Chapter 1: Exit Exam


The symptoms were sly, innocuous nuisances that were easily forgotten in Ann’s busy schedule. She always forgot to take her Claritin and wheezing was typical for an under-medicated, tired grad student in late spring. After all, she had had grass and tree allergies since her youth; these symptoms could easily have been seasonal. The weight loss, too, didn’t seem significant. A sigh left Ann’s lips as she remembered thinking that her New Year’s fitness plan was finally working. Even when her phlegm was a little darker than usual, she didn’t bother checking it out. She’d spent the weekend at a monster truck convention (event 8 of 10 on a “Before We Get Married” bucket list Eric had planned) where the dust could have easily discolored the expelled lung fluid. The last thing Ann suspected was lung cancer—weight loss from the copious amount of nutrients the tumor was stealing from her otherwise healthy body, breathlessness as the tumor grew into the visceral pleura and a main bronchus of her right lung, partially blocking her airways and bloodying her phlegm (10).

To be honest, things weren’t concerning until the chest pain. She tried everything from antacids to the leftover pain meds she received after getting her wisdom teeth out. Even the doctor was hesitant to scan her—there was no history of lung cancer in her immediate family and Ann was not a smoker. Moreover, she was young, barely 28. Data was on her side, too: CDC surveys showed that Chinese women were the 2nd least diagnosed with lung cancer of White, Hispanic, Black and Native American demographic groups (7). If it wasn’t for her Eric’s concern, she might have declined the CT scan. She didn’t like small, tight spaces or the metallic whirring of machines—two things the CT scan promised to provide, along with radiation exposure (2).
Her fiancée had been so supportive throughout the process. His optimism made her want to believe that it would be okay, that they could get through this together. He’d told her not to look at any of the survival statistics. He didn’t know, but she had. NSCLC, Stage IIA. It stood for non-small cell lung cancer, of which there were four types: adenocarcinoma of the lung, squamous cell carcinoma, large cell carcinoma and other subtypes. Ann had an adenocarcinoma of the right lung. Apparently, that meant that cells that were supposed to be harmlessly becoming mucus secretion cells turned into evil masterminds spearheading the disease (1). She knew it wasn’t the most scientific image, but that’s how Ann thought of it. It certainly felt like the disease had a rational mind of its own, the way friends, family and doctors spoke about it. Lung Adenocarcinoma, Stage IIA. The words rolled around in her mouth. If someone had said those words to her two months ago, Ann would have thought they were talking about the name of a foreign play and the section of the theatre they were being seated. Now it was a phrase that filled her thoughts. The associated numbers bounced inside her head like rubber balls bouncing on hard cement. 5-year survival rate: 30%. Percent of lung cancers that are adenocarcinomas: 40%. Size of the tumor: 6 cm. Classification: T2b, N0, M0 (1). That was her tag. Lung Adenocarcinoma, Stage IIA: T2b, N0, M0. Ann felt a sense of disgust at how cold the diagnosis sounded. Her graduate dissertation was on the de-individualization of Asians in film. Ann prided herself on trying her best to be a genuine person, and showed her individuality in that way. The cold, numeric taste of the words Lung Adenocarcinoma, Stage IIA: T2b, N0, M0 was the opposite of how Ann would describe herself. Regardless, it was now a part her.

Often, when images of bleached white papers with fine black print and cold clammy doctor’s hands kept her from sleep, Ann would imagine herself as an observer of her case. Diagnostic documents, in their excruciating detail, were easier to read when she pretended they were not talking about her. She’d made a mental habit of replacing Ann with Patient 88 when reading official documents:

Patient 88 Profile
May 2016

Patient 88 was diagnosed with Non-Small Cell Lung Cancer (NSCLC). The lung adenocarcinoma was found in the epithelium of the right lung, where lining of organs and gland formation takes place (9). Using the individual characteristics of the cancer such as tumor size (T), the state of lymph nodes (N) and incidence of metastases (M), we have grouped her tumor to help narrow down treatment plans. Patient 88’s tumor is 6 cm across. It is thus labeled as a T2b tumor because the main tumor is between 5 and 7 cm across. The tumor has grown into the visceral pleura and a main bronchus, as determined by a bronchoscopy. Additionally, a pulmonary function test has confirmed that Patient 88’s airway is partially obstructed. Lung capacity is lower than average due to the obstruction. The cancer has not spread to lymph nodes or distant sites, indicated by the labels N0 and M0 (10). From the previously determined standards, we characterize Patient 88’s tumor as T2b, N0, M0, indicating she is in Stage IIA of NSCLC.

When studying patient 88, Ann could appreciate the nuances of the disease. As an observer, she marveled at rapid proliferation of the organism that had only one goal—to survive. She held a bitter respect for its adaptability and persistence as well as its ability to slither around the body, evading detection. Lung cancer was especially creative in its individuality from patient to patient. The individuality of lung tumors reminded Ann of her dissertation. In her studies, Asian actors fought to be seen as individuals in media instead of their reoccurring portrayal as interchangeable minions and sidekicks. In media and popular culture, individuality and representation was a privilege. Ironically, in cancers, it was a curse.

Still, there was much to be grateful for. Grateful that Eric had pushed her to get the CT scan. Grateful that she was diagnosed pre-metastases. Grateful that she had health insurance. Ann struggled to hold on to the positives. It was a daily battle; more often than not she felt cheated out of a life she had so meticulously planned.

At least she had support. Ann couldn’t imagine facing this alone. Eric could make light of anything, even when he felt lost and distraught, too. He reminded her to stay in the moment, and somehow always knew when she was crawling into that dark hole of frustration and self-pity. They could not change the facts. The only promise of physical and emotional recovery was in the future. It was time to gather data, decide on treatment options, and enroll in clinical trials. There, in the methodology of the process at least, was something Ann could take solace in. Graduate studies had taught Ann patience and perseverance. Perhaps her cancer would be her exit exam. Her grimace softened, and she fell asleep.

Chapter 2: Language Barriers


Three counts in, three counts out. Three counts in, three counts out. Brian focused on his breathing to slow his heart rate. He’d barely made the train and had to yell from across the platform for the conductor to wait. They were irritated, for sure, but when people saw his scrubs they usually cut him some slack. Maybe that’s why he was always late; he generally got away with it.

Eric had scanned the tumor sequencing results to Brian a couple days ago. Brian had looked over them meticulously every chance he had; a page here had coffee stains and another was creased from being in his pocket during rounds. He was the one who asked Ann to get the tumor sequenced not only for the traditional mutations, but also for a fusion recently detected in a subset of NSCLC patients called the EML4-ALK fusion.



You’re in a room with 200 people, and you all have cancer. 26 of you have lung cancer, and of that 26, 20 of you have non small cell lung cancer. 1 of the 20 has a tumor with an EML4-ALK translocation (19). Why study this translocation? At 1 in 20, it doesn’t really matter does it?

It does if it’s you.

Well, you and the 70,000 people worldwide whose cancer is caused by this translocation (19). NSCLC can be traced to a variety of somatic mutations; Ann’s case is particular in that she is young, ethnically Chinese and does not have a smoking history (Supplemental Figure 1). Clinically, her history points to two probable mutations causing her disease: a point mutation in the epidermal growth factor receptor (EGFR), or an EML4-ALK translocation (24). Though both mutations exhibit similar clinical phenotypes, their differences are stark. Most EML4-ALK positive tumors will pathologically exhibit “a solid growth pattern with >10% signet-ring cells”, a characteristic rare in positive EGFR tumors (Supplemental Figure 2) (19). How the each mutation mechanistically leads to cancer differs as well. EGFR positive tumors mainly exhibit EGFR mutations in the tyrosine kinase domain that leads to dimerization and hyperphosphorylation of the wild type EGFR, activating ligand independent signaling. Tumor cell proliferation, invasion and metastasis are some downstream effects of this unregulated signaling (26). EML4-ALK fusions also produce these hallmarks in their tumors (and do so through a continually active kinase) but vary significantly in mutation acquisition and kinase activation mechanism (20). Still, the overlap in what hallmarks the two mutations produces independently is notable. The manifestation of the functional overlap may be in the fact that EML4-ALK fusions and EGFR mutations are mutually exclusive and acquisition of both mutations is exceedingly rare (19).

Ann’s tumor is EML4-ALK positive. As ominous as that sounds, it’s important to note that EML4 and ALK are perfectly ordinary genes, regulated meticulously. EML4 belongs to a class of proteins that interact with soluble tubulin and microtubules (20). ALK most likely contributes to the development of the nervous system (20). The two genes dutifully carry out their purpose, save in the case of a fusion. A disruption 3.6 bp downstream of EML4, subsequent inversion then ligation to ALK 297 bp upstream of exon 21 hijacks this highly regulated system (22).

EML4-ALK Fusion picture.jpg
Figure 1. EML4 is disrupted at a position ~3.6 kb downstream of exon 13 and is ligated to a position 297 bp upstream of exon 21 of ALK, giving rise to the EML4–ALK (variant 1) fusion gene. Filled and open horizontal arrows indicate the direction of transcription and the positions of the Fusion-genome primers, respectively (22).

The disruption cuts regions of the EML4 protein that, when fused to ALK, drive ALK activation. This region is called the trimerisation domain (TD) (20). An inversion must occur to create an open reading frame. The inversion is then ligated to a portion of the ALK gene coding for the tyrosine kinase domain. The translocation cuts out the sequence for the transmembrane portion of the ALK protein. This results in an intracellular fusion protein with an active tyrosine kinase domain whose production is promoted by portions of the EML4 protein (20, 22). The TD of EML4 drives ALK activation through self-association of the kinase domains. ALK fires signals at will, independent of ligands—quite literally a loose cannon as it is no longer bound to the cell membrane. Variants in the fusion event and fusion protein localize to different areas within the cell including the cytosol, nucleus and microtubules (20).

This simple flip and ligation process is enough to circumvent the highly regulated process of EML4 and ALK gene expression. Functional, dutiful genes become oncogenic by this single fusion event. When expressed, these genes—once a working part in a well-oiled machine—can activate neoplastic phenotypes, induce cell proliferation and promote cell survival (20). Cells exhibiting these (among other) oncogenic hallmarks are eventually detected as cancer, and, for our particular patient, as EML4-ALK positive non-small cell lung cancer.



Sir, your ticket please.

The conductor jolted Brian out of his cogitation. He flashed his pass and returned to his thoughts. How would he explain to Ann the details of her cancer? As a scientist, he found her mutations fascinating, but fascinating was not the word Eric and Ann wanted to hear. He thought of Ann in the hospital and a mixture of emotion passed through him. He was amazed at her disease, captivated by the singularity of the fusion event and its oncogenic ability. The case was like an unfinished puzzle; mechanism was mostly filled but still had pieces missing and the treatments section was almost completely empty. There were a lot of pieces to fit into the picture and that was a daunting but exhilarating challenge. But as he thought of who housed this anomaly and who suffered at its hands, his stomach knotted and he felt guilt and distress.

Ann and Brian studied together in high school. These charts he had to explain, though higher stakes, were no different than assignments they’d worked on together. The twins had always been great study partners and Ann always said he had a teacher’s mind. Eric and Ann were studious; he just had to find the words to meet them halfway on the road to understanding.

Ann and Eric wouldn’t care about the statistical significance of getting both an EGFR and EML4-ALK fusion, or how many variants of EML4-ALK fusion there were. The important thing, to them, was the mutations and specific variant related to Ann. They would care about treatment options. To be honest, Brian wasn’t sure what the best treatment options were. Drugs for ALK inhibition were the first on his mind, but he would have to study the newest ones available and discuss them with Ann’s doctors.

Brian's eyes watered and he realized how dry his contacts were. It was 3 minutes until his stop. He texted Eric that he'd be arriving soon, and placed Ann's documents neatly into a manila folder.

Chapter 3: Cost Benefit Analysis


Dr. Yu flipped the page and saw the bright red line on her fingertip before she felt the sharp bite of the paper cut. This happened so easily during the winter, the cold air vacuuming the moisture out of her skin. It didn’t help that she washed her hands frequently, but such was the life of a doctor. Now she’d be late for her next appointment. Perhaps she would be more irritated by her Band-Aid detour if she wasn’t looking for a reason to delay her meeting with Eric and Ann.

Dr. Yu had prescribed Ann Crizotinib, a tyrosine kinase inhibitor that disrupts the ligand independent firing of the EML4-ALK fusion protein (27). It’d been almost a year and tumor had been shrinking steadily. But it was a short-lived victory, as Dr. Yu had learned to anticipate in her years in the field. Still, one couldn’t help but hope.

Maybe Eric and Ann already knew. They had called her for an appointment earlier than her usual check-in. Ann was having difficulty breathing again and increased irritation in her lungs. The files on Dr. Yu’s desk showed that the tumor mass had increased in size since her last check-up. Ann was already on 250 mg of Crizotinib, twice daily, which was the dosage recommended by the FDA (28). She felt the side effects intensely, but wouldn’t compromise for the lower dosage. Like so many of Dr. Yu’s patients, she would do anything and everything to defeat her cancer.

Dr. Yu wrapped her index finger tightly in a Band-Aid. Within a few days, the wound would heal and she wouldn’t need cumbersome protective covering. Within a few days, it would be like it never happened. If only all medicine were that simple. Ann was diagnosed last Spring. For 9 months she lived with intense side effects of her chemotherapy, in the hope that she, too, could emerge from the disease like it never happened. But 9 months rolled around and what was shrinking came back with a vengeance. Was it worth it? Sometimes Dr. Yu didn’t know the answer to that question.

Screen Shot 2016-06-09 at 11.44.30 AM.png
Figure 1. Side effects of Crizotinib. Percentages in parenthesis indicate percent of patients in clinical trial that exhibited these side effects from 250 mg of Crizotinib, twice daily. (27)

1 year was the average time that tumors like Ann’s acquired resistance to Crizotinib (27). Mutations in the active site of the tyrosine kinase that prevented Crizotinib binding to the ligand-independent fusion protein was a possible way Ann's tumor could have gained resistance (27). There were chemotherapy options besides Crizotinib, each with their slew of side effects and promises of possibly prolonging the patient’s life for a year or two. The question rang again: Is it worth it?

Ann and Eric wouldn’t want to hear her doubts; they wanted options. She wouldn’t breathe words like palliative care unless they mentioned it first, or the treatment options were exhausted. Dr. Yu would suggest another drug called Ceritinib. It was FDA approved; and clinical trials had shown that 56% of patients who had previously received Crizotinib had tumors that were Ceritinib sensitive (29). Ceritinib advertised as a more specific drug than Crizotinib, though mechanisms in the trial were not explicitly stated. Speculations like “ceritinib may inhibit an unknown kinase that has not yet been found to play a role in the biology of these [NSCLC] tumors” gave few insights into the true mechanism. Still, the numbers didn’t lie about the therapeutic effect. Patients with Crizotinib resistance reached an average of almost 7 months of progression free survival (29). Dr. Yu was sure that Ann wanted as much time as she could get.
Screen Shot 2016-06-09 at 11.48.27 AM.png

There would be similar costs, though, to trying the new drug. The side effects of Ceritinib would be close to those of Crizotinib: diarrhea, vomiting, dehydration, among others (29). Ann would continue to be weak from the chemotherapy. She could barely speak at their meetings. Eric told Dr. Yu that Ann slept most of the day. Is it worth it, she asked herself for the third time that day.

She was already 10 minutes late for their appointment. The cost was for Ann to decide; it was her job as a physician to give her professional opinion about the best course of action for Ann's goal—to survive. It was not her place to ask if just surviving was enough. Her paper cut stung as she opened the door to the conference room.

Epilogue


Eric watched Annie and Chelsea lay on the carpeted living room floor, coloring diligently. The house was silent, save the sound of crayons and colored pencils hitting the paper. It was in these quiet moments he thought of Ann and the family they might have had together.
Ann, one of the 70,000 women who die yearly from lung cancer (1), passed 25 months after her initial diagnosis. It had been 7 years since her passing, but Eric accepted many years ago that the experience and heartbreak would stay with him for the rest of his life. He kept in contact with Brian and Ann’s family, and often felt her presence in peaceful moments. He was sure she was happier now, cancer free in a dimension unknown to those still in this world. A tug on hand brought him out of his musings; Annie wanted to show him a picture she drew of a pretty garden she imagined. Eric stroked her hair and returned to the familiarity of everyday life, a privilege he was grateful he could enjoy.



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