PMC2676304.

[4] Ruan M, Liu J, Ren X, Li C, Zhao AZ, Li L, Yang H, Dai Y, Wang Y. Whole transcriptome sequencing analyses of DHA treated glioblastoma cells. J Neurol Sci. 2019 Jan 15;396:247-253. doi: 10.1016/j.jns.2018.11.027. Epub 2018 Nov 22. PMID: 30529802.

Gastrointestinal cancers are a heterogeneous group of cancers that can be caused by H. pylori bacterial or Epstein-Barr virus infection, chronic inflammation, or inherited or spontaneous genetic mutations. Advances in solid tumor immunotherapy for gastrointestinal cancers include the development of methods that improve the screening, evaluation, and development of more precise and robust treatments. Breakthroughs in basic and translational research are leading to better treatment options for gastrointestinal cancer, and CRISPR/Cas9-based (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) gene editing technology is at the forefront of these discoveries.

CRISPR/Cas9-based gene editing technology was originally identified in bacteria and archaea as an antiviral defense mechanism^[1]. As a gene editing application, CRISPR/Cas9 uses the Cas9 nuclease to cleave specific sequences in the target DNA and introduces modifications such as knock-in or knock-out mutations^[2]. The DNA sequence is targeted using a single-guide RNA (sgRNA) comprised of CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracRNA), and these RNAs can be expressed on the same plasmid as the Cas9 nuclease upon delivery into target cells. The crRNA/tracrRNA duplex can bind to the complementary sequence in the genomic DNA and recruit Cas9, which cleaves the target sequence and allows for DNA repair by either homology-directed repair or non-homologous end pairing. This repaired sequence is now a part of the genomic DNA and leaves virtually no trace of gene editing.

CRISPR/Cas9 gene editing has been used for several applications in oncology research and more recently to improve immune-oncology strategies. One of the earliest applications involves knockout screens in which a library of sgRNAs is used to transfect a pool of knockouts that can be used for gain-of-function or small molecule/drug screens. Genome-wide screens of cancer cell lines have been useful in identifying genes that are essential to cancer cell growth but can be prone to false-positive hits if the screens are not correctly designed or analyzed^[3]. Genome-wide screens have also been used to identify genes linked to resistance, and such gene hits have been identified in a melanoma library screen when treating with the inhibitor vemurafenib^[4]. Combinatorial CRISPR/Cas9 screens are now being used to target multiple genes, and this approach can be used for defining genetic or cellular pathways involved in cancer or characterizing drugs that target multiple genes^[5].

CRISPR/Cas9 has moved beyond in vitro cell culture and can be used for human organoid models for studying oncogenesis. ARID1A is one of the most frequently mutated genes in solid tumors, including gastric tumors^[6]. ARID1A encodes a BAF complex subunit that normally targets BAF to AT-rich DNA sequences to regulate transcription. Mouse studies have suggested that ARID1A is involved in gastrointestinal cancer oncogenesis, but this was not validated in humans until a recent study that used CRISPR/Cas9-mediated depletion of ARID1A wild-type human gastric organoids. This ARID1A-knockout organoid system established a forward genetics model of gastric cancer that resembled gastric cancer phenotypically and identified BIRC5/Survivin as a key player in early tumorigenesis. This type of organoid model is not only useful for basic oncogenesis studies but can be used for small molecule inhibitor screens.

CRISPR/Cas9 screens can be used to validate mutations found in patients with gastrointestinal tumors. Activin A receptor type 2A (ACVR2A) is frequently mutated in patients with microsatellite instability-high gastric cancer, and a 2021 study used CRISPR/Cas9 to generate ACVR2A-knockout human gastric cancer cells^[7]. These cells exhibited less aggressive proliferation, migration, and invasion in vitro, and patients with ACVR2A mutations had better prognoses than patients with wild-type ACVR2A. Gastrointestinal stromal tumors (GIST) have been typically characterized by activation mutations in the receptor tyrosine kinase KIT, but a 2022 study using genome-wide CRISPR screening identified the complementary chromatin-modifying complexes MOZ and Menin-MLL as being essential to GIST^[8]. This finding highlights a trend in oncology research elucidating a role for chromatin regulation in tumorigenesis, which has the potential to be targeted therapeutically.

Beyond basic research, CRISPR/Cas9 is starting to be used in applications for clinical trials. A Phase II trial has recently launched that is using CRISPR/Cas9 to delete an intracellular checkpoint molecule called cytokine-induced SH2 (CISH) protein^[9]. Preclinical studies have shown that CRISPR/Cas9-mediated deletion of CISH enhanced antitumor responses, and the Phase II trial is using patient-derived CRISPR-modified T cells to treat individuals with metastatic gastrointestinal tumors.

CAR T-cells (Chimeric Antigen Receptor) have been an incredible progress in personalized therapy targeting cancer.^[10] However, different challenges hampered the availability, efficacy, and safety of this promising cell therapy. CRISPR-Cas9 technology can address many of these limitations. Desired genetic modification can be achieved with cellular precision engineering, leveraging CRISPR-Cas9-based gene editing. In addition, this approach can be exploited to overcome T-cell exhaustion, lack of CAR T-cell persistence, and toxicity related to cytokine release.

In particular, the implementation of CRISPR-Cas9 technology generated universal CAR T Cells resistant to PD1 Inhibition; or enhanced T cell function against bladder cancer disrupting CTLA-4.^[11]  In the oncolytic therapy field, it has been demonstrated that HSV-1-derived CD40L-armed oncolytic therapy by CRISPR-Cas9-based gene editing boosted endogenous immunity in pancreatic ductal adenocarcinoma.^[12]

CRISPR/Cas9 gene editing will continue to transform basic and clinical research, immunotherapy, and cellular therapy providing effective and safe therapeutic strategies. Regulatory agencies are now developing frameworks to allow for the use of this revolutionary tool in a wide range of diseases.

[1] Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature. 2012 Feb 15;482(7385):331-8.

[2] Barrangou R, Doudna JA. Applications of CRISPR technologies in research and beyond. Nat. Biotechnol. 2016;34(9):933-941.

[3] Munoz DM, Cassiani PJ, Li L, Billy E, Korn JM, Jones MD, Golji J, Ruddy DA, Yu K, McAllister G, DeWeck A. CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. Cancer Discovery. 2016 Aug 1;6(8):900-13.

[4] Shalem O, Sanjana NE, Hartenian E, Shi X , Scott DA , et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014. 343:84–87.

[5] Han K, Jeng EE, Hess GT, Morgens DW, Li A, Bassik MC. Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions. Nat. Biotechnol. 2017 May;35(5):463-74.

[6] Lo YH, Kolahi KS, Du Y, Chang CY, Krokhotin A, Nair A, Sobba WD, Karlsson K, Jones SJ, Longacre TA, Mah AT, Tercan B, Sockell A, Xu H, Seoane JA, Chen J, Shmulevich I, Weissman JS, Curtis C, Califano A, Fu H, Crabtree GR, Kuo CJ. A CRISPR/Cas9-Engineered ARID1A-Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation. Cancer Discov. 2021 Jun;11(6):1562-1581.

[7] Yuza K, Nagahashi M, Ichikawa H, Hanyu T, Nakajima M, Shimada Y, Ishikawa T, Sakata J, Takeuchi S, Okuda S, Matsuda Y, Abe M, Sakimura K, Takabe K, Wakai T. Activin a Receptor Type 2A Mutation Affects the Tumor Biology of Microsatellite Instability-High Gastric Cancer. J. Gastrointest. Surg. 2021 Jan 8. doi: 10.1007/s11605-020-04889-9. Epub ahead of print.

[8] Hemming ML, Benson MR, Loycano MA, Anderson JA, Andersen JL, Taddei ML, Krivtsov AV, Aubrey BJ, Cutler JA, Hatton C, Sicinska E. MOZ and Menin-MLL Complexes are Complementary Regulators of Chromatin Association and Transcriptional Output in Gastrointestinal Stromal Tumor. Cancer Discovery. 2022 May 2.

[9] https://twin-cities.umn.edu/news-events/university-minnesota-opens-first-its-kind-clinical-trial-treat-metastatic-gi-cancers

[10] Jogalekar MP, Rajendran RL, Khan F, Dmello C, Gangadaran P, Ahn BC.Front Immunol. 2022 Jul 22;13:925985. doi: 10.3389/fimmu.2022.925985. eCollection 2022.

[11] Zhang W, Shi L, Zhao Z, Du P, Ye X, Li D, Cai Z, Han J, Cai J. Disruption of CTLA-4 expression on peripheral blood CD8 + T cell enhances anti-tumor efficacy in bladder cancer. Cancer Chemother Pharmacol. 2019;83:911–20.

[12] Wang R, Chen J, Wang W, Zhao Z, Wang H, Liu S, et al. CD40L-armed oncolytic herpes simplex virus suppresses pancreatic ductal adenocarcinoma by facilitating the tumor microenvironment favorable to cytotoxic T cell response in the syngeneic mouse model. J Immunother Cancer. 2022;10(1):e003809.